Publications acknowledging the Hoffman2 Cluster¶
The following is the list of publications across multiple disciplines known to us to acknowledge the use of the Hoffman2 Cluster within their research process. See Acknowledging Hoffman2 to learn how to acknowledge work performed on the Hoffman2 Cluster in papers, presentations and other publications.
Important
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- As of 2025/10/10 there are (not including preprints):
1038 known publications acknowledging the Hoffman2 Cluster, of which:
884 Journal Articles
117 Theses
27 Conference Papers
4 Reports
3 Book Sections
2 Presentations
1 Newspaper Articles
2025¶
- 67 publications for 2025 as of 2025/10/10
5 Theses
Journal Articles for 2025 as of 2025/10/10¶
Agarwal, Shivam and Lihua Jin. “Architected Lattices with a Topological Transition.” Advanced Engineering Materials 27 no. 11 (2025): 2301192. 10.1002/adem.202301192.
“This work was supported by the Hellman fellowship. It used computational and storage services associated with the Hoffman2 Shared Cluster provided by Institute for Digital Research and Education’s Research Technology Group at the University of California, Los Angeles (UCLA).” (Agarwal and Jin, 2025, p. 10)
Bennett, Ronan; Marco Morselli; Kseniya Petrova; Leonid Peshkin, and Matteo Pellegrini. “An epigenetic clock for Xenopus tropicalis.” npj Aging 11 no. 1 (2025): 38. 10.1038/s41514-025-00236-x.
“This project used computational and storage services associated with the Hoffman2 Cluster, operated by the UCLA Office of Advanced Research Computing’s Research Technology Group, and the High Performance Computing facility at the University of Parma (Parma, Italy).” (Bennett et al., 2025, p. 9)
Bern, Zvi; Enrico Herrmann; Radu Roiban; Michael S. Ruf, and Mao Zeng. “Global bases for nonplanar loop integrands, generalized unitarity, and the double copy to all loop orders.” Journal of High Energy Physics 2025 no. 6 (2025): 115. 10.1007/JHEP06(2025)115.
“In addition, this work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Bern et al., 2025, p. 45)
Biswas, Souvick; Jack Cokas; Winston Gee; Dababrata Paul; Nureshan Dias; Harry W. T. Morgan; Matthew T. Finn; Bethany M. Hudak; Perrin M. Godbold; Christopher A. Klug; Albert Epshteyn; Anastassia N. Alexandrova; Musahid Ahmed, and Ralf I. Kaiser. “Unconventional low temperature decomposition of a saturated hydrocarbon over atomically-dispersed titanium-aluminum-boron catalyst.” Nature Communications 16 no. 1 (2025): 6793. 10.1038/s41467-025-62112-2.
“This work used computational and storage services associated with the DOD HPC, National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC0205CH11231, and UCLA IDRE Shared Cluster Hoffman2.” (Biswas et al., 2025, p. 13)
Boatner, Lisa M.; Jerome Eberhardt; Flowreen Shikwana; Matthew Holcomb; Peiyuan Lee; Kendall N. Houk; Stefano Forli, and Keriann M. Backus. “CIAA: Integrated Proteomics and Structural Modeling for Understanding Cysteine Reactivity with Iodoacetamide Alkyne.” ACS Chemical Biology 20 no. 7 (2025): 1669-1682. 10.1021/acschembio.5c00225.
This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Boatner et al., 2025, p. 1680)
Chen, Kyle; Barry Y. Li; Tucker Allen, and Daniel Neuhauser. “Mixed Planewave and Localized Orbital Basis for Sparse-Stochastic Hybrid Time-Dependent Density Functional Theory.” Journal of Chemical Theory and Computation 21 no. 17 (2025): 8509-8517. 10.1021/acs.jctc.5c01025.
“Computational resources for simulations were provided by both the Expanse cluster at the San Diego Supercomputer Center through allocation CHE-230099 under the Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) program and the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Chen et al., 2025, p. 8515-6)
Chen, Pan-Pan; Meng Duan; Qingyang Zhou; Fang Liu; Yi Tang; Neil K. Garg, and K. N. Houk. “Origin of the Different Binding Affinities of (9R)- and (9S)-Hexahydrocannabinol (HHC) for the CB1 and CB2 Cannabinoid Receptors.” ACS Chemical Biology 20 no. 8 (2025): 2006-2013. 10.1021/acschembio.5c00399.
“Calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles, and Expanse at SDSC through allocation CHE040014 from the Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) program.” (Chen et al., 2025, p. 2011)
Chen, Pan-Pan; Tomás G. Santiago; Carlota Odena; Chi Zhang; Ruben Martin, and K. N. Houk. “Unraveling the Dichotomy Exerted by Boron Reagents in Site-Selective Functionalization of C(sp2)– and C(sp3)–OMe Bonds.” Journal of the American Chemical Society 147 no. 38 (2025): 34575-34588. 10.1021/jacs.5c09306.
“Calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575).” (Chen et al., 2025, p. 34586)
Cheng, Dongfang; Khanh-Ly C. Nguyen; Vaidish Sumaria; Ziyang Wei; Zisheng Zhang; Winston Gee; Yichen Li; Carlos G. Morales-Guio; Markus Heyde; Beatriz Roldan Cuenya; Anastassia N. Alexandrova, and Philippe Sautet. “Structure Sensitivity and Catalyst Restructuring for CO2 Electro-reduction on Copper.” Nature Communications 16 no. 1 (2025): 4064. 10.1038/s41467-025-59267-3.
“Computational resources for this work were provided by the UCLA-shared cluster Hoffman2, the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program at the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC0206CH11357 and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant No. ACI-1548562, through allocation TGCHE170060.” (Cheng et al., 2025, p. 14)
Cheng, Dongfang; Ziyang Wei, and Philippe Sautet. “Elucidating the Proton Source for CO2 Electro-Reduction on Cu(100) Using Many-Body Perturbation Theory.” Journal of the American Chemical Society 147 no. 13 (2025): 10954-10965. 10.1021/jacs.4c14108.
“Computational resources for this work were provided by the UCLA-shared cluster Hoffman2, and the Expanse cluster through the allocation CHE170060 at the San Diego Supercomputing Center through ACCESS.” (Cheng et al., 2025, p. 10963)
Dahal, Laxman; Henry Burton, and Kuanshi Zhong. “High-Fidelity High-Resolution Regional Seismic Risk and Resilience Assessment of Large Building Inventories.” Earthquake Engineering & Structural Dynamics 54 no. 5 (2025): 1376-1396. 10.1002/eqe.4313.
“The computations are performed in Hoffman2, an HPC cluster operated by the Institute for Digital Research and Education (IDRE) at the University of California, Los Angeles.” (Dahal et al., 2025, p. 1391)
Dalichaouch, T. N.. “Fully plasma-based electron injector for a linear collider or XFEL.” Physical Review Research 7 no. 2 (2025). 10.1103/PhysRevResearch.7.023118.
“The simulations were performed on the National Energy Research Scientific Computing Center (NERSC) and Hoffman2 at UCLA.” (Dalichaouch, 2025, p. 6)
DiRusso, Jonathan A.; Lingyu Zhan; Yu Tao; Allison L. Wang; Xinyu Xiang; Alexander C. Robbins; Azra J. Cruz; Wanlu Liu, and Amander T. Clark. “Sex-specific expression and function of TRIM28 during mouse primordial germ differentiation.” iScience 28 no. 10 (2025). 10.1016/j.isci.2025.113474.
“Data were processed using the UCLA IDRE Hoffman2 High Performance Cluster and the UCLA Collaboratory.” (DiRusso et al., 2025, p. 1)
Drozdov, A. Y.; P. Kollmann; Y. Hao; D. Wang, and E. E. Woodfield. “Electron Acceleration and Zebra Stripe Formation in Saturn’s Radiation Belts.” Journal of Geophysical Research: Space Physics 130 no. 5 (2025): e2025JA033898. 10.1029/2025JA033898.
“This work used computational and storage services associated with the Hoffman2 Cluster which is operated by the UCLA Office of Advanced Research Computing’s Research Technology Group.” (Drozdov et al., 2025, p. 13)
Du, Xiaolong; Daniel Gilman; Tommaso Treu; Andrew Benson, and Charles Gannon. “Empirical model for the tidal evolution of dark matter substructure around strong gravitational lenses.” Physical Review D 112 no. 2 (2025): 023009. 10.1103/6tbt-w3nv.
“This work used computational and storage services associated with the Hoffman2 Cluster which is operated by the UCLA Office of Advanced Research Computing’s Research Technology Group.” (Du et al., 2025, p. 16)
Elgindy, Cecile; Achyut R. Gogoi; Ángel Rentería-Gómez; Bumsu Park; Deborshee Das; Carys E. Obertone; Balu D. Dherange; Osvaldo Gutierrez, and Mark D. Levin. “Mechanisms and Synthetic Applications of Cyclic, Nonstabilized Isodiazenes: Nitrogen-Atom Insertion into Pyrrolidines and Related Rearrangements.” Journal of the American Chemical Society 147 no. 31 (2025): 28179-28188. 10.1021/jacs.5c08361.
“O.G. acknowledges UCLA for funding and UCLA’s Office of Advanced Research Computing’s Research Technology Group and Hoffman Cluster for (Hoffman2) Cluster computing resources.” (Elgindy et al., 2025, p. 28187)
Feng, Shijia; Ziang Liu; Dongfang Cheng; Yunfeng Hu; Sizhe Chen; Xinyuan Zhang; Jiabao Li; Xiaorui Dong; Tianyu Wang; Ziwei Wang; Yulun Wu; Ya Yin; Hongzhi Zheng; Philippe Sautet; Xiaojun Wang, and Jia Zhu. “Proton-donating cations enable efficient and stable acidic CO2 reduction in membrane electrode assemblies.” National Science Review 12 no. 10 (2025): nwaf312. 10.1093/nsr/nwaf312.
“Philippe Sautet and Dongfang Cheng have been solely supported by Computational resources from the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE).” (Feng et al., 2025, p. 12)
Finnerty, Luke; Julie Inglis; Michael P. Fitzgerald; Daniel Echeverri; Nemanja Jovanovic; Dimitri Mawet; Geoffrey A. Blake; Ashley Baker; Randall Bartos; Benjamin Calvin; Sylvain Cetre; Jacques-Robert Delorme; Greg Doppmann; Katelyn Horstman; Chih-Chun Hsu; Joshua Liberman; Ronald A. López; Evan Morris; Jacklyn Pezzato-Rovner; Jean-Baptiste Ruffio; Ben Sappey; Tobias Schofield; Andrew Skemer; J. Kent Wallace; Nicole L. Wallack; Jason J Wang; Ji Wang; Yinzi Xin, and Jerry W. Xuan. “The Watery Atmosphere of HD 209458 b Revealed by Joint K- and L-band High-resolution Spectroscopy.” The Astronomical Journal 170 no. 4 (2025): 223. 10.3847/1538-3881/adfb71.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Finnerty et al., 2025)
Fu, Xiaoyang; Dongfang Cheng; Ao Zhang; Jingxuan Zhou; Sibo Wang; Chengzhang Wan; Xun Zhao; Jun Chen; Philippe Sautet; Yu Huang, and Xiangfeng Duan. “High-Performance Cu6Sn5 Alloy Electrocatalysts for Formaldehyde Oxidative Dehydrogenation and Bipolar Hydrogen Production.” Angewandte Chemie International Edition 64 no. 28 (2025): e202503828. 10.1002/anie.202503828.
“D.C. used the HOFFMAN2 cluster at the UCLA Institute for Digital Research and Education (IDRE) and the Expanse cluster through the allocation CHE170060 at the San Diego Supercomputing Center through ACCESS.” (Fu et al., 2025, p. 8)
Fukami, Kai. “Extreme vortex-gust airfoil interactions at Reynolds number 5000.” Physical Review Fluids 10 no. 8 (2025). 10.1103/vcbd-tvz1.
“This study used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Fukami, 2025, p. 20)
Gangan, Abhijeet Sadashiv; Ekin Dogus Cubuk; Samuel S. Schoenholz; Mathieu Bauchy, and N. M. Anoop Krishnan. “Force-Field Optimization by End-to-End Differentiable Atomistic Simulation.” Journal of Chemical Theory and Computation 21 no. 12 (2025): 5867-5879. 10.1021/acs.jctc.4c01784.
“This work also used computational and storage services associated with the Hoffman2 Cluster, which is operated by the UCLA Office of Advanced Research Computing’s Research Technology Group.” (Gangan et al., 2025, p. 5878)
Gilman, Daniel; Jo Bovy; Neige Frankel, and Andrew Benson. “Dark Galactic Subhalos and the Gaia Snail.” The Astrophysical Journal 980 no. 1 (2025): 24. 10.3847/1538-4357/ada963.
“This work used computational and storage services associated with the Hoffman2 Cluster, which is operated by the UCLA Office of Advanced Research Computing’s Research Technology Group.” (Gilman et al., 2025, p. 16)
Gladkov, Nikita; Igor Pak, and Aleksandr Zimin. “The bunkbed conjecture is false.” Proceedings of the National Academy of Sciences 122 no. 24 (2025): e2420725122. 10.1073/pnas.2420725122.
“We are grateful to Lisa Snyder (UCLA Advanced Research Computing) for help with the HOFFMAN2 cluster” (Gladkov et al., 2025, p. 11)
Green, J.. “Mapping the three-dimensional fermiology of the triangular lattice magnet <math xmlns=”http://www.w3.org/1998/Math/MathML”><mrow><msub><mi>EuAg</mi><mn>4</mn></msub><msub><mi>Sb</mi><mn>2</mn></msub></mrow></math>.” Physical Review B 111 no. 8 (2025). 10.1103/PhysRevB.111.085139.
“The computational work was supported by the DOE-BES Grant No. DE-SC0024987 to A.N.A. and used the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Green, 2025, p. 8)
Guan, Yani; Justus Kümper; Simran Kumari; Nick Heiming; Sonja D. Mürtz; Stephan N. Steinmann; Stefan Palkovits; Regina Palkovits, and Philippe Sautet. “Probing the Electric Double-Layer Capacitance to Understand the Reaction Environment in Conditions of Electrochemical Amination of Acetone.” ACS Applied Materials & Interfaces 17 no. 2 (2025): 4087-4097. 10.1021/acsami.4c14134.
“Computational resources for this work were provided by the UCLA-shared cluster Hoffman2 and the Expanse cluster through the allocation CHE170060 at the San Diego Supercomputing Center through ACCESS. P.S. and S.N.S. thank the support of CNRS and UCLA via the International Research Project ‘Electrified Interfaces for Better Energy’ (ELINE).” (Guan et al., 2025, p. 4096)
Gupta, Akash; Lars Stixrude, and Hilke E. Schlichting. “The Miscibility of Hydrogen and Water in Planetary Atmospheres and Interiors.” The Astrophysical Journal Letters 982 no. 2 (2025): L35. 10.3847/2041-8213/adb631.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group and Princeton Research Computing resources at Princeton University, which is a consortium of groups led by the Princeton Institute for Computational Science and Engineering (PICSciE) and Office of Information Technology’s Research Computing.” (Gupta et al., 2025, p. 6)
He, Ling; Daria Azizad; Kruttika Bhat; Angeliki Ioannidis; Carter J. Hoffmann; Evelyn Arambula; Mansoureh Eghbali; Aparna Bhaduri; Harley I. Kornblum, and Frank Pajonk. “Radiation-induced cellular plasticity primes glioblastoma for forskolin-mediated differentiation.” Proceedings of the National Academy of Sciences 122 no. 9 (2025): e2415557122. 10.1073/pnas.2415557122.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (He et al., 2025, p. 11)
Insixiengmay, Leslie and Lars Stixrude. “MgO miscibility in liquid iron.” Earth and Planetary Science Letters 654 (2025): 119242. 10.1016/j.epsl.2025.119242.
“Calculations were carried out using the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Insixiengmay and Stixrude, 2025, p. 6)
Isakov, Avital; Patricia Poths; Edison Cummings; Borna Zandkarimi, and Anastassia N. Alexandrova. “Role of Sn Content in the Activity and Selectivity of PtSn/SiO2 Clusters for Ethane Dehydrogenation.” The Journal of Physical Chemistry C 129 no. 36 (2025): 16020-16026. 10.1021/acs.jpcc.5c03264.
“This work used computational and storage services associated with the DOD HPC, National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC0205CH11231, and UCLA IDRE Shared Cluster Hoffman2.” (Isakov et al., 2025, p. 16025)
Kogan, Sophie; Anastassia N. Alexandrova, and Harry W. T. Morgan. “5d Orbital Covalency Controls the High-Pressure Polymorphism of BaO.” Chemistry – A European Journal 31 no. 50 (2025): e202501536. 10.1002/chem.202501536.
“This work was supported by computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group, and Bridges-2 at Pittsburgh Supercomputing Center through allocation CHE240146 from the ACCESS program, which is supported by NSF grants #2138259, #2138286, #2138307, #2137603, and #2138296.” (Kogan et al., 2025, p. 4)
Lam, Ching Ching and Kendall N. Houk. “Exploring reaction dynamics involving post-transition state bifurcations based on quantum mechanical ambimodal transition states.” Pure and Applied Chemistry 97 no. 9 (2025): 1135-1148. 10.1515/pac-2025-0462.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Lam and Houk, 2025, p. 1145)
Lao, Guanming; Taras Khvorost; Antonio Macias; Harry W. T. Morgan; Robert H. Lavroff; Ryan Choi; Haowen Zhou; Denis Usvyat; Guo-Zhu Zhu; Miguel A. García-Garibay; Anastassia N. Alexandrova; Eric R. Hudson, and Wesley C. Campbell. “Bottom-up approach to making larger hydrocarbon molecules capable of optical cycling.” Nature Chemistry (2025): 1-8. 10.1038/s41557-025-01965-y.
“Computational resources were provided by XSEDE and UCLA IDRE shared cluster hoffman2.” (Lao et al., 2025, p. 10)
Li, Barry Y.; Tim Duong; Tucker Allen; Nadine C. Bradbury; Justin R. Caram, and Daniel Neuhauser. “Parameterized attenuated exchange for generalized TDHF@vW applications.” The Journal of Chemical Physics 163 no. 3 (2025): 034102. 10.1063/5.0273771.
“We also acknowledge the computational resources provided by the Expanse cluster at San Diego Supercomputer Center (SDSC) through allocation CHE-240183 under the Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support (ACCESS) program and the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Li et al., 2025, p. 6)
Li, Guangjing; Shawn Chiu; Harry W. T. Morgan; Autumn T. Fuchs; Avital Isakov; Patricia Poths; Zisheng Zhang; Anastassia N. Alexandrova, and Scott L. Anderson. “Size-dependent effects of Ge addition on the coking and sintering tendency of PtnGem/alumina (n = 4,7,11) model catalysts.” Journal of Catalysis 448 (2025): 116196. 10.1016/j.jcat.2025.116196.
“This work used computational and storage services associated with the DOD HPC, National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, and UCLA IDRE Shared Cluster Hoffman2.” (Li et al., 2025, p. 17)
Li, Yichen; Dongfang Cheng; Giyeong Son; Anna V. Shneidman; Kang Rui Garrick Lim; Joanna Aizenberg, and Philippe Sautet. “Modeling electron storage at the interface between Au and anatase-TiO2 under ambient conditions.” Chem Catalysis 5 no. 9 (2025). 10.1016/j.checat.2025.101430.
“Computations in this work were performed on the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE) and the Bridges2 cluster through allocation CHE170060 from the Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) supported by the National Science Foundation.” (Li et al., 2025, p. 8)
Lyu, Huida; Jung Tae Kim; Dongfang Cheng; Xintong Yuan; Mackenzie Anderson; Keyue Liang; Jiayi Yu; Philippe Sautet; Richard Kaner, and Yuzhang Li. “Localized Eutectic Electrolytes for Stable Aqueous Zinc-Ion Batteries.” ACS Energy Letters 10 no. 6 (2025): 2924-2933. 10.1021/acsenergylett.5c00491.
“We acknowledge the use of the UCLA-CNSI EICN Facilities and the support provided by UCLA Molecular Instrumentation Center. H.L. sincerely acknowledges Guohao Hao for his help in battery testing, the support of Hui-Chun Chin and TsungDao Lee Chinese Undergraduate Research Endowment (CURE), and the Hoffman2 high-performance cluster at UCLA.” (Lyu et al., 2025, p. 2931)
Mohanna, Saeed; Lingsen Meng; Tung-Cheng Ho; Chao An, and Liuwei Xu. “The 2024 Noto earthquake and tsunami: insights from the static and adjoint state inversion methods.” Earth, Planets and Space 77 no. 1 (2025): 130. 10.1186/s40623-025-02197-7.
“This work used computational and storage services associated with the Hoffman2 Cluster, which is operated by the UCLA Office of Advanced Research Computing’s Research Technology Group.” (Mohanna et al., 2025, p. 10)
Mouton, Alice; Deborah J Bird; Gang Li; Brent A Craven; Jonathan M Levine; Marco Morselli; Matteo Pellegrini; Blaire Van Valkenburgh; Robert K Wayne, and William J Murphy. “Genetic and Anatomical Determinants of Olfaction in Dogs and Wild Canids.” Molecular Biology and Evolution 42 no. 3 (2025): msaf035. 10.1093/molbev/msaf035.
“A.M. used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Mouton et al., 2025, pp. 10-1)
Niknam, Mohamad and Louis-S. Bouchard. “Microstructural geometry revealed by NMR line shape analysis.” The Journal of Chemical Physics 162 no. 8 (2025): 084113. 10.1063/5.0245237.
“The computational and storage services used in this work are part of the Hoffman2 Shared Cluster, provided by the UCLA Institute for Digital Research and Education’s (IDRE) Research Technology Group.” (Niknam and Bouchard, 2025, p. 8)
Pinto Pereira Junior, Marcus Vinicius; Eric P. Geunes; Huiling Shao; Yiran Zhang; Jinkai Cheng; Samantha V. Magpantay; Brandon Q. Mercado; James M. Mayer; Kendall N. Houk; Robert R. Knowles, and Scott J. Miller. “Enantioselective Hydrodifluoroalkylation of Alkenes with Conformationally Tuned Peptidyl Hydrogen Atom Transfer Catalysts.” Journal of the American Chemical Society 147 no. 13 (2025): 11412-11424. 10.1021/jacs.5c01166.
“All DFT calculations were performed with Gaussian 1630 on UCLA Hoffman2 andXSEDE 31 supercomputers.” (Pinto Pereira Junior et al., 2025, p. 11419)
Pomfret, Meredith N.; Lucy P. Miller; Nicholas P. Serck; Ángel Rentería-Gómez; Bob Li; Sarah M. Zeitler; Sebastian M. Krajewski; Werner Kaminsky; Rajan Paranji; Osvaldo Gutierrez, and Matthew R. Golder. “Macrocyclic Ruthenium Ring Expansion Metathesis Polymerization Initiators Exhibit Tether Length-Dependent Behavior.” Organometallics 44 no. 18 (2025): 2083-2091. 10.1021/acs.organomet.5c00226.
“O.G. acknowledges NIH NIGMS (R35GM137797) for funding; his work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Pomfret et al., 2025, p. 2090)
Ready, Austin D.; Varun Tej Raviprolu; Tyler A. Kerr; Joseph W. Treacy; Mei L. Matsumoto; Prairie E. Hammer; Ellen M. Sletten; K. N. Houk, and Alexander M. Spokoyny. “Carboranes without Cage Carbons: closo-Dodecaborate Mimics of Neutral closo-Carboranes.” Journal of the American Chemical Society 147 no. 29 (2025): 25478-25488. 10.1021/jacs.5c05637.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Ready et al., 2025, p. 25486)
Reus, Lianne M.; Toni Boltz; Marcelo Francia; Merel Bot; Naren Ramesh; Maria Koromina; Yolande A. L. Pijnenburg; Anouk den Braber; Wiesje M. van der Flier; Pieter Jelle Visser; Sven J. van der Lee; Betty M. Tijms; Charlotte E. Teunissen; Loes Olde Loohuis, and Roel A. Ophoff. “Quantitative trait loci mapping of circulating metabolites in cerebrospinal fluid to uncover biological mechanisms involved in brain-related phenotypes.” Molecular Psychiatry 30 no. 8 (2025): 3478-3490. 10.1038/s41380-025-02934-0.
This work used computational and storage services associated with the Hoffman2 Cluster which is operated by the UCLA Office of Advanced Research Computing’s Research Technology Group.” (Reus et al., 2025, p. 3490)
Routh, Prahlad K.; Xihan Liu; Evgeniy Redekop; Jin Soo Lim; Sebastian Prodinger; Jessi E. S. van der Hoeven; Joanna Aizenberg; Maarten Nachtegaal; Adam H. Clark; Philippe Sautet, and Anatoly I. Frenkel. “Unraveling the Kinetics of Hydride Formation and Decomposition at Pd–Au Bimetallic Interfaces: A Combined Spectroscopic and Computational Study.” Journal of the American Chemical Society 147 no. 13 (2025): 11378-11389. 10.1021/jacs.5c00842.
“X.L. used the HOFFMAN2 cluster atthe UCLA Institute forDigital Research and Education (IDRE).” (Routh et al., 2025, p. 11387)
Shariat, Cheyanne; Smadar Naoz; Kareem El-Badry; Kyle Akira Rocha; Vicky Kalogera; Alexander P. Stephan; Kevin B. Burdge, and Isabel Angelo. “Triple Evolution Pathways to Black Hole Low-mass X-Ray Binaries: Insights from V404 Cygni.” The Astrophysical Journal 983 no. 2 (2025): 115. 10.3847/1538-4357/adbf01.
“This work used computational and storage services associated with the Hoffman2 Cluster, which is operated by the UCLA Office of Advanced Research Computing’s Research Technology Group, and the Resnick High-Performance Computing Center, a facility supported by the Resnick Sustainability Institute at the California Institute of Technology.” (Shariat et al., 2025, p. 16)
Song, Kaidong; Jingyuan Zhou; Chen Wei; Ashok Ponnuchamy; Md Omarsany Bappy; Yuxuan Liao; Qiang Jiang; Yipu Du; Connor J. Evans; Brian C. Wyatt; Thomas O’ Sullivan; Ryan K. Roeder; Babak Anasori; Anthony J. Hoffman; Lihua Jin; Xiangfeng Duan, and Yanliang Zhang. “A Printed Microscopic Universal Gradient Interface for Super Stretchable Strain-Insensitive Bioelectronics.” Advanced Materials 37 no. 11 (2025): 2414203. 10.1002/adma.202414203.
“This work used the computational and storage services associated with the Hoffman2 Shared Cluster provided by Institute for Digital Research and Education’s Research Technology Group at the University of California, Los Angeles.” (Song et al., 2025, p. 9)
Sun, Jiayang; Mojhgan A. Haghnegahdar; Julianne M. Fernandez; Cédric Magen, and James Farquhar. “Controls on concentrations and clumped isotopologues of vehicle exhaust methane.” PLOS ONE 20 no. 2 (2025): e0315304. 10.1371/journal.pone.0315304.
“All electronic structure calculations in this study are made using the Gaussian09 software package (Gaussian 09: AM6 4 L-G09RevB.01 12 August 2010) on the UCLA Hoffman2 cluster.” (Sun et al., 2025, p. 21-22)
Tena Meza, Arismel; Christina A. Rivera; Huiling Shao; Andrew V. Kelleghan; K. N. Houk, and Neil K. Garg. “σ-Bond insertion reactions of two strained diradicaloids.” Nature 640 no. 8059 (2025): 683-690. 10.1038/s41586-025-08745-1.
“Calculations were performed on the Hoffman2 cluster and the UCLA Institute of Digital Research and Education (IDRE) at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575).” (Tena Meza et al., 2025, p. 691)
Travis, Christopher R.; Jake R. Wilkinson; Ryan G. Dumais; Hanne C. Henriksen; Joseph W. Treacy; Noah K. Schomburg; K.n. Houk, and Marcey L. Waters. “Negative Cooperativity in the UHRF1 TTD-PHD Dual Domain Masks the Contributions of Cation-π Interactions between Trimethyllysine and the TTD Aromatic Cage.” Chemistry – A European Journal 31 no. 28 (2025): e202500848. 10.1002/chem.202500848.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Travis et al., 2025, p. 7)
Treacy, Joseph W.; James A. R. Tilden; Elaine Y. Chao; Zihuan Fu; Alexander M. Spokoyny; K. N. Houk, and Heather D. Maynard. “In silico screening of P,N-ligands facilitates optimization of Au(III)-mediated S-arylation.” Chemical Science 16 no. 9 (2025): 3878-3887. 10.1039/D4SC05920D.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Treacy et al., 2025, p. 3885)
Verardi, Peter J.; Elizabeth A. Ryutov; Poulami Mukherjee; Remy Lalisse; Karina Targos; Tetsuya Inagaki; Megan Kelly; Ilia A. Guzei; Marcel Schreier; Osvaldo Gutierrez, and Zachary K. Wickens. “Stereo-reversed E2 unlocks Z-selective C–H functionalization.” Science 389 no. 6766 (2025): 1239-1245. 10.1126/science.adv7630.
“O.G. acknowledges NIH NIGMS (R35GM137797) for funding and Texas A&M University HPRC resources and the Hoffman2 Cluster at UCLA Office of Advanced Research Computing’s Research Technology Group for providing computational resources (https://hprc.tamu.edu).” (Verardi et al., 2025, p. 1245)
Walters, Zach G.; Dominick C. Witkowski; K. N. Houk, and Neil K. Garg. “Mechanisms of Kobayashi eliminations for the generation of highly strained arynes, cyclic cumulenes, and anti-Bredt olefins.” Chemical Science 16 no. 35 (2025): 16047-16056. 10.1039/D5SC03943F.
“Calculations were performed on the Hoffman2 cluster and the UCLA Institute of Digital Research and Education (IDRE) at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575).” (Witkowski et al., 2025, p. 1015)
Wan, Jing; Antoinette van Ouwerkerk; Jean-Christophe Mouren; Carla Heredia; Lydie Pradel; Benoit Ballester; Jean-Christophe Andrau, and Salvatore Spicuglia. “Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits.” Nucleic Acids Research 53 no. 4 (2025): gkae1270.
“The chromatin state annotation data was downloaded from full-stack ChromHMM model trained with 1032 datasets from 127 reference epigenomes (https://public.hoffman2.idre.ucla.edu/ernst/2K9RS/ full_stack/full_stack_annotation_public_release/hg38/) (40).” (Wan et al., p. 4)
Wang, Haley R.; Zhen-Qi Liu; Hajer Nakua; Catherine E. Hegarty; Melanie Blair Thies; Pooja K. Patel; Charles H. Schleifer; Thomas P. Boeck; Rachel A. McKinney; Danielle Currin; Logan Leathem; Pamela DeRosse; Carrie E. Bearden; Bratislav Misic, and Katherine H. Karlsgodt. “Decoding Early Psychoses: Unraveling Stable Microstructural Features Associated With Psychopathology Across Independent Cohorts.” Biological Psychiatry 97 no. 2 (2025): 167-177. 10.1016/j.biopsych.2024.06.011.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the University of California, Los Angeles, Institute for Digital Research and Education’s Research Technology Group” (Wang et al., 2025, p. 175)
Wang, Qian; Jin-Kai Cheng; Shi-Xiong Tang; Kendall N. Houk, and Fei Wang. “Stereoselective synthesis of tetra- and tri-substituted alkenyl nitriles via aminative ring-opening of cyclopropenes with iron-aminyl radical.” Nature Communications 16 no. 1 (2025): 3168. 10.1038/s41467-025-58555-2.
“K.N.H. and J.-K. C. acknowledge the computational resources at UCLA (Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group).” (Wang et al., 2025, p. 9)
Wang, Yicheng; Hio Tong Ngan; Ho-Yi Lam; George Yan; Ryan T. Hannagan; Volkan Çınar; Nathaniel M. Eagan; Prashant Deshlahra; Philippe Sautet, and E. Charles H. Sykes. “Direct Comparison of the Activity and Selectivity of Rh1Cu and Ni1Cu Single-Atom Alloy Sites for Ethanol Decomposition.” ACS Catalysis 15 no. 8 (2025): 6046-6057. 10.1021/acscatal.4c07556.
“DFT calculations reported in this work used computational and storage resources on the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE), the National Energy Research Scientific Computing Center (NERSC), andtheBridges-2 cluster60 through the allocation CHE170060 at the Pittsburgh Supercomputing Center through ACCESS.” (Wang et al., 2025, p. 6055)
Weldon, Grant C.; Smadar Naoz, and Bradley M. S. Hansen. “The Cold Jupiter Eccentricity Distribution is Consistent with EKL Driven by Stellar Companions.” The Astrophysical Journal Letters 980 no. 2 (2025): L31. 10.3847/2041-8213/adb157.
“The authors also acknowledge the use of the UCLA cluster Hoffman2 for computational resources.” (Weldon et al., 2025, p. 10)
Williams, Claire E.; Smadar Naoz; William Lake; Blakesley Burkhart; Federico Marinacci; Mark Vogelsberger; Naoki Yoshida; Shyam H. Menon; Avi Chen, and Angela Adamo. “ΛCDM Star Clusters at Cosmic Dawn: Stellar Densities, Environment, and Equilibrium.” The Astrophysical Journal 990 no. 2 (2025): 135. 10.3847/1538-4357/adf19d.
“This work used computational and storage services associated with the Hoffman2 Cluster, which is operated by the UCLA Office of Advanced Research Computing’s Research Technology Group.” (Williams et al., 2025, p. 16)
Witkowski, Dominick C.; Daniel W. Turner; Ana S. Bulger; K. N. Houk, and Neil K. Garg. “Synthesis and reactivity of nitrogen-containing strained cyclic 1,2,3-trienes.” Nature Synthesis 4 no. 8 (2025): 1009-1016. 10.1038/s44160-025-00793-9.
“Calculations were performed on the Hoffman2 cluster and the UCLA Institute of Digital Research and Education (IDRE) at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575).” (Witkowski et al., 2025, p. 1015)
Xue, Albert; Jingyou Rao; Sriram Sankararaman, and Harold Pimentel. “dotears: Scalable and consistent directed acyclic graph estimation using observational and interventional data.” iScience 28 no. 2 (2025): 111673. 10.1016/j.isci.2024.111673.
“In Figure S5, we benchmark wallclock time and memory usage for all methods in p = 40 simulations30 on the UCLA hoffman2 cluster.” (Xue et al., 2025, p. 8.e1)
Yalcin, Refet A.; Patricia E. McNeil; Abhinav Bhanawat; Ricardo Martinez; Glareh N. Kashanchi; Sarah H. Tolbert; Bruce S. Dunn, and Laurent Pilon. “Dependent scattering and fractal microstructure determine the transparency of aerogel monoliths.” APL Photonics 10 no. 4 (2025): 046103. 10.1063/5.0238739.
“This work also used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Yalcin et al., 2025, p. 11)
Zengin, Esra; Yousef Bozorgnia, and Jonathan P. Stewart. “Response of BART’s Berkeley Hills tunnel to fault displacement and impact on system functionality.” Tunnelling and Underground Space Technology 164 (2025): 106813. 10.1016/j.tust.2025.106813.
“This work used computational and storage services associated with the Hoffman2 Cluster which is operated by the UCLA Office of Advanced Research Computing’s Research Technology Group.” (Zengin et al., 2025, p. 11)
Theses for 2025 as of 2025/10/10¶
DiRusso, Jonathan Adam. “Transposable Elements and Their Epigenetic Regulators are Necessary to Orchestrate the Transcriptome of the Developing Germline.” Ph.D. Thesis, University of California, Los Angeles, 2025. ProQuest, https://www.proquest.com/docview/3173129785.
“Data was processed using the UCLA IDRE Hoffman2 High Performance Cluster and the UCLA Collaboratory.” (DiRusso, 2025, p. 65)
Hao, Zhuonan. “Design, Modeling and Control of Flexible Structures in Robotics Applications.” Ph.D. Thesis, University of California, Los Angeles, 2025. ProQuest, https://www.proquest.com/docview/3250360105.
“The inflation behavior of the actuator was simulated using Finite Element Analysis (FEA) in AbaqusTM (Academic Edition on UCLA Hoffman2 cluster).” (Hao, 2025, p. 48)
Lavroff, Robert Harris. “Tackling Electron-Electron and Electron-Phonon Effects in Solids With a Novel Quantum Embedding Technique and Chemical Bonding Analysis.” Ph.D. Thesis, University of California, Los Angeles, 2025. ProQuest, https://www.proquest.com/docview/3178975487.
“Thank you also to the UCLA-IDRE administrators for help with the Hoffman2 cluster” (Lavroff, 2025, p. xiv)
Sandoval Belmar, Marco Sebastián. “Examining the Interplay Between Terrestrial Nutrient Inputs and Harmful Algal Blooms in the California Current.” Ph.D. Thesis, University of California, Los Angeles, 2025. ProQuest, https://www.proquest.com/docview/3207099186.
“Computational resources were provided by the Expanse system at the San Diego Supercomputer Center through allocation TG-OCE170017 from the Advanced Cyber Infrastructure Coordination Ecosystem: Services and Support (ACCESS) program, supported by National Science Foundation grants 2138259, 2138286, 2138307, 2137603, and 2138296, and by the Hoffman2 cluster at UCLA’s Institute for Digital Research and Education (IDRE).” (Sandoval Belmar, 2025, p. xvi)
Wang, Jason Yiheng. “Application of Machine Learning and Data Science in Synthetic Organic Chemistry.” Ph.D. Thesis, University of California, Los Angeles, 2025. ProQuest, https://www.proquest.com/docview/3175454571.
“More specifically, Auto-QChem supports job syntax for Princeton University’s computer cluster and UCLA’s Hoffman2 cluster.” (Wang, 2025, p. 43)
2024¶
- 137 publications for 2024
111 Journal Articles
22 Theses
1 Reports
Journal Articles for 2024¶
Achiro, Jennifer M.; Yang Tao; Fuying Gao; Chia-Ho Lin; Marika Watanabe; Sylvia Neumann; Giovanni Coppola; Douglas L. Black, and Kelsey C. Martin. “Aging differentially alters the transcriptome and landscape of chromatin accessibility in the male and female mouse hippocampus.” Frontiers in Molecular Neuroscience 17 (2024). 10.3389/fnmol.2024.133486.
“This study used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Achiro et al., 2024, p. 3)
Agarwal, Shivang and Amartya S. Banerjee. “Solution of the Schrödinger equation for quasi-one-dimensional materials using helical waves.” Journal of Computational Physics 496 (2024): 112551. 10.1016/j.jcp.2023.112551.
“All simulations involving HelicES were carried out using dedicated desktop workstations (Dell Precision 7920 Tower, iMac, and iMac Pro) or on single nodes of the Hoffman2 cluster at UCLA’s Institute for Digital Research and Education (IDRE).” (Agarwal and Banerjee, 2024, p. 15)
Bern, Zvi; Enrico Herrmann; Radu Roiban; Michael S. Ruf; Alexander V. Smirnov; Vladimir A. Smirnov, and Mao Zeng. “Amplitudes, supersymmetric black hole scattering at \(O(G^5)\), and loop integration.” Journal of High Energy Physics 2024 no. 10 (2024): 23. 10.1007/JHEP10(2024)023.
“In addition, this work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Bern et al., 2024, p. 33)
Bhanawat, Abhinav; Ricardo Martinez; Refet Ali Yalcin; Thomas Lee, and Laurent Pilon. “Dependent scattering and plasmon coupling in concentrated suspensions of optically hard nanoparticles.” Applied Physics Letters 125 no. 2 (2024): 021106. 10.1063/5.0192977.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Bhanawat et al., 2024, p. 8)
Bhimineni, Sree Harsha; Shu-Ting Ko; Casey Cornwell; Yantao Xia; Sarah H. Tolbert; Jian Luo, and Philippe Sautet. “First Principles Study of Aluminum Doped Polycrystalline Silicon as a Potential Anode Candidate in Li-ion Batteries.” Advanced Energy Materials 14 no. 34 (2024): 2400924. 10.1002/aenm.202400924.
“This work utilized the computational and storage services of the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Educational Research Technology Group (IDRE).” (Bhimineni et al., 2024, p. 10)
Bonney, Matthew J.; Celine Tesvara; Philippe Sautet, and Michael G. White. “Understanding the Decomposition of Dimethyl Methyl Phosphonate on Metal-Modified TiO2(110) Surfaces Using Ensembles of Product Configurations.” ACS Applied Materials & Interfaces 16 no. 19 (2024): 25483-25497. 10.1021/acsami.4c01250.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Office of Advanced Research Computing’s Research Technology Group.” (Bonney et al., 2024, p. 25496)
Borgini, Matteo; Qi-Nan Huang; Pan-Pan Chen; Steven J. Geib; K. N. Houk, and Peter Wipf. “Rhodium(I)-Catalyzed Annulation of Bicyclo[1.1.0]butyl-Substituted Dihydroquinolines and Dihydropyridines.” Journal of the American Chemical Society 146 no. 22 (2024): 14927-14934. 10.1021/jacs.4c04081.
“Calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI−1053575).” (Borgini et al., 2024, p. 14933-14934)
Bradbury, Nadine C.; Barry Y. Li; Tucker Allen; Justin R. Caram, and Daniel Neuhauser. “No more gap-shifting: Stochastic many-body-theory based TDHF for accurate theory of polymethine cyanine dyes.” The Journal of Chemical Physics 161 no. 14 (2024): 141101. 10.1063/5.0223783.
“This work also used computational services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Bradbury et al., 2024, p. 5)
Buth, Jessie E; Catherine E Dyevich; Alexandra Rubin; Chengbing Wang; Lei Gao; Tessa Marks; Michael RM Harrison; Jennifer H Kong; M Elizabeth Ross; Bennett G Novitch, and Caroline Alayne Pearson. “Foxp1 suppresses cortical angiogenesis and attenuates HIF-1alpha signaling to promote neural progenitor cell maintenance.” EMBO reports 25 no. 5 (2024): 2202-2219. 10.1038/s44319-024-00131-8.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Buth et al., 2024, p. 2210-2211) Num Pages: 2219
Cabezas-Escares, J.; Nicolás F. Barrera; Robert H. Lavroff; Anastassia N. Alexandrova; C. Cardenas, and F. Munoz. “Electronic structure and vibrational stability of copper-substituted lead apatite LK-99.” Physical Review B 109 no. 14 (2024): 144515. 10.1103/PhysRevB.109.144515.
“RHL performed calculations on UCLA’s IDRE Hoffman2 cluster” (Cabezas-Escares et al., 2024, p. 7)
Campbell, Steven J.; Chris La; Qingyang Zhou; Jason Le; Jennyfer Galvez-Reyes; Catherine Banach; K. N. Houk; Jie Rou Chen, and Suzanne E. Paulson. “Characterizing Hydroxyl Radical Formation from the Light-Driven Fe(II)–Peracetic Acid Reaction, a Key Process for Aerosol-Cloud Chemistry.” Environmental Science & Technology 58 no. 17 (2024): 7505-7515. 10.1021/acs.est.3c10684.
“Calculations were performed on the IDRE (Institute of Digital Research and Education) Hoffman2 Cluster at the University of California, Los Angeles. This work also used Expanse at SDSC through allocation CHE040014 from the Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) program, which is supported by National Science Foundation grants #2138259, #2138286, #2138307, #2137603, and #2138296.” (Campbell et al., 2024, p. I)
Cantarella, Simona; Marco Vezzoli; Davide Carnevali; Marco Morselli; Nathan R. Zemke; Barbara Montanini; Coralie F. Daussy; Harald Wodrich; Martin Teichmann; Matteo Pellegrini; Arnold J. Berk; Giorgio Dieci, and Roberto Ferrari. “Adenovirus small E1A directs activation of Alu transcription at YAP/TEAD- and AP-1-bound enhancers through interactions with the EP400 chromatin remodeler.” Nucleic Acids Research 52 no. 16 (2024): 9481-9500. 10.1093/nar/gkae615.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Cantarella et al., 2024, p. 9496) PMID: 39011896 PMCID: PMC11381368
Capel, Samantha L R; Natalie M Hamilton; Devaughn Fraser; Merly Escalona; Oanh Nguyen; Samuel Sacco; Ruta Sahasrabudhe; William Seligmann; Juan M Vazquez; Peter H Sudmant; Michael L Morrison; Robert K Wayne, and Michael R Buchalski. “Reference genome of Townsend’s big-eared bat, Corynorhinus townsendii.” Journal of Heredity 115 no. 2 (2024): 203-211. 10.1093/jhered/esad078.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Capel et al., 2023, p. 8)
Cheng, Dongfang; Anastassia N. Alexandrova, and Philippe Sautet. “H-Induced Restructuring on Cu(111) Triggers CO Electroreduction in an Acidic Electrolyte.” The Journal of Physical Chemistry Letters 15 no. 4 (2024): 1056-1061. 10.1021/acs.jpclett.3c03202.
“Computational resources for this work were provided by the UCLA-shared cluster Hoffman2, the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program at the Argonne Leadership Computing Facility, which is a U.S. Department of Energy (DOE) Office of Science User Facility supported under Contract DE-AC02-06CH11357, and the Expanse cluster through the allocation CHE170060 at the San Diego Supercomputing Center through ACCESS.” (Cheng et al., 2024, p. 1060)
Choudhary, Krishna; Sven Berberich; Thomas T. G. Hahn; James M. McFarland, and Mayank R. Mehta. “Spontaneous persistent activity and inactivity in vivo reveals differential cortico-entorhinal functional connectivity.” Nature Communications 15 no. 1 (2024): 3542. 10.1038/s41467-024-47617-6.
“All simulations were performed using MATLAB on the UCLA Hoffman2 Computing Cluster with time-step 0.2 ms using the Runge-Kutta method.” (Choudhary et al., 2024, p. 11) “This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Choudhary et al., 2024, p. 14)
Culver, Adrian B.; Pratik Sathe, and Rahul Roy. “Scattering expansion for localization in one dimension.” Physical Review B 109 no. 6 (2024): L060201. 10.1103/PhysRevB.109.L060201.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Culver et al., 2024, p. 5)
Curti, Joseph N; Devaughn Fraser; Merly Escalona; Colin W Fairbairn; Samuel Sacco; Ruta Sahasrabudhe; Oanh Nguyen; William Seligmann; Peter H Sudmant; Erin Toffelmier; Juan Manuel Vazquez; Robert Wayne; H Bradley Shaffer, and Michael R Buchalski. “A genome assembly of the Yuma myotis bat, Myotis yumanensis.” Journal of Heredity 115 no. 1 (2024): 139-148. 10.1093/jhered/esad053.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Curti et al., 2023, p. 8)
Dahal, Laxman; Henry Burton; Zhengxiang Yi, and Zizhao He. “Auto-WoodSDA: A scalable end-to-end automation framework to perform probabilistic seismic risk and recovery assessment of new residential woodframe buildings.” Journal of Building Engineering 96 (2024): 110545. 10.1016/j.jobe.2024.110545.
“IDRE maintains Hoffman2, an HPC cluster at the University of California Los Angeles.” (Dahal et al., 2024, p. 19)
David, Maya; Thomas Leirikh; Omri Shelef; Sara Gutkin; Tal Kopp; Qingyang Zhou; Pengchen Ma; Micha Fridman; Kendall N. Houk, and Doron Shabat. “Chemiexcitation Acceleration of 1,2-Dioxetanes by Spiro-Fused Six-Member Rings with Electron-Withdrawing Motifs.” Angewandte Chemie International Edition 63 no. 46 (2024): e202410057. 10.1002/anie.202410057.
“D.S. thanks the Israel Science Foundation (ISF) for financial support. K.N.H. thanks the US National Science Foundation for financial support (CHE-2153972) and the UCLA Institute for Digital Research for access to the Hoffman2 shared cluster. K.N.H., P.M., and Q.Z. thank the SDSC Expanse calculation resource. O.S. acknowledges support from the Adams Fellowship Program of the Israel Academy of Science and Humanities. P.M. is thankful to the National Natural Science Foundation of China (No. 22103060).” (David et al., 2024, p. 9)
De Abreu, Maxime; Torben Rogge; Matteo Lanzi; Tomas J. Saiegh; Kendall N. Houk, and Joanna Wencel-Delord. “Cyclic Diaryl λ3-Bromanes as a Precursor for Regiodivergent Alkynylation Reactions.” Angewandte Chemie 136 no. 16 (2024): e202319960. 10.1002/ange.202319960.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles.” (De Abreu et al., 2024, p. 6)
Dobynde, Mikhail and Jingnan Guo. “Guidelines for radiation-safe human activities on the Moon.” Nature Astronomy 8 no. 8 (2024): 991-999. 10.1038/s41550-024-02287-8.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the Institute for Digital Research and Education’s Research Technology Group at the University of California, Los Angeles.” (Dobynde and Guo, 2024, p. 999)
Doud, Evan A.; James A. R. Tilden; Joseph W. Treacy; Elaine Y. Chao; Hayden R. Montgomery; Grace E. Kunkel; Eileen J. Olivares; Nima Adhami; Tyler A. Kerr; Yu Chen; Arnold L. Rheingold; Joseph A. Loo; Christopher G. Frost; K. N. Houk; Heather D. Maynard, and Alexander M. Spokoyny. “Ultrafast Au(III)-Mediated Arylation of Cysteine.” Journal of the American Chemical Society 146 no. 18 (2024): 12365-12374. 10.1021/jacs.3c12170.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Doud et al., 2024, p. 12372)
Dragulet, Francis and Lars Stixrude. “Partitioning of Iron Between (Mg,Fe)SiO3 Liquid and Bridgmanite.” Geophysical Research Letters 51 no. 12 (2024): e2023GL107979. 10.1029/2023GL107979.
“This project is supported by the National Science Foundation under Grant EAR2223935 to L.S. Calculations were carried out using the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Dragulet and Stixrude, 2024, p. 7)
Drozdov, A. Y.; H. J. Allison; A. A. Saikin; Q. Schiller, and D. Wang. “Distribution of Seed Electron Phase Space Density Minima in Earth’s Radiation Belts.” Geophysical Research Letters 51 no. 7 (2024): e2023GL108028. 10.1029/2023GL108028.
“This work used computational, andstorage services associated with theHoffman2 Shared Cluster provided bytheUCLA Institute for Digital Research andEducation’s Research Technology Group.” (Drozdov et al., 2024, p. 7)
Duan, Meng; Qianzhen Shao; Qingyang Zhou; Phil S. Baran, and K. N. Houk. “Why •CF2H is nucleophilic but •CF3 is electrophilic in reactions with heterocycles.” Nature Communications 15 no. 1 (2024): 4630. 10.1038/s41467-024-48949-z.
“Calculations were performed on the Hoffman2 cluster at UCLA, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575 to K.N.H.).” (Duan et al., 2024, p. 8)
Dutta, Subhabrata; Yi-Lin Lu; Johannes E. Erchinger; Huiling Shao; Emanuel Studer; Felix Schäfer; Huamin Wang; Debanjan Rana; Constantin G. Daniliuc; K. N. Houk, and Frank Glorius. “Double Strain-Release [2π+2σ]-Photocycloaddition.” Journal of the American Chemical Society 146 no. 8 (2024): 5232-5241. 10.1021/jacs.3c11563.
“DFT calculations were performed ontheIDRE Hoffman2 cluster attheUniversity ofCalifornia, LosAngeles, andthe Extreme Science and Engineering Discovery Environment (XSEDE)” (Dutta et al., 2024, p. 5239)
Enders, Craig K.; Juan Diego Vera; Brian T. Keller; Agatha Lenartowicz, and Sandra K. Loo. “Building a simpler moderated nonlinear factor analysis model with Markov Chain Monte Carlo estimation.” Psychological Methods (2024). 10.1037/met0000712.
Place: US
Esra Zengin, Ph D. and Yousef Bozorgnia. “Evaluating the Seismic Vulnerability and Resilience of BART’s Berkeley Hills Tunnel.” (2024). 10.7922/G22J697K.
“his work used computational and storage services associated with the Hoffman2 Cluster which is operated by the UCLA Office of Advanced Research Computing’s Research Technology Group” (Esra Zengin, 2024, p. 3)
Feng, Shijia; Xiaojun Wang; Dongfang Cheng; Yao Luo; Mengxin Shen; Jingyang Wang; Wei Zhao; Susu Fang; Hongzhi Zheng; Liyao Ji; Xing Zhang; Weigao Xu; Yongye Liang; Philippe Sautet, and Jia Zhu. “Stabilizing CO2 Intermediates at the Acidic Interface using Molecularly Dispersed Cobalt Phthalocyanine as Catalysts for CO2 Reduction.” *Angewandte Chemie 136 no. 8 (2024): e202317942. 10.1002/ange.202317942.
“Prof. Jia Zhu acknowledges the support from the XPLORER PRIZE. D. C. and P.S. acknowledged the National Science Foundation CBET Grant 2103116, the Audi CO2 Cy Pres Award, and Computational resources from the Hoffman2 cluster at UCLA Institute for Digital Research and Education (IDRE).” (Feng et al., p. 8)
Finnerty, Luke; Jerry W. Xuan; Yinzi Xin; Joshua Liberman; Tobias Schofield; Michael P. Fitzgerald; Shubh Agrawal; Ashley Baker; Randall Bartos; Geoffrey A. Blake; Benjamin Calvin; Sylvain Cetre; Jacques-Robert Delorme; Greg Doppmann; Daniel Echeverri; Chih-Chun Hsu; Nemanja Jovanovic; Ronald A. López; Emily C. Martin; Dimitri Mawet; Evan Morris; Jacklyn Pezzato; Jean-Baptiste Ruffio; Ben Sappey; Andrew Skemer; Taylor Venenciano; J. Kent Wallace; Nicole L. Wallack; Jason J. Wang, and Ji Wang. “Atmospheric Metallicity and C/O of HD 189733 b from High-resolution Spectroscopy.” The Astronomical Journal 167 no. 1 (2024): 43. 10.3847/1538-3881/ad1180.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Educations Research Technology Group.” (Finnerty et al., 2024, p. 10)
Frieder, Christina A.; Fayçal Kessouri; Minna Ho; Martha Sutula; Daniele Bianchi; James C. McWilliams; Curtis Deutsch, and Evan Howard. “Effects of urban eutrophication on pelagic habitat capacity in the Southern California Bight.” Frontiers in Marine Science 11 (2024). 10.3389/fmars.2024.1392671.
“Additional computational resources were provided by the Hoffman2 computer cluster at the University of California Los Angeles, Institute for Digital Research and Education (IDRE).” (Frieder et al., 2024, p. 10)
Fu, Hongxiang; Harry Pickering; Liudmilla Rubbi; Ted M. Ross; Elaine F. Reed, and Matteo Pellegrini. “Longitudinal analysis of influenza vaccination implicates regulation of RIG-I signaling by DNA methylation.” Scientific Reports 14 no. 1 (2024): 1455. 10.1038/s41598-024-51665-9.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Fu et al., 2024, p. 11) Number: 1
Fu, Xiaoyang; Dongfang Cheng; Ao Zhang; Jingxuan Zhou; Sibo Wang; Xun Zhao; Jun Chen; Philippe Sautet; Yu Huang, and Xiangfeng Duan. “Ag–Ru interface for highly efficient hydrazine assisted water electrolysis.” Energy & Environmental Science 17 no. 6 (2024): 2279-2286. 10.1039/D3EE02981F.
“D. C. used the HOFFMAN2 cluster at the UCLA Institute for Digital Research Education (IDRE).” (Fu et al., 2024, p. 7-8)
Fu, Zihuan; Joseph W. Treacy; Brock M. Hosier; K. N. Houk, and Heather D. Maynard. “Controlling rates and reversibilities of elimination reactions of hydroxybenzylammoniums by tuning dearomatization energies.” Chemical Science 15 no. 27 (2024): 10448-10454. 10.1039/D4SC02985B.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Fu et al., 2024, p. 10453) Edge Article
Gardner, Anna; Eric Baxter; Srinivasan Raghunathan; Weiguang Cui, and Daniel Ceverino. “Prospects for studying the mass and gas in protoclusters with future CMB observations.” The Open Journal of Astrophysics 7 (2024). 10.21105/astro.2307.15309.
“This work also used the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Gardner et al., 2024, p. 12)
Gautam, Abhimat K.; Tuan Do; Andrea M. Ghez; Devin S. Chu; Matthew W. Hosek; Shoko Sakai; Smadar Naoz; Mark R. Morris; Anna Ciurlo; Zoë Haggard, and Jessica R. Lu. “An Estimate of the Binary Star Fraction among Young Stars at the Galactic Center: Possible Evidence of a Radial Dependence.” The Astrophysical Journal 964 no. 2 (2024): 164. 10.3847/1538-4357/ad26e6.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Gautam et al., 2024, p. 27)
Gilman, Daniel; Simon Birrer; Anna Nierenberg, and Maverick S H Oh. “Turbocharging constraints on dark matter substructure through a synthesis of strong lensing flux ratios and extended lensed arcs.” Monthly Notices of the Royal Astronomical Society 533 no. 2 (2024): 1687-1713. 10.1093/mnras/stae1810.
“Computations performed for this analysis were performed on the Midway2 and Midway3 clusters hosted by the University of Chicago’s Research Computing Center, the Niagara supercomputer at the SciNet HPC Consortium, and the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Gilman et al., 2024, p. 1709)
Goldstein, David. “Divergence-time estimation in Indo-European: The case of Latin.” Diachronica 41 no. 1 (2024): 1-45. 10.1075/dia.22031.gol.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Goldstein, 2024, p. 42)
Guan, Yani; Justus Kümper; Sonja D. Mürtz; Simran Kumari; Peter J. C. Hausoul; Regina Palkovits, and Philippe Sautet. “Origin of copper dissolution under electrocatalytic reduction conditions involving amines.” Chemical Science 15 no. 35 (2024): 14485-14496. 10.1039/D4SC01944J.
“Computational resources for this work were provided by the UCLA-shared cluster Hoffman2 and the Expanse cluster through the allocation CHE170060 at the San Diego Supercomputing Center through ACCESS.” (Guan et al., 2024, p. 14495)
Guo, Yuxuan; Yang Luo; Roshan Plamthottam; Siyou Pei; Chen Wei; Ziqing Han; Jiacheng Fan; Mason Possinger; Kede Liu; Yingke Zhu; Zhangqing Fei; Isabelle Winardi; Hyeonji Hong; Yang Zhang; Lihua Jin, and Qibing Pei. “Haptic artificial muscle skin for extended reality.” Science Advances 10 no. 43 (2024): eadr1765. 10.1126/sciadv.adr1765.
“This work used computational and storage services associated with the hoffman2 Shared cluster provided by institute for digital Research and education’s Research technology Group at the University of california, los Angeles.” (Guo et al., 2024, p. 11)
Gutkin, Sara; Omri Shelef; Zuzana Babjaková; Laura Anna Tomanová; Matej Babjak; Tal Kopp; Qingyang Zhou; Pengchen Ma; Micha Fridman; Urs Spitz; Kendall N. Houk, and Doron Shabat. “Boosting Chemiexcitation of Phenoxy-1,2-dioxetanes through 7-Norbornyl and Homocubanyl Spirofusion.” JACS Au 4 no. 9 (2024): 3558-3566. 10.1021/jacsau.4c00493.
“K.N.H. thanks the US National Science Foundation for financial support (CHE-2153972) and the UCLA Institute for Digital Research for access to the Hoffman2 shared cluster.” (Gutkin et al., 2024, p. 3565)
Hayes-Larson, Eleanor; Yixuan Zhou; L. Paloma Rojas-Saunero; Crystal Shaw; Marissa J. Seamans; M. Maria Glymour; Audrey R. Murchland; Daniel Westreich, and Elizabeth Rose Mayeda. “Methods for Extending Inferences From Observational Studies: Considering Causal Structures, Identification Assumptions, and Estimators.” Epidemiology 35 no. 6 (2024): 753. 10.1097/EDE.0000000000001780.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Office of Advanced Research Computing’s Research Technology Group.” (Hayes-Larson et al., 2024, p. 762)
He, Sicong; Brian D. Wirth; Lance Snead; Jason R. Trelewicz; Yutai Katoh; Steve J. Zinkle, and Jaime Marian. “Simulations of radiation damage accumulation in Fe-9Cr under pulsed irradiation conditions representative of inertial fusion energy.” Journal of Nuclear Materials 601 (2024): 155325. 10.1016/j.jnucmat.2024.155325.
“All numerical simulations were performed on the Hoffman2 computer cluster at UCLA’s Institute for Digital Research and Education.” (He et al., 2024, p. 11)
Hoel, Paige; Allison R. Moreno, and Daniele Bianchi. “Mechanisms controlling lower trophic ecosystem response to ocean outfall discharges: Role of nitrogen form and freshwater volume.” Regional Studies in Marine Science 78 (2024): 103739. 10.1016/j.rsma.2024.103739.
“Additional computational resources were provided by the Hoffman2 computer cluster at the University of California Los Angeles, Institute for Digital Research and Education (IDRE).” (Hoel et al., 2024, p. 10)
Ippoliti, Francesca M.; Laura G. Wonilowicz; Nathan J. Adamson; Evan R. Darzi; Joyann S. Donaldson; Daniel J. Nasrallah; Milauni M. Mehta; Andrew V. Kelleghan; K. N. Houk, and Neil K. Garg. “Total Synthesis of Lissodendoric Acid A.” Angewandte Chemie International Edition 63 no. 32 (2024): e202406676. 10.1002/anie.202406676.
“Calculations were performed ontheHoffman2 cluster and theUCLA Institute ofDigital Research andEducation (IDRE) atUCLA andtheExtreme Science and Engineering Discovery Environment (XSEDE), which issupported bytheNational Science Foundation (OCI1053575).” (Ippoliti et al., 2024, p. 11)
Jung, Su Yon; Herbert Yu; Xianglong Tan, and Matteo Pellegrini. “Novel DNA methylation-based epigenetic signatures in colorectal cancer from peripheral blood leukocytes.” American Journal of Cancer Research 14 no. 5 (2024): 2253-2271. 10.62347/MXWJ1398.
“All statistical analyses were performed with R through UCLA’s Hoffman2 high-performance computing cluster.” (Jung et al., 2024, p. 2257) PMID: 38859857 PMCID: PMC11162685
Kelleghan, Andrew V.; Arismel Tena Meza, and Neil K. Garg. “Generation and reactivity of unsymmetrical strained heterocyclic allenes.” Nature Synthesis 3 (2024): 329-336. 10.1038/s44160-023-00432-1.
“Calculations were performed on the Hoffman2 cluster and the University of California, Los Angeles (UCLA) Institute of Digital Research and Education and the Extreme Science and Engineering Discovery Environment, which is supported by the NSF (OCI-1053575). We thank K. N. Houk (UCLA) for computational resources and helpful discussions and S. Khan (UCLA) for X-ray analysis.” (Kelleghan et al., 2023).
Kessouri, Fayçal; Martha A. Sutula; Daniele Bianchi; Minna Ho; Pierre Damien; James C. McWilliams; Christina A. Frieder; Lionel Renault; Hartmut Frenzel; Karen McLaughlin, and Curtis Deutsch. “Cross-shore transport and eddies promote large scale response to urban eutrophication.” Scientific Reports 14 no. 1 (2024): 7240. 10.1038/s41598-024-57626-6.
“Additional computational resources were provided by the Hoffman2 computer cluster at the University of California, Los Angeles, Institute for Digital Research and Education (IDRE).” (Kessouri et al., 2024, p. 17)
Kim, Youngjae; Vedasri Godavarthi; Laura Victoria Rolandi; Joseph T. Klamo, and Kunihiko Taira. “Influence of three-dimensionality on wake synchronisation of an oscillatory cylinder.” Journal of Fluid Mechanics 1001 (2024): A24. 10.1017/jfm.2024.1079.
“This work used Expanse at the San Diego Supercomputing Center (SDSC) through allocation PHY230016 from the Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support (ACCESS) program and Hoffman2 provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Kim et al., 2024, p. 22)
Kowalski, Robert Michael; Avishek Banerjee; Chudi Yue; Sara G. Gracia; Dongfang Cheng; Carlos G. Morales-Guio, and Philippe Sautet. “Electroreduction of Captured CO2 on Silver Catalysts: Influence of the Capture Agent and Proton Source.” Journal of the American Chemical Society 146 no. 30 (2024): 20728-20741. 10.1021/jacs.4c03915.
“Computational calculations were run on the UCLA Institute for Digital Research and Education’s Research Technology Group’s cluster Hoffman2 and Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support’s (ACCESS) clusters Expanse and Bridges2 through the allocation CHE170060 at the San Diego Supercomputing Center through ACCESS.” (Kowalski et al., 2024, p. 20740)
Kunkel, Grace E.; Joseph W. Treacy; Magdalena F. Polite; Hayden R. Montgomery; Evan A. Doud; Kendall N. Houk; Alexander M. Spokoyny, and Heather D. Maynard. “Heterotelechelic Organometallic PEG Reagents Enable Modular Access to Complex Bioconjugates.” ACS Macro Letters 13 no. 11 (2024): 1551-1557. 10.1021/acsmacrolett.4c00588.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Kunkel et al., 2024, p. 1556)
Lake, William; Claire E. Williams; Smadar Naoz; Federico Marinacci; Blakesley Burkhart; Mark Vogelsberger; Naoki Yoshida; Gen Chiaki; Avi Chen, and Yeou S. Chiou. “The Supersonic Project: Early Star Formation with the Streaming Velocity.” The Astrophysical Journal 973 no. 2 (2024): 115. 10.3847/1538-4357/ad6762.
“W.L., S.N., Y.S.C, B.B., F.M., and M.V. are grateful for the support of NASA ATP grant No. 80NSSC20K0500 (19ATP19-0020) and the XSEDE AST180056 allocation, as well as to the Simons Foundation Center for Computational Astrophysics and the UCLA cluster Hoffman2 for computational resources.” (Lake et al., 2024, p. 9)
Lee, Woojin; Tyler R. Benton; Arkajyoti Sengupta, and K. N. Houk. “Molecular Dynamics of the Norbornyl Cation in Solution and Its Generation in Winstein–Trifan Solvolysis: The Timing of Sigma Bridging.” The Journal of Organic Chemistry 89 no. 2 (2024): 1140-1146. 10.1021/acs.joc.3c02325.
“All calculations were performed on computational resources provided by the UCLA Institute of Digital Research and Education and the NSF Extreme Science and Engineering Discovery Environment.” (Lee et al., 2024, p. 1144)
Levandowski, Brian J.; Brian J. Graham; K. N. Houk, and Ronald T. Raines. “Click Organocatalysis: Acceleration of Azide–Alkyne Cycloadditions with Mutually Orthogonal Click Reactions.” The Journal of Organic Chemistry 89 no. 4 (2024): 2232-2237. 10.1021/acs.joc.3c02182.
“This work used computational and storage services associated with theHoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Levandowski et al., 2024, p. 2236)
Liepuoniute, Ieva; Jing-Ran Shan; K. N. Houk, and Miguel A. Garcia-Garibay. “Computational Study of Ground-State Destabilization Effects and Dipole–Dipole Interaction Energies in Amphidynamic Crystals.” The Journal of Organic Chemistry 89 no. 1 (2024): 9-15. 10.1021/acs.joc.3c00465.
“Computations were performed ontheHoffman2 cluster at UCLA” (Liepuoniute et al., 2023, p. 6)
Lubinski, Thomas; Carleton Coffrin; Catherine McGeoch; Pratik Sathe; Joshua Apanavicius; David Bernal Neira, and Quantum Economic Development Consortium(QED-C) Collaboration. “Optimization Applications as Quantum Performance Benchmarks.” ACM Transactions on Quantum Computing 5 no. 3 (2024): 18:1–18:44. 10.1145/3678184.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute of Digital Research and Education’s Research Technology Group.” (Lubinski et al., 2024, p. 1)
Ma, Pengchen; Dennis Svatunek; Zixi Zhu; Dale L. Boger; Xin-Hua Duan, and K. N. Houk. “Computational Studies of Reactions of 1,2,4,5-Tetrazines with Enamines in MeOH and HFIP.” Journal of the American Chemical Society 146 no. 27 (2024): 18706-18713. 10.1021/jacs.4c06067.
“K.N.H. and P.M. are thankful for computation resources from Hoffman2 cluster at UCLA and Expanse at SDSC through allocation CHE040014 from the Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) program.” (Ma et al., 2024, p. 18711)
Mao, Runze; Doris Mia Taylor; Daniel J. Wackelin; Torben Rogge; Sophia J. Wu; Kathleen M. Sicinski; K. N. Houk, and Frances H. Arnold. “Biocatalytic, stereoconvergent alkylation of (Z/E)-trisubstituted silyl enol ethers.” Nature Synthesis 3 no. 2 (2024): 256-264. 10.1038/s44160-023-00431-2.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles.” (Mao et al., 2023).
McDermott, Luca; Zach G. Walters; Sarah A. French; Allison M. Clark; Jiaming Ding; Andrew V. Kelleghan; K. N. Houk, and Neil K. Garg. “A solution to the anti-Bredt olefin synthesis problem.” Science 386 no. 6721 (2024): eadq3519. 10.1126/science.adq3519.
“Calculations were performed on the UCLA Hoffman2 cluster and at the UCLA Institute of Digital Research and Education (IDRE).” (McDermott et al., 2024, p. 9)
Mei, Kenneth J.; William R. Borrelli; José L. Guardado Sandoval, and Benjamin J. Schwartz. “How to Probe Hydrated Dielectrons Experimentally: Ab Initio Simulations of the Absorption Spectra of Aqueous Dielectrons, Electron Pairs, and Hydride.” The Journal of Physical Chemistry Letters 15 no. 38 (2024): 9557-9565. 10.1021/acs.jpclett.4c02404.
“We gratefully acknowledge the Institute for Digital Research and Education (IDRE) at UCLA for use of the Hoffman2 computing cluster and ACCESS under computational project TG-CHE230086.” (Mei et al., 2024, p. 9563)
Mei, Kenneth J.; William R. Borrelli; Andy Vong, and Benjamin J. Schwartz. “Using Machine Learning to Understand the Causes of Quantum Decoherence in Solution-Phase Bond-Breaking Reactions.” The Journal of Physical Chemistry Letters 15 no. 4 (2024): 903-911. 10.1021/acs.jpclett.3c03474.
“We gratefully acknowledge the Institute for Digital Research and Education (IDRE) at UCLA for use of the Hoffman2 computing cluster.” (Mei et al., 2024, p. 909)
Mei, Kenneth J. and Benjamin J. Schwartz. “How Solvation Alters the Thermodynamics of Asymmetric Bond-Breaking: Quantum Simulation of NaK+ in Liquid Tetrahydrofuran.” The Journal of Physical Chemistry Letters 15 no. 32 (2024): 8187-8195. 10.1021/acs.jpclett.4c01636.
“We gratefully acknowledge the Institute for Digital Research and Education (IDRE) at UCLA for use of the Hoffman2 computing cluster.” (Mei and Schwartz, 2024, p. 8193)
Miao, Yu; Tianxiang Zhou; Xiaoru Zheng, and Shaily Mahendra. “Investigating Biodegradation of 1,4-Dioxane by Groundwater and Soil Microbiomes: Insights into Microbial Ecology and Process Prediction.” ACS ES&T Water 4 no. 3 (2024): 1046-1060. 10.1021/acsestwater.3c00185.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Miao et al., 2024, p. L)
Ming Yu, Husan; Shivam Sharma; Shivang Agarwal; Olivia Liebman, and Amartya S. Banerjee. “Carbon Kagome nanotubes—quasi-one-dimensional nanostructures with flat bands.” RSC Advances 14 no. 2 (2024): 963-981. 10.1039/D3RA06988E.
“The authors would like to thank UCLA’s Institute for Digital Research and Education (IDRE) and the Minnesota Supercomputing Institute (MSI) for making available some of the computing resources used in this work.” (Ming Yu et al., 2024, p. 977)
Minor, Christine M.; Allen Takayesu; Sung Min Ha; Lukasz Salwinski; Michael R. Sawaya; Matteo Pellegrini, and Robert T. Clubb. “A genomic analysis reveals the diversity of cellulosome displaying bacteria.” Frontiers in Microbiology 15 (2024). 10.3389/fmicb.2024.1473396.
“This work used computational and storage services associated with the Hoffman2 Cluster which is operated by the UCLA Office of Advanced Research Computing’s Research Technology Group.” (Minor et al., 2024, p. 15)
Morgan, H. W. T.; W. T. Laderer, and A. N. Alexandrova. “δ-Bonding and Spin-Orbit Coupling Make SrAg4Sb2 a Topological Insulator.” Chemistry – A European Journal 30 no. 17 (2024): e202303679. 10.1002/chem.202303679.
“This work was supported by the Brown Science Foundation Award 1168 to A.N.A. and computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Morgan et al., 2024, p. 5)
Ngan, Hio Tong and Philippe Sautet. “Tuning the Hydrogenation Selectivity of an Unsaturated Aldehyde via Single-Atom Alloy Catalysts.” Journal of the American Chemical Society 146 no. 4 (2024): 2556-2567. 10.1021/jacs.3c10994.
“DFT calculations reported in this work used computational and storage resources on the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE), the National Energy Research Scientific Computing Center (NERSC) of the U.S.Department of Energy, and the Bridges-2 cluster through the allocation CHE170060 at the Pittsburgh Supercomputing Center through ACCESS.” (Ngan and Sautet, 2024, p. K)
Niknam, Mohamad and Louis-S. Bouchard. “Nuclear induction line shape: Non-Markovian diffusion with boundaries.” The Journal of Chemical Physics 160 no. 2 (2024): 024305. 10.1063/5.0179178.
“The computational and storage services used in this work are part of the Hoffman2 Shared Cluster, provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Niknam and Bouchard, 2024, p. 9)
Ou, Feiyang; Fahim Abdullah; Henrik Wang; Matthew Tom; Gerassimos Orkoulas, and Panagiotis D. Christofides. “Sparse identification modeling and predictive control of wafer temperature in an atomic layer etching reactor.” Chemical Engineering Research and Design 202 (2024): 1-11. 10.1016/j.cherd.2023.12.024.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Ou et al., 2024, p. 11)
Ou, Feiyang; Henrik Wang; Chao Zhang; Matthew Tom; Sthitie Bom; James F. Davis, and Panagiotis D. Christofides. “Industrial data-driven machine learning soft sensing for optimal operation of etching tools.” Digital Chemical Engineering 13 (2024): 100195. 10.1016/j.dche.2024.100195.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Ou et al., 2024, p. 17)
Pathrudkar, Shashank; Ponkrshnan Thiagarajan; Shivang Agarwal; Amartya S. Banerjee, and Susanta Ghosh. “Electronic structure prediction of multi-million atom systems through uncertainty quantification enabled transfer learning.” npj Computational Materials 10 no. 1 (2024): 1-15. 10.1038/s41524-024-01305-7.
“Raw data were generated at Hoffman2 High-Performance Compute Cluster at UCLA’s Institute for Digital Research and Education (IDRE) and National Energy Research Scientific Computing Center (NERSC).” (Pathrudkar et al., 2024, p. 12)
Prabhu, K.; S. Raghunathan; M. Millea; G. P. Lynch; P. A. R. Ade; E. Anderes; A. J. Anderson; B. Ansarinejad; M. Archipley; L. Balkenhol; K. Benabed; A. N. Bender; B. A. Benson; F. Bianchini; L. E. Bleem; F. R. Bouchet; L. Bryant; E. Camphuis; J. E. Carlstrom; T. W. Cecil; C. L. Chang; P. Chaubal; P. M. Chichura; A. Chokshi; T.-L. Chou; A. Coerver; T. M. Crawford; A. Cukierman; C. Daley; T. de Haan; K. R. Dibert; M. A. Dobbs; A. Doussot; D. Dutcher; W. Everett; C. Feng; K. R. Ferguson; K. Fichman; A. Foster; S. Galli; A. E. Gambrel; R. W. Gardner; F. Ge; N. Goeckner-Wald; R. Gualtieri; F. Guidi; S. Guns; N. W. Halverson; E. Hivon; G. P. Holder; W. L. Holzapfel; J. C. Hood; A. Hryciuk; N. Huang; F. Kéruzoré; L. Knox; M. Korman; K. Kornoelje; C.-L. Kuo; A. T. Lee; K. Levy; A. E. Lowitz; C. Lu; A. Maniyar; F. Menanteau; J. Montgomery; Y. Nakato; T. Natoli; G. I. Noble; V. Novosad; Y. Omori; S. Padin; Z. Pan; P. Paschos; K. A. Phadke; A. W. Pollak; W. Quan; M. Rahimi; A. Rahlin; C. L. Reichardt; M. Rouble; J. E. Ruhl; E. Schiappucci; G. Smecher; J. A. Sobrin; A. A. Stark; J. Stephen; A. Suzuki; C. Tandoi; K. L. Thompson; B. Thorne; C. Trendafilova; C. Tucker; C. Umilta; A. Vitrier; J. D. Vieira; Y. Wan; G. Wang; N. Whitehorn; W. L. K. Wu; V. Yefremenko; M. R. Young, and J. A. Zebrowski. “Testing the ΛCDM Cosmological Model with Forthcoming Measurements of the Cosmic Microwave Background with SPT-3G.” The Astrophysical Journal 973 no. 1 (2024): 4. 10.3847/1538-4357/ad5ff1.
This work made use of the following computing resources: Illinois Campus Cluster, a computing resource that is operated by the Illinois Campus Cluster Program (ICCP) in conjunction with the National Center for Supercomputing Applications (NCSA) and which is supported by funds from the University of Illinois at Urbana-Champaign; the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group; the computing resources provided on Crossover, a high-performance computing cluster operated by the Laboratory Computing Resource Center at Argonne National Laboratory; and the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the US Department of Energy under contract No. DE-AC02-05CH11231.” (Prabhu et al., 2024, p. 17)
Psaras, Catherine; Annette Regan; Roch Nianogo; Onyebuchi A Arah, and Marissa J Seamans. “The impact of maternal pertussis vaccination recommendation on infant pertussis incidence and mortality in the USA: an interrupted time series analysis.” International Journal of Epidemiology 53 no. 1 (2024): dyad161. 10.1093/ije/dyad161.
“UCLA Institute for Digital Research and Education’s Research Technology Group provided computational and storage services associated with the Hoffman2 Shared Cluster.” (Psaras et al., 2023, p. 7)
Quarshie, Henry Elorm; Henry Martin; Eric Kwabena Kyeh Abavare, and Alessandra Continenza. “Ab-initio study of the transition pathways for single and double interstitial solute (H, N, O, H-H, N-N, and O-O) within bcc refractory metals (Mo and Nb).” MRS Advances (2024). 10.1557/s43580-024-01028-3.
“This work was conducted using resources from the Lengau Cluster at the Centre for High-Performance Computing (CHPC) in Cape Town, South Africa, the CINECA high-performance computing (HPC) Center in Italy through project name IsCa5_VIMFIML and code HP10CURIS1, and the Hoffman2 shared cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Quarshie et al., 2024, p. 7)
Riu, Martin-Louis Y.; Stasik Popov; Benjamin Wigman; Zhenqi Zhao; Jonathan Wong; Kendall N. Houk, and Hosea M. Nelson. “Carbon–Carbon Bond Forming Reactions of Vinyl Cations: A Personal Perspective.” European Journal of Organic Chemistry 27 no. 43 (2024): e202400567. 10.1002/ejoc.202400567.
“Work by the Houk group used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Riu et al., 2024, p. 8)
Rogge, Torben; Qingyang Zhou; Nicholas J. Porter; Frances H. Arnold, and K. N. Houk. “Iron Heme Enzyme-Catalyzed Cyclopropanations with Diazirines as Carbene Precursors: Computational Explorations of Diazirine Activation and Cyclopropanation Mechanism.” Journal of the American Chemical Society 146 no. 5 (2024): 2959-2966. 10.1021/jacs.3c06030.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and Expanse at the San Diego Supercomputer Center(SDSC).” (Rogge et al., 2024, p. G)
Sedillo, Kassandra; Flora Fan; Robert R. Knowles, and Abigail G. Doyle. “Cooperative Phosphine-Photoredox Catalysis Enables N–H Activation of Azoles for Intermolecular Olefin Hydroamination.” Journal of the American Chemical Society 146 no. 29 (2024): 20349-20356. 10.1021/jacs.4c05881.
“Financial support for this work was provided by the NIGMS (R35GM126986 to AGD and R35-GM134893 to RRK). These studies were also supported by shared instrumentation grants from the National Science Foundation (CHE-1048804), NIH Office of Research Infrastructure Programs (S10OD028644), and used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Sedillo et al., 2024, p. 20355)
Shariat, Cheyanne; Smadar Naoz; Kareem El-Badry; Antonio C. Rodriguez; Bradley M. S. Hansen; Isabel Angelo, and Alexander P. Stephan. “Once a Triple, Not Always a Triple: The Evolution of Hierarchical Triples That Yield Merged Inner Binaries.” The Astrophysical Journal 978 no. 1 (2024): 47. 10.3847/1538-4357/ad944a.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computings Research Technology Group.” (Shariat et al., 2024, p. 14)
Shen, Mengxin; Liyao Ji; Dongfang Cheng; Ziwei Wang; Qinwen Xue; Shijia Feng; Yao Luo; Shuying Chen; Jiahao Wang; Hongzhi Zheng; Xiaojun Wang; Philippe Sautet, and Jia Zhu. “Hierarchical design enables sufficient activated CO2 for efficient electrolysis of bicarbonate to CO.” Joule 8 no. 7 (2024): 1999-2015. 10.1016/j.joule.2024.04.006.
“The authors acknowledge the micro-fabrication center of the National Laboratory of Solid State Microstructures (NLSSM) for technical support. This study has been supported by the New Cornerstone Science Foundation through the XPLORER PRIZE. D.C. and P.S. acknowledged the National Science Foundation CBET grant 2103116, the Audi CO2 Cy Pres Award, and computational resources from the Hoffman2 cluster at UCLA Institute for Digital Research and Education (IDRE).” (Shen et al., 2024, p. 2014)
Si, Yidongfang; Andrew L. Stewart; Alessandro Silvano, and Alberto C. Naveira Garabato. “Antarctic Slope Undercurrent and onshore heat transport driven by ice shelf melting.” Science Advances 10 no. 16 (2024): eadl0601. 10.1126/sciadv.adl0601.
“This work used the hoffman2 cluster, which is supported by the IDRE Research technology Group at UCLA. This work also used the Extreme Science and engineering discovery environment (XSede) (61), which is supported by the national Science Foundation grant number Aci-1548562.” (Si et al., 2024, p. 14)
SPT-3G and SPTpol Collaboration; S. Raghunathan; P. A. R. Ade; A. J. Anderson; B. Ansarinejad; M. Archipley; J. E. Austermann; L. Balkenhol; J. A. Beall; K. Benabed; A. N. Bender; B. A. Benson; F. Bianchini; L. E. Bleem; J. Bock; F. R. Bouchet; L. Bryant; E. Camphuis; J. E. Carlstrom; T. W. Cecil; C. L. Chang; P. Chaubal; H. C. Chiang; P. M. Chichura; T.-L. Chou; R. Citron; A. Coerver; T. M. Crawford; A. T. Crites; A. Cukierman; C. Daley; K. R. Dibert; M. A. Dobbs; A. Doussot; D. Dutcher; W. Everett; C. Feng; K. R. Ferguson; K. Fichman; A. Foster; S. Galli; J. Gallicchio; A. E. Gambrel; R. W. Gardner; F. Ge; E. M. George; N. Goeckner-Wald; R. Gualtieri; F. Guidi; S. Guns; N. Gupta; T. de Haan; N. W. Halverson; E. Hivon; G. P. Holder; W. L. Holzapfel; J. C. Hood; J. D. Hrubes; A. Hryciuk; N. Huang; J. Hubmayr; K. D. Irwin; F. Kéruzoré; A. R. Khalife; L. Knox; M. Korman; K. Kornoelje; C.-L. Kuo; A. T. Lee; K. Levy; D. Li; A. E. Lowitz; C. Lu; A. Maniyar; E. S. Martsen; J. J. McMahon; F. Menanteau; M. Millea; J. Montgomery; C. Corbett Moran; Y. Nakato; T. Natoli; J. P. Nibarger; G. I. Noble; V. Novosad; Y. Omori; S. Padin; Z. Pan; P. Paschos; S. Patil; K. A. Phadke; K. Prabhu; C. Pryke; W. Quan; M. Rahimi; A. Rahlin; C. L. Reichardt; M. Rouble; J. E. Ruhl; B. R. Saliwanchik; K. K. Schaffer; E. Schiappucci; C. Sievers; G. Smecher; J. A. Sobrin; A. A. Stark; J. Stephen; A. Suzuki; C. Tandoi; K. L. Thompson; B. Thorne; C. Trendafilova; C. Tucker; C. Umilta; T. Veach; J. D. Vieira; M. P. Viero; Y. Wan; G. Wang; N. Whitehorn; W. L. K. Wu; V. Yefremenko; M. R. Young; J. A. Zebrowski, and M. Zemcov. “First Constraints on the Epoch of Reionization Using the Non-Gaussianity of the Kinematic Sunyaev-Zel’dovich Effect from the South Pole Telescope and Herschel-SPIRE Observations.” Physical Review Letters 133 no. 12 (2024): 121004. 10.1103/PhysRevLett.133.121004.
“This work made use of the following computing resources: Illinois Campus Cluster, a computing resource that is operated by the Illinois Campus Cluster Program (ICCP) in conjunction with the National Center for Supercomputing Applications (NCSA) and which is supported by funds from the University of Illinois at Urbana-Champaign; the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group; and the computing resources provided on Crossover, a high-performance computing cluster operated by the Laboratory Computing Resource Center at Argonne National Laboratory. The South Pole Telescope program is supported by the National Science Foundation (NSF) through grant OPP-1852617.” (SPT-3G and SPTpol Collaboration et al., 2024, p. 6-7)
Stephan, Alexander P.; David V. Martin; Smadar Naoz; Nathan R. Hughes, and Cheyanne Shariat. “Two Novel Hot Jupiter Formation Pathways: How White Dwarf Kicks Shape the Hot Jupiter Population.” The Astrophysical Journal Letters 977 no. 1 (2024): L11. 10.3847/2041-8213/ad94d8.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computingʼs Research Technology Group, and the resources provided by the Vanderbilt Advanced Computing Center for Research and Education (ACCRE).” (Stephan et al., 2024, p. 9)
Su, Erica; Robert E. Weiss; Kouros Nouri-Mahdavi, and Andrew J. Holbrook. “A spatially varying hierarchical random effects model for longitudinal macular structural data in glaucoma patients.” The Annals of Applied Statistics 18 no. 4 (2024): 3444-3466. 10.1214/24-AOAS1944.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Su et al., 2024, p. 3463)
Svatunek, Dennis; Anton Murnauer; Zhuoting Tan; K. N. Houk, and Kathrin Lang. “How cycloalkane fusion enhances the cycloaddition reactivity of dibenzocyclooctynes.” Chemical Science 15 no. 6 (2024): 2229-2235. 10.1039/D3SC05789E.
“Computational results presented were obtained using the Vienna Scientific Cluster (VSC) at TU Wien and the Hoffman2 cluster at UCLA.” (Svatunek et al., 2024, p. 2234)
Tang, Yu; George Yan; Shiran Zhang; Yuting Li; Luan Nguyen; Yasuhiro Iwasawa; Tomohiro Sakata; Christopher Andolina; Judith C. Yang; Philippe Sautet, and Franklin Feng Tao. “Turning on Low-Temperature Catalytic Conversion of Biomass Derivatives through Teaming Pd1 and Mo1 Single-Atom Sites.” Journal of the American Chemical Society 146 no. 47 (2024): 32366-32382. 10.1021/jacs.4c07075.
“The calculations in this work used computational and storage services associated with the Hoffman2 shared computational cluster located at UCLA.” (Tang et al., 2024, p. O)
Tannous, Rozan; Omri Shelef; Sara Gutkin; Maya David; Thomas Leirikh; Liang Ge; Qais Jaber; Qingyang Zhou; Pengchen Ma; Micha Fridman; Urs Spitz; Kendall N. Houk, and Doron Shabat. “Spirostrain-Accelerated Chemiexcitation of Dioxetanes Yields Unprecedented Detection Sensitivity in Chemiluminescence Bioassays.” ACS Central Science 10 no. 1 (2024): 28-42. 10.1021/acscentsci.3c01141.
“K.N.H. thanks the US National Science Foundation for financial support (CHE-2153972) andtheUCLA Institute for Digital Research for access to the Hoffman2 shared cluster.” (Tannous et al., 2024, p. 40)
Tesvara, Celine; Md Raian Yousuf; Malik Albrahim; Diego Troya; Abhijit Shrotri; Eli Stavitski; Ayman M. Karim, and Philippe Sautet. “Unraveling the CO Oxidation Mechanism over Highly Dispersed Pt Single Atom on Anatase TiO2 (101).” ACS Catalysis 14 no. 10 (2024): 7562-7575. 10.1021/acscatal.4c01018.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group and by the hardware at Virginia Tech’s Advanced Research Computing.” (Tesvara et al., 2024, p. 7573)
Tom, Matthew; Henrik Wang; Feiyang Ou; Gerassimos Orkoulas, and Panagiotis D. Christofides. “Machine Learning Modeling and Run-to-Run Control of an Area-Selective Atomic Layer Deposition Spatial Reactor.” Coatings 14 no. 1 (2024): 38. 10.3390/coatings14010038.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Tom et al., 2024, p. 16)
Travis, Christopher R.; Ryan G. Dumais; Joseph W. Treacy; Kelsey M. Kean; K. N. Houk, and Marcey L. Waters. “Contribution of Electrostatic CH3–π Interactions to Recognition of Histone Asymmetric Dimethylarginine by the SPIN1 Triple Tudor Domain.” Journal of the American Chemical Society 146 no. 30 (2024): 20678-20684. 10.1021/jacs.4c03463.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Travis et al., 2024, p. 20683)
Travis, Christopher R.; Hanne C. Henriksen; Jake R. Wilkinson; Noah K. Schomburg; Joseph W. Treacy; Kelsey M. Kean; K. N. Houk, and Marcey L. Waters. “WDR5 Binding to Histone Serotonylation Is Driven by an Edge–Face Aromatic Interaction with Unexpected Electrostatic Effects.” Journal of the American Chemical Society 146 no. 40 (2024): 27451-27459. 10.1021/jacs.4c07277.
“This work used computational and storage services associated with the Hoff-man2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Travis et al., 2024, p. 27457)
Travis, Christopher R.; Kelsey M. Kean; Katherine I. Albanese; Hanne C. Henriksen; Joseph W. Treacy; Elaine Y. Chao; K. N. Houk, and Marcey L. Waters. “Trimethyllysine Reader Proteins Exhibit Widespread Charge-Agnostic Binding via Different Mechanisms to Cationic and Neutral Ligands.” Journal of the American Chemical Society 146 no. 5 (2024): 3086-3093. 10.1021/jacs.3c10031.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided bythe UCLA Institute for Digital Research and Education’s Research Technology Group.” (Travis et al., 2024, p. F)
Treacy, Joseph W.; Elaine Y. Chao; Grace E. Kunkel; Thomas Louis-Goff; James A. R. Tilden; Alexander M. Spokoyny; Heather D. Maynard, and K. N. Houk. “Electronic Effects of Bidentate P,N-Ligands on the Elementary Steps of Au(I)/Au(III) Reactions Relevant to Cross-Coupling Chemistry.” Organic Letters 26 no. 50 (2024): 10875-10879. 10.1021/acs.orglett.4c04045.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Treacy et al., 2024, p. 10878)
Tyler, Jasper L.; Felix Schäfer; Huiling Shao; Colin Stein; Audrey Wong; Constantin G. Daniliuc; K. N. Houk, and Frank Glorius. “Bicyclo[1.1.0]butyl Radical Cations: Synthesis and Application to [2π + 2σ] Cycloaddition Reactions.” Journal of the American Chemical Society 146 no. 23 (2024): 16237-16247. 10.1021/jacs.4c04403.
“DFT calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI1053575).” (Tyler et al., 2024, p. 16246)
Wang, Henrik; Feiyang Ou; Julius Suherman; Matthew Tom; Gerassimos Orkoulas, and Panagiotis D. Christofides. “Data-Driven Machine Learning Predictor Model for Optimal Operation of a Thermal Atomic Layer Etching Reactor.” Industrial & Engineering Chemistry Research 63 no. 45 (2024): 19693-19706. 10.1021/acs.iecr.4c03150.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Office of Advanced Research Computing’s Research Technology Group.” (Wang et al., 2024, p. 19705)
Wang, Henrik; Matthew Tom; Feiyang Ou; Gerassimos Orkoulas, and Panagiotis D. Christofides. “Integrating run-to-run control with feedback control for a spatial atomic layer etching reactor.” Chemical Engineering Research and Design 203 (2024): 1-10. 10.1016/j.cherd.2024.01.030.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group” (Wang et al., 2024, p. 7)
Wang, Henrik; Matthew Tom; Feiyang Ou; Gerassimos Orkoulas, and Panagiotis D. Christofides. “Multiscale computational fluid dynamics modeling of an area-selective atomic layer deposition process using a discrete feed method.” Digital Chemical Engineering 10 (2024): 100140. 10.1016/j.dche.2024.100140.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Wang et al., 2024, p. 14)
Weldon, Grant C.; Smadar Naoz, and Bradley M. S. Hansen. “Analytical Models for Secular Descents in Hierarchical Triple Systems.” The Astrophysical Journal 974 no. 2 (2024): 302. 10.3847/1538-4357/ad77a9.
“The authors also acknowledge the use of the UCLA cluster Hoffman2 for computational resources.” (Weldon et al., 2024, p. 9)
Weng, Guorong; William Laderer, and Anastassia N. Alexandrova. “Understanding the Adiabatic Evolution of Surface States in Tetradymite Topological Insulators under Electrochemical Conditions.” The Journal of Physical Chemistry Letters 15 no. 10 (2024): 2732-2739. 10.1021/acs.jpclett.4c00064.
“The computations utilized the following resources: (1) computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group” (Weng et al., 2024, p. 2737)
Williams, Chloe G.; Sepand K. Nistanaki; Krista Dong; Woojin Lee; Kendall N. Houk, and Hosea M. Nelson. “Main Group-Catalyzed Cationic Claisen Rearrangements via Vinyl Carbocations.” Organic Letters 26 no. 23 (2024): 4847-4852. 10.1021/acs.orglett.4c00837.
“Work by the Houk group used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Williams et al., 2024, p. 4851)
Williams, Claire E.; William Lake; Smadar Naoz; Blakesley Burkhart; Tommaso Treu; Federico Marinacci; Yurina Nakazato; Mark Vogelsberger; Naoki Yoshida; Gen Chiaki; Yeou S. Chiou, and Avi Chen. “The Supersonic Project: Lighting Up the Faint End of the JWST UV Luminosity Function.” The Astrophysical Journal Letters 960 no. 2 (2024): L16. 10.3847/2041-8213/ad1491.
“C.E.W., W.L., S.N., Y.S.C., B.B., F.M., and M.V. are thankful for the support of NASA grant No. 80NSSC20K0500 and the XSEDE/ACCESS AST180056 allocation, as well as the UCLA cluster Hoffman2 for computational resources.” (Williams et al., 2024, p. 7)
Wu, Huan and Yongjie Hu. “Ab initio investigations on hydrodynamic phonon transport: From diffusion to convection.” International Journal of Heat and Mass Transfer 220 (2024): 124988. 10.1016/j.ijheatmasstransfer.2023.124988.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group” (Wu and Hu, 2024, p. 7)
Yan, Wenzhong; Talmage Jones; Christopher L. Jawetz; Ryan H. Lee; Jonathan B. Hopkins, and Ankur Mehta. “Self-deployable contracting-cord metamaterials with tunable mechanical properties.” Materials Horizons 11 no. 16 (2024): 3805-3818. 10.1039/D4MH00584H.
“We also acknowledge the use of computational and storage services from the Hoffman2 Shared Cluster, courtesy of the UCLA Office of Advanced Research Computing’s Research Technology Group.” (Yan et al., 2024, p. 3816)
Yeung, Christopher; Benjamin Pham; Zihan Zhang; Katherine T. Fountaine, and Aaswath P. Raman. “Hybrid supervised and reinforcement learning for the design and optimization of nanophotonic structures.” Optics Express 32 no. 6 (2024): 9920-9930. 10.1364/OE.512159.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Yeung et al., 2024, p. 9929)
Yuan, Xintong; Dongfang Cheng; Bo Liu; Kaiyan Liang; Keyue Liang; Jiayi Yu; Matthew Mecklenburg; Philippe Sautet, and Yuzhang Li. “Engineering battery corrosion films by tuning electrical double layer composition.” Joule 8 no. 11 (2024): 3038-3053. 10.1016/j.joule.2024.07.011.
“We thank Dr. Ankun Yang at Oakland University for his assistance with the Raman cell and experiment design. D.C. and P.S. acknowledge the National Science Foundation CBET grant 2103116, the Audi Cy Pres fund award, and computational resources from the Hoffman2 cluster at UCLA Institute for Digital Research and Education (IDRE) and the Expanse cluster through the allocation CHE170060 at the San Diego Supercomputing Center through ACCESS.” (Yuan et al., 2024, p. 14)
Zapata, Felipe; José Cerca; Dana McCarney; Claudia L Henriquez; Bashir B Tiamiyu; John E McCormack; Kelsey R Reckling; Jaime A Chaves, and Gonzalo Rivas-Torres. “Darwin’s overlooked radiation: genomic evidence points to the early stages of a radiation in the Galápagos prickly pear cactus (Opuntia: Cactaceae).” Evolutionary Journal of the Linnean Society 3 no. 1 (2024): kzae021. 10.1093/evolinnean/kzae021.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group, and the Norwegian national infrastructure for high-performance computing and storage.” (Zapata et al., 2024, p. 10)
Zhang, Zisheng; Winston Gee; Philippe Sautet, and Anastassia N. Alexandrova. “H and CO Co-Induced Roughening of Cu Surface in CO2 Electroreduction Conditions.” Journal of the American Chemical Society 146 no. 23 (2024): 16119-16127. 10.1021/jacs.4c03515.
“Computational resources for this work were provided by UCLA shared cluster Hoffman2 and the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program at the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under contract DE-AC02-06CH11357.” (Zhang et al., 2024, p. 16126)
Zhao, Zhenqi; Stasik Popov; Woojin Lee; Jessica E. Burch; David A. Delgadillo; Lee Joon Kim; Mona Shahgholi; Naiara Lebrón-Acosta; K. N. Houk, and Hosea M. Nelson. “Accessing Medium-Sized Rings via Vinyl Carbocation Intermediates.” Organic Letters 26 no. 5 (2024): 1000-1005. 10.1021/acs.orglett.3c04014.
“Computational resources were provided by the UCLA Institute for Digital Research and Education.” (Zhao et al., 2024, p. 1004)
Zhou, Qingyang; Garrett Kukier; Igor Gordiy; Roald Hoffmann; Jeffrey I. Seeman, and K. N. Houk. “A 21st Century View of Allowed and Forbidden Electrocyclic Reactions.” The Journal of Organic Chemistry 89 no. 2 (2024): 1018-1034. 10.1021/acs.joc.3c02103.
“The Houk group acknowledges the National Science Foundation (CHE-2153972) and computational resources at UCLA (Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group) and the NSF XSEDE (now ACCESS) (ACI-1548562).” (Zhou et al., 2024, pp. 1031)
Zhou, Xinran; Annie Barnett; Emily H. Mang; Michael L. Falk; Mitra L. Taheri, and Jaime Marian. “Self-interstitial atom properties in Nb–Mo–Ta–W alloys.” Computational Materials Science 234 (2024): 112765. 10.1016/j.commatsci.2023.112765.
“Computer time allocations at UCLA’s IDRE Hoffman2 supercomputer are acknowledged.” (Zhou et al., 2024, p. 7)
Zhou, Xinran; Sicong He, and Jaime Marian. “Temperature dependence of the strength of Nb-Mo-Ta-W alloys due to screw dislocations.” Scripta Materialia 239 (2024): 115815. 10.1016/j.scriptamat.2023.115815.
“Computer time allocations at UCLA’s IDRE Hoffman2 supercomputer are acknowledged.” (Zhou et al., 2024, p. 5)
Zhu, Guo-Zhu; Guanming Lao; Claire E. Dickerson; Justin R. Caram; Wesley C. Campbell; Anastassia N. Alexandrova, and Eric R. Hudson. “Extending the Large Molecule Limit: The Role of Fermi Resonance in Developing a Quantum Functional Group.” The Journal of Physical Chemistry Letters 15 no. 2 (2024): 590-597. 10.1021/acs.jpclett.3c03177.
“Computational resources were provided by ACCESS and UCLA IDRE.” (Zhu et al., 2024, p. 596)
Theses for 2024¶
Agarwal, Shivang. “Design and Applications of Novel Computational Methods for the Study of Quantum Properties of Emergent Nanomaterials and Biomolecules.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3067598818.
“A lot of the simulations in this work were also performed on the Hoffman2 cluster at UCLA’s Institute for Digital Research and Education (IDRE).” (Agarwal, 2024, p. xxvii)
Alhawaj, Walaa Sameer. “Theoretical Exploration of Carbon Dioxide Hydrogenation to High-Value Hydrocarbons via Heterogeneous Catalysis.” M.S. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3105620994.
“This work utilized the UCLA Institute for Digital Research and Education (IDRE) Hoffman2 Cluster and the Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support’s (ACCESS) San Diego Supercomputer Center’s (SDSC) Expanse and Pittsburg Supercomputing Center’s (PSC) Bridges2 clusters through the allocation CHE170060.” (Alhawaj, 2024, p. xi)
Bhanawat, Abhinav. “Solar Radiation Transfer Through Semitransparent Scattering Media Across Length Scales.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3068717320.
“This work used computational and storage services associated with the Hoffman2 shared cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Bhanawat, 2024, p. xxiv)
Bøen, Rune. “Effects of rare recurrent copy number variations on brain structure.” Doctoral thesis Thesis, Univeristy of Oslo, 2024. www.duo.uio.no, https://www.duo.uio.no/handle/10852/110516.
“For study III, samples were deidentified and stored at a secure high-performance cluster (The Hoffman2 Cluster, Institute for Digital Research and Education Cluster Hosting Program).” (Bøen, 2024, p. 58) Accepted: 2024-04-09T06:34:40Z
Curti, Joseph Nikko. “Species Conservation in the Big Data Era: Leveraging Genomic and Community Science Datasets for Conservation Management.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3144918353.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Curti, 2024, p. 64)
Guan, Yani. “Modeling the Electrocatalytic Interface in the Conditions of Electrochemical Amination of Acetone with Methylamine as Nitrogen Source.” M.S. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/2973883051.
“I acknowledge UCLA for providing the necessary resources and facilities for conducting this research, specifically the UCLA Institute for Digital Research and Education (IDRE) and the computational resources on the Hoffman2 cluster.” (Guan, 2024, pp. xi)
Guo, Wenbin. “Computational Method Development and Analysis for DNA Methylome Studies.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3145827628.
“I want to thank Harray Zhang, Hongxiang Fu, and Junxi Feng for their valuable input and discussion and the Hoffman2 at UCLA for providing essential computational support.” (Guo, 2024, p. 36)
Guo, Wenbin. “Modeling Site-Site Dependency in DNA Methylation Sequencing Data.” M.S. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3144751019.
“We downloaded this data to the UCLA IDRE hoffman2 cluster, where subsequent data processing and analysis steps were performed.” (Guo, 2024, p. 12)
Insixiengmay, Leslie. “Chemical Reactions at the Earth’s Core-Mantle Boundary.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3064054148.
“Most of this work was carried out locally on an 8-core MacBook Pro or through High Performance Computing (HPC) such as the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Insixiengmay, 2024, p. 56)
Kowalski, Robert Michael. “Comparing the reactivity of capture agents and proton source for captured carbon dioxide reduction reaction. A theoretical assessment.” Thesis, UCLA, 2024. escholarship.org, https://escholarship.org/uc/item/65z8v7j8.
“Computational calculations were run on the UCLA Institute for Digital Research and Education’s Research Technology Group’s cluster Hoffman2 and Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support’s (ACCESS) clusters Expanse and Bridges2 through the allocation CHE170060 at the San Diego Supercomputing Center through ACCESS.” (Kowalski, 2024, pp. xi)
Lake, William. “Formation of the First Stars Under the Influence of Streaming.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3144929401.
“This work was made possible through the support of the UCLA Graduate Division through the Dissertation Year Fellowship, as well as the NASA ATP grants 19- ATP19-0020 and 3-ATP23-0149 and the XSEDE and ACCESS AST180056 allocation, as well as the Simons Foundation Center for Computational Astrophysics and the UCLA cluster Hoffman2.” (Lake, 2024, p. xxiii)
Lewis, Briley Lynn. “Applications of High-Contrast Imaging Techniques and Polarimetry to (Exo-)Planetary Science.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3106217273.
“Lastly, this research made use of computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Lewis, 2024, p. xxvi)
McGreevy, Kristen. “DNA Methylation Based Biomarkers, Imputation, and Prediction Algorithms.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3061584085.
“All computation was performed using R version 4.1.0 and the Hoffman2 Cluster, which is a Linux compute cluster.” (McGreevy, 2024, p. 43)
Mei, Kenneth Jun Ru. “Electronic Dynamics in Solution Phase Chemical Reactions: Photodissociation of Alkali Dimer Cations and the Hydrogen Evolution Reaction of Hydrated Electrons.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3130505270.
“We gratefully acknowledge the Institute for Digital Research and Education (IDRE) at UCLA for use of the Hoffman2 computing cluster and ACCESS under computational project TG-CHE230086.” (Mei, 2024, p. 76)
Ngan, Hio Tong. “Dilute Alloy Catalysts: Unraveling Enhanced Selectivity and Reactivity in (De)Hydrogenation Reactions Through Theoretical Exploration.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3040201680.
“The DFT calculations in this work used computational and storage services associated with the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE), the National Energy Research Scientific Computing Center (NERSC) of the U.S. Department of Energy, and the Bridges-2 cluster through the allocation TG-CHE170060 at the Pittsburgh Supercomputing Center (supported by National Science Foundation award number ACI-1928147) through the Extreme Science and Engineering Discovery Environment (supported by National Science Foundation grant number ACI-1548562).” (Ngan, 2024, p. xxxiv)
Sedlak, Alexander Paul Woodward. “Field Shift Fractionations in Novel Isotope Systems.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3064085358.
“All molecular geometry optimizations are performed with the Gaussian09 software package (Frisch et al., 2009) on the UCLA Hoffman2 computing cluster.” (Sedlak, 2024, p. 33) “Geometry optimization and vibrational analyses for molecules and molecular complexes are performed using the software Gaussian09 (Frisch et al. 2009), on the Hoffman2 cluster at UCLA.” (Sedlak, 2024, p. 93) “Calculations were performed in the software Gaussian09 (Frisch, 2009) on the Hoffman2 cluster at UCLA.” (Sedlak, 2024, p. 150)
Tesvara, Celine. “Understanding the Stability and Reactivity of Highly Dispersed Metal Catalysts Supported on Titania for the Decomposition of Chemical Warfare Agents.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3062334697.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Tesvara, 2024, p. 28)
Thapa, Laura Hughes. “Improving the Representation of Fresh Wildfire Smoke Plumes in Air Quality Forecasts.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3101937386.
“Xinxin Ye configured WRF-Chem to run on the UCLA Hoffman2 cluster.” (Thapa, 2024, p. 30)
Tibbe, Tristan Dale. “A Comprehensive Comparison of Missing Data Procedures for Tree-Based Machine Learning Methods.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3145627461.
“The R code was executed on the University of California, Los Angeles’ Hoffman2 supercomputer due to its ability to run conditions in parallel, vastly increasing the speed with which the computationally intensive simulation could be completed.” (Tibbe, 2024, p. 38)
Tom, Matthew Cheuk-Woh. “First-Principles and Machine Learning Modeling for Design and Operation of Area-Selective Atomic Layer Deposition.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3050055747.
“I would like to extend my appreciation for the support of the UCLA Hoffman2 Cluster Support Team including Raffaella D’Auria, Shao-Ching Huang, John Pedersen, Brian Pape, and Charles Peterson, for their technical support.” (Tom, 2024, p. xix)
Yu, Hsuan Ming. “Nanotubes from First Principle and Data-Driven Methods: Real and Reimagined.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/2973884572.
“All simulations involving Helical DFT were run using a dedicated desktop workstation (Dell Precision 7920 Tower) or single nodes of the Hoffman2 cluster at UCLA’s Institute for Digital Research and Education (IDRE).” (Yu, 2024, p. 36)
Zhang, Zisheng. “Grand Canonical Approach to Modeling Dynamic Catalysts: From Thermal to Electro-Catalysis, From Clusters to Surfaces.” Ph.D. Thesis, University of California, Los Angeles, 2024. ProQuest, https://www.proquest.com/docview/3062239492.
“The computations in this work were performed on: Hoffman2, the UCLAshared cluster” (Zhang, 2024, p. xxxv)
Conference Papers for 2024¶
Rolandi, L. Victoria; Luke Smith, and Kunihiko Taira. “RESOLVENT ANALYSIS OF SEPARATED FLOWSOVERNACA0012 WINGS: REYNOLDS NUMBEREFFECTS.” In 13th International Symposium on Turbulence and Shear Flow Phenomena (TSFP13): 13th International Symposium on Turbulence and Shear Flow Phenomena (TSFP13) Montreal, Canada, 2024: 1-6. http://www.tsfp-conference.org/proceedings/2023/9.pdf.
“This work used computational and storage services hosted by the Hoffman2 Shared Cluster at UCLA’s Institute for Digital Research and Education’s Research Technology Group.” (Rolandi et al., 2024, p. 5)
Tamhidi, Aidin and Yousef Bozorgnia. “Near-Real-Time Framework For Seismic Performance Characterization Of A Large Portfolio Of Buildings.” In 18th World Conference on Earthquake Engineering (WCEE2024): 18th World Conference on Earthquake Engineering (WCEE2024) Milan, 2024. https://proceedings-wcee.org/view.html?id=24880&conference=18WCEE.
“The procedure including the ground motion time series simulation and nonlinear response history analyses of the SS buildings, is conducted on the University of California Los Angeles computational and storage services associated with the Hoffman2 Shared Cluster for Digital Research and Education’s Research Technology Group.” (Tamhidi and Bozorgnia, 2024, p. 9)
Reports for 2024¶
Wilson, Bianca D. M. and Lauren J. A. Bouton. “LGBTQ Parenting in the US.” UCLA: The Williams Institute, 2024. https://escholarship.org/uc/item/4n14x2dd.
“Thank you to Raffaella D’Auria, Ph.D., who facilitated the use of the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Wilson and Bouton, 2024, p. 36)
Presentations for 2024¶
Shaked, Gideon; Jingyuan Fu, and Jason Ernst. “Identifying Functional Genomic Regions in iPSC Reprogramming with ChromHMM.” 2024.
“This work used computational and storage services associated with the Hoffman2 Cluster which is operated by the UCLA Office of Advanced Research Computing’s Research Technology Group.” (Shaked et al., 2024, p. 1) – B.I.G. Summer 2024 Poster Presentation
2023¶
- 134 publications for 2023
107 Journal Articles
20 Theses
Journal Articles for 2023¶
Acosta, Adrian; J. Mark P. Martirez; Norleakvisoth Lim; Jane P. Chang, and Emily A. Carter. “Effect of thickness and surface composition on the stability of polarization in ferroelectric Hf_{x}Zr_{1-x}O_{2} thin films.” Physical Review Materials 7 no. 12 (2023): 124401. 10.1103/PhysRevMaterials.7.124401.
“This paper used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Acosta et al., 2023, p. 9)
Agarwal, Shivang; Daniel R. Kattnig; Clarice D. Aiello, and Amartya S. Banerjee. “The Biological Qubit: Calcium Phosphate Dimers, Not Trimers.” The Journal of Physical Chemistry Letters 14 no. 10 (2023): 2518-2525. 10.1021/acs.jpclett.2c03945.
“Lastly, the authors would like to thank UCLA’s Institute for Digital Research and Education (IDRE) for making available the computing resources used in this work.” (Agarwal et al., 2023, p. 2524)
Alcock, Emma; Pamela Mackey; Aneta Turlik; Khushi Bhatt; Mark E. Light; Kendall N. Houk, and Gerard P. McGlacken. “The Aldol-Tishchenko Reaction of Butanone, Cyclobutanone and a 3-Pentanone Derived Sulfinylimine and DFT Calculations of the Stereo-determining Step.” Chemistry – A European Journal 29 no. 22 (2023): e202203029. 10.1002/chem.202203029.
“Calculations were performed ontheHoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI1053575).” (Alcock et al., 2023, p. 6)
Almisbaa, Zahra; Hassan A. Aljama; Khalid Almajnouni; Luigi Cavallo, and Philippe Sautet. “Acetylene Semi-Hydrogenation on Intermetallic Ni–In Catalysts: Ni Ensemble and Acetylene Coverage Effects from a Theoretical Analysis.” ACS Catalysis 13 no. 11 (2023): 7358-7370. 10.1021/acscatal.3c01175.
“This work was supported by the Supercomputing Laboratory at King Abdullah University of Science &Technology (KAUST) inThuwal, Saudi Arabia, the Extreme Science and Engineering Discovery Environment (XSEDE) Expanse and Bridges-2 clusters at San Diego Supercomputer Center through allocation TG-CHE170060, and the UCLA Institute of Digital Research and Education (IDRE) for computational resources on the UCLA Hoffman2 cluster.” (Almisbaa et al., 2023, p. 7368)
Apostol, Michael R.; Timothy Jordan; Andrew F. Leuchter, and Nicole Petersen. “Effects of transcranial magnetic stimulation to the dorsolateral prefrontal cortex on craving and state anxiety in tobacco use disorder.” Nature Mental Health 1 no. 12 (2023): 1001-1012. 10.1038/s44220-023-00154-5.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education Research Technology Group.” (Apostol et al., 2023). Number: 12
Barr, Kelly; Christen M. Bossu; Rachael A. Bay; Eric C. Anderson; Jim Belthoff; Lynne A. Trulio; Debra Chromczak; Colleen L. Wisinski; Thomas B. Smith, and Kristen C. Ruegg. “Genetic and environmental drivers of migratory behavior in western burrowing owls and implications for conservation and management.” Evolutionary Applications 16 no. 12 (2023): 1889-1900. 10.1111/eva.13600.
“Computational allocations from the Extreme Science and Engineering Discovery Environment (Xsede), as well as UCLA’s Shared Hoffman2 Cluster made this work possible.” (Barr et al., 2023, p. 9)
Bhanawat, Abhinav and Laurent Pilon. “Light transfer through bubble-filled electrolyte for solar water splitting.” Sustainable Energy & Fuels 7 no. 2 (2023): 448-460. 10.1039/D2SE01168A.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Bhanawat and Pilon, 2023, p. 459)
Bhanawat, Abhinav; Refet Ali Yalcin; Ricardo Martinez, and Laurent Pilon. “Critical review and experimental validation of radiative transfer models for semitransparent media containing large gas bubbles.” Journal of Quantitative Spectroscopy and Radiative Transfer 311 (2023): 108781. 10.1016/j.jqsrt.2023.108781.
“This work used computational and storage services associated with the Hoffman2 shared cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Bhanawat et al., 2023, p. 11)
Brewer, John; Sachin Kulkarni, and Aaswath P. Raman. “Resonant Anti-Reflection Metasurfaces for Infrared Transmission Optics.” Nano Letters 23 no. 19 (2023): 8940-8946. 10.1021/acs.nanolett.3c02375.
“Additionally, this work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Brewer et al., 2023, p. 8944-8945)
Cendejas, Melissa C.; Oscar A. Paredes Mellone; Unni Kurumbail; Zisheng Zhang; Jacob H. Jansen; Faysal Ibrahim; Son Dong; John Vinson; Anastassia N. Alexandrova; Dimosthenis Sokaras; Simon R. Bare, and Ive Hermans. “Tracking Active Phase Behavior on Boron Nitride during the Oxidative Dehydrogenation of Propane Using Operando X-ray Raman Spectroscopy.” Journal of the American Chemical Society 145 no. 47 (2023): 25686-25694. 10.1021/jacs.3c08679.
“The computations inthis work were performed onHoffman2 theUCLA-shared cluster” (Cendejas et al., 2023, p. 25693)
Chen, Hao; Lorenz J. Falling; Heath Kersell; George Yan; Xiao Zhao; Judit Oliver-Meseguer; Max Jaugstetter; Slavomir Nemsak; Adrian Hunt; Iradwikanari Waluyo; Hirohito Ogasawara; Alexis T. Bell; Philippe Sautet, and Miquel Salmeron. “Elucidating the active phases of CoOx films on Au(111) in the CO oxidation reaction.” Nature Communications 14 no. 1 (2023): 6889. 10.1038/s41467-023-42301-7.
“The DFT calculations in this work used computational and storage services associated with the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE), and the Bridges-2 cluster at the Pittsburgh Supercomputing Center (supported by National Science Foundation award number ACI-1928147) through the Extreme Science and Engineering Discovery Environment (supported by National Science Foundation grant number ACI-1548562) grant TG-CHE170060.” (Chen et al., 2023, p. 8) Publication Title: Nature …
Chen, Peng-Yu; Nikolaos Lesgidis; Anastasios Sextos, and Ertugrul Taciroglu. “A method for automated development of model and fragility inventories of nonductile reinforced concrete buildings.” Resilient Cities and Structures 2 no. 3 (2023): 87-103. 10.1016/j.rcns.2023.08.002.
“This work used computational and storage services associated with the Hoffman2 shared cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Chen et al., 2023, p. 11)
Chen, Ximin; Laurence C. Chen; Mobina Khericha; Xiangzhi Meng; Emma Salvestrini; Amanda Shafer; Neha Iyer; Anya S. Alag; Yunfeng Ding; Demetri M. Nicolaou, and Yvonne Y. Chen. “Rational Protein Design Yields a CD20 CAR with Superior Antitumor Efficacy Compared with CD19 CAR.” Cancer Immunology Research 11 no. 2 (2023): 150-163. 10.1158/2326-6066.CIR-22-0504.
“This work was performed with instrumentation and computational resources from the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell ResearchMolecular, Cell, and Developmental Biology Microscopy Core, the UCLA Jonsson Comprehensive Cancer Center (JCCC) Flow Cytometry Core Facility supported by the National Institutes of Health (P30 CA016042), and the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Chen et al., 2023, p. 162)
Cheng, Dongfang; Ziyang Wei; Zisheng Zhang; Peter Broekmann; Anastassia N. Alexandrova, and Philippe Sautet. “Restructuring and Activation of Cu(111) under Electrocatalytic Reduction Conditions.” Angewandte Chemie International Edition 62 no. 20 (2023): e202218575. 10.1002/anie.202218575.
“Computational resources for this work were performed ontheHoffman2 cluster at UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant No. ACI-1548562, through allocation TGCHE170060.” (Cheng et al., 2023, p. 7)
Chu, Benjamin B; Seyoon Ko; Jin J Zhou; Aubrey Jensen; Hua Zhou; Janet S Sinsheimer, and Kenneth Lange. “Multivariate genome-wide association analysis by iterative hard thresholding.” Bioinformatics 39 no. 4 (2023): btad193. 10.1093/bioinformatics/btad193.
“The UCLA Institute for Digital Research and Education’s Research Technology Group supplied computational and storage services through its Hoffman2 Shared Cluster.” (Chu et al., 2023, p. 5)
Contina, Andrea; Christen M. Bossu; Daniel Allen; Michael B. Wunder, and Kristen C. Ruegg. “Genetic and ecological drivers of molt in a migratory bird.” Scientific Reports 13 no. 1 (2023): 814. 10.1038/s41598-022-26973-7.
“Computational allocations from the Extreme Science and Engineering Discovery Environment (Xsede), as well as UCLA’s Shared Hoffman2 Cluster made this work possible.” (Contina et al., 2023, p. 13)
Delisle, Marie-Pierre C.; Yeulwoo Kim, and Timu W. Gallien. “A Numerical Study of Dam-Break Driven Swash and Beach Groundwater Interactions.” Journal of Geophysical Research: Oceans 128 no. 9 (2023): e2022JC019615. 10.1029/2022JC019615.
“Numerical simulations presented in this study were carried out using the Hoffman2 cluster at the University of California, Los Angeles.” (Delisle et al., 2023, p. 19)
Deng, Jie; Haiyang Niu; Junwei Hu; Mingyi Chen, and Lars Stixrude. “Melting of MgSi O 3 determined by machine learning potentials.” Physical Review B 107 no. 6 (2023): 064103. 10.1103/PhysRevB.107.064103.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Deng et al., 2023, p. 11)
Dike, Veronica; Daniel Gilman, and Tommaso Treu. “Strong lensing constraints on primordial black holes as a dark matter candidate.” Monthly Notices of the Royal Astronomical Society 522 no. 4 (2023): 5434-5441. 10.1093/mnras/stad1313.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by University of California Los Angeles Institute for Digital Research and Education’s Research Technology Group.” (Dike et al., 2023, p. 5439)
Durr, Steven; Youssef Mroueh; Yuhai Tu, and Shenshen Wang. “Effective Dynamics of Generative Adversarial Networks.” Physical Review X 13 no. 4 (2023): 041004. 10.1103/PhysRevX.13.041004.
“This work used computational and storage services associated with the Hoffman2 Cluster hosted by the UCLA Institute for Digital Research and Education.” (Durr et al., 2023, p. 11)
Finnerty, Luke; Tobias Schofield; Ben Sappey; Jerry W. Xuan; Jean-Baptiste Ruffio; Jason J. Wang; Jacques-Robert Delorme; Geoffrey A. Blake; Cam Buzard; Michael P. Fitzgerald; Ashley Baker; Randall Bartos; Charlotte Z. Bond; Benjamin Calvin; Sylvain Cetre; Greg Doppmann; Daniel Echeverri; Nemanja Jovanovic; Joshua Liberman; Ronald A. López; Emily C. Martin; Dimitri Mawet; Evan Morris; Jacklyn Pezzato; Caprice L. Phillips; Sam Ragland; Andrew Skemer; Taylor Venenciano; J. Kent Wallace; Nicole L. Wallack; Ji Wang, and Peter Wizinowich. “Keck Planet Imager and Characterizer Emission Spectroscopy of WASP-33b.” The Astronomical Journal 166 no. 1 (2023): 31. 10.3847/1538-3881/acda91.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Educations Research Technology Group.” (Finnerty et al., 2023, p. 15)
Flores, Marcos M.; Chris Kouvaris, and Alexander Kusenko. “Defrosting and Blast Freezing Dark Matter.” Physical Review D 108 no. 10 (2023): 103545. 10.1103/PhysRevD.108.103545.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Flores et al., 2023, p. 6)
Flores, Marcos M.; Alexander Kusenko; Lauren Pearce, and Graham White. “Fireball baryogenesis from early structure formation due to Yukawa forces.” Physical Review D 108 no. 9 (2023): L091705. 10.1103/PhysRevD.108.L091705.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Flores et al., 2023, p. 6)
Flores, Marcos M.; Alexander Kusenko, and Misao Sasaki. “Gravitational Waves from Rapid Structure Formation on Microscopic Scales before Matter-Radiation Equality.” Physical Review Letters 131 no. 1 (2023): 011003. 10.1103/PhysRevLett.131.011003.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Flores et al., 2023, p. 6)
Foucher, Alexandre C.; Hio Tong Ngan; Tanya Shirman; Amanda Filie; Kaining Duanmu; Michael Aizenberg; Robert J. Madix; Cynthia M. Friend; Joanna Aizenberg; Philippe Sautet, and Eric A. Stach. “Influence of Pd Concentration in Au–Pd Nanoparticles for the Hydrogenation of Alkynes.” ACS Applied Nano Materials 6 no. 24 (2023): 22927-22938. 10.1021/acsanm.3c04278.
“The DFT calculations used computational and storage services associated with the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE)” (Foucher et al., 2023, p. J)
Freedman, Adam H.; Ryan J. Harrigan; Ying Zhen; Alison M. Hamilton, and Thomas B. Smith. “Evidence for ecotone speciation across an African rainforest-savanna gradient.” Molecular Ecology 32 no. 9 (2023): 2287-2300. 10.1111/mec.16867.
“The computations in this study were run on UCLA’s Hoffman2 cluster, and the cluster supported by the FAS Division of Science, Research Computing Group at Harvard University.” (Freedman et al., 2023, p. 2297)
Fu, Xiaoyang; Dongfang Cheng; Chengzhang Wan; Simran Kumari; Hongtu Zhang; Ao Zhang; Huaixun Huyan; Jingxuan Zhou; Huaying Ren; Sibo Wang; Zipeng Zhao; Xun Zhao; Jun Chen; Xiaoqing Pan; Philippe Sautet; Yu Huang, and Xiangfeng Duan. “Bifunctional Ultrathin RhRu0.5-Alloy Nanowire Electrocatalysts for Hydrazine-Assisted Water Splitting.” Advanced Materials 35 no. 23 (2023): 2301533. 10.1002/adma.202301533.
“D.C. and S.K. used the HOFFMAN2 cluster at the UCLA Institute for Digital Research and Education (IDRE).” (Fu et al., 2023, p. 8)
Fuller, Jack T.; Steven Barnes; Lorenzo A. Sadun; Pujan Ajmera; Anastassia N. Alexandrova, and Alfredo A. Sadun. “Coenzyme Q10 trapping in mitochondrial complex I underlies Leber’s hereditary optic neuropathy.” Proceedings of the National Academy of Sciences 120 no. 39 (2023): e2304884120. 10.1073/pnas.2304884120.
“The Hoffman2 Shared Cluster provided by the University of California at Los Angeles (UCLA) Institute for Digital Research and Education’s Research Technology Group was used for simulations.” (Fuller et al., 2023, p. 5)
Galeotti, M; WJ Lee; S Sisti; M Casciotti; M Salamone; KN Houk, and M Bietti. “Radical and Cationic Pathways in C(sp 3)-H Bond Oxygenation by Dioxiranes of Bicyclic and Spirocyclic Hydrocarbons Bearing Cyclopropane Moieties.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 145 no. 44 (2023): 24021-24034. 10.1021/jacs.3c07163.
“Calculations were performed oncomputational resources provided bythe UCLA Institute ofDigital Research and Education (IDRE) and theExtreme Science and Engineering Discovery Environment (XSEDE).” (Galeotti et al., 2023, p. 24032)
Gilman, Daniel; Yi-Ming Zhong, and Jo Bovy. “Constraining resonant dark matter self-interactions with strong gravitational lenses.” Physical Review D 107 no. 10 (2023): 103008. 10.1103/PhysRevD.107.103008.
“We also used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Gilman et al., 2023, p. 10)
Goyal, Karan; Garrett A. Kukier; Xiangyang Chen; Aneta Turlik; K. N. Houk, and Richmond Sarpong. “Rearrangement of a carboxy-substituted spiro[4.4]nonatriene to annulated fulvenes through a Pd(II)-mediated 1,5-vinyl shift.” Chemical Science 14 no. 42 (2023): 11809-11817. 10.1039/D3SC03222A.
“Calculations were performed at the MGCF, which is supported by NIH grant S10OD023532, and on the Hoffman2 cluster at UCLA.” (Goyal et al., 2023, p. 11816)
He, Sicong; Xinran Zhou; Dan Mordehai, and Jaime Marian. “Thermal super-jogs control the high-temperature strength plateau in Nb-Mo-Ta-W alloys.” Acta Materialia 244 (2023): 118539. 10.1016/j.actamat.2022.118539.
“We thank UCLA’s IDRE for computer time allocations on the Hoffman2 supercomputer.” (He et al., 2023, p. 11)
Hejna, Benjamin G.; Jacob M. Ganley; Huiling Shao; Haowen Tian; Jonathan D. Ellefsen; Nicholas J. Fastuca; Kendall N. Houk; Scott J. Miller, and Robert R. Knowles. “Catalytic Asymmetric Hydrogen Atom Transfer: Enantioselective Hydroamination of Alkenes.” Journal of the American Chemical Society 145 no. 29 (2023): 16118-16129. 10.1021/jacs.3c04591.
“DFT calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science” (Hejna et al., 2023, p. 16127)
Hester, Eric W.; Sean Carney; Vishwesh Shah; Alyssa Arnheim; Bena Patel; Dino Di Carlo, and Andrea L. Bertozzi. “Fluid dynamics alters liquid–liquid phase separation in confined aqueous two-phase systems.” Proceedings of the National Academy of Sciences 120 no. 49 (2023): e2306467120. 10.1073/pnas.2306467120.
“We acknowledge computing resources on Hoffman2 provided through the Institute for Digital Research and Education at UCLA.” (Hester et al., 2023, p. 8)
Ho, Minna; Fayçal Kessouri; Christina A. Frieder; Martha Sutula; Daniele Bianchi, and James C. McWilliams. “Effect of ocean outfall discharge volume and dissolved inorganic nitrogen load on urban eutrophication outcomes in the Southern California Bight.” Scientific Reports 13 no. 1 (2023): 22148. 10.1038/s41598-023-48588-2.
“Additional computational resources were provided by the Hoffman2 computer cluster at the University of California Los Angeles, Institute for Digital Research and Education (IDRE).” (Ho et al., 2023, p. 15-16) Publication Title: Scientific Reports
Hu, Liang; Guangrong Meng; Xiangyang Chen; Joseph S. Yoon; Jing-Ran Shan; Nikita Chekshin; Daniel A. Strassfeld; Tao Sheng; Zhe Zhuang; Rodolphe Jazzar; Guy Bertrand; K. N. Houk, and Jin-Quan Yu. “Enhancing Substrate–Metal Catalyst Affinity via Hydrogen Bonding: Pd(II)-Catalyzed β-C(sp3)–H Bromination of Free Carboxylic Acids.” Journal of the American Chemical Society 145 no. 30 (2023): 16297-16304. 10.1021/jacs.3c04223.
“Calculations were performed on the Hoffman2 cluster at UCLA” (Hu et al., 2023, p. 16302)
Huang, Jireh and Qing Zhou. “Bayesian Causal Bandits with Backdoor Adjustment Prior.” Transactions on Machine Learning Research (2023).
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group” (Huang and Zhou, 2022, p. 18)
Insixiengmay, Leslie and Lars Stixrude. “Hydrogen bond symmetrization and high-spin to low-spin transition of ε-FeOOH at the pressure of Earth’s lower mantle.” American Mineralogist 108 no. 12 (2023): 2209-2218. 10.2138/am-2022-8839.
“Calculations were carried out using the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Insixiengmay and Stixrude, 2023, p. 2216)
Jimenez, Amy M.; Peter E. Clayson; Arpi S. Hasratian; Junghee Lee; Eric A. Reavis; Jonathan K. Wynn; Michael F. Green, and William P. Horan. “Neuroimaging of social motivation during winning and losing: Associations with social anhedonia across the psychosis spectrum.” Neuropsychologia 188 (2023): 108621. 10.1016/j.neuropsychologia.2023.108621.
“fMRI data analysis for this study used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Jimenez et al., 2023, p. 9)
Kaasik, Mikk; Pan-Pan Chen; Sebastijan Ričko; Karl Anker Jørgensen, and K. N. Houk. “Asymmetric [4 + 2], [6 + 2], and [6 + 4] Cycloadditions of Isomeric Formyl Cycloheptatrienes Catalyzed by a Chiral Diamine Catalyst.” Journal of the American Chemical Society 145 no. 43 (2023): 23874-23890. 10.1021/jacs.3c09551.
“Calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles.” (Kaasik et al., 2023, p. 23888)
Kaiser, Selina K.; Jessi E. S. van der Hoeven; George Yan; Kang Rui Garrick Lim; Hio Tong Ngan; Sadhya Garg; Mustafa Karatok; Michael Aizenberg; Joanna Aizenberg; Philippe Sautet; Cynthia M. Friend, and Robert J. Madix. “Identifying the Optimal Pd Ensemble Size in Dilute PdAu Alloy Nanomaterials for Benzaldehyde Hydrogenation.” ACS Catalysis 13 no. 18 (2023): 12092-12103. 10.1021/acscatal.3c02671.
“The DFT calculations int his work used computational and storage services associated with the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE)” (Kaiser et al., 2023, p. 12102)
Kelleghan, Andrew V.; Ana S. Bulger; Dominick C. Witkowski, and Neil K. Garg. “Strain-promoted reactions of 1,2,3-cyclohexatriene and its derivatives.” Nature 618 no. 7966 (2023): 748-754. 10.1038/s41586-023-06075-8.
“Calculations were performed on the Hoffman2 cluster and the UCLA Institute of Digital Research and Education (IDRE) at UCLA” (Kelleghan et al., 2023, p. 755) Number: 7966
Kim, Sangmin; Joseph W. Treacy; Yessica A. Nelson; Jordan A. M. Gonzalez; Milan Gembicky; K. N. Houk, and Alexander M. Spokoyny. “Arene C–H borylation strategy enabled by a non-classical boron cluster-based electrophile.” Nature Communications 14 no. 1 (2023): 1671. 10.1038/s41467-023-37258-6.
“J.W.T. and K.N.H. acknowledge that this work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Kim et al., 2023, p. 8) Number: 1
Kuatsjah, Eugene; Michael Zahn; Xiangyang Chen; Ryo Kato; Daniel J. Hinchen; Mikhail O. Konev; Rui Katahira; Christian Orr; Armin Wagner; Yike Zou; Stefan J. Haugen; Kelsey J. Ramirez; Joshua K. Michener; Andrew R. Pickford; Naofumi Kamimura; Eiji Masai; K. N. Houk; John E. McGeehan, and Gregg T. Beckham. “Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation.” Proceedings of the National Academy of Sciences 120 no. 4 (2023): e2212246120. 10.1073/pnas.2212246120.
“Computations were performed on the Hoffman2 cluster at UCLA” (Kuatsjah et al., 2023, p. 8)
Kumari, Simran; Anastassia N. Alexandrova, and Philippe Sautet. “Nature of Zirconia on a Copper Inverse Catalyst Under CO2 Hydrogenation Conditions.” Journal of the American Chemical Society 145 no. 48 (2023): 26350-26362. 10.1021/jacs.3c09947.
“This work used computational and storage services associated with theHoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education Research Technology Group.T” (Kumari et al., 2023, p. 26360)
Kumari, Simran; Tsugunosuke Masubuchi; Henry S. White; Anastassia Alexandrova; Scott L. Anderson, and Philippe Sautet. “Electrocatalytic Hydrogen Evolution at Full Atomic Utilization over ITO-Supported Sub-nano-Ptn Clusters: High, Size-Dependent Activity Controlled by Fluxional Pt Hydride Species.” Journal of the American Chemical Society 145 no. 10 (2023): 5834-5845. 10.1021/jacs.2c13063.
“This work used computational andstorage services associated with theHoffman2 Shared Cluster provided bytheUCLA Institute forDigital Research andEducation Research Technology Group.” (Kumari et al., 2023, p. 5843)
Kumari, Simran and Philippe Sautet. “Elucidation of the Active Site for the Oxygen Evolution Reaction on a Single Pt Atom Supported on Indium Tin Oxide.” The Journal of Physical Chemistry Letters 14 no. 10 (2023): 2635-2643. 10.1021/acs.jpclett.3c00160.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided bytheUniversity of California, LosAngeles (UCLA) Institute for Digital Research and Education Research Technology Group.” (Kumari and Sautet, 2023, p. 2641)
Lake, William; Smadar Naoz; Blakesley Burkhart; Federico Marinacci; Mark Vogelsberger; Gen Chiaki; Yeou S. Chiou; Naoki Yoshida; Yurina Nakazato, and Claire E. Williams. “The Supersonic Project: The Early Evolutionary Path of Supersonically Induced Gas Objects.” The Astrophysical Journal 943 no. 2 (2023): 132. 10.3847/1538-4357/acac8d.
“The authors thank the anonymous reviewer for their helpful comments and suggestions. W.L., S.N., Y.S.C, B.B., F.M., and M.V. thank the support of NASA grant No. 80NSSC20K0500 and the XSEDE AST180056 allocation, as well as the Simons Foundation Center for Computational Astrophysics and the UCLA cluster Hoffman2 for computational resources.” (Lake et al., 2023, p. 13)
Lake, William; Smadar Naoz; Federico Marinacci; Blakesley Burkhart; Mark Vogelsberger; Claire E. Williams; Yeou S. Chiou; Gen Chiaki; Yurina Nakazato, and Naoki Yoshida. “The Supersonic Project: Star Formation in Early Star Clusters without Dark Matter.” Astrophysical Journal Letters 956 no. 1 (2023): L7. 10.3847/2041-8213/acfa9b.
“The authors thank the anonymous reviewer for the thoughtful comments that have substantially improved the paper. W.L., S.N., Y.S.C, B.B., F.M., and M.V. thank the support of NASA grant No. 80NSSC20K0500 and the XSEDE AST180056 allocation, as well as the Simons Foundation Center for Computational Astrophysics and the UCLA cluster Hoffman2 for computational resources.” (Lake et al., 2023, p. 7)
Lanzi, Matteo; Torben Rogge; Tan Sang Truong; K. N. Houk, and Joanna Wencel-Delord. “Cyclic Diaryl λ3-Chloranes: Reagents and Their C–C and C–O Couplings with Phenols via Aryne Intermediates.” Journal of the American Chemical Society 145 no. 1 (2023): 345-358. 10.1021/jacs.2c10090.
“Calculations were performed ontheHoffman2 cluster at the University of California, Los Angeles.” (Lanzi et al., 2023, p. 357)
Lee, Hao and Jacob Rosen. “Lower Limb Exoskeleton - Energy Optimization of Bipedal Walking With Energy Recycling - Modeling and Simulation.” IEEE Robotics and Automation Letters 8 no. 3 (2023): 1579-1586. 10.1109/LRA.2023.3234813.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Lee and Rosen, 2023, p. 7) Conference Name: IEEE Robotics and Automation Letters
Lee, Woojin; Hosea M. Nelson, and K. N. Houk. “Computational Exploration of the Nature of Li+-Ureide Anion Catalysis on Formation of Highly Reactive Vinyl Carbocations and Subsequent C–C Bond Forming Reactions.” The Journal of Organic Chemistry 88 no. 6 (2023): 3403-3408. 10.1021/acs.joc.2c02178.
“Computations were performed on the UCLA Institute of Digital Research and Education Hoffman2 Cluster.” (Lee et al., 2023, p. 3407)
Levy, Kevin; Srinivasan Raghunathan, and Kaustuv Basu. “A foreground-immune CMB-cluster lensing estimator.” Journal of cosmology and astroparticle physics 2023 no. 8 (2023): 20-. 10.1088/1475-7516/2023/08/020.
“This work made use of the following computing resources: the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group” (Levy et al., 2023, p. 18) Place: Bristol
Lewis, Briley; Michael P. Fitzgerald; Rupert H. Dodkins; Kristina K. Davis, and Jonathan Lin. “Speckle Space–Time Covariance in High-contrast Imaging.” The Astronomical Journal 165 no. 2 (2023): 59. 10.3847/1538-3881/aca761.
“We take advantage of this capability by using UCLA’s Hoffman2 Cluster.”
Li, Man; Huan Wu; Erin M. Avery; Zihao Qin; Dominic P. Goronzy; Huu Duy Nguyen; Tianhan Liu; Paul S. Weiss, and Yongjie Hu. “Electrically gated molecular thermal switch.” Science 382 no. 6670 (2023): 585-589. 10.1126/science.abo4297.
“We acknowledge support from UCLA Nanolab and California NanoSystems Institute and the computational and storage services associated with the Hoffman 2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group; from the Bridges-2 at Pittsburgh Supercomputing Center through allocation no. DMR180111 from Extreme Science and Engineering Discovery Environment supported by NSF grant no. 1548562; and from the Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) program supported by NSF grants no. 2138259, no. 2138286, no. 2138307, no. 2137603, and no. 2138296.” (Li et al., 2023, p. 4-5)
Li, Yichen; Dongfang Cheng; Ziyang Wei, and Philippe Sautet. “Photoelectron Storage at the WO3/TiO2 Interface: Modeling in Ambient Conditions from First-Principles Calculations.” ACS Catalysis 13 no. 15 (2023): 9979-9986. 10.1021/acscatal.3c01756.
“Computations in this work were performed ontheHoffman2 cluster at UCLA Institute for Digital Research and Education (IDRE)” (Li et al., 2023, p. 9985)
Liu, Han Jie and Jennifer L. Wilson. “Drug target, class level, and PathFX pathway information share utility for machine learning prediction of common drug-induced side effects.” Frontiers in Drug Safety and Regulation 3 (2023). 10.3389/fdsfr.2023.1287535.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Office of Advanced Research Computing’s Research Technology Group.” (Liu and Wilson, 2023, p. 13)
Liu, Jiawang; Jiayan Lu; Chen Zhang; Qingyang Zhou; Cooper S. Jamieson; Changhui Shang; K. N. Houk; Jiahai Zhou, and Youcai Hu. “Tandem intermolecular [4 + 2] cycloadditions are catalysed by glycosylated enzymes for natural product biosynthesis.” Nature Chemistry 15 no. 8 (2023): 1083-1090. 10.1038/s41557-023-01260-8.
“All calculations were performed on the Hoffman2 cluster at UCLA and the UCLA Institute of Digital Research and Education (IDRE).” (Liu et al., 2023, p. 1094) Publication Title: Nature Chemistry
Liu, ZW; S Rivera; SA Newmister; JN Sanders; QY Nie; S Liu; FL Zhao; JD Ferrara; HW Shih; S Patil; WJ Xu; MD Miller; GN Phillips; KN Houk; DH Sherman, and X Gao. “An NmrA-like enzyme-catalysed redox-mediated Diels-Alder cycloaddition with anti-selectivity.” NATURE CHEMISTRY 15 no. 4 (2023): 526-+. 10.1038/s41557-022-01117-6.
“Computational resources for DFT computations were provided by the UCLA Institute for Digital Research and Education (IDRE) and by the San Diego Supercomputing Center (SDSC) through XSEDE (ACI-1548562).” (Liu et al., 2023, p. 538)
Luo, Jinwen; Ludovica De Carolis; Biao Zeng, and Minjeong Jeon. “Bayesian Estimation of Latent Space Item Response Models with JAGS, Stan, and NIMBLE in R.” Psych 5 no. 2 (2023): 396-415. 10.3390/psych5020027.
“All of the analysis was done within the R environment on the Hoffman2 Linux Compute Cluster hosted at UCLA and each run was conducted within a node with two cores and 16GB RAM.” (Luo et al., 2023, p. 400) Number: 2
Mao, Runze; Daniel J. Wackelin; Cooper S. Jamieson; Torben Rogge; Shilong Gao; Anuvab Das; Doris Mia Taylor; K. N. Houk, and Frances H. Arnold. “Enantio- and Diastereoenriched Enzymatic Synthesis of 1,2,3-Polysubstituted Cyclopropanes from (Z/E)-Trisubstituted Enol Acetates.” Journal of the American Chemical Society 145 no. 29 (2023): 16176-16185. 10.1021/jacs.3c04870.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles.” (Mao et al., 2023, p. 16184)
Martin-Somer, Ana; Xiao-Song Xue; Cooper S. Jamieson; Yike Zou, and K.N. Houk. “Computational Design of a Tetrapericyclic Cycloaddition and the Nature of Potential Energy Surfaces with Multiple Bifurcations.” Journal of the American Chemical Society 145 no. 7 (2023): 4221-4230. 10.1021/jacs.2c12871.
“We are grateful to the National Science Foundation (CHE1764328 to K.N.H.) for financial support of this research and for access to XSEDE and UCLA Hoffman 2 for computer time and for this study.” (Martin-Somer et al., 2023, p. 4229)
Martirez, John Mark P. and Emily A. Carter. “Solvent Dynamics Are Critical to Understanding Carbon Dioxide Dissolution and Hydration in Water.” Journal of the American Chemical Society 145 no. 23 (2023): 12561-12575. 10.1021/jacs.3c01283.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group and Princeton University’s Terascale Infrastructure for Groundbreaking Research in Engineering and Science (TIGRESS).” (Martirez and Carter, 2023, p. 12573)
McElfresh, Cameron and Jaime Marian. “Initial grain orientation controls static recrystallization outcomes in cold-worked iron: Insight from coupled crystal plasticity/vertex dynamics modeling.” Acta Materialia 245 (2023): 118631. 10.1016/j.actamat.2022.118631.
“Computer time allocations at UCLA’s IDRE Hoffman2 computer cluster are gratefully acknowledged.” (McElfresh and Marian, 2023, p. 15) Publication Title: Acta Materialia
Nigenda-Morales, Sergio F.; Meixi Lin; Paulina G. Nuñez-Valencia; Christopher C. Kyriazis; Annabel C. Beichman; Jacqueline A. Robinson; Aaron P. Ragsdale; Jorge Urbán R.; Frederick I. Archer; Lorena Viloria-Gómora; María José Pérez-Álvarez; Elie Poulin; Kirk E. Lohmueller; Andrés Moreno-Estrada, and Robert K. Wayne. “The genomic footprint of whaling and isolation in fin whale populations.” Nature Communications 14 no. 1 (2023): 5465. 10.1038/s41467-023-40052-z.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Nigenda-Morales et al., 2023, p. 17) Number: 1
Niknam, Mohamad and Louis-S. Bouchard. “Nuclear induction lineshape modeling via hybrid SDE and MD approach.” The Journal of Chemical Physics 159 no. 12 (2023): 124201. 10.1063/5.0163782.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Niknam and Bouchard, 2023, pp. 7)
Niwa, Kanji; Masao Ohashi; Kaili Xie; Chen-Yu Chiang; Cooper S. Jamieson; Michio Sato; Kenji Watanabe; Fang Liu; K. N. Houk, and Yi Tang. “Biosynthesis of Polycyclic Natural Products from Conjugated Polyenes via Tandem Isomerization and Pericyclic Reactions.” Journal of the American Chemical Society 145 no. 25 (2023): 13520-13525. 10.1021/jacs.3c02380.
“The computational resources from theUCLA Institute ofDigital Research and Education (IDRE) aregratefully acknowledged.” (Niwa et al., 2023, p. 13524)
Ohashi, M; D Tan; JY Lu; CS Jamieson; D Kanayama; JH Zhou; KN Houk, and Y Tang. “Enzymatic cis-Decalin Formation in Natural Product Biosynthesis.” Journal of the American Chemical Society 145 no. 6 (2023): 3301-3305. 10.1021/jacs.2c12854.
“The computational resources from the UCLA Institute of Digital Research and Education (IDRE) are gratefully acknowledged.” (Ohashi et al., 2023, p. 5)
Patel, Dipna A.; Georgios Giannakakis; George Yan; Hio Tong Ngan; Peng Yu; Ryan T. Hannagan; Paul L. Kress; Junjun Shan; Prashant Deshlahra; Philippe Sautet, and E. Charles H. Sykes. “Mechanistic Insights into Nonoxidative Ethanol Dehydrogenation on NiCu Single-Atom Alloys.” ACS Catalysis 13 no. 7 (2023): 4290-4303. 10.1021/acscatal.3c00275.
“The DFT calculations in this work used computational and storage services associated with the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE),” (Patel et al., 2023, p. 4301)
Peng, Marie; Chang-Sheng Wang; Pan-Pan Chen; Thierry Roisnel; Henri Doucet; K. N. Houk, and Jean-François Soulé. “Merging C–H Bond Activation, Alkyne Insertion, and Rearrangements by Rh(III)-Catalysis: Oxindole Synthesis from Nitroarenes and Alkynes.” Journal of the American Chemical Society 145 no. 8 (2023): 4508-4516. 10.1021/jacs.2c10932.
“Calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles” (Peng et al., 2023, p. 4514)
Raghunathan, Srinivasan and Yuuki Omori. “A Cross-internal Linear Combination Approach to Probe the Secondary CMB Anisotropies: Kinematic Sunyaev–Zel’dovich Effect and CMB Lensing.” The Astrophysical Journal 954 no. 1 (2023): 83. 10.3847/1538-4357/ace0c6.
“This work made use of the following computing resources: Illinois Campus Cluster, a computing resource that is operated by the Illinois Campus Cluster Program (ICCP) in conjunction with the National Center for Supercomputing Applications (NCSA) and which is supported by funds from the University of Illinois at Urbana-Champaign; the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group; and the computing resources provided on Crossover, a high performance computing cluster operated by the Laboratory Computing Resource Center at Argonne National Laboratory.” (Raghunathan and Omori, 2023, p. 12)
Richard, Derek; Matthew Tom; Joonbaek Jang; Sungil Yun; Panagiotis D. Christofides, and Carlos G. Morales-Guio. “Quantifying transport and electrocatalytic reaction processes in a gastight rotating cylinder electrode reactor via integration of Computational Fluid Dynamics modeling and experiments.” Electrochimica Acta 440 (2023): 141698. 10.1016/j.electacta.2022.141698.
“All simulations were performed on the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group using a 36-core dual processor with 192 GB of RAM.” (Richard et al., 2023, p. 9)
Rueda-Hernández, Rafael; Christen M. Bossu; Thomas B. Smith; Andrea Contina; Ricardo Canales del Castillo; Kristen Ruegg, and Blanca E. Hernández-Baños. “Winter connectivity and leapfrog migration in a migratory passerine.” Ecology and Evolution 13 no. 2 (2023): e9769. 10.1002/ece3.9769.
“Computational allocations from the Extreme Science and Engineering Discovery Environment (Xsede), as well as UCLA’s Shared Hoffman2 Cluster, made this work possible.” (Rueda-Hernández et al., 2023, p. 8)
Sandoval-Belmar, Marco; Jayme Smith; Allison R. Moreno; Clarissa Anderson; Raphael M. Kudela; Martha Sutula; Fayçal Kessouri; David A. Caron; Francisco P. Chavez, and Daniele Bianchi. “A cross-regional examination of patterns and environmental drivers of Pseudo-nitzschia harmful algal blooms along the California coast.” Harmful Algae 126 (2023): 102435. 10.1016/j.hal.2023.102435.
“Additional computational resources were provided by the Hoffman2 computer cluster at the University of California Los Angeles, Institute for Digital Research and Education (IDRE).” (Sandoval-Belmar et al., 2023, p. 12)
Sengupta, Arkajyoti and K. N. Houk. “Origins of Periselectivity and Regioselectivity in Ambimodal Tripericyclic [8+6]/[6+4]/[4+2] Intramolecular Cycloadditions of a Heptafulvenyl-Fulvene.” The Journal of Physical Chemistry A 127 no. 38 (2023): 7976-7983. 10.1021/acs.jpca.3c05656.
“Calculations were performed on the Hoffman2 cluster at the UCLA” (Sengupta and Houk, 2023, p. 7982)
Shajib, Anowar J.; Pritom Mozumdar; Geoff C.-F. Chen; Tommaso Treu; Michele Cappellari; Shawn Knabel; Sherry H. Suyu; Vardha N. Bennert; Joshua A. Frieman; Dominique Sluse; Simon Birrer; Frederic Courbin; Christopher D. Fassnacht; Lizvette Villafaña, and Peter R. Williams. “TDCOSMO - XII. Improved Hubble constant measurement from lensing time delays using spatially resolved stellar kinematics of the lens galaxy.” Astronomy & Astrophysics 673 (2023): A9. 10.1051/0004-6361/202345878.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Shajib et al., 2023, p. 20)
Shaw, Crystal; Yingyan Wu; Scott C. Zimmerman; Eleanor Hayes-Larson; Thomas R. Belin; Melinda C. Power; M. Maria Glymour, and Elizabeth Rose Mayeda. “Comparison of Imputation Strategies for Incomplete Longitudinal Data in Lifecourse Epidemiology.” American Journal of Epidemiology 192 no. 12 (2023): 2075-2084. 10.1093/aje/kwad139.
“We used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Shaw et al., 2023, p. 2078)
Shen, Kangze; Dongfang Cheng; Eber Reyes-Lopez; Joonbaek Jang; Philippe Sautet, and Carlos G. Morales-Guio. “On the origin of carbon sources in the electrochemical upgrade of CO2 from carbon capture solutions.” Joule 7 no. 6 (2023): 1260-1276. 10.1016/j.joule.2023.05.010.
“Computational resources for this work were provided by the UCLA-shared cluster Hoffman2 and Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation grant no. ACI-1548562 through allocation TGCHE170060XXX.” (Shen et al., 2023, p. 1276)
Shen, Kangze; Simran Kumari; Yu-Chao Huang; Joonbaek Jang; Philippe Sautet, and Carlos G. Morales-Guio. “Electrochemical Oxidation of Methane to Methanol on Electrodeposited Transition Metal Oxides.” Journal of the American Chemical Society 145 no. 12 (2023): 6927-6943. 10.1021/jacs.3c00441.
“This work also used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education Research Technology Group.” (Shen et al., 2023, p. 6942)
Shende, Vikram V.; Natalia R. Harris; Jacob N. Sanders; Sean A. Newmister; Yogan Khatri; Mohammad Movassaghi; Kendall N. Houk, and David H. Sherman. “Molecular Dynamics Simulations Guide Chimeragenesis and Engineered Control of Chemoselectivity in Diketopiperazine Dimerases.” Angewandte Chemie International Edition 62 no. 20 (2023): e202210254. 10.1002/anie.202210254.
“Additional computational resources were provided bytheUCLA Institute forDigital Research andEducation (IDRE).” (Shende et al., 2023, p. 5)
Shi, Junjie; Hio Tong Ngan; Philippe Sautet, and Jason F. Weaver. “High Selectivity and Activity of Ti-Cu(111) Dilute Alloys for the Deoxygenation of Ethanol to Ethylene.” ACS Catalysis 13 no. 17 (2023): 11244-11255. 10.1021/acscatal.3c02530.
DFT calculations reported in this work use computational and storage resources ontheHoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE).” (Shi et al., 2023, p. 11254)
Shoemaker, William R.. “A macroecological perspective on genetic diversity in the human gut microbiome.” PLOS ONE 18 no. 7 (2023): e0288926. 10.1371/journal.pone.0288926.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Shoemaker, 2023, p. 22)
Si, Yidongfang; Andrew L. Stewart, and Ian Eisenman. “Heat transport across the Antarctic Slope Front controlled by cross-slope salinity gradients.” Science Advances 9 no. 18 (2023): eadd7049. 10.1126/sciadv.add7049.
“This work also used the Hoffman2 Cluster, which is supported b the IDRE Research Technology Group at UCLA.” (Si et al., 2023, p. 13)
Spaulding-Astudillo, Francisco E. and Jonathan L. Mitchell. “Effects of Varying Saturation Vapor Pressure on Climate, Clouds, and Convection.” Journal of the Atmospheric Sciences 80 no. 5 (2023): 1247-1266. 10.1175/JAS-D-22-0063.1.
“Simulations with the ECHAM6 climate model were carried out on UCLA’s Hoffman2 Cluster.” (Spaulding-Astudillo and Mitchell, 2023, p. 1265)
Staples, F. A.; Q. Ma; A. Kellerman; I. J. Rae; C. Forsyth; J. K. Sandhu, and J. Bortnik. “Differentiating Between Simultaneous Loss Drivers in Earth’s Outer Radiation Belt: Multi-Dimensional Phase Space Density Analysis.” Geophysical Research Letters 50 no. 23 (2023): e2023GL106162. 10.1029/2023GL106162.
“The computations employed computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Staples et al., 2023, p. 9)
Svatunek, Dennis; Konrad Chojnacki; Titas Deb; Hannah Eckvahl; K. N. Houk, and Raphael M. Franzini. “Orthogonal Inverse-Electron-Demand Cycloaddition Reactions Controlled by Frontier Molecular Orbital Interactions.” Organic Letters 25 no. 34 (2023): 6340-6345. 10.1021/acs.orglett.3c02265.
“Calculations were performed on the Hoffman2 system provided by the University of California, Los Angeles (UCLA) Institute for Digital Research and Education and the Vienna Scientific Cluster.” (Svatunek et al., 2023, p. 6344)
Tesvara, Celine; Christopher J. Karwacki, and Philippe Sautet. “Decomposition of the Toxic Nerve Agent Sarin on Oxygen Vacancy Sites of Rutile TiO2(110).” The Journal of Physical Chemistry C 127 no. 17 (2023): 8006-8015. 10.1021/acs.jpcc.2c08525.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Tesvara et al., 2023, p. 8014)
Tom, Matthew; Henrik Wang; Feiyang Ou; Sungil Yun; Gerassimos Orkoulas, and Panagiotis D. Christofides. “Computational fluid dynamics modeling of a discrete feed atomic layer deposition reactor: Application to reactor design and operation.” Computers & Chemical Engineering 178 (2023): 108400. 10.1016/j.compchemeng.2023.108400.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Tom et al., 2023, p. 11)
Tonelli, Benjamin A.; Casey Youngflesh, and Morgan W. Tingley. “Geomagnetic disturbance associated with increased vagrancy in migratory landbirds.” Scientific Reports 13 no. 1 (2023): 414. 10.1038/s41598-022-26586-0.
“Models were run using the UCLA Hoffman2 Cluster using parallelization with each chain of the Bayesian models being run on a separate core.” (Tonelli et al., 2023, p. 10) Number: 1
Turba, Rachel; Glory H. Thai, and David K. Jacobs. “Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities.” Peer Community Journal 3 (2023). 10.24072/pcjournal.256.
“Sequence data was bioinformatically processed in Hoffman2, the High Performance Computing cluster at UC Los Angeles” (Turba et al., 2023, p. 6)
Wang, Huamin; Huiling Shao; Ankita Das; Subhabrata Dutta; Hok Tsun Chan; Constantin Daniliuc; K. N. Houk, and Frank Glorius. “Dearomative ring expansion of thiophenes by bicyclobutane insertion.” Science 381 no. 6653 (2023): 75-81. 10.1126/science.adh9737.
“DFT calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles.” (Wang et al., 2023, p. 7)
Wei, Ziyang; George Yan, and Philippe Sautet. “Toward more accurate surface properties of ceria using many-body perturbation theory.” The Journal of Chemical Physics 159 no. 5 (2023): 054708. 10.1063/5.0161084.
“The calculations were performed on the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE)” (Wei et al., 2023, p. 5)
Weng, Yangyang; Yetong Zhang; Aneta Turlik; Xianqing Wu; Haiyan Li; Fan Fei; Yongkang Yao; Chenglong Wang; Zhiqian Guo; Jingping Qu; K. N. Houk, and Yifeng Chen. “Nickel-catalysed regio- and stereoselective acylzincation of unsaturated hydrocarbons with organozincs and CO.” Nature Synthesis 2 no. 3 (2023): 261-274. 10.1038/s44160-022-00208-z.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (grant no. OCI-1053575).” (Weng et al. 2023) Number: 3
Williams, Claire E.; Smadar Naoz; William Lake; Yeou S. Chiou; Blakesley Burkhart; Federico Marinacci; Mark Vogelsberger; Gen Chiaki; Yurina Nakazato, and Naoki Yoshida. “The Supersonic Project: The Eccentricity and Rotational Support of SIGOs and DM GHOSts.” The Astrophysical Journal 945 no. 1 (2023): 6. 10.3847/1538-4357/acb820.
“C.E. W., W.L., S.N., Y.S.C, B.B., F.M., and M.V. thank the support of NASA grant No. 80NSSC20K0500 and the XSEDE AST180056 allocation, as well as the Simons Foundation Center for Computational Astrophysics and the UCLA cluster Hoffman2 for computational resources.” (Williams et al., 2023, p. 15)
Wu, Eric C. and Benjamin J. Schwartz. “Does the Traditional Band Picture Describe the Electronic Structure of Doped Conjugated Polymers? TD-DFT and Natural Transition Orbital Study of Doped P3HT.” Journal of Chemical Theory and Computation 19 no. 19 (2023): 6761-6769. 10.1021/acs.jctc.3c00743.
“Computations were performed on the Hoffman 2 cluster operated by the UCLA Institute for Digital Research and Education.” (Wu and Schwartz, 2023, p. 6767)
Yanagawa, Jane; Linh M. Tran; Ramin Salehi-Rad; Raymond J. Lim; Camelia Dumitras; Eileen Fung; William D. Wallace; Ashley E. Prosper; Gregory Fishbein; Conor Shea; Rui Hong; Bitta Kahangi; John J. Deng; Adam C. Gower; Bin Liu; Joshua D. Campbell; Sarah A. Mazzilli; Jennifer E. Beane; Humam Kadara; Marc E. Lenburg; Avrum E. Spira; Denise R. Aberle; Kostyantyn Krysan, and Steven M. Dubinett. “Single-Cell Characterization of Pulmonary Nodules Implicates Suppression of Immunosurveillance across Early Stages of Lung Adenocarcinoma.” Cancer Research 83 no. 19 (2023): 3305-3319. 10.1158/0008-5472.CAN-23-0128.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Yanagawa et al., 2023, p. 3317)
Yeung, Christopher; Benjamin Pham; Ryan Tsai; Katherine T. Fountaine, and Aaswath P. Raman. “DeepAdjoint: An All-in-One Photonic Inverse Design Framework Integrating Data-Driven Machine Learning with Optimization Algorithms.” ACS Photonics 10 no. 4 (2023): 884-891. 10.1021/acsphotonics.2c00968.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Yeung et al., 2023, p. 890)
Yu, Yikang; Hyeongjun Koh; Zisheng Zhang; Zhenzhen Yang; Anastassia N. Alexandrova; Mangilal Agarwal; Eric A. Stach, and Jian Xie. “Kinetic pathways of fast lithium transport in solid electrolyte interphases with discrete inorganic components.” Energy & Environmental Science 16 no. 12 (2023): 5904-5915. 10.1039/D3EE02048G.
“The computations in this work were performed on Hoffman2, the UCLA-shared cluster.” (Yu et al., 2023, p. 5914)
Yue, Xiaolin; Qingyang Zhou, and K. N. Houk. “Computational Exploration of the Thermal Rearrangement of Basketene: One Forbidden versus Two Allowed Pericyclic Reactions.” The Journal of Organic Chemistry 88 no. 20 (2023): 14303-14307. 10.1021/acs.joc.3c00993.
“Calculations were performed on the IDRE (Institute of Digital Research and Education) Hoffman2 Cluster at the University of California, Los Angeles.” (Yue et al., 2023, p. 14307)
Yun, Sungil; Henrik Wang; Matthew Tom; Feiyang Ou; Gerassimos Orkoulas, and Panagiotis D. Christofides. “Multiscale CFD Modeling of Area-Selective Atomic Layer Deposition: Application to Reactor Design and Operating Condition Calculation.” Coatings 13 no. 3 (2023): 558. 10.3390/coatings13030558.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Yun et al., 2023, p. 23) Number: 3
Zhang, Jian; Jingnan Guo, and Mikhail I. Dobynde. “What Is the Radiation Impact of Extreme Solar Energetic Particle Events on Mars?.” Space Weather 21 no. 6 (2023): e2023SW003490. 10.1029/2023SW003490.
“Part of this work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Zhang et al., 2023, p. 12)
Zhang, Zhenyu; Akihiko Nishimura; Nídia S. Trovão; Joshua L. Cherry; Andrew J. Holbrook; Xiang Ji; Philippe Lemey, and Marc A. Suchard. “Accelerating Bayesian inference of dependency between mixed-type biological traits.” PLOS Computational Biology 19 no. 8 (2023): e1011419. 10.1371/journal.pcbi.1011419.
“This work uses computational and storage services provided by the Hoffman2 Shared Cluster through the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Zhang et al., 2023, p. 19)
Zhang, Zisheng; Ive Hermans, and Anastassia N. Alexandrova. “Off-Stoichiometric Restructuring and Sliding Dynamics of Hexagonal Boron Nitride Edges in Conditions of Oxidative Dehydrogenation of Propane.” Journal of the American Chemical Society 145 no. 31 (2023): 17265-17273. 10.1021/jacs.3c04613.
“The computations in this work were performed on Hoffman2 the UCLA-shared cluster; Coriand Perlmutter of the National Energy Research Scientific Computing Center (NERSC), a U.S.Department of Energy Office of Science User Facility operated under Contract DEAC02-05CH11231; Theta of the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program at the Argonne Leadership Computing Facility, a U.S. Department of Energy Office of Science User Facility operated under Contract DE-AC02-06CH11357.” (Zhang et al., 2023, p. 17272)
Zhang, Zisheng; Tsugunosuke Masubuchi; Philippe Sautet; Scott L. Anderson, and Anastassia N. Alexandrova. “Hydrogen Evolution on Electrode-Supported Ptn Clusters: Ensemble of Hydride States Governs the Size Dependent Reactivity.” Angewandte Chemie International Edition 62 no. 20 (2023): e202218210. 10.1002/anie.202218210.
“The computations in this work were performed on:Hoffman2 the UCLA-shared cluster; Cori and Perlmutter of the National Energy Research Scientific Computing Center (NERSC), a U.S.Department of Energy Office of Science User Facility operated under Contract DE-AC02-05CH11231; Theta of the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program at the Argonne Leadership Computing Facility, a U.S.Department of Energy Office of Science User Facility operated under Contract DE-AC0206CH11357.” (Zhang et al., 2023, p. 8]
Zhou, Min and Nicholas V. DiRago. “The trajectory of the colour line in a US immigrant gateway: hyperdiverse spatialization in Los Angeles.” Ethnic and Racial Studies 46 no. 11 (2023): 2474-2501. 10.1080/01419870.2023.2168498.
“We have benefited from facilities and resources, provided by the California Center for Population Research at UCLA, and computational and storage services associated with the Hoffman2 Shared Cluster, provided by the UCLA Institute for Digital Research and Education.” (Zhou and DiRago, 2023, p. 2497)
Zhou, Yu; Yuzhen Chen, and Lihua Jin. “Three-dimensional postbuckling analysis of thick hyperelastic tubes.” Journal of the Mechanics and Physics of Solids 173 (2023): 105202. 10.1016/j.jmps.2023.105202.
“This work used the computational and storage services associated with the Hoffman2 Shared Cluster provided by Institute for Digital Research and Education’s Research Technology Group at UCLA.” (Zhou et al., 2023, p. 16)
Zieba, Jennifer; Lisette Nevarez; Davis Wachtell; Jorge H. Martin; Alexander Kot; Sereen Wong; Daniel H. Cohn, and Deborah Krakow. “Altered Sox9 and FGF signaling gene expression in Aga2 OI mice negatively affects linear growth.” JCI Insight 8 no. 21 (2023). 10.1172/jci.insight.171984.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Zieba et al., 2023, p. 18)
Theses for 2023¶
Abularrage, Nile S.. “Bioorthogonal Reagents: Design, Synthesis, and Reactivity.” Thesis Thesis, Massachusetts Institute of Technology, 2023. dspace.mit.edu, https://dspace.mit.edu/handle/1721.1/150556.
“Computations were performed using Gaussian09 Rev D.01236 on the Hoffman2 cluster of the Institute for Digital Research and Education (IDRE) at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE).” (Abularrage, 2023, p. 66) Accepted: 2023-04-25T14:21:29Z
Barr, Kelly. “Expanding Genomics Toolkits to Facilitate the Conservation and Recovery of Two Protected Species, the Tricolored Blackbird and Burrowing Owl.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2864476603.
“Computational allocations from the Extreme Science and Engineering Discovery Environment (Xsede), as well as UCLA’s Shared Hoffman2 Cluster made this work possible.” (Barr, 2023, p. 79)
Brewer, John Benjamin. “Photonic Control of Thermal Infrared Radiation.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2898157702.
“Special thanks to: UCLA Hoffman2 Computational Cluster” (Brewer, 2023, p. 16)
Delisle, Marie-Pierre Chloe. “A High-Resolution Numerical Investigation of Beach Groundwater and Swash Interactions.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2823427170.
“Numerical simulations presented in this dissertation were carried out using computational and storage services associated with the Hoffman2 Shared Cluster provided by the Institute for Digital Research and Education’s Research Technology Group at the University of California, Los Angeles” (Delisle, 2023, p. xx)
Dike, Veronica Jane. “Light From Dark Stars and Light Through Dark Matter: Emission as a Tool to Study the Unseen.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2867055176.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Dike, 2023, p. xii-xiii)
Evans, Declan Marshall. “Mechanistic Insight from Physical Models of Laboratory-Engineered Catalysts.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2781119044.
“Calculations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant no. ACI-1548562.” (Evans, 2023, p. xi)
Gupta, Akash. “From the Galactic to Atomic Scale: Understanding Planet Formation and Evolution.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2827890722.
“In addition, part of this thesis was facilitated by the computational and storage support provided by the UCLA Institute for Digital Research and Education’s Research Technology Group/Hoffman2 Cluster.” (Gupta, 2023, p. xxxiv) “These calculations were primarily performed on the UCLA Hoffman 2 Cluster and took roughly 3 million CPU hours.” (Gupta, 2023, p. 167)
Higa, Justin Takeshi. “Multi-Scale Investigations on the Impacts of Geologic Fractures.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2827870868.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Higa, 2023, pp. xix)
Kang, Bo. “Condition-Specific Variations in 30-Day Episode Cost and Admission Rates Among All-Payer Beneficiaries in Emergency Department.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2902850938.
“I also would like to thank Raffaella D’Auria, a computational scientist from IDRE, who guided me on using Hoffman2 cluster to array my heavy data workload, to solve the challenge of massive calculation.” (Kang, 2023, p. 14)
Kumari, Simran. “Probing Active Sites and Their Evolution in Surface Catalysts: From Electrochemical to Thermal Environments.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2825760922.
“This work was funded by DOE-BES grant DESC0020125. This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education Research Technology Group.” (Kumari, 2023, p. 31)
Lee, Woojin. “Exploring Reaction Mechanisms of Short-Lived Carbocation and Radical Intermediates via Synergetic Modern Computational Methods and Collaborative Experiments.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2866184471.
“Tyler and Gina familiarized me with the Hoffman2 cluster, Gaussian, and CREST” (Lee, 2023, p. 23)
Liu, Xihan. “Hydride Formation Modeling and Ethanol Dehydrogenation Simulation in Transition Metal Catalyst Systems.” M.S. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2825092778.
“I sincerely appreciate the support from the University of California, Los Angeles, specifically the UCLA Institute for Digital Research and Education (IDRE) and the computational resources on the Hoffman2 cluster.” (Liu, 2023, p. 9)
Mashhadi, Andrew Amir Ali. “An Application of Split-Attention Networks: Melanoma Detection.” M.A.S. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2819235566.
“The set of images consisted of over 110GB, so the data was hosted on UCLA’s Hoffman2 Linux Cluster. To support the size of each image and the large number of individual images within the data set, computing resources from the Hoffman2 cluster and Google Colab were used to tune, train, and test our models with powerful Graphical Processing Units (GPUs).” (Mashhadi, 2023, p. 13)
Richard, Derek Michael. “A Smart Manufacturing Inspired Approach to Research in Electrochemistry Applied to Electrochemical Carbon Dioxide Reduction and Steam Methane Reforming.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2872524954.
“All simulations were performed on the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group using a 36core dual processor with 192 GB of RAM.” (Richard, 2023, p. 64) “Simulations were performed using Ansys Fluent 2022R2 software running on the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group using a 48-core dual processor with 512 GB of RAM.” (Richard, 2023, p. 90)
Shaw, Crystal Ruth Michelle. “Link, Transport, Integrate: A Bayesian Latent Class Mixture Modeling Framework for Scalable Algorithmic Dementia Classification in Population-Representative Studies.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2777368412.
“This dissertation used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Shaw, 2023, p. 28)
Smith, Stephen Vincent. “Local Causal Structure Learning With the Coordinated Multi-Neighborhood Learning Algorithm.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2901721832.
“All numerical results in this work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Smith, 2023, p. xiii)
Su, Erica. “Bayesian Spatial Longitudinal Modeling for Local Rates of Glaucoma Progression.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2821521624.
“This work was supported by an NIH R01 grant (R01-EY029792) and used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Su, 2023, p. xxi)
Sumaria, Vaidish Pravin. “Modeling Transition Metal Surface Reconstruction in CO Gas Environment.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2778541651.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Sumaria, 2023, p. xxviii)
Xia, Yantao. “Self-limited Etching for Atomic Scale Surface Engineering of Metals: Understanding and Design.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2866269331.
“The author gratefully acknowledges the support from UCLA Institute of Digital Research and Education(IDRE) for computational resources on the UCLA Hoffman2 cluster.” (Xia, 2023, p. xiii)
Yun, Sungil. “First-Principles and Multiscale Modeling for Design and Operation of Atomic Layer Processing.” Ph.D. Thesis, University of California, Los Angeles, 2023. ProQuest, https://www.proquest.com/docview/2834034789.
“Facilitated by the Hoffman2 Cluster at UCLA, the Fluent computations are implemented with 24 parallel central processing units (CPU) with 16 GB memory for each core processor so that the parallel processing splits the gas-phase domain into multiple partitions to improve the computation efficiency.” (Yun, 2023, p. 52)
Conference Papers for 2023¶
Delisle, Marie-Pierre C.; Yeulwoo Kim, and Timu W. Gallien. “A numerical study of swash-groundwater interactions using openfoam.” In Coastal Sediments 2023: 2023: 305-313. 10.1142/9789811275135_0027.
“Numerical simulations were carried out using the UCLA Hoffman2 cluster.” (Delisle et al., 2023, p. 311) DOI: 10.1142/9789811275135_0027
Finnerty, Luke; Katelyn Horstman; Jean-Baptiste Ruffio; Jason J. Wang; Dimitri Mawet; Tobias Schofield; Ben Sappey; Jerry Xuan; Jacques-Robert Delorme; Nemanja Jovanovic; Geoffrey A. Blake, and Michael P. Fitzgerald. “Characterization of hot Jupiter atmospheres with Keck/KPIC.” In Techniques and Instrumentation for Detection of Exoplanets XI: Techniques and Instrumentation for Detection of Exoplanets XI 2023: 41-49. 10.1117/12.2677777.
“The contributed Hoffman2 computing node used for this work was supported by the Heising-Simons Foundation grant #2020-1821.” (Finnerty et al., 2023, p. 7)
Krishnamoorthy, Siddarth; Satvik Mashkaria, and Aditya Grover. “Diffusion models for black-box optimization.” In Proceedings of the 40th International Conference on Machine Learning: Honolulu, Hawaii, USA, 2023: 17842–17857.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Krishnamoorthy et al., 2023, p. 9)
Mashkaria, Satvik Mehul; Siddarth Krishnamoorthy, and Aditya Grover. “Generative Pretraining for Black-Box Optimization.” In Proceedings of the 40th International Conference on Machine Learning: International Conference on Machine Learning Honolulu, Hawaii, USA, 2023: 24173-24197. https://proceedings.mlr.press/v202/mashkaria23a.html.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Mashkaria et al., 2023, p. 9) ISSN: 2640-3498
Tom, Matthew; Sungil Yun; Henrik Wang; Feiyang Ou; Gerassimos Orkoulas, and Panagiotis D. Christofides. “Multiscale Modeling of Spatial Area-Selective Thermal Atomic Layer Deposition.” In Computer Aided Chemical Engineering: 2023: 71-76. 10.1016/B978-0-443-15274-0.50012-3.
“The multiscale simulation is performed autonomously through a Linux cluster system through the UCLA Hoffman2 Cluster and allows the interconnection of various programming languages and application software.” (Tom et al., 2023, p. 73) DOI: 10.1016/B978-0-443-15274-0.50012-3
Yalcin, Refet Ali; Patricia E. McNeil; Glareh N. Kashanchi; Ricardo Martinez; Sarah H. Tolbert; Bruce S. Dunn, and Laurent Pilon. “DEPENDENT SCATTERING IN SILICA AMBIGEL MONOLITHS - EXPERIMENTS AND SIMULATIONS.” Proceedings of the 10th International Symposium on Radiative Transfer, RAD-23 Thessaloniki, Greece, 12–16 June 2023 2023. 10.1615/RAD-23.260.
“This work also used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Yalcin et al., 2023, p. 218)
Presentations for 2023¶
Winjum, Bejamin J.; Roman Lee; Simon Bolaños; Frank S Tsung, and Warren Mori. “Enhancement and mitigation of kinetic stimulated Raman scattering by a magnetic field.” Denver, Colorado: 2023. https://meetings.aps.org/Meeting/DPP23/Session/JO06.3.
“Simulations were performed on the UCLA Hoffman2 Cluster.” (Benjum et al., 2023)
2022¶
- 106 publications for 2022
Journal Articles for 2022¶
Albanese, Katherine I.; Andrew Leaver-Fay; Joseph W. Treacy; Rodney Park; K. N. Houk; Brian Kuhlman, and Marcey L. Waters. “Comparative Analysis of Sulfonium−π, Ammonium−π, and Sulfur−π Interactions and Relevance to SAM-Dependent Methyltransferases.” Journal of the American Chemical Society 144 no. 6 (2022): 2535-2545. 10.1021/jacs.1c09902.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Albanese et al., 2022, p. 2543)
An, Hua; Geng Sun; Max J. Hülsey; Philippe Sautet, and Ning Yan. “Demonstrating the Electron–Proton-Transfer Mechanism of Aqueous Phase 4-Nitrophenol Hydrogenation Using Unbiased Electrochemical Cells.” ACS Catalysis 12 no. 24 (2022): 15021-15027. 10.1021/acscatal.2c03133.
“This work used computational and storage services associated withtheHoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (An et al., 2022, p. 15026)
Andorfer, Mary C.; Declan Evans; Song Yang; Cyndi Qixin He; Anna M. Girlich; Jaylie Vergara-Coll; Narayanasami Sukumar; K. N. Houk, and Jared C. Lewis. “Analysis of laboratory-evolved flavin-dependent halogenases affords a computational model for predicting halogenase site selectivity.” Chem Catalysis 2 no. 10 (2022): 2658-2674. 10.1016/j.checat.2022.07.003.
“Calculations were performed on the Hoffman2 cluster at UCLA, and the Extreme Science and Engineering Discovery Environment (XSEDE)” (Andorfer et al., 2022, p. 2674) Publication Title: Chem Catalysis
Bellotti, Peter; Torben Rogge; Fritz Paulus; Ranjini Laskar; Nils Rendel; Jiajia Ma; K. N. Houk, and Frank Glorius. “Visible-Light Photocatalyzed peri-(3 + 2) Cycloadditions of Quinolines.” Journal of the American Chemical Society 144 no. 34 (2022): 15662-15671. 10.1021/jacs.2c05687.
“The NMR laboratory of the Organic Chemistry Institute (WWU Münster) is acknowledged for experimental assistance with the NMR measurements. Calculations were performed ontheHoffman2 cluster at the University of California, Los Angeles.” (Bellotti et al., 2022, p. 15669)
Bossu, Christen M.; Julie A. Heath; Gregory S. Kaltenecker; Barbara Helm, and Kristen C. Ruegg. “Clock-linked genes underlie seasonal migratory timing in a diurnal raptor.” Proceedings of the Royal Society B: Biological Sciences 289 no. 1974 (2022): 20212507. 10.1098/rspb.2021.2507.
“Computational allocations from the Extreme Science and Engineering Discovery Environment (Xsede), as well as UCLA’s Shared Hoffman2 Cluster made this work possible.” (Bossu et al., 2022, p. 8)
Braithwaite, James and Lars Stixrude. “Partitioning of Iron Between Liquid and Crystalline Phases of (Mg,Fe)O.” Geophysical Research Letters 49 no. 16 (2022): e2022GL099116. 10.1029/2022GL099116.
“Calculations were carried out using the IRIDIS cluster partly owned by University College London, ARCHER of the UK national high-performance computing service, and MARENOSTRUM at the Barcelona Supercomputing Center, Spain of the PRACE Consortium, and the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Braithwaite and Stixrude, 2022, p. 5)
Bím, D; M Navrátil; O Gutten; J Konvalinka; Z Kutil; M Culka; V Navrátil; AN Alexandrova; C Barinka, and L Rulísek. “Predicting Effects of Site-Directed Mutagenesis on Enzyme Kinetics by QM/MM and QM Calculations: A Case of Glutamate Carboxypeptidase II.” JOURNAL OF PHYSICAL CHEMISTRY B 126 no. 1 (2022): 132-143. 10.1021/acs.jpcb.1c09240.
“Computational 1” (Bím et al., 2022, p. 11) “resources were in part provided by the IT4Innovations National Supercomputing Center, under the project LM2015070 (Large Infrastructures for Research, Experimental Development and Innovations), UCLA-IDRE cluster Hoffman2, and Extreme Science and Engineering Discovery Environment (XSEDE)” (Bím et al., 2022, p. 12)
Chen, Pan-Pan; Peter Wipf, and K. N. Houk. “How mono- and diphosphine ligands alter regioselectivity of the Rh-catalyzed annulative cleavage of bicyclo[1.1.0]butanes.” Nature Communications 13 no. 1 (2022): 7292. 10.1038/s41467-022-34837-x.
“Calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles” (Chen et al., 2022, p. 9) Publication Title: Nature Communications
Chen, Yen-Wei; Graciel Diamante; Jessica Ding; Thien Xuan Nghiem; Jessica Yang; Sung-Min Ha; Peter Cohn; Douglas Arneson; Montgomery Blencowe; Jennifer Garcia; Nima Zaghari; Paul Patel, and Xia Yang. “PharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning tool.” iScience 25 no. 4 (2022): 104052. 10.1016/j.isci.2022.104052.
“We thank the UCLA Hoffman2 engineers John Pedersen, Shao-Ching Huang, Brian Pape, and Raffaella D’Auria for technical support.” (Chen et al., 2022, p. 16)
Chen, Yuzhen; Alexa S. Kuenstler; Ryan C. Hayward, and Lihua Jin. “Formation of rolls from liquid crystal elastomer bistrips.” Soft Matter 18 no. 21 (2022): 4077-4089. 10.1039/D1SM01830B.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by Institute for Digital Research and Education’s Research Technology Group at the University of California, Los Angeles.” (Chen et al., 2022, p. 15)
Chen, Yuzhen; Tianzhen Liu, and Lihua Jin. “Spatiotemporally Programmable Surfaces via Viscoelastic Shell Snapping.” Advanced Intelligent Systems 4 no. 9 (2022): 2100270. 10.1002/aisy.202100270.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Chen et al., 2022, p. 7)
Cheung, Clifford; James Mangan; Julio Parra-Martinez, and Nabha Shah. “Nonperturbative Double Copy in Flatland.” Physical Review Letters 129 no. 22 (2022): 221602. 10.1103/PhysRevLett.129.221602.
“Numerical simulations were performed on the Hoffman2 Cluster at the Institute for Digital Research and Education at UCLA.” (Cheung et al., 2022, p. 7)
Deger, Caner; Shaun Tan; K. N. Houk; Yang Yang, and Ilhan Yavuz. “Lattice strain suppresses point defect formation in halide perovskites.” Nano Research 15 no. 6 (2022): 5746-5751. 10.1007/s12274-022-4141-9.
“The numerical calculations reported in this paper were performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources) and Hoffman2 cluster at the University of California, Los Angeles. Computational analysis was performed at the Simulations and Modelling Research Lab (Simulab), Physics Department of MU.” (Deger et al., 2022, p. 4)
Delisle, Marie-Pierre C.; Yeulwoo Kim; Ryan S. Mieras, and Timu W. Gallien. “Numerical investigation of sheet flow driven by a near-breaking transient wave using SedFoam.” European Journal of Mechanics - B/Fluids 96 (2022): 51-64. 10.1016/j.euromechflu.2022.07.002.
“Numerical simulations presented in this study were carried out using the Hoffman2 cluster at the University of California, Los Angeles.” (Delisle et al., 2022, p. 62)
Dickerson, Claire E.; Cecilia Chang; Han Guo, and Anastassia N. Alexandrova. “Fully Saturated Hydrocarbons as Hosts of Optical Cycling Centers.” The Journal of Physical Chemistry A 126 no. 51 (2022): 9644-9650. 10.1021/acs.jpca.2c06647.
“Computational resources at XSEDE and UCLA shared cluster hoffman2 are acknowledged.” (Dickerson et al., 2022, p. 9648)
DiRago, Nicholas V.; Meiying Li; Thalia Tom; Will Schupmann; Yvonne Carrillo; Colleen M. Carey, and S. Michael Gaddis. “COVID-19 Vaccine Rollouts and the Reproduction of Urban Spatial Inequality: Disparities Within Large US Cities in March and April 2021 by Racial/Ethnic and Socioeconomic Composition.” Journal of Urban Health 99 no. 2 (2022): 191-207. 10.1007/s11524-021-00589-0.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster, provided by the UCLA Institute for Digital Research and Education.” (DiRago et al., 2022, p. 201)
Drozdov, A. Y.; H. J. Allison; Y. Y. Shprits; M.e. Usanova; A. Saikin, and D. Wang. “Depletions of Multi-MeV Electrons and Their Association to Minima in Phase Space Density.” Geophysical Research Letters 49 no. 8 (2022): e2021GL097620. 10.1029/2021GL097620.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Drozdov et al., 2022, p. 9)
Espinoza, Rosa V.; Mark A. Maskeri; Aneta Turlik; Anjanay Nangia; Yogan Khatri; John Montgomery; K. N. Houk, and David H. Sherman. “Epoxidation and Late-Stage C–H Functionalization by P450 TamI Are Mediated by Variant Heme-Iron Oxidizing Species.” ACS Catalysis 12 no. 6 (2022): 3731-3742. 10.1021/acscatal.2c00364.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), supported by the National Science Foundation (Grant TG-CHE040013N).” (Espinoza et al., 2022, pp. -)
Fan, Zhoulong; Xiangyang Chen; Keita Tanaka; Han Seul Park; Nelson Y. S. Lam; Jonathan J. Wong; K. N. Houk, and Jin-Quan Yu. “Molecular editing of aza-arene C–H bonds by distance, geometry and chirality.” Nature 610 no. 7930 (2022): 87-93. 10.1038/s41586-022-05175-1.
“We gratefully acknowledge The Scripps Research Institute and the NIH (National Institute of General Medical Sciences grant R01 GM102265) for their financial support. Computations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Fan et al., 2022, p. 7)
Galy, Tiphaine and Laurent Pilon. “Dependent scattering effects in aggregates with touching or overlapping non-absorbing spherical particles.” Journal of Quantitative Spectroscopy and Radiative Transfer 278 (2022): 108018. 10.1016/j.jqsrt.2021.108018.
“Overall, it took between a couple of minutes and 18 h to perform the different simulations on UCLA Hoffman2 computing cluster.” (Galy and Pilon, 2022, p. 6)
Ge, Yijun and Timothy S. Fisher. “First-principles calculations of the optical response of single-layer and bilayer armchair graphene nanoribbons.” Frontiers in Nanotechnology 4 (2022).
“This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562 and computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Ge and Fisher, 2022, p. 11)
Ghahari, Farid; Niloofar Malekghaini; Hamed Ebrahimian, and Ertugrul Taciroglu. “Bridge Digital Twinning Using an Output-Only Bayesian Model Updating Method and Recorded Seismic Measurements.” Sensors 22 no. 3 (2022): 1278. 10.3390/s22031278.
“The authors would like to thank D’Auria from UCLA Institute for Digital Research and Education whose help was instrumental to carry out analyses on the UCLA Hoffman cluster.” (Ghahari et al., 2022, p. 24) Number: 3
Goldstein, David. “Correlated grammaticalization: The rise of articles in Indo-European.” Diachronica 39 no. 5 (2022): 658-706. 10.1075/dia.20033.gol.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Goldstein, 2022, p. 1)
Guiet, J; D Bianchi; O Maury; N Barrier, and F Kessouri. “Movement Shapes the Structure of Fish Communities Along a Cross-Shore Section in the California Current.” FRONTIERS IN MARINE SCIENCE 9 (2022). 10.3389/fmars.2022.785282.
“Computational resources were provided by the Extreme Science and Engineering Discovery Environment (XSEDE) through allocation TGOCE170017, and by the super-computer Hoffman2 at the University of California Los Angeles, at the Institute for Digital Research and Education (IDRE, UCLA).” (Guiet et al., 2022, p. 17) Publication Title: Frontiers in Marine … Type: 10.3389/fmars.2022.785282
Hassan, Isra S.; Jack T. Fuller; Vanessa N. Dippon; Angeline N. Ta; Michael W. Danneman; Brian R. McNaughton; Anastassia N. Alexandrova, and Tomislav Rovis. “Tuning through-space interactions via the secondary coordination sphere of an artificial metalloenzyme leads to enhanced Rh(III)-catalysis.” Chemical Science 13 no. 32 (2022): 9220-9224. 10.1039/D2SC03674F.
“NIGMS grants GM80442 to T. R., GM107520, B. R. M., and 1R01GM134047 to A. N. A., NSF predoctoral fellowship to I. S. H., Societe de Chemie summer fellowship to V. N. D., and UCLAIDRE cluster Hoffman2 and XSEDE are acknowledged.” (Hassan et al., 2022, p. 4)
Hosek, Matthew W.; Tuan Do; Jessica R. Lu; Mark R. Morris; Andrea M. Ghez; Gregory D. Martinez, and Jay Anderson. “Measuring the Orbits of the Arches and Quintuplet Clusters Using HST and Gaia: Exploring Scenarios for Star Formation near the Galactic Center.” The Astrophysical Journal 939 no. 2 (2022): 68. 10.3847/1538-4357/ac8bd6.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group” (Hosek et al., 2022, p. 21)
Huang, Huan-Ming; Peter Bellotti; Pan-Pan Chen; Kendall N. Houk, and Frank Glorius. “Allylic C(sp3)–H arylation of olefins via ternary catalysis.” Nature Synthesis 1 no. 1 (2022): 59-68. 10.1038/s44160-021-00006-z.
“Calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles, and the Vienna Scientific Cluster.” Number: 1
Jänner, Sven; Daniel Isak; Yuli Li; Kendall N. Houk, and Aubry K. Miller. “Bioinspired Asymmetric Total Synthesis of Emeriones A–C**.” Angewandte Chemie International Edition 61 no. 32 (2022): e202205878. 10.1002/anie.202205878.
“K.N.H. thanks the National Science Foundation (CHE1764328) for financial support, and the UCLA IDRE for computational resources.” (Jänner et al., 2022, p. 6)
Kean, Kelsey M.; Stefanie A. Baril; Kelsey N. Lamb; Sarah N. Dishman; Joseph W. Treacy; Kendall N. Houk; Eric M. Brustad; Lindsey I. James, and Marcey L. Waters. “Systematic Variation of Both the Aromatic Cage and Dialkyllysine via GCE-SAR Reveal Mechanistic Insights in CBX5 Reader Protein Binding.” Journal of Medicinal Chemistry 65 no. 3 (2022): 2646-2655. 10.1021/acs.jmedchem.1c02049.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Kean et al., 2022, p. 2654)
Kessouri, F; L Renault; JC McWilliams; P Damien, and D Bianchi. “Enhancement of Oceanic Eddy Activity by Fine-Scale Orographic Winds Drives High Productivity, Low Oxygen, and Low pH Conditions in the Santa Barbara Channel.” JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS 127 no. 12 (2022): e2022JC018947. 10.1029/2022JC018947.
“Computational resources were provided by the Extreme Science and Engineering Discovery Environment (XSEDE) through allocation TG-OCE170017, and by the super-computer Hoffman2 at the University of California Los Angeles, at the Institute for Digital Research and Education (IDRE, UCLA).” (Kessouri et al., 2022, p. 13)
Kim, Suhong; Pan-Pan Chen; K. N. Houk, and Robert R. Knowles. “Reversible Homolysis of a Carbon–Carbon σ-Bond Enabled by Complexation-Induced Bond-Weakening.” Journal of the American Chemical Society 144 no. 34 (2022): 15488-15496. 10.1021/jacs.2c01229.
“We are grateful to the NIH (R35 GM134893 to R.R.K.) and the National Science Foundation (CHE-1764328 to K.N.H.) for financial support of this research. Calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles.” (Kim et al., 2022, p. 15495)
Lao, GM; GZ Zhu; CE Dickerson; BL Augenbraun; AN Alexandrova; JR Caram; ER Hudson, and WC Campbell. “Laser Spectroscopy of Aromatic Molecules with Optical Cycling Centers: Strontium(I) Phenoxides.” The Journal of Physical Chemistry Letters 13 no. 47 (2022): 11029-11035. 10.1021/acs.jpclett.2c03040.
“Computational resources were provided by XSEDE and UCLA IDRE shared cluster hoffman2.” (Lao et al., 2022, p. 11034)
Laroche, Alexander; Daniel Gilman; Xinyu Li; Jo Bovy, and Xiaolong Du. “Quantum fluctuations masquerade as haloes: bounds on ultra-light dark matter from quadruply imaged quasars.” Monthly Notices of the Royal Astronomical Society 517 no. 2 (2022): 1867-1883. 10.1093/mnras/stac2677.
“Secondly, we used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Laroche et al., 2022, pp. -)
Lee, Woojin; Daniel Polyak; Bokai Xu; K. N. Houk, and Isaac J. Krauss. “A Mechanistic Switch from Homoallylation to Cyclopropylcarbinylation of Aldehydes.” Organic Letters 24 no. 25 (2022): 4660-4664. 10.1021/acs.orglett.2c01790.
“K.N.H. acknowledges the generous financial support of the National Science Foundation (No. CHE1764328) and the computational support of UCLA (Hoffman2 cluster).” (Lee et al., 2022, p. 4663)
Li, Bo; Xingyi Guan; Song Yang; Yike Zou; Wen Liu, and K. N. Houk. “Mechanism of the Stereoselective Catalysis of Diels–Alderase PyrE3 Involved in Pyrroindomycin Biosynthesis.” Journal of the American Chemical Society 144 no. 11 (2022): 5099-5107. 10.1021/jacs.2c00015.
“All calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (grant OCI1053575).” (Li et al., 2022, p. 5105)
Li, Bo; Hui Xu; Yanfeng Dang, and K. N. Houk. “Dispersion and Steric Effects on Enantio-/Diastereoselectivities in Synergistic Dual Transition-Metal Catalysis.” Journal of the American Chemical Society 144 no. 4 (2022): 1971-1985. 10.1021/jacs.1c12664.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI-1053575).” (Li et al., 2022, p. 1981)
Lin, Meixi; Merly Escalona; Ruta Sahasrabudhe; Oanh Nguyen; Eric Beraut; Michael R Buchalski, and Robert K Wayne. “A Reference Genome Assembly of the Bobcat, Lynx rufus.” Journal of Heredity 113 no. 6 (2022): 615-623. 10.1093/jhered/esac031.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Lin et al., 2022, p. 622)
Liu, Wen-Deng; Woojin Lee; Hanyu Shu; Chuyu Xiao; Huiwei Xu; Xiangyang Chen; Kendall N. Houk, and Jiannan Zhao. “Diastereoselective Radical Aminoacylation of Olefins through N-Heterocyclic Carbene Catalysis.” Journal of the American Chemical Society 144 no. 49 (2022): 22767-22777. 10.1021/jacs.2c11209.
“Computations were performed on the UCLA Institute of Digital Research and Education Hoffman2 Cluster.” (Liu et al., 2022, p. 22774)
Lleras-Muney, Adriana and Flavien Moreau. “A Unified Model of Cohort Mortality.” Demography 59 no. 6 (2022): 2109-2134. 10.1215/00703370-10286336.
“This work used computational and storage services associated with the Shared Hoffman2 Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Lleras-Muney and Moreau, 2022, p. 2131)
Ma, Jiajia; Shuming Chen; Peter Bellotti; Tobias Wagener; Constantin Daniliuc; Kendall N. Houk, and Frank Glorius. “Facile access to fused 2D/3D rings via intermolecular cascade dearomative [2 + 2] cycloaddition/rearrangement reactions of quinolines with alkenes.” Nature Catalysis 5 no. 5 (2022): 405-413. 10.1038/s41929-022-00784-5.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI-1053575).” (Ma et al., 2022, p. 413) Number: 5
MacDougall, Mason G.; Erik A. Petigura; Tara Fetherolf; Corey Beard; Jack Lubin; Isabel Angelo; Natalie M. Batalha; Aida Behmard; Sarah Blunt; Casey Brinkman; Ashley Chontos; Ian J. M. Crossfield; Fei Dai; Paul A. Dalba; Courtney Dressing; Benjamin Fulton; Steven Giacalone; Michelle L. Hill; Andrew W. Howard; Daniel Huber; Howard Isaacson; Stephen R. Kane; Molly Kosiarek; Andrew Mayo; Teo Močnik; Joseph M. Akana Murphy; Daria Pidhorodetska; Alex Polanski; Malena Rice; Paul Robertson; Lee J. Rosenthal; Arpita Roy; Ryan A. Rubenzahl; Nicholas Scarsdale; Emma V. Turtelboom; Dakotah Tyler; Judah Van Zandt; Lauren M. Weiss; Emma Esparza-Borges; Akihiko Fukui; Keisuke Isogai; Kiyoe Kawauchi; Mayuko Mori; Felipe Murgas; Norio Narita; Taku Nishiumi; Enric Palle; Hannu Parviainen; Noriharu Watanabe; Jon M. Jenkins; David W. Latham; George R. Ricker; S. Seager; Roland K. Vanderspek; Joshua N. Winn; Allyson Bieryla; Douglas A. Caldwell; Diana Dragomir; M. M. Fausnaugh; Ismael Mireles, and David R. Rodriguez. “The TESS–Keck Survey. XIII. An Eccentric Hot Neptune with a Similar-mass Outer Companion around TOI-1272.” The Astronomical Journal 164 no. 3 (2022): 97. 10.3847/1538-3881/ac7ce1.
“This work also used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (MacDougall et al., 2022, p. 12)
Marcella, Nicholas; Jin Soo Lim; Anna M. Płonka; George Yan; Cameron J. Owen; Jessi E. S. Van Der Hoeven; Alexandre C. Foucher; Hio Tong Ngan; Steven B. Torrisi; Nebojsa S. Marinkovic; Eric A. Stach; Jason F. Weaver; Joanna Aizenberg; Philippe Sautet; Boris Kozinsky, and Anatoly I. Frenkel. “Decoding reactive structures in dilute alloy catalysts.” Nature Communications 13 no. 1 (2022): 832. 10.1038/s41467-022-28366-w.
“G.Y. and H.T.N. used the HOFFMAN2 cluster at the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE)5” (Marcella et al., 2022, p. 9) Publication Title: Nature …
Martin, Henry; Eric Kwabena Kyeh Abavare, and Peter Amoako-Yirenkyi. “Thermodynamic stable site for interstitial solute (N or O) in bcc refractory metals (Mo and Nb) using density functional theory.” MRS Advances 7 no. 22 (2022): 474-481. 10.1557/s43580-022-00280-9.
“The authors would like to thank Prof. Jaime Marian and his group at the Department of Materials Science and Engineering and Mechanical and Aerospace Engineering, University of California Los Angeles (UCLA), Los Angeles, USA, for his helpful discussion, insightful advice, access, and usage of the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Martin et al., 2022, p. 479)
Maskeri, Mark A.; Anthony J. Fernandes; Giovanni Di Mauro; Nuno Maulide, and K. N. Houk. “Taming Keteniminium Reactivity by Steering Reaction Pathways: Computational Predictions and Experimental Validations.” Journal of the American Chemical Society 144 no. 51 (2022): 23358-23367. 10.1021/jacs.2c09146.
“Computations for this work were performed ontheHoffman2 cluster available through the UCLA Institute for Digital Research and Education (IDRE).” (Maskeri et al., 2022, p. 23366)
McElfresh, C; C Roberts; SC He; S Prikhodko, and J Marian. “Using machine-learning to understand complex microstructural effects on the mechanical behavior of Ti-6Al-4V alloys.” COMPUTATIONAL MATERIALS SCIENCE 208 (2022). 10.1016/j.commatsci.2022.111267.
“Computer time allocations at UCLA’s IDRE Hoffman2 supercomputer are acknowledged.” (McElfresh et al., 2022, p. 20)
McLeod, David; Nicolaj Inunnguaq Jessen; Thanh V. Q. Nguyen; Marcus Espe; Jeremy David Erickson; Karl Anker Jørgensen; Limin Yang, and K. N. Houk. “Influence of Achiral Phosphine Ligands on a Synergistic Organo‐ and Palladium‐Catalyzed Asymmetric Allylic Alkylation.” Chemistry – A European Journal 28 no. 71 (2022): e202202951. 10.1002/chem.202202951.
“K.N.H.and L.Y. thank the National Science Foundation (CHE-1764328 to K.N.H.) and the UCLA IDRE for use of the Hoffman2 cluster.” (McLeod et al., 2022, p. 8)
Moreno, Allison R.; Clarissa Anderson; Raphael M. Kudela; Martha Sutula; Christopher Edwards, and Daniele Bianchi. “Development, calibration, and evaluation of a model of Pseudo-nitzschia and domoic acid production for regional ocean modeling studies.” Harmful Algae 118 (2022): 102296. 10.1016/j.hal.2022.102296.
“D. Bianchi acknowledges computational support by the Extreme Science and Engineering Discovery Environment through allocation TG-OCE170017, and by the supercomputer Hoffman2 at the University of California Los Angeles, at the Institute for Digital Research and Education.” (Moreno et al., 2022, p. 14)
Munarriz, Julen; Zisheng Zhang; Philippe Sautet, and Anastassia N. Alexandrova. “Graphite-Supported Ptn Cluster Electrocatalysts: Major Change of Active Sites as a Function of the Applied Potential.” ACS Catalysis 12 no. 23 (2022): 14517-14526. 10.1021/acscatal.2c04643.
“The authors acknowledge the computational resources and technical assistance from NERSC, INCITE, and UCLA shared cluster, Hoffman2.” (Munarriz et al., 2022, p. 14524)
Narvaez, Wilberth A.; Eric C. Wu; Sanghyun J. Park; Mariah Gomez, and Benjamin J. Schwartz. “Trap-Seeking or Trap-Digging? Photoinjection of Hydrated Electrons into Aqueous NaCl Solutions.” The Journal of Physical Chemistry Letters 13 no. 37 (2022): 8653-8659. 10.1021/acs.jpclett.2c02243.
“Computational resources were provided by the UCLA Institute for Digital Research and Education and byXSEDE under computational Project No. CHE-170065.” (Narvaez et al., 2022, p. 8657-8)
Ngan, Hio Tong; George Yan; Jessi E. S. van der Hoeven; Robert J. Madix; Cynthia M. Friend, and Philippe Sautet. “Hydrogen Dissociation Controls 1-Hexyne Selective Hydrogenation on Dilute Pd-in-Au Catalysts.” ACS Catalysis 12 no. 21 (2022): 13321-13333. 10.1021/acscatal.2c03560.
“The DFT calculations in this work used computational and storage services associated with the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE)” (Ngan et al., 2022, p. 13331)
Nistanaki, Sepand K.; Chloe G. Williams; Benjamin Wigman; Jonathan J. Wong; Brittany C. Haas; Stasik Popov; Jacob Werth; Matthew S. Sigman; K. N. Houk, and Hosea M. Nelson. “Catalytic asymmetric C–H insertion reactions of vinyl carbocations.” Science 378 no. 6624 (2022): 1085-1091. 10.1126/science.ade5320.
“Work by the Houk group used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Nistanaki et al., 2022, p. 7)
Padilla, Robin; K. Peter C. Vollhardt; Kendall N. Houk, and Jonathan J. Wong. “Bis(η5-cyclopentadienyl)[μ-(4b,5,5a-η3:9b,10,10a-η3)-2,3,7,8-tetrakis(trimethylsilyl)benzo[3,4]cyclobuta[1,2-b]biphenylene]-syn-dicobalt (Co–Co), a Dinuclear π-Complex of the Linear [3]Phenylene Framework.” Synlett 33 no. 1 (2022): 34-37. 10.1055/a-1659-7656.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and in the Extreme Science and Engineering Discovery Environment (XSEDE), which is funded by the National Science Foundation (Grant OCI-1053575).” (Padilla et al., 2022, p. 37)
Penchoff, Deborah A.; Charles C. Peterson; Eleigha M. Wrancher; George Bosilca; Robert J. Harrison; Edward F. Valeev, and Paul D. Benny. “Evaluations of molecular modeling and machine learning for predictive capabilities in binding of lanthanum and actinium with carboxylic acids.” Journal of Radioanalytical and Nuclear Chemistry 331 no. 12 (2022): 5469-5485. 10.1007/s10967-022-08620-7.
“Part of this work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Penchoff et al., 2022, p. 5482)
Raghunathan, Srinivasan. “Assessing the Importance of Noise from Thermal Sunyaev–Zel′dovich Signals for CMB Cluster Surveys and Cluster Cosmology.” The Astrophysical Journal 928 no. 1 (2022): 16. 10.3847/1538-4357/ac510f.
“This work also used the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Raghunathan, 2022, p. 11)
Raghunathan, Srinivasan; Nathan Whitehorn; Marcelo A. Alvarez; Han Aung; Nicholas Battaglia; Gilbert P. Holder; Daisuke Nagai; Elena Pierpaoli; Christian L. Reichardt, and Joaquin D. Vieira. “Constraining Cluster Virialization Mechanism and Cosmology Using Thermal-SZ-selected Clusters from Future CMB Surveys.” The Astrophysical Journal 926 no. 2 (2022): 172. 10.3847/1538-4357/ac4712.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Raghunathan et al., 2022, p. 17)
Ricciardi, Tulio R.; William R. Wolf, and Kunihiko Taira. “Transition, intermittency and phase interference effects in airfoil secondary tones and acoustic feedback loop.” Journal of Fluid Mechanics 937 (2022): A23. 10.1017/jfm.2022.129.
“The authors thank CENAPAD-SP (Project 551), UCLA cluster Hoffman2 and LNCC-Cluster SDumont (Project SimTurb) for providing the computational resources used in this study.” (Ricciardi et al., 2022, p. 29)
Riedel, Philipp; Junghee Lee; Christopher G. Watson; Amy M. Jimenez; Eric A. Reavis, and Michael F. Green. “Reorganization of the functional connectome from rest to a visual perception task in schizophrenia and bipolar disorder.” Psychiatry Research: Neuroimaging 327 (2022): 111556. 10.1016/j.pscychresns.2022.111556.
“fMRI data analysis for this study used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Riedel et al., 2022, p. 13)
Rose, Douglas A.; Joseph W. Treacy; Zhongyue J. Yang; Jeong Hoon Ko; K. N. Houk, and Heather D. Maynard. “Self-Immolative Hydroxybenzylamine Linkers for Traceless Protein Modification.” Journal of the American Chemical Society 144 no. 13 (2022): 6050-6058. 10.1021/jacs.2c01136.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Rose et al., 2022, p. 6057) PMID: 35321547
Ruiz-Ramos, Dannise V.; Rachel S. Meyer; Daniel Toews; Molly Stephens; Monique K. Kolster, and Jason P. Sexton. “Environmental DNA (eDNA) detects temporal and habitat effects on community composition and endangered species in ephemeral ecosystems: A case study in vernal pools.” Environmental DNA 5 no. 1 (2022): 85-101. 10.1002/edn3.360.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Ruiz-Ramos et al., 2023, p. 98)
Saikin, A. A.; A. Y. Drozdov, and D. M. Malaspina. “Low Frequency Plasmaspheric Hiss Wave Activity Parameterized by Plasmapause Location: Models and Simulations.” Journal of Geophysical Research: Space Physics 127 no. 9 (2022): e2022JA030687. 10.1029/2022JA030687.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Saikin et al., 2022, p. 13)
Sarwal, Varuni; Sebastian Niehus; Ram Ayyala; Minyoung Kim; Aditya Sarkar; Sei Chang; Angela Lu; Neha Rajkumar; Nicholas Darfci-Maher; Russell Littman; Karishma Chhugani; Arda Soylev; Zoia Comarova; Emily Wesel; Jacqueline Castellanos; Rahul Chikka; Margaret G Distler; Eleazar Eskin; Jonathan Flint, and Serghei Mangul. “A comprehensive benchmarking of WGS-based deletion structural variant callers.” Briefings in Bioinformatics 23 no. 4 (2022): bbac221. 10.1093/bib/bbac221.
“The CPU time was computed using either the GNU time program that is inbuilt in make bash terminals or the Hoffman2 Cluster qsub command” (Sarwal et al., 2022, p. 10)
Sengupta, Arkajyoti; Bo Li; Dennis Svatunek; Fang Liu, and K. N. Houk. “Cycloaddition Reactivities Analyzed by Energy Decomposition Analyses and the Frontier Molecular Orbital Model.” Accounts of Chemical Research 55 no. 17 (2022): 2467-2479. 10.1021/acs.accounts.2c00343.
“All calculations were performed oncomputational resources provided bytheUCLA Institute ofDigital Research and Education andtheVienna Scientific Cluster andtheExtreme Science andEngineering Discovery Environment (XSEDE).” (Sengupta et al., 2022, p. 2477)
Senthilvelan, Jayasuriya and Neema Jamshidi. “A pipeline for automated deep learning liver segmentation (PADLLS) from contrast enhanced CT exams.” Scientific Reports 12 no. 1 (2022): 15794. 10.1038/s41598-022-20108-8.
“The authors appreciatively acknowledge the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group at UCLA.” (Senthilvelan and Jamshidi, 2022, p. 11)
Shajib, A. J.; K. C. Wong; S. Birrer; S. H. Suyu; T. Treu; E. J. Buckley-Geer; H. Lin; C. E. Rusu; J. Poh; A. Palmese; A. Agnello; M. W. Auger-Williams; A. Galan; S. Schuldt; D. Sluse; F. Courbin; J. Frieman, and M. Millon. “TDCOSMO - IX. Systematic comparison between lens modelling software programs: Time-delay prediction for WGD 2038−4008.” Astronomy & Astrophysics 667 (2022): A123. 10.1051/0004-6361/202243401.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Shajib et al., 2022, p. 32)
Staples, F. A.; A. Kellerman; K. R. Murphy; I. J. Rae; J. K. Sandhu, and C. Forsyth. “Resolving Magnetopause Shadowing Using Multimission Measurements of Phase Space Density.” Journal of Geophysical Research: Space Physics 127 no. 2 (2022): e2021JA029298. 10.1029/2021JA029298.
“The computations employed computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Staples et al., 2022, p. 12)
Svatunek, Dennis; Martin Wilkovitsch; Lea Hartmann; K. N. Houk, and Hannes Mikula. “Uncovering the Key Role of Distortion in Bioorthogonal Tetrazine Tools That Defy the Reactivity/Stability Trade-Off.” Journal of the American Chemical Society 144 no. 18 (2022): 8171-8177. 10.1021/jacs.2c01056.
“The computational results presented have been achieved using the Vienna Scientific cluster (VSC) at TU Wien and the Hoffman2 cluster at UCLA.” (Svatunek et al., 2022, p. 8176)
Tesvara, Celine; Constantin Walenta, and Philippe Sautet. “Oxidative decomposition of dimethyl methylphosphonate on rutile TiO2(110): the role of oxygen vacancies.” Physical Chemistry Chemical Physics 24 no. 38 (2022): 23402-23419. 10.1039/D2CP02246J.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Tesvara et al., 2022, p. 23414)
Tom, Matthew; Sungil Yun; Henrik Wang; Feiyang Ou; Gerassimos Orkoulas, and Panagiotis D. Christofides. “Machine learning-based run-to-run control of a spatial thermal atomic layer etching reactor.” Computers & Chemical Engineering 168 (2022): 108044. 10.1016/j.compchemeng.2022.108044.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Tom et al., 2022, p. 20)
Tran, Zachary; Nikhil Chervu; Catherine Williamson; Arjun Verma; Joseph Hadaya; Matthew Gandjian; Sha’Shonda Revels, and Peyman Benharash. “The Impact of Expedited Discharge on 30-Day Readmission After Lung Resection: A National Study.” The Annals of Thoracic Surgery 113 no. 4 (2022): 1274-1281. 10.1016/j.athoracsur.2021.04.009.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Tran et al., 2022, p. 1280)
Tran, Zachary; Roland Hernandez; Josef Madrigal; Samuel T. Kim; Arjun Verma; David G. Rabkin, and Peyman Benharash. “Center-Level Variation in Transplant Rates Following the Heart Allocation Policy Change.” JAMA cardiology 7 no. 3 (2022): 277-285. 10.1001/jamacardio.2021.5370.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Tran et al., 2022, p. 284) PMID: 35044415 PMCID: PMC8771429
Turba, Rachel; Jonathan Q. Richmond; Sorel Fitz-Gibbon; Marco Morselli; Robert N. Fisher; Camm C. Swift; Gorgonio Ruiz-Campos; Adam R. Backlin; Chris Dellith, and David K. Jacobs. “Genetic structure and historic demography of endangered unarmoured threespine stickleback at southern latitudes signals a potential new management approach.” Molecular Ecology 31 no. 24 (2022): 6515-6530. 10.1111/mec.16722.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group (IDRE), and access was sponsored by the Pellegrini laboratory.” (Turba et al., 2022, p. 6526)
van der Hoeven, Jessi E. S.; Hio Tong Ngan; George Yan; Joanna Aizenberg; Robert J. Madix; Philippe Sautet, and Cynthia M. Friend. “Unraveling 1-Hexene Hydrogenation over Dilute Pd-in-Au Alloys.” The Journal of Physical Chemistry C 126 no. 37 (2022): 15710-15723. 10.1021/acs.jpcc.2c04982.
“The DFT calculations in this work used computational and storage services associated with the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE)” (Hoeven et al., 2022, p. 15721)
Vidal, Lucas; Pan-Pan Chen; Eva Nicolas; Andrew Hackett; Craig M. Robertson; Kendall N. Houk, and Christophe Aïssa. “Enantioselective Intramolecular Iridium-Catalyzed Cyclopropanation of α-Carbonyl Sulfoxonium Ylides.” Organic letters 24 no. 46 (2022): 8503-8508. 10.1021/acs.orglett.2c03396.
“Calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575).” (Vidal et al., 2022, p. 8506)
Vong, Andy; Kenneth J. Mei; Devon R. Widmer, and Benjamin J. Schwartz. “Solvent Control of Chemical Identity Can Change Photodissociation into Photoisomerization.” The Journal of Physical Chemistry Letters 13 no. 34 (2022): 7931-7938. 10.1021/acs.jpclett.2c01955.
“We gratefully acknowledge the Institute for Digital Research and Education (IDRE) at UCLA for use of the Hoffman2 computing cluster.” (Vong et al., 2022, p. 7937)
Vong, Andy and Benjamin J. Schwartz. “Bond-Breaking Reactions Encounter Distinct Solvent Environments Causing Breakdown of Linear Response.” The Journal of Physical Chemistry Letters 13 no. 29 (2022): 6783-6791. 10.1021/acs.jpclett.2c01656.
“We gratefully acknowledge the Institute for Digital Research and Education (IDRE) at UCLA for use of the hoffman2 computing cluster.” (Vong and Schwartz, 2022, p. 6790)
Watanabe, Momoko; Jessie E. Buth; Jillian R. Haney; Neda Vishlaghi; Felix Turcios; Lubayna S. Elahi; Wen Gu; Caroline A. Pearson; Arinnae Kurdian; Natella V. Baliaouri; Amanda J. Collier; Osvaldo A. Miranda; Natassia Dunn; Di Chen; Shan Sabri; Luis de la Torre-Ubieta; Amander T. Clark; Kathrin Plath; Heather R. Christofk; Harley I. Kornblum; Michael J. Gandal, and Bennett G. Novitch. “TGFβ superfamily signaling regulates the state of human stem cell pluripotency and capacity to create well-structured telencephalic organoids.” Stem Cell Reports 17 no. 10 (2022): 2220-2238. 10.1016/j.stemcr.2022.08.013.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Watanabe et al., 2022, p. 2236)
Wei, Ziyang; Florian Göltl; Stephan N. Steinmann, and Philippe Sautet. “Modeling Electrochemical Processes with Grand Canonical Treatment of Many-Body Perturbation Theory.” The Journal of Physical Chemistry Letters 13 no. 26 (2022): 6079-6084. 10.1021/acs.jpclett.2c01376.
“The calculations were performed on the Hoffman2 cluster at UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE),53 which is supported by National Science Foundation Grant No. ACI-1548562, through allocation TGCHE170060.” (Wei et al., 2022, p. 6083)
Wei, Ziyang and Philippe Sautet. “Revisiting the link between magnetic properties and chemisorption at graphene nanoribbon zigzag edge.” The Journal of Chemical Physics 156 no. 4 (2022): 044706. 10.1063/5.0079064.
“The calculations were performed on the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE),45 which is supported by the National Science Foundation under Grant No. ACI-1548562, through Grant No. TG-CHE170060.” (Wei and Sautet, 2022, p. 8)
Wei, Ziyang and Philippe Sautet. “Improving the Accuracy of Modelling CO2 Electroreduction on Copper Using Many-Body Perturbation Theory.” Angewandte Chemie 134 no. 43 (2022): e202210060. 10.1002/ange.202210060.
“The calculations were performed ontheHoffman2 cluster at UCLA Institute for Digital Research and Education (IDRE) and at the Extreme Science and Engineering Discovery Environment (XSEDE),[46] which is supported by National Science Foundation grant number ACI-1548562, through allocation TG-CHE170060.” (Wei and Sautet, 2022, p. 5)
Wigman, Benjamin; Woojin Lee; Wenjing Wei; Kendall N. Houk, and Hosea M. Nelson. “Electrochemical Fluorination of Vinyl Boronates through Donor-Stabilized Vinyl Carbocation Intermediates**.” Angewandte Chemie 134 no. 12 (2022): e202113972. 10.1002/ange.202113972.
“Computations were performed ontheHoffman2 cluster at UCLA.” (Wigman et al., 2022, p. 5)
Wu, Boliang; Tianzhen Liu; Yuzhen Chen, and Lihua Jin. “Photo-induced spatiotemporal bending of shape memory polymer beams.” Smart Materials and Structures 31 no. 12 (2022): 125011. 10.1088/1361-665X/ac9d75.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by Institute for Digital Research and Education’s Research Technology Group at the University of California, Los Angeles (UCLA).” (Wu et al., 2022, p. 16)
Wu, Xianqing; Aneta Turlik; Baixue Luan; Feng He; Jingping Qu; K. N. Houk, and Yifeng Chen. “Nickel‐Catalyzed Enantioselective Reductive Alkyl‐Carbamoylation of Internal Alkenes.” Angewandte Chemie 134 no. 36 (2022): e202207536.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (grant OCI-1053575).” (Wu et al., 2022, p. 7)
Wu, Zhi-Chen; K. N. Houk; Dale L. Boger, and Dennis Svatunek. “Mechanistic Insights into the Reaction of Amidines with 1, 2, 3-Triazines and 1, 2, 3, 5-Tetrazines.” Journal of the American Chemical Society 144 no. 24 (2022): 10921-10928.
“The computational results presented have been achieved using the Vienna Scientific cluster (VSC) at TU Wien and the Hoffman2 cluster at UCLA.” (Wu et al., 2022, p. 10928)
Xia, Yantao and Philippe Sautet. “Plasma Oxidation of Copper: Molecular Dynamics Study with Neural Network Potentials.” ACS Nano 16 no. 12 (2022): 20680-20692. 10.1021/acsnano.2c07712.
“The authors gratefully acknowledge the support from UCLA Institute of Digital Research and Education (IDRE) for computational resources ontheUCLAHoffman2 cluster.” (Xia and Sautet, 2022, p. 20691)
Yalcin, Refet Ali; Thomas Lee; Glareh Natalie Kashanchi; Johannes Markkanen; Ricardo Martinez; Sarah H. Tolbert, and Laurent Pilon. “Dependent Scattering in Thick and Concentrated Colloidal Suspensions.” ACS Photonics 9 no. 10 (2022): 3318-3332. 10.1021/acsphotonics.2c00664.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Yalcin et al., 2022, p. 3331)
Yan, George; Yu Tang; Yuting Li; Yixiao Li; Luan Nguyen; Tomohiro Sakata; Kotaro Higashi; Franklin Feng Tao, and Philippe Sautet. “Reaction product-driven restructuring and assisted stabilization of a highly dispersed Rh-on-ceria catalyst.” Nature Catalysis 5 no. 2 (2022): 119-127. 10.1038/s41929-022-00741-2.
“The calculations in this work used computational and storage services associated with the Hoffman2 shared computational cluster located at University of California Los Angeles.” (Yan et al., 2022, p. 127) Number: 2
Yeung, Christopher; David Ho; Benjamin Pham; Katherine T. Fountaine; Zihan Zhang; Kara Levy, and Aaswath P. Raman. “Enhancing Adjoint Optimization-Based Photonic Inverse Design with Explainable Machine Learning.” ACS Photonics 9 no. 5 (2022): 1577-1585. 10.1021/acsphotonics.1c01636.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Yeung et al., 2022, p. 1584)
Yu, HM and AS Banerjee. “Density functional theory method for twisted geometries with application to torsional deformations in group-IV nanotubes.” JOURNAL OF COMPUTATIONAL PHYSICS 456 (2022). 10.1016/j.jcp.2022.111023.
“All simulations involving Helical DFT were run using a dedicated desktop workstation (Dell Precision 7920 Tower) or single nodes of the Hoffman2 cluster at UCLA’s Institute for Digital Research and Education (IDRE). The desktop workstation has an 18-core Intel Xeon Gold 5220 processor (24.75 MB cache, running at 2.2 GHz), 256 GB of RAM and a 1 TB SATA Class 20 Solid State Drive (SSD). Each compute node of the Hoffman2 cluster has two 18-core Intel Xeon Gold 6140 processors (with 24.75 MB cache, running at 2.3 GHz), 192 GB of RAM and local SSD storage. MATLAB version 9.7.0 (R2019b) was used for the simulations. Compilation of C language routines was carried out using MinGW (on the workstation) and GCC (on the Hoffman2 nodes) software suites.” (Yu and Banerjee, 2022, p. 24) “ASB acknowledges startup support from the Samueli School Of Engineering at UCLA, as well as funding from UCLA’s Council on Research (COR) Faculty Research Grant. ASB would like to thank Neha Bairoliya (Univ. of Southern California) for providing encouragement and support during the preparation of this manuscript. HMY would like to thank Elliona Li for her help in preparing some of the figures in this work. ASB would like to thank Vikram Gavini (University of Michigan) and Swarnava Ghosh (Oak Ridge National Lab) for insightful discussions during the early stages of preparation of the manuscript. ASB and HMY would like to thank UCLA’s Institute for Digital Research and Education (IDRE) for making available some of the computing resources used in this work.” (Yu and Banerjee, 2022, p. 41)
Yu, Qianran; Giacomo Po, and Jaime Marian. “Physics-based model of irradiation creep for ferritic materials under fusion energy operation conditions.” Journal of Applied Physics 132 no. 22 (2022): 225101. 10.1063/5.0101561.
“Computer time allocations at UCLA’s IDRE Hoffman2 computer cluster are gratefully acknowledged.” (Yu et al., 2022, p. 15)
Yun, Sungil; Feiyang Ou; Henrik Wang; Matthew Tom; Gerassimos Orkoulas, and Panagiotis D. Christofides. “Atomistic-mesoscopic modeling of area-selective thermal atomic layer deposition.” Chemical Engineering Research and Design 188 (2022): 271-286. 10.1016/j.cherd.2022.09.051.
“This work used computational and storage services associated with theHoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Yun et al., 2022, p. 285)
Yun, Sungil; Matthew Tom; Gerassimos Orkoulas, and Panagiotis D. Christofides. “Multiscale computational fluid dynamics modeling of spatial thermal atomic layer etching.” Computers & Chemical Engineering 163 (2022): 107861. 10.1016/j.compchemeng.2022.107861.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute of Digital Research and Educations Research Technology Group.” (Yun et al., 2022, p. 12)
Yun, Sungil; Matthew Tom; Feiyang Ou; Gerassimos Orkoulas, and Panagiotis D. Christofides. “Multiscale computational fluid dynamics modeling of thermal atomic layer etching: Application to chamber configuration design.” Computers & Chemical Engineering 161 (2022): 107757. 10.1016/j.compchemeng.2022.107757.
“In addition, technical support from the UCLA Institute for Digital Research and Education (IDRE) is thankfully acknowledged.” (Yun et al., 2022, p. 11)
Zhang, Zisheng; Ziyang Wei; Philippe Sautet, and Anastassia N. Alexandrova. “Hydrogen-Induced Restructuring of a Cu(100) Electrode in Electroreduction Conditions.” Journal of the American Chemical Society 144 no. 42 (2022): 19284-19293. 10.1021/jacs.2c06188.
“Computational resources for this work were provided by the UCLA-shared cluster Hoffman2 and the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program at the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.” (Zhang et al., 2022, p. 19292)
Zhang, Zisheng; Borna Zandkarimi; Julen Munarriz; Claire E. Dickerson, and Anastassia N. Alexandrova. “Fluxionality of Subnano Clusters Reshapes the Activity Volcano of Electrocatalysis.” ChemCatChem 14 no. 15 (2022): e202200345. 10.1002/cctc.202200345.
“We acknowledge the support from the U.S.Department of Energy grant DE-SC0020125, and the computational resources at NERSC and UCLA shared cluster, Hoffman2.” (Zhang et al., 2022, p. 5)
Zhou, Chen; Hio Tong Ngan; Jin Soo Lim; Zubin Darbari; Adrian Lewandowski; Dario J. Stacchiola; Boris Kozinsky; Philippe Sautet, and Jorge Anibal Boscoboinik. “Dynamical Study of Adsorbate-Induced Restructuring Kinetics in Bimetallic Catalysts Using the PdAu(111) Model System.” Journal of the American Chemical Society 144 no. 33 (2022): 15132-15142. 10.1021/jacs.2c04871.
“H.T.N. used the HOFFMAN2 cluster at the UCLA Institute for Digital Research and Education (IDRE).” (Zhou et al., 2022, p. 15140)
Zhou, Qingyang; Mathias K. Thøgersen; Nomaan M. Rezayee; Karl Anker Jørgensen, and K. N. Houk. “Ambimodal Bispericyclic [6 + 4]/[4 + 6] Transition State Competes with Diradical Pathways in the Cycloheptatriene Dimerization: Dynamics and Experimental Characterization of Thermal Dimers.” Journal of the American Chemical Society 144 no. 48 (2022): 22251-22261. 10.1021/jacs.2c10407.
“All calculations were performed on computational resources provided by the UCLA Institute of Digital Research and Education.” (Zhou et al., 2022, p. 22260)
Zhu, Ledong; Mark A. Maskeri; Melissa Ramirez; F. Le Bideau; Léon Ghosez, and K. N. Houk. “Computational Exploration of Anomalous Regioselectivities in Cycloadditions of Ketenes to Oxazolines.” The Journal of Organic Chemistry 87 no. 5 (2022): 3613-3622. 10.1021/acs.joc.2c00001.
“Computations were performed on the Hoffman2 cluster at UCLA and the Expanse cluster available from the NSF XSEDE program under grant OCI-1053575.” (Zhu et al., 2022, p. 3621)
Theses for 2022¶
de Paula, Rachel Turba. “Conservation Genetics in the Age of High-Throughput Sequencing: New Tools for Old Dilemmas.” Ph.D. Thesis, University of California, Los Angeles, 2022. ProQuest, https://www.proquest.com/docview/2731388070.
“All the work listed here used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group (IDRE), and access was sponsored by the Pellegrini lab.” (Paula, 2022, p. 20)
Engel, Ruth Aliza. “Assessing Urban Ecosystem Alternatives for Changing Land Use Dynamics in the Los Angeles Region.” Ph.D. Thesis, University of California, Los Angeles, 2022. ProQuest, https://www.proquest.com/docview/2673640195.
“We ran identical versions of our static vegetation model in the sequential (traditional) and the parallel versions of DHSVM3.2 (Wigmosta et al. 1994; Perkins et al. 2019) on the UCLA Hoffman2 Cluster.” (Engel, 2022, p. 127)
Huang, Jireh Kyle. “Directed Acyclic Graphs: Partitioned Hybrid Structure Learning and Bayesian Causal Bandits.” Ph.D. Thesis, University of California, Los Angeles, 2022. ProQuest, https://www.proquest.com/docview/2670031189.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Huang, 2022, p. xii)
Huang, Shu. “Multi-Scale Modeling and Simulations for Materials Phenomena.” Ph.D. Thesis, University of California, Los Angeles, 2022. ProQuest, https://www.proquest.com/docview/2705483419.
“Computer time allocations at UCLA’s IDRE Hoffman2 supercomputer are acknowledged.” (Huang, 2022, p. 15)
Ren, Yi Ming. “Machine Learning Modeling with Application to Laser Powder Bed Fusion Additive Manufacturing Process.” Thesis, UCLA, 2022. escholarship.org, https://escholarship.org/uc/item/4tz9j6b8.
“Furthermore, to enhance the simulation computational efficiency, job distribution is realized with distributed cloud computing, where more than 100 of 8 GB RAMs are allocated on the UCLA hoffman2 cluster.” (Ren, 2022, p. 50)
Wei, Ziyang. “Computational Modeling of Electrochemical Systems for Energy Conversion Using Density Functional Theory and Many-Body Perturbation Theory.” Ph.D. Thesis, University of California, Los Angeles, 2022. ProQuest, https://www.proquest.com/docview/2681030738.
“The calculations were performed on the Hoffman2 cluster at UCLA Institute for Digital Research and Education (IDRE), The National Energy Research Scientific Computing Center (NERSC), and the Extreme Science and Engineering Discovery Environment (XSEDE)” (Wei, 2022, p. xxx)
Yan, George Xu. “Theoretical Modeling of Highly Dispersed Catalysts Under Reactive Gas Environments.” Ph.D. Thesis, University of California, Los Angeles, 2022. ProQuest, https://www.proquest.com/docview/2715597267.
“The calculations in this work used computational and storage services associated with the Hoffman2 shared computational cluster located at University of California Los Angeles.” (Yan, 2022, p. 37)
Zhou, Chen. “Surface Science Study of Bimetallic Catalysts and Confined Chemistry with 2-Dimensional Model System.” Ph.D. Thesis, State University of New York at Stony Brook, 2022. ProQuest, https://www.proquest.com/docview/2714145528.
“H.T.N. used the HOFFMAN2 cluster at the UCLA Institute for Digital Research and Education (IDRE).” (Zhou, 2022, p. 7)
Conference Papers for 2022¶
Goel, Shashank; Hritik Bansal; Sumit Bhatia; Ryan Rossi; Vishwa Vinay, and Aditya Grover. “CyCLIP: Cyclic Contrastive Language-Image Pretraining.” In Advances in Neural Information Processing Systems: 2022: 6704-6719. https://proceedings.neurips.cc/paper_files/paper/2022/hash/2cd36d327f33d47b372d4711edd08de0-Abstract-Conference.html.
“This research is supported by an Adobe Data Science Research Award for Aditya Grover. We would like to thank the IDRE’s Research Technology group for the GPU computing resources on the UCLA Hoffman2 Cluster.” (Goel et al., 2022, p. 10)
2021¶
- 100 publications for 2021
2 Theses
Journal Articles for 2021¶
Agak, George W.; Alice Mouton; Rosane M.B. Teles; Thomas Weston; Marco Morselli; Priscila R. Andrade; Matteo Pellegrini, and Robert L. Modlin. “Extracellular traps released by antimicrobial TH17 cells contribute to host defense.” Journal of Clinical Investigation 131 no. 2 (2021): e141594. 10.1172/JCI141594.
“We used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Agak et al., 2021, p. 12)
Agarwal, Shivang; Clarice D. Aiello; Daniel R. Kattnig, and Amartya S. Banerjee. “The Dynamical Ensemble of the Posner Molecule Is Not Symmetric.” The Journal of Physical Chemistry Letters 12 no. 42 (2021): 10372-10379. 10.1021/acs.jpclett.1c02796.
“The authors would also like to thank UCLA’s Institute for Digital Research and Education (IDRE) for making available the computing resources used in this work.” (Agarwal et al., 2021, p. 10378)
Allred, Tyler K.; Michael B. Shaghafi; Pan-Pan Chen; Quan Tran; K. N. Houk, and Larry E. Overman. “Constructing Saturated Guanidinum Heterocycles by Cycloaddition of N-Amidinyliminium Ions with Indoles.” Organic Letters 23 no. 19 (2021): 7618-7623. 10.1021/acs.orglett.1c02832.
“Calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles.” (Allred et al., 2021, p. 7622)
Anthony, S. M.; V. Tona; Y. Zou, and L. A. Morrill. “Total synthesis of (−)-strictosidine and interception of aryne natural product derivatives “strictosidyne” and “strictosamidyne”.” Journal of the American Chemical Society 143 no. 19 (2021): 7471-7479. 10.1021/jacs.1c02004.
“Calculations were performed on the Hoffman2 cluster and the UCLA Institute of Digital Research and Education (IDRE) at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE)”
Banerjee, Amartya S.. “Ab initio framework for systems with helical symmetry: Theory, numerical implementation and applications to torsional deformations in nanostructures.” Journal of the Mechanics and Physics of Solids 154 (2021): 104515. 10.1016/j.jmps.2021.104515.
“Finally, ASB would like to acknowledge the anonymous reviewers for suggestions which helped in improving the manuscript, as well as the Minnesota Supercomputing Institute (MSI) and UCLA’s Institute for Digital Research and Education (IDRE) for making available the computing resources used in this work.” (Banerjee, 2021, p. 65)
Bennert, Vardha N.; Tommaso Treu; Xuheng Ding; Isak Stomberg; Simon Birrer; Tomas Snyder; Matthew A. Malkan; Andrew W. Stephens, and Matthew W. Auger. “A Local Baseline of the Black Hole Mass Scaling Relations for Active Galaxies. IV. Correlations Between MBH and Host Galaxy σ, Stellar Mass, and Luminosity.” The Astrophysical Journal 921 no. 1 (2021): 36. 10.3847/1538-4357/ac151a.
“This research has made use of the Dirac computer cluster at the California Polytechnic State University in San Luis Obispo, maintained by Dr. Brian Granger and Dr. Ashley Ringer McDonald, and the Hoffman2 Cluster at the University of California Los Angeles, managed and operated by the IDRE Research Technology Group under the direction of Lisa Snyder.” (Bennert et al., 2021, p. 16)
Bím, D and AN Alexandrova. “Electrostatic regulation of blue copper sites.” CHEMICAL SCIENCE 12 no. 34 (2021): 11406-11413. 10.1039/d1sc02233d.
“We also acknowledge the UCLA-IDRE cluster Hoffman2 and XSEDE for computational resources.” (Bím and Alexandrova, 2021, p. 6) Publication Title: Chemical science
Bím, Daniel and Anastassia N. Alexandrova. “Local Electric Fields As a Natural Switch of Heme-Iron Protein Reactivity.” ACS Catalysis 11 no. 11 (2021): 6534-6546. 10.1021/acscatal.1c00687.
“We also acknowledge the UCLA-IDRE cluster Hoffman2 and XSEDE for computational resources.” (Bím and Alexandrova, 2021, p. 6545)
Chen, Pan-Pan; Pengchen Ma; Xue He; Dennis Svatunek; Fang Liu, and Kendall N. Houk. “Computational Exploration of Ambiphilic Reactivity of Azides and Sustmann’s Paradigmatic Parabola.” The Journal of Organic Chemistry 86 no. 8 (2021): 5792-5804. 10.1021/acs.joc.1c00239.
“Calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles, and the Vienna Scientific Cluster.” (Chen et al., 2021, p. 5802)
Chen, Shuming; Tuo Hu, and K. N. Houk. “Energy of Concert and Origins of Regioselectivity for 1,3-Dipolar Cycloadditions of Diazomethane.” The Journal of Organic Chemistry 86 no. 9 (2021): 6840-6846. 10.1021/acs.joc.1c00743.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and SCIURus, the Oberlin College HPC cluster (NSF MRI 1427949).” (Chen et al., 2021, p. 6845)”
Chen, Xiangyang; Mathias Kirk Thøgersen; Limin Yang; Rune F. Lauridsen; Xiao-Song Xue; Karl Anker Jørgensen, and K. N. Houk. “[8+2] vs [4+2] Cycloadditions of Cyclohexadienamines to Tropone and Heptafulvenes—Mechanisms and Selectivities.” Journal of the American Chemical Society 143 no. 2 (2021): 934-944. 10.1021/jacs.0c10966.
“Computations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575).” (Chen et al., 2021, p. 942)
Chen, Yuzhen and Lihua Jin. “Reusable Energy-Absorbing Architected Materials Harnessing Snapping-Back Buckling of Wide Hyperelastic Columns.” Advanced Functional Materials 31 no. 31 (2021): 2102113. 10.1002/adfm.202102113.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by Institute for Digital Research and Education’s Research Technology Group at UCLA.” (Chen and Jin, 2021, p. 8)
Cui, Ying; Zihao Qin; Huan Wu; Man Li, and Yongjie Hu. “Flexible thermal interface based on self-assembled boron arsenide for high-performance thermal management.” Nature Communications 12 no. 1 (2021): 1284. 10.1038/s41467-021-21531-7.
“This work used computational and storage services associated with the Hoffman 2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant No. ACI-1548562.” (Cui et al., 2021, p. 7) Number: 1
De Pascalis, Lucrezia; Mei-Kwan Yau; Dennis Svatunek; Zhuoting Tan; Srinivas Tekkam; K. N. Houk, and M. G. Finn. “The Influence of Substitution on Thiol-Induced Oxanorbornadiene Fragmentation.” Organic Letters 23 no. 9 (2021): 3751-3754. 10.1021/acs.orglett.1c01164.
“Calculations were performed on the Hoffman2 system provided by the UCLA Institute for Digital Research and Education and the Vienna Scientific Cluster.” (De Pascalis et al., 2021, p. 3754)
Deng, J; SC Lin; JT Fuller; B Zandkarimi; HM Chen; AN Alexandrova, and C Liu. “Electrocatalytic Methane Functionalization with d0 Early Transition Metals Under Ambient Conditions.” ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 60 no. 51 (2021): 26630-26638. 10.1002/anie.202107720.
“A.N.A. acknowledges the NSF Career Award (CHE-1351968) and the UCLA-IDRE cluster Hoffman2 and CSM HPC clusters for computational resources.” (Deng et al., 2021, p. 12)
Deng, Jie and Lars Stixrude. “Thermal Conductivity of Silicate Liquid Determined by Machine Learning Potentials.” Geophysical Research Letters 48 no. 17 (2021): e2021GL093806. 10.1029/2021GL093806.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Deng and Stixrude, 2021, p. 8)
Deng, Jie and Lars Stixrude. “Deep fractionation of Hf in a solidifying magma ocean and its implications for tungsten isotopic heterogeneities in the mantle.” Earth and Planetary Science Letters 562 (2021): 116873. 10.1016/j.epsl.2021.116873.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Deng and Stixrude, 2021, p. 7)
Dinh, Cuc K.; Jesus M. Salas; Mark R. Morris, and Smadar Naoz. “Effects of Turbulence in the Circumnuclear Disk.” The Astrophysical Journal 920 no. 2 (2021): 79. 10.3847/1538-4357/ac185b.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Dinh et al., 2021, p. 11)
Dobynde, Mikhail I. and Jingnan Guo. “Radiation Environment at the Surface and Subsurface of the Moon: Model Development and Validation.” Journal of Geophysical Research: Planets 126 no. 11 (2021): e2021JE006930. 10.1029/2021JE006930.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Dobynde and Guo, 2021, p. 11)
Drozdov, A. Y.; H. J. Allison; Y. Y. Shprits; S. R. Elkington, and N. A. Aseev. “A Comparison of Radial Diffusion Coefficients in 1‐D and 3‐D Long‐Term Radiation Belt Simulations.” Journal of Geophysical Research: Space Physics 126 no. 8 (2021): e2020JA028707. 10.1029/2020JA028707.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Drozdov et al., 2021, p. 19)
Duan, Meng; Christian David Díaz-Oviedo; Yang Zhou; Xiangyang Chen; Peiyuan Yu; Benjamin List; Kendall N. Houk, and Yu Lan. “Chiral Phosphoric Acid Catalyzed Conversion of Epoxides into Thiiranes: Mechanism, Stereochemical Model, and New Catalyst Design.” Angewandte Chemie International Edition 61 no. 9 (2021): e202113204. 10.1002/anie.202113204.
“Calculations were performed ontheHoffman2 cluster at UCLA, Center for Computational Science and Engineering at Southern University of Science and Technology, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575).” (Duan et al., 2022, p. 6)
Einsiedler, Manuel; Cooper S. Jamieson; Mark A. Maskeri; Kendall N. Houk, and Tobias A. M. Gulder. “Fungal Dioxygenase AsqJ Is Promiscuous and Bimodal: Substrate-Directed Formation of Quinolones versus Quinazolinones.” Angewandte Chemie 133 no. 15 (2021): 8378-8383. 10.1002/ange.202017086.
“All calculations were performed oncomputing resources made available bythe UCLA Institute ofDigital Research and Education.” (Einsiedler et al., 2021, p. 8383)
Farrell, Colin; Michael Thompson; Anela Tosevska; Adewale Oyetunde, and Matteo Pellegrini. “BiSulfite Bolt: A bisulfite sequencing analysis platform.” GigaScience 10 no. 5 (2021): giab033. 10.1093/gigascience/giab033.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Farrell et al., 2021, p. 7)
Fereyduni, E; O Lahtigui; JN Sanders; BM Tomiczek; MD Mannchen; RA Yu; KN Houk, and AJ Grenning. “Overcoming Kinetic and Thermodynamic Challenges of Classic Cope Rearrangements.” JOURNAL OF ORGANIC CHEMISTRY 86 no. 3 (2021): 2632-2643. 10.1021/acs.joc.0c02690.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE).” (Fereyduni et al., 2021, p. 18)
Giannakakis, Georgios; Paul Kress; Kaining Duanmu; Hio Tong Ngan; George Yan; Adam S. Hoffman; Zhen Qi; Antonios Trimpalis; Leelavathi Annamalai; Mengyao Ouyang; Jilei Liu; Nathaniel Eagan; Juergen Biener; Dimosthenis Sokaras; Maria Flytzani-Stephanopoulos; Simon R. Bare; Philippe Sautet, and E. Charles H. Sykes. “Mechanistic and Electronic Insights into a Working NiAu Single-Atom Alloy Ethanol Dehydrogenation Catalyst.” Journal of the American Chemical Society 143 no. 51 (2021): 21567-21579. 10.1021/jacs.1c09274.
“DFT calculations were performed on the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE) and the National Energy Research Scientific Computing Center (NERSC) of the U.S. Department of Energy.” (Giannakakis et al., 2021, p. 21577)
Gilli, Gabriella; Thomas Navarro; Sebastien Lebonnois; Diogo Quirino; Vasco Silva; Aurelien Stolzenbach; Franck Lefèvre, and Gerald Schubert. “Venus upper atmosphere revealed by a GCM: II. Model validation with temperature and density measurements.” Icarus 366 (2021): 114432. 10.1016/j.icarus.2021.114432.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group, as well as the High-Performance Computing (HPC) resources of Centre Informatique National de l’Enseignement Superieur 1(CINES) under the allocations A0060110391 and A0080110391 made by Grand Equipment National de Calcul Intensif (GENCI).” (Gilli et al., 2021, p. 17)
Gorla, Aditya; Brandon Jew; Luke Zhang, and Jae Hoon Sul. “xGAP: a python based efficient, modular, extensible and fault tolerant genomic analysis pipeline for variant discovery.” Bioinformatics 37 no. 1 (2021): 9-16. 10.1093/bioinformatics/btaa1097.
“The authors thank the support from Hoffman2 and Cerebrum BMAP HPC administrators at UCLA.” (Gorla et al., 2021, p. 16)
Guo, Han; Claire E. Dickerson; Ashley J. Shin; Changling Zhao; Timothy L. Atallah; Justin R. Caram; Wesley C. Campbell, and Anastassia N. Alexandrova. “Surface chemical trapping of optical cycling centers.” Physical Chemistry Chemical Physics 23 no. 1 (2021): 211-218. 10.1039/D0CP04525J.
“This work used computational and storage services associated with the Hoffman2 cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group, the NSF-supported Extreme Science and Engineering Discovery Environment (XSEDE) (TG-CHE160054).” (Guo et al., 2021, p. 21)
Hardy, Anthony J.; Maryam Bostani; Erin Angel; Chris Cagnon; Ioannis Sechopoulos, and Michael F. McNitt‐Gray. “Reference dataset for benchmarking fetal doses derived from Monte Carlo simulations of CT exams.” Medical Physics 48 no. 1 (2021): 523-532. 10.1002/mp.14573.
“The MCNPX simulations were conducted using the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Hardy et al., 2021, p. 6)
Hardy, Anthony James; Maryam Bostani; Grace Hyun J. Kim; Christopher H. Cagnon; Maria Agnes Zankl, and Michael McNitt-Gray. “Evaluating Size-Specific Dose Estimate (SSDE) as an estimate of organ doses from routine CT exams derived from Monte Carlo simulations.” Medical Physics 48 no. 10 (2021): 6160-6173. 10.1002/mp.15128.
“MCNPX simulations were performed using the computational and storage service associated with the Hoffman2 Shared Cluster provided by UCLA Institute of Digital and Education’s Research Technology Group.” (Hardy et al., 2021, p. 6165)v
Hoffarth, Elesha R.; Kersti Caddell Haatveit; Eugene Kuatsjah; Gregory A. MacNeil; Simran Saroya; Charles J. Walsby; Lindsay D. Eltis; K. N. Houk; Marc Garcia-Borràs, and Katherine S. Ryan. “A shared mechanistic pathway for pyridoxal phosphate–dependent arginine oxidases.” Proceedings of the National Academy of Sciences 118 no. 40 (2021): e2012591118. 10.1073/pnas.2012591118.
“Computations were performed on the Hoffman2 cluster at the University of California, Los Angeles and the Extreme Science and Engineering Discovery Environment, which is supported by the NSF (OCI-1053575).” (Hoffarth et al., 2021, p. 10)
Hohlman, RM; SA Newmister; JN Sanders; Y Khatri; SS Li; NR Keramati; AN Lowell; KN Houk, and DH Sherman. “Structural Diversification of Hapalindole and Fischerindole Natural Products via Cascade Biocatalysis.” ACS CATALYSIS 11 no. 8 (2021): 4670-4681. 10.1021/acscatal.0c05656.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and by the San Diego Supercomputing Center (SDSC) through XSEDE (ACI-1548562).” (Hohlman et al., 2021, p. 14)
Hou, Bao-Long; Jonathan J. Wong; Na Lv; Yong-Qiang Wang; K. N. Houk, and Chuang-Chuang Li. “Facile generation of bridged medium-sized polycyclic systems by rhodium-catalysed intramolecular (3+2) dipolar cycloadditions.” Nature Communications 12 no. 1 (2021): 5239. 10.1038/s41467-021-25513-7.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI-1053575).” (Hou et al., 2021, p. 8)
Huffman, Benjamin J.; Tiffany Chu; Yusuke Hanaki; Jonathan J. Wong; Shuming Chen; Kendall N. Houk, and Ryan A. Shenvi. “Stereodivergent Attached-Ring Synthesis via Non-Covalent Interactions: A Short Formal Synthesis of Merrilactone A.” Angewandte Chemie International Edition 61 no. 3 (2021): e202114514. 10.1002/anie.202114514.
“Calculations were performed ontheHoffman2 cluster at the University of California, Los Angeles ,and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI-1053575).” (Huffman et al., 2022, p. 6)
Hülsey, Max J.; Geng Sun; Philippe Sautet, and Ning Yan. “Observing Single-Atom Catalytic Sites During Reactions with Electrospray Ionization Mass Spectrometry.” Angewandte Chemie International Edition 60 no. 9 (2021): 4764-4773. 10.1002/anie.202011632.
“The computational work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562. We also thank computational and storage services associated with theHoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s ResearchTechnology Group.” (Hülsey et al., 2021, p. 4771)
Jamieson, Cooper S.; Arkajyoti Sengupta, and K. N. Houk. “Cycloadditions of Cyclopentadiene and Cycloheptatriene with Tropones: All Endo-[6+4] Cycloadditions Are Ambimodal.” Journal of the American Chemical Society 143 no. 10 (2021): 3918-3926. 10.1021/jacs.0c13401.
“All calculations were performed on computational resources provided by the UCLA Institute of Digital Research and Education.” (Jamieson et al., 2021, p. 3925)
Jellen, Marcus J.; Ieva Liepuoniute; Mingoo Jin; Christopher G. Jones; Song Yang; Xing Jiang; Hosea M. Nelson; K. N. Houk, and Miguel A. Garcia-Garibay. “Enhanced Gearing Fidelity Achieved Through Macrocyclization of a Solvated Molecular Spur Gear.” Journal of the American Chemical Society 143 no. 20 (2021): 7740-7747. 10.1021/jacs.1c01885.
“Computations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Jellen et al., 2021, p. 7746)
Jung, Su Yon; Peter A. Scott; Jeanette C. Papp; Eric M. Sobel; Matteo Pellegrini; Herbert Yu; Sihao Han, and Zuo-Feng Zhang. “Genome-wide Association Analysis of Proinflammatory Cytokines and Gene–lifestyle Interaction for Invasive Breast Cancer Risk: The WHI dbGaP Study.” Cancer Prevention Research 14 no. 1 (2021): 41-54. 10.1158/1940-6207.CAPR-20-0256.
“During the data QC process, dose2plink script (http://genepi.qimr.edu.au/staff/sarahMe/ dose2plink), PLINK1.9/2.0, KING kinship estimator, and R stats package on UCLA’s Hoffman2 high performance computing cluster were used.” (Jung et al., 2021, p. 45)
Kellerman, Adam C.. “Trapped Electron Energy Inferred From Cosmic Noise Absorption Signals Through Drift‐Time Analysis in Empirical Electric and Semi‐Empirical Magnetic Fields.” Journal of Geophysical Research: Space Physics 126 no. 3 (2021): e2020JA028887. 10.1029/2020JA028887.
“The electron PSD data employed computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Kellerman, 2021, p. 8)
Kessouri, Faycal; James C. McWilliams; Daniele Bianchi; Martha Sutula; Lionel Renault; Curtis Deutsch; Richard A. Feely; Karen McLaughlin; Minna Ho; Evan M. Howard; Nina Bednaršek; Pierre Damien; Jeroen Molemaker, and Stephen B. Weisberg. “Coastal eutrophication drives acidification, oxygen loss, and ecosystem change in a major oceanic upwelling system.” Proceedings of the National Academy of Sciences 118 no. 21 (2021): e2018856118. 10.1073/pnas.2018856118.
“Computational resources were provided by the Extreme Science and Engineering Discovery Environment through allocation TG-OCE170017; and by the supercomputer Hoffman2 at the University of California Los Angeles, at the Institute for Digital Research and Education.” (Kessouri et al., 2021, p. 7)
Khan, Arshad H. and Desmond J. Smith. “Cost-Effective Mapping of Genetic Interactions in Mammalian Cells.” Frontiers in Genetics 12 (2021). 10.3389/fgene.2021.703738.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education Research Technology Group.” (Khan and Smith, 2021, p. 10)
Kim, Yeulwoo; Ryan S. Mieras; Dylan Anderson, and Timu Gallien. “A Numerical Study of Sheet Flow Driven by Skewed-Asymmetric Shoaling Waves Using SedWaveFoam.” Journal of Marine Science and Engineering 9 no. 9 (2021): 936. 10.3390/jmse9090936.
“Numerical simulations presented in this study were carried out using the Hoffman2 cluster at the University of California, Los Angeles.” (Kim et al., 2021, p. 24)
Kim, Yeulwoo; Sangyoung Son; Taehwa Jung, and Timu Gallien. “An analytical and numerical study of a vertically discretized multi-paddle wavemaker for generating free surface and internal waves.” Coastal Engineering 165 (2021): 103840. 10.1016/j.coastaleng.2021.103840.
“Numerical simulations presented in this study were carried out using the Hoffman2 cluster at the University of California, Los Angeles.” (Kim et al., 2021, p. 19)
Kochocki, Alina; Volodymyr Takhistov; Alexander Kusenko, and Nathan Whitehorn. “Contribution of Secondary Neutrinos from Line-of-sight Cosmic-Ray Interactions to the IceCube Diffuse Astrophysical Flux.” The Astrophysical Journal 914 no. 2 (2021): 91. 10.3847/1538-4357/abf830.
“We also acknowledge use of the Hoffman2 Shared Cluster computational and storage services provided by UCLA’s Institute for Digital Research & Education.” (Kochocki et al., 2021, p. 9)
Kumari, Simran and Philippe Sautet. “Highly dispersed Pt atoms and clusters on hydroxylated indium tin oxide: a view from first-principles calculations.” Journal of Materials Chemistry A 9 no. 28 (2021): 15724-15733. 10.1039/D1TA03177E.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education Research Technology Group.” (Kumari and Sautet, 2021, p. 17)
Layman, Rick R.; Anthony J. Hardy; Hyun J. Kim; Ei Ne Chou; Maryam Bostani; Chris Cagnon; Dianna Cody, and Michael McNitt‐Gray. “A comparison of breast and lung doses from chest CT scans using organ‐based tube current modulation (OBTCM) vs. Automatic tube current modulation (ATCM).” Journal of Applied Clinical Medical Physics 22 no. 5 (2021): 97-109. 10.1002/acm2.13198.
“MCNPX simulations were performed using the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Layman et al., 2021, p. 101)
Li, Bo; Yuli Li; Yanfeng Dang, and K. N. Houk. “Post-Transition State Bifurcation in Iron-Catalyzed Arene Aminations.” ACS Catalysis 11 no. 12 (2021): 6816-6824. 10.1021/acscatal.1c01291.
“DFT calculations and MD simulations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI1053575).” (Li et al., 2021, p. 6823)
Liu, Tianzhen; Yuzhen Chen; Liwu Liu; Yanju Liu; Jinsong Leng, and Lihua Jin. “Effect of imperfections on pseudo-bistability of viscoelastic domes.” Extreme Mechanics Letters 49 (2021): 101477. 10.1016/j.eml.2021.101477.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Liu et al., 2021, p. 11)
Llorente, I. L.; Y. Xie; J. A. Mazzitelli, and E. A. Hatanaka. “Patient-derived glial enriched progenitors repair functional deficits due to white matter stroke and vascular dementia in rodents.” Science Translational … 13 no. 590 (2021): eaaz6747. 10.1126/scitranslmed.aaz6747.
“Tophat was used to align reads to the hg19 genome assembly using the default settings in Galaxy (http://galaxy.hoffman2.idre.ucla.edu).” (Llorente et al., 2021, p. 13)
Llorente, Irene L.; Emily A. Hatanaka; Michael E. Meadow; Yuan Xie; William E. Lowry, and S. Thomas Carmichael. “Reliable generation of glial enriched progenitors from human fibroblast-derived iPSCs.” Stem Cell Research 55 (2021): 102458. 10.1016/j.scr.2021.102458.
“Tophat was used to align reads to the hg19 genome assembly using the default settings in Galaxy (http://galaxy.hoffman2.idre.ucla.edu).” (Llorente et al., 2021, p. 6)
Mackey, Pamela; Aneta Turlik; Kaori Ando; Mark E. Light; K. N. Houk, and Gerard P. McGlacken. “Stereoselective Installation of Five Contiguous Stereogenic Centers in a Double Aldol–Tishchenko Cascade and Evaluation of the Key Transition State through DFT Calculation.” Organic Letters 23 no. 16 (2021): 6372-6376. 10.1021/acs.orglett.1c02179.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE),” (Mackey et al., 2021, p. 6375)
Madson, Austin and Yongwei Sheng. “Coulomb stress analysis for several filling and operational scenarios at the Grand Ethiopian Renaissance Dam impoundment.” Environmental Earth Sciences 80 no. 7 (2021): 286. 10.1007/s12665-021-09591-w.
“A portion of this research utilized computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Madson and Sheng, 2021, p. 15)
Madson, Austin and Yongwei Sheng. “Automated Water Level Monitoring at the Continental Scale from ICESat-2 Photons.” Remote Sensing 13 no. 18 (2021): 3631. 10.3390/rs13183631.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Madson and Sheng, 2021, p. 15)
Manwani, P.; N. Majernik; M. Yadav; C. Hansel, and J. B. Rosenzweig. “Resonant excitation of very high gradient plasma wakefield accelerators by optical-period bunch trains.” Physical Review Accelerators and Beams 24 no. 5 (2021): 051302. 10.1103/PhysRevAccelBeams.24.051302.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Educations Research Technology Group and the SCARF cluster provided by the STFC Scientific Computing Department.” (Manwani et al., 2021, p. 12)
McElfresh, Cameron; Yinan Cui; Sergei L. Dudarev; Giacomo Po, and Jaime Marian. “Discrete stochastic model of point defect-dislocation interaction for simulating dislocation climb.” International Journal of Plasticity 136 (2021): 102848. 10.1016/j.ijplas.2020.102848.
“Computer time allocations at UCLA’s IDRE Hoffman2 supercomputer are acknowledged.” (McElfresh et al., 2021, p. 15)
Meng, Dong; Rui Wang; Janice B. Lin; Jonathan Lee Yang; Selbi Nuryyeva; Yu-Che Lin; Shuai Yuan; Zhao-Kui Wang; Elizabeth Zhang; Chengyi Xiao; Danlei Zhu; Lang Jiang; Yepin Zhao; Zhenxing Li; Chenhui Zhu; Kendall N. Houk, and Yang Yang. “Chlorinated Spiroconjugated Fused Extended Aromatics for Multifunctional Organic Electronics.” Advanced Materials 33 no. 12 (2021): 2006120. 10.1002/adma.202006120.
“Calculations were performed on the Hoffman2 cluster provided by the UCLA Institute of Digital Research and Education’s Research Technology Group and on the NSF-supported Extreme Science and Engineering Discovery Environment (XSEDE)’s Gordon supercomputer (OCI-1053575) at the San Diego Supercomputing Center.” (Meng et al., 2021, p. 8)
Mishra, Amrendra; Hamed Mirzaei; Novella Guidi; Manlio Vinciguerra; Alice Mouton; Marina Linardic; Francesca Rappa; Rosario Barone; Gerardo Navarrete; Min Wei; Sebastian Brandhorst; Stefano Di Biase; Todd E. Morgan; S. Ram Kumar; Peter S. Conti; Matteo Pellegrini; Michel Bernier; Rafael de Cabo, and Valter D. Longo. “Fasting-mimicking diet prevents high-fat diet effect on cardiometabolic risk and lifespan.” Nature Metabolism 3 no. 10 (2021): 1342-1356. 10.1038/s42255-021-00469-6.
“We used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Mishra et al., 2021, p. 1356) Number: 10
Morselli, Marco; Colin Farrell; Liudmilla Rubbi; Heather L. Fehling; Rebecca Henkhaus, and Matteo Pellegrini. “Targeted bisulfite sequencing for biomarker discovery.” Methods 187 (2021): 13-27. 10.1016/j.ymeth.2020.07.006.
“All example code was run on the UCLA Hoffman2 cluster, running UGE (v8.6.4) with 8 requested cores and 32GB ram.” (Morselli et al., 2021, p. 19)
Nadel, Brian B; David Lopez; Dennis J Montoya; Feiyang Ma; Hannah Waddel; Misha M Khan; Serghei Mangul, and Matteo Pellegrini. “The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data.” GigaScience 10 no. 2 (2021): giab002. 10.1093/gigascience/giab002.
“We installed and ran GEDIT, CIBERSORT, DeconRNASeq, and dtangle on the hoffman2 computational cluster at UCLA.” (Nadel et al., 2021, p. 11)
Nadel, Brian B; Meritxell Oliva; Benjamin L Shou; Keith Mitchell; Feiyang Ma; Dennis J Montoya; Alice Mouton; Sarah Kim-Hellmuth; Barbara E Stranger; Matteo Pellegrini, and Serghei Mangul. “Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples.” Briefings in Bioinformatics 22 no. 6 (2021): bbab265. 10.1093/bib/bbab265.
“all other tools were installed on the Hoffman2 Cluster at University of California, Los Angeles (UCLA).” (Nadel et al., 2021, p. 10)
Nadvornick, Warren; Hsing-Yin Chang; Andrew Alvarado; Pablo Molina; Jaime Marian, and Nasr Ghoniem. “A linked-scale coupled model of mass erosion and redistribution in plasma-exposed micro-foam surfaces.” Journal of Nuclear Materials 553 (2021): 153010. 10.1016/j.jnucmat.2021.153010.
“All simulations were run at UCLA’s Hoffman2 shared cluster using Intel Xeon E5-2650v4 2.2GHz processors.” (Nadvornick et al., 2021, p. 17)
Navarro, Thomas; Gabriella Gilli; Gerald Schubert; Sébastien Lebonnois; Franck Lefèvre, and Diogo Quirino. “Venus’ upper atmosphere revealed by a GCM: I. Structure and variability of the circulation.” Icarus 366 (2021): 114400. 10.1016/j.icarus.2021.114400.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group, as well as the High-Performance Computing (HPC) resources of Centre Informatique National de l’Enseignement Suérieur (CINES) under the allocations A0060110391 and A0080110391 made by Grand Equipment National de Calcul Intensif (GENCI).” (Navarro et al., 2021, p. 18)
Perri, Angela R.; Kieren J. Mitchell; Alice Mouton; Sandra Álvarez-Carretero; Ardern Hulme-Beaman; James Haile; Alexandra Jamieson; Julie Meachen; Audrey T. Lin; Blaine W. Schubert; Carly Ameen; Ekaterina E. Antipina; Pere Bover; Selina Brace; Alberto Carmagnini; Christian Carøe; Jose A. Samaniego Castruita; James C. Chatters; Keith Dobney; Mario Dos Reis; Allowen Evin; Philippe Gaubert; Shyam Gopalakrishnan; Graham Gower; Holly Heiniger; Kristofer M. Helgen; Josh Kapp; Pavel A. Kosintsev; Anna Linderholm; Andrew T. Ozga; Samantha Presslee; Alexander T. Salis; Nedda F. Saremi; Colin Shew; Katherine Skerry; Dmitry E. Taranenko; Mary Thompson; Mikhail V. Sablin; Yaroslav V. Kuzmin; Matthew J. Collins; Mikkel-Holger S. Sinding; M. Thomas P. Gilbert; Anne C. Stone; Beth Shapiro; Blaire Van Valkenburgh; Robert K. Wayne; Greger Larson; Alan Cooper, and Laurent A. F. Frantz. “Dire wolves were the last of an ancient New World canid lineage.” Nature 591 no. 7848 (2021): 87-91. 10.1038/s41586-020-03082-x.
“A.M. used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group. D” (Perri et al., 2021, p. 6)
Ramirez, Melissa; Evan R. Darzi; Joyann S. Donaldson; Kendall N. Houk, and Neil K. Garg. “Cycloaddition Cascades of Strained Alkynes and Oxadiazinones.” Angewandte Chemie 133 no. 33 (2021): 18349-18356. 10.1002/ange.202105244.
“Calculations were performed on the Hoffman2 cluster and the UCLA Institute of Digital Research and Education (IDRE) at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575).” (Ramirez et al., 2021, p. 9)
Ramirez, Melissa; Dennis Svatunek; Fang Liu; Neil K. Garg, and Kendall N. Houk. “Origins of Endo Selectivity in Diels–Alder Reactions of Cyclic Allene Dienophiles.” Angewandte Chemie 133 no. 27 (2021): 15116-15124. 10.1002/ange.202101809.
“This study used computational and storage services associated with theHoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education. Calculations were in part performed at the Vienna Scientific Cluster.” (Ramirez et al., 2021, p. 15123)
Ramirez, Melissa; Vito Vece; Stephen Hanessian, and K. N. Houk. “Computational and Further Experimental Explorations of the Competing Cascades Following Claisen Rearrangements of Aryl Propargyl Ethers: Substituent Effects on Reactivity and Regioselectivity.” The Journal of Organic Chemistry 86 no. 24 (2021): 17955-17964. 10.1021/acs.joc.1c02296.
“This study used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Ramirez et al., 2021, p. 17962)
Reilley, David J.; Jian Wang; Nikolay V. Dokholyan, and Anastassia N. Alexandrova. “Titr-DMD-A Rapid, Coarse-Grained Quasi-All-Atom Constant pH Molecular Dynamics Framework.” Journal of Chemical Theory and Computation 17 no. 7 (2021): 4538-4549. 10.1021/acs.jctc.1c00338.
“Simulations were performed on AMD Opteron 2380 (2.5 GHz) cores on Hoffman2 at UCLA IDRE.” (Reilley et al., 2021, p. 11) PMID: 34165292 PMCID: PMC10662685
Reilley, DJ; Z Arraf, and AN Alexandrova. “Contrasting Effects of Inhibitors Li+ and Be2+ on Catalytic Cycle of Glycogen Synthase Kinase-3β.” JOURNAL OF PHYSICAL CHEMISTRY B 125 no. 33 (2021): 9480-9489. 10.1021/acs.jpcb.1c05099.
“We also acknowledge UCLA-IDRE and XSEDE for providing computational resources.” (Reilley et al., 2021, p. 10)
Ren, Yi Ming; Yichi Zhang; Yangyao Ding; Tao Liu; Cody S. Lough; Ming C. Leu; Edward C. Kinzel, and Panagiotis D. Christofides. “Finite element modeling of direct metal laser solidification process: Sensor data replication and use in defect detection and data reduction via machine learning.” Chemical Engineering Research and Design 171 (2021): 254-267. 10.1016/j.cherd.2021.05.018.
“Furthermore, to enhance the simulation computational efficiency, job distribution is realized with distributed cloud computing, where more than 100 of 8 GB RAMs are allocated on the UCLA hoffman2 cluster.” (Ren et al., 2021, p. 12)
Rezayee, Nomaan M.; Valdemar J. Enemærke; Sif T. Linde; Johannes N. Lamhauge; Gabriel J. Reyes-Rodríguez; Karl Anker Jørgensen; Chenxi Lu, and K. N. Houk. “An Asymmetric SN2 Dynamic Kinetic Resolution.” Journal of the American Chemical Society 143 no. 19 (2021): 7509-7520. 10.1021/jacs.1c02193.
“Computations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI1053575).” (Rezayee et al., 2021, p. 7518)
Rossman, Gabriel and Jacob C. Fisher. “Network hubs cease to be influential in the presence of low levels of advertising.” Proceedings of the National Academy of Sciences 118 no. 7 (2021): e2013391118. 10.1073/pnas.2013391118.
“Simulations for this project were conducted using the Duke Compute Cluster, the University of Michigan–Institute for Social Research’s Likert cluster, and the University of California, Los Angeles (UCLA) Hoffman2 cluster.” (Rossman and Fisher, 2021, p. 4)
Saikin, A. A.; Y. Y. Shprits; A. Y. Drozdov; D. A. Landis; I. S. Zhelavskaya, and S. Cervantes. “Reconstruction of the Radiation Belts for Solar Cycles 17–24 (1933–2017).” Space Weather 19 no. 3 (2021): e2020SW002524. 10.1029/2020SW002524.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Saikin et al., 2021, p. 21)
Salas, Jesus M.; Mark R. Morris, and Smadar Naoz. “Modeling Turbulence in Galactic Centers.” The Astronomical Journal 161 no. 5 (2021): 243. 10.3847/1538-3881/abefd3.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Salas et al., 2021, p. 10)
Scott, Wendell A.; Eric G. Gharakhanian; Alexandra G. Bell; Declan Evans; Ehab Barun; K. N. Houk, and Timothy J. Deming. “Active Controlled and Tunable Coacervation Using Side-Chain Functional α-Helical Homopolypeptides.” Journal of the American Chemical Society 143 no. 43 (2021): 18196-18203. 10.1021/jacs.1c07925.
“All calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles.” (Scott et al., 2021, p. 18202)
Shajib, Anowar J; Tommaso Treu; Simon Birrer, and Alessandro Sonnenfeld. “Dark matter haloes of massive elliptical galaxies at <i>z</i> ∼ 0.2 are well described by the Navarro–Frenk–White profile.” Monthly Notices of the Royal Astronomical Society 503 no. 2 (2021): 2380-2405. 10.1093/mnras/stab536.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and EducationâĂŹs Research Technology Group.” (Shajib et al., 2021, p. 20)
Sheil, Ryan; J. Mark P. Martirez; Xia Sang; Emily A. Carter, and Jane P. Chang. “Precise Control of Nanoscale Cu Etching via Gas-Phase Oxidation and Chemical Complexation.” The Journal of Physical Chemistry C 125 no. 3 (2021): 1819-1832. 10.1021/acs.jpcc.0c08932.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group. J” (Sheil et al., 2021, p. 1830)
Shen, Zican; Morgan M. Walker; Shuming Chen; Giovanny A. Parada; Duc M. Chu; Sun Dongbang; James M. Mayer; K. N. Houk, and Jonathan A. Ellman. “General Light-Mediated, Highly Diastereoselective Piperidine Epimerization: From Most Accessible to Most Stable Stereoisomer.” Journal of the American Chemical Society 143 no. 1 (2021): 126-131. 10.1021/jacs.0c11911.
“Calculations were performed on the Hoffman2 cluster at UCLA, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (Grant OCI-1053575).” (Shen et al., 2021, p. 130)
Shi, Junjie; Cameron J. Owen; Hio Tong Ngan; Siyu Qin; Vikram Mehar; Philippe Sautet, and Jason F. Weaver. “Formation of a Ti–Cu(111) single atom alloy: Structure and CO binding.” The Journal of Chemical Physics 154 no. 23 (2021): 234703. 10.1063/5.0050800.
“The calculations by H.T.N. were performed on the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE) and the National Energy Research Scientific Computing Center (NERSC) of the U.S. Department of Energy.” (Shi et al., 2021, p. 12)
Sun, Geng; Jack T. Fuller; Anastassia N. Alexandrova, and Philippe Sautet. “Global Activity Search Uncovers Reaction Induced Concomitant Catalyst Restructuring for Alkane Dissociation on Model Pt Catalysts.” ACS Catalysis 11 no. 3 (2021): 1877-1885. 10.1021/acscatal.0c05421.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Sun et al., 2021, p. 17)
Sun, Geng and Philippe Sautet. “Active Site Fluxional Restructuring as a New Paradigm in Triggering Reaction Activity for Nanocluster Catalysis.” Accounts of Chemical Research 54 no. 20 (2021): 3841-3849. 10.1021/acs.accounts.1c00413.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Sun and Sautet, 2021, p. 18)
Svatunek, Dennis; Thomas Hansen; Kendall N. Houk, and Trevor A. Hamlin. “How the Lewis Base F <sup>–</sup> Catalyzes the 1,3-Dipolar Cycloaddition between Carbon Dioxide and Nitrilimines.” The Journal of Organic Chemistry 86 no. 5 (2021): 4320-4325. 10.1021/acs.joc.0c02963.
“Quantum chemical calculations were performed on the Vienna Scientific Cluster (Austria), the Hoffman2 Cluster (UCLA Institute for Digital Research and Education), and the Cartesius supercomputer (SURFsara, Amsterdam).” (Svatunek et al., 2021, p. 4324)
Turlik, Aneta; Kaori Ando; Pamela Mackey; Emma Alcock; Mark Light; Gerard P. McGlacken, and K. N. Houk. “Mechanism and Origins of Stereoselectivity of the Aldol-Tishchenko Reaction of Sulfinimines.” The Journal of Organic Chemistry 86 no. 5 (2021): 4296-4303. 10.1021/acs.joc.0c02862.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (grant OCI-1053575).” (Turlik et al., 2021, p. 4302)
Turlik, Aneta; K. N. Houk, and Dennis Svatunek. “Origin of Increased Reactivity in Rhenium-Mediated Cycloadditions of Tetrazines.” The Journal of Organic Chemistry 86 no. 18 (2021): 13129-13133. 10.1021/acs.joc.1c01564.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Vienna Scientific Cluster.” (Turlik et al., 2021, p. 13132)
Urner, Lorenz M.; Ga Young Lee; Joseph W. Treacy; Aneta Turlik; Saeed I. Khan; K. N. Houk, and Michael E. Jung. “Intramolecular N−H⋅⋅⋅F Hydrogen Bonding Interaction in a Series of 4-Anilino-5-Fluoroquinazolines: Experimental and Theoretical Characterization of Electronic and Conformational Effects.” Chemistry – A European Journal 28 no. 2 (2021): e202103135. 10.1002/chem.202103135.
“Calculations were performed ontheHoffman2 cluster at the University of California, Los Angeles. A.T. acknowledges the support of the National Institutes of Health under Ruth L. Kirschstein National Research Service Award F32GM134709.” (Urner et al., 2022, p. 9)
Vargas, Santiago; Matthew R. Hennefarth; Zhihao Liu, and Anastassia N. Alexandrova. “Machine Learning to Predict Diels–Alder Reaction Barriers from the Reactant State Electron Density.” Journal of Chemical Theory and Computation 17 no. 10 (2021): 6203-6213. 10.1021/acs.jctc.1c00623.
“We also acknowledge the UCLA-IDRE cluster Hoffman2 computational resources.” (Vargas et al., 2021, p. 6210)”
Wei, Ziyang; Shona M. Becwar; Bradley F. Chmelka, and Philippe Sautet. “Atomic Environments in N-Containing Graphitic Carbon Probed by First-Principles Calculations and Solid-State Nuclear Magnetic Resonance.” The Journal of Physical Chemistry C 125 no. 16 (2021): 8779-8787. 10.1021/acs.jpcc.1c00511.
“The calculations were performed on the Hoffman2 cluster at UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE),56 which is supported by National Science Foundation grant number ACI-1548562, through allocation TG-CHE170060.” (Wei et al., 2021, p. 21)
Wei, Ziyang; Florian Göltl, and Philippe Sautet. “Diffusion Barriers for Carbon Monoxide on the Cu(001) Surface Using Many-Body Perturbation Theory and Various Density Functionals.” Journal of Chemical Theory and Computation 17 no. 12 (2021): 7862-7872. 10.1021/acs.jctc.1c00946.
“The calculations were performed on the Hoffman2 cluster at UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE),69 which is supported by National Science Foundation grant number ACI-1548562, through allocation TGCHE170060.” (Wei et al., 2021, p. 7870)
Whang, Grace; Qizhang Yan; Da Li; Ziyang Wei; Danielle Butts; Philippe Sautet; Jian Luo, and Bruce Dunn. “Avoiding dendrite formation by confining lithium deposition underneath Li–Sn coatings.” Journal of Materials Research 36 no. 4 (2021): 797-811. 10.1557/s43578-020-00047-8.
“The calculations were performed on the Hoffman2 cluster at the UCLA Institute for Digital Research and Education (IDRE), and the Extreme Science and Engineering Discovery Environment (XSEDE) [67], which is supported by National Science Foundation grant number ACI- 1548562, through allocation TG-CHE170060.” (Whang et al., 2021, p. 808)
Wong, Jonathan J.; Xiangyang Chen; Kendall N. Houk, and K. Peter C. Vollhardt. “The Trajectory of the (η5-Cyclopentadienyl)cobalt-Mediated Cycloisomerization of Ene-Yne-Ene-Type Allyl Propargylic Ethers to Furans: A DFT Appraisal.” Synthesis 53 no. 22 (2021): 4279-4289. 10.1055/a-1645-2632.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575).” (Wong et al., 2021, p. 4288)
Wu, Huan; Hang Fan, and Yongjie Hu. “Ab initio determination of ultrahigh thermal conductivity in ternary compounds.” Physical Review B 103 no. 4 (2021): L041203. 10.1103/PhysRevB.103.L041203.
“This work used computational and storage services associated with the Hoffman 2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation through Grant No. ACI-1548562.” (Wu et al., 2021, p. 4)
Xia, Yantao and Philippe Sautet. “Thermodynamics of Atomic Layer Etching Chemistry on Copper and Nickel Surfaces from First Principles.” Chemistry of Materials 33 no. 17 (2021): 6774-6786. 10.1021/acs.chemmater.1c01324.
“The authors gratefully acknowledge the support from UCLA Institute of Digital Research and Education (IDRE) for computational resources on the UCLA Hoffman2 cluster.” (Xia and Sautet, 2021, p. 6785)
Yu, Qianran; Sabyasachi Chatterjee; Kenneth J. Roche; Giacomo Po, and Jaime Marian. “Coupling crystal plasticity and stochastic cluster dynamics models of irradiation damage in tungsten.” Modelling and Simulation in Materials Science and Engineering 29 no. 5 (2021): 055021. 10.1088/1361-651X/ac01ba.
“Computer time allocations at UCLA’s IDRE Hoffman2 computer cluster are gratefully acknowledged.” (Yu et al., 2021, p. 21)
Zhang, Hong; Alexander J. E. Novak; Cooper S. Jamieson; Xiao-Song Xue; Shuming Chen; Dirk Trauner, and K. N. Houk. “Computational Exploration of the Mechanism of Critical Steps in the Biomimetic Synthesis of Preuisolactone A, and Discovery of New Ambimodal (5 + 2)/(4 + 2) Cycloadditions.” Journal of the American Chemical Society 143 no. 17 (2021): 6601-6608. 10.1021/jacs.1c01856.
“All calculations were performed on computational resources provided by the UCLA Institute of Digital Research and Education.” (Zhang et al., 2021, p. 6607)
Zhang, Hong; Mathias Kirk Thøgersen; Cooper S. Jamieson; Xiao-Song Xue; Karl Anker Jørgensen, and Kendall N. Houk. “Ambimodal Transition States in Diels–Alder Cycloadditions of Tropolone and Tropolonate with N-Methylmaleimide**.” Angewandte Chemie International Edition 60 no. 47 (2021): 24991-24996. 10.1002/anie.202109608.
“All calculations were performed on computational resources provided by the UCLA Institute of Digital Research and Education.” (Zhang et al., 2021, p. 24996)
Zhang, Song; Masato Koizumi; Zhiqiang Cao; Keyou S. Mao; Zhiyuan Qian; Luke A. Galuska; Lihua Jin, and Xiaodan Gu. “Directly Probing the Fracture Behavior of Ultrathin Polymeric Films.” ACS Polymers Au 1 no. 1 (2021): 16-29. 10.1021/acspolymersau.1c00005.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by Institute for Digital Research and Education’s Research Technology Group at the University of California, Los Angeles.” (Zhang et al., 2021, p. 27)
Zhou, X. and J. Marian. “Temperature and stress dependence of screw dislocation mobility in nb-v-ta alloys using kinetic monte carlo simulations.” Frontiers in Materials 8 (2021). 10.3389/fmats.2021.801141.
Publication Title: Frontiers in Materials “We thank UCLA’s IDRE for computer time allocations on the Hoffman2 supercomputer.” (Zhou and Marian, 2021, p. 9) Type: 10.3389/fmats.2021.801141
Zhou, Xinran; Sicong He, and Jaime Marian. “Cross-kinks control screw dislocation strength in equiatomic bcc refractory alloys.” Acta Materialia 211 (2021): 116875. 10.1016/j.actamat.2021.116875.
“We thank UCLA’s IDRE for computer time allocations on the Hoffman2 supercomputer.” (Zhou et al., 2021, p. 11)
Zou, Yike and K. N. Houk. “Mechanisms and Dynamics of Synthetic and Biosynthetic Formation of Delitschiapyrones: Solvent Control of Ambimodal Periselectivity.” Journal of the American Chemical Society 143 no. 30 (2021): 11734-11740. 10.1021/jacs.1c05293.
“All DFT calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI-1053575).” (Zou and Houk, 2021, p. 7)
Theses for 2021¶
Almisbaa, Zahra Nasser. “Computational Modeling of Ni-Based Catalysts for Selective Hydrogenation of Acetylene to Ethylene.” M.S. Thesis, University of California, Los Angeles, 2021. ProQuest, https://www.proquest.com/docview/2563674401.
“This work received support from UCLA Institute of Digital Research and Education (IDRE) for computational resources on the UCLA Hoffman2 cluster.” (Almisbaa, 2021, p. 11)
Reilley, David John. “Accounting for Chemical Change in Classical and QM-Hybrid Molecular Dynamics Simulations of Proteins and Metalloproteins.” Ph.D. Thesis, University of California, Los Angeles, 2021. ProQuest, https://www.proquest.com/docview/2553309167.
“Simulations were performed on AMD Opteron 2380 (2.5 GHz) cores on Hoffman2 at UCLA IDRE.” (Reilley, 2021, p. 108)
2020¶
- 99 publications for 2020
Journal Articles for 2020¶
Abreu, S.; F. Febres Cordero; H. Ita; M. Jaquier; B. Page; M. S. Ruf, and V. Sotnikov. “Two-Loop Four-Graviton Scattering Amplitudes.” Physical Review Letters 124 no. 21 (2020): 211601. 10.1103/PhysRevLett.124.211601.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Abreu et al., 2020, p. 5)
Ascenzi, Maria-Grazia; Andrea Zonca, and Joyce H. Keyak. “Effect of cortical bone micro-structure in fragility fracture patients on lamellar stress.” Journal of Biomechanics 100 (2020): 109596. 10.1016/j.jbiomech.2019.109596.
“We acknowledge Jennifer Lourenço and Hasan Muqri for preliminary calculations, UCLA’s Academic Technology Services for Hoffman2 Cluster resources, Extreme Science and Engineering Discovery Environment (XSEDE) for Supercomputer Comet at UC San Diego resources with dedicated support of a High Performance Computing consultant through the Extended Collaborative Support Service (ECSS).” (Ascenzi et al., 2020, p. 109603) PMID: 31898977
Beşken, Mert; Shouvik Datta, and Per Kraus. “Quantum thermalization and Virasoro symmetry.” Journal of Statistical Mechanics: Theory and Experiment 2020 no. 6 (2020): 063104. 10.1088/1742-5468/ab900b.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Beşken et al., 2020, p. 24)
Bostanci Ceran, Basak; Alp Karakoç, and Ertuğrul Taciroğlu. “Airborne pathogen projection during ophthalmic examination.” Graefe’s Archive for Clinical and Experimental Ophthalmology = Albrecht Von Graefes Archiv Fur Klinische Und Experimentelle Ophthalmologie 258 no. 10 (2020): 2275-2282. 10.1007/s00417-020-04815-4.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Bostanci Ceran et al., 2020, p. 2281) PMID: 32588166 PMCID: PMC7315910
Brito, Jaqueline J; Thiago Mosqueiro; Jeremy Rotman; Victor Xue; Douglas J Chapski; Juan De la Hoz; Paulo Matias; Lana S Martin; Alex Zelikovsky; Matteo Pellegrini, and Serghei Mangul. “Telescope: an interactive tool for managing large-scale analysis from mobile devices.” GigaScience 9 no. 1 (2020): giz163. 10.1093/gigascience/giz163.
“We successfully tested Telescope at the University of California, Los Angeles (UCLA) campus-wide computational cluster” (Brito et al., 2020, p. 2)
Chang, Jonathan; Daniel L Rabosky, and Michael E Alfaro. “Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions.” Systematic Biology 69 no. 3 (2020): 602-611. 10.1093/sysbio/syz081.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group. This research was supported in part through computational resources and services provided by Advanced Research Computing at the University of Michigan, Ann Arbor.” (Chang et al., 2020, p. 610)
Chen, Pan-Pan; Jeffrey I. Seeman, and Kendall N. Houk. “Rolf Huisgen’s Classic Studies of Cyclic Triene Diels–Alder Reactions Elaborated by Modern Computational Analysis.” Angewandte Chemie International Edition 59 no. 30 (2020): 12506-12519. 10.1002/anie.202003279.
“Calculations were performed on the IDRE Hoffman2 cluster at the University of California, Los Angeles.” (Chen et al., 2020, p. 12518)
Chen, Shuming; Jonathan J. Wong, and K. N. Houk. “Mechanism of the Manolikakes Enamide-Based Domino Reaction for the Stereospecific Construction of Tetrahydropyrans.” The Journal of Organic Chemistry 85 no. 5 (2020): 3806-3811. 10.1021/acs.joc.9b03440.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI1053575).” (Chen et al., 2020, p. 3810)
Cheung, Clifford and Mikhail P. Solon. “Tidal Effects in the Post-Minkowskian Expansion.” Physical Review Letters 125 no. 19 (2020): 191601. 10.1103/PhysRevLett.125.191601.
“The calculations here used the computer algebra system Mathematica [49] in combination with FeynCalc [50] and xAct [51], as well as the On-Line Encyclopedia of Integer Sequences [52] and the Hoffman2 Cluster at the Institute for Digital Research and Education at UCLA.” (Cheung and Solon, 2020, p. 6)
Chu, Benjamin B; Kevin L Keys; Christopher A German; Hua Zhou; Jin J Zhou; Eric M Sobel; Janet S Sinsheimer, and Kenneth Lange. “Iterative hard thresholding in genome-wide association studies: Generalized linear models, prior weights, and double sparsity.” GigaScience 9 no. 6 (2020): giaa044. 10.1093/gigascience/giaa044.
“We thank UCLA for providing the computing resources via the Hoffman2 cluster.” (Chu et al., 2020, p. 11)
Dalichaouch, T. N.; X. L. Xu; F. Li; A. Tableman; F. S. Tsung; W. An, and W. B. Mori. “Generating high quality ultrarelativistic electron beams using an evolving electron beam driver.” Physical Review Accelerators and Beams 23 no. 2 (2020): 021304. 10.1103/PhysRevAccelBeams.23.021304.
“The simulations were performed on Blue Waters, the National Energy Research Scientific Computing Center (NERSC), and Hoffman2 at UCLA.” (Dalichaouch et al., 2020, p. 5)
Debrauwer, Vincent; Aneta Turlik; Lénaic Rummler; Alessandro Prescimone; Nicolas Blanchard; K. N. Houk, and Vincent Bizet. “Ligand-Controlled Regiodivergent Palladium-Catalyzed Hydrogermylation of Ynamides.” Journal of the American Chemical Society 142 no. 25 (2020): 11153-11164. 10.1021/jacs.0c03556.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (grant OCI-1053575).” (Debrauwer et al., 2020, p. 11162)
Demoret, Robert M.; Meghan A. Baker; Masaki Ohtawa; Shuming Chen; Ching Ching Lam; Sophia Khom; Marisa Roberto; Stefano Forli; Kendall N. Houk, and Ryan A. Shenvi. “Synthetic, Mechanistic, and Biological Interrogation of Ginkgo biloba Chemical Space En Route to (−)-Bilobalide.” Journal of the American Chemical Society 142 no. 43 (2020): 18599-18618. 10.1021/jacs.0c08231.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), supported by the National Science Foundation (OCI-1053575).” (Demoret et al., 2020, p. 18614)
Deng, J; SC Lin; J Fuller; JA Iñiguez; DL Xiang; D Yang; GR Chan; HM Chen; AN Alexandrova, and C Liu. “Ambient methane functionalization initiated by electrochemical oxidation of a vanadium (V)-oxo dimer.” NATURE COMMUNICATIONS 11 no. 1 (2020). 10.1038/s41467-020-17494-w.
“A.N.A. acknowledges the NSF Career Award (CHE-1351968), and the XSEDE and the UCLA-IDRE cluster Hoffman2 for computational resources.” (Deng et al., 2020, p. 10) Publication Title: Nature …
Ding, Yangyao; Yichi Zhang; Gerassimos Orkoulas, and Panagiotis D. Christofides. “Microscopic modeling and optimal operation of plasma enhanced atomic layer deposition.” Chemical Engineering Research and Design 159 (2020): 439-454. 10.1016/j.cherd.2020.05.014.
“To boost the computational speed and efficiently utilize all available computational resources, we adopt a distributed computation using the UCLA Hoffman2 cluster.” (Ding et al., 2020, p. 450)
Dobynde, M. I. and Y. Y. Shprits. “Radiation environment created with GCRs inside a spacecraft.” Life Sciences in Space Research 24 (2020): 116-121. 10.1016/j.lssr.2019.09.001.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA’s Institute for Digital Research and Education’s Research Technology Group.” (Dobynde and Shprits, 2020, p. 121) PMID: 31987475
Drozdov, A. Y.; M. E. Usanova; M. K. Hudson; H. J. Allison, and Y. Y. Shprits. “The Role of Hiss, Chorus, and EMIC Waves in the Modeling of the Dynamics of the Multi-MeV Radiation Belt Electrons.” Journal of Geophysical Research: Space Physics 125 no. 9 (2020): e2020JA028282. 10.1029/2020JA028282.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Drozdov et al., 2020, p. 11)
Eger, E; A Simon; M Sharma; S Yang; WB Breukelaar; G Grogan; KN Houk, and W Kroutil. “Inverted Binding of Non-natural Substrates in Strictosidine Synthase Leads to a Switch of Stereochemical Outcome in Enzyme-Catalyzed Pictet-Spengler Reactions.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 142 no. 2 (2020): 792-800. 10.1021/jacs.9b08704.
“Computational resources from the UCLA Institute of Digital Research and Education (IDRE) are gratefully acknowledged.” (Eger et al., 2020, p. 798)
Enders, Craig K.; Han Du, and Brian T. Keller. “A model-based imputation procedure for multilevel regression models with random coefficients, interaction effects, and nonlinear terms.” Psychological Methods 25 no. 1 (2020): 88-112. 10.1037/met0000228.
“Computational tasks were executed on UCLA’s Shared Hoffman2 Cluster, and we used a Linux shell script to coordinate simulation tasks.” (Enders et al., 2020, p. 102) Num Pages: 88-112 Place: Washington, US
Fan, Zhoulong; Katherine L Bay; Xiangyang Chen; Zhe Zhuang; Han Seul Park; Kap‐Sun Yeung; KN Houk, and Jin‐Quan Yu. “Rational development of remote C− H functionalization of biphenyl: Experimental and computational studies.” Angewandte Chemie 132 no. 12 (2020): 4800-4807.
“Computations were performed ontheHoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI1053575).” (Fan et al., 2020, p. 4776)
Fraley, AE; KC Haatveit; Y Ye; SP Kelly; SA Newmister; FA Yu; RM Williams; JL Smith; KN Houk, and DH Sherman. “Molecular Basis for Spirocycle Formation in the Paraherquamide Biosynthetic Pathway.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 142 no. 5 (2020): 2244-2252. 10.1021/jacs.9b09070.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1 053575).” (Fraley et al., 2020, p. 8)
Galy, Tiphaine; Daniel Huang, and Laurent Pilon. “Revisiting independent versus dependent scattering regimes in suspensions or aggregates of spherical particles.” Journal of Quantitative Spectroscopy and Radiative Transfer 246 (2020): 106924. 10.1016/j.jqsrt.2020.106924.
“This work also used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Galy et al., 2020, p. 14)
Gamble, Amandine; Romain Garnier; Thierry Chambert; Olivier Gimenez, and Thierry Boulinier. “Next-generation serology: integrating cross-sectional and capture–recapture approaches to infer disease dynamics.” Ecology 101 no. 2 (2020): e02923. 10.1002/ecy.2923.
“This work used computational and storage services associated with the shared clusters provided by CEFE-CNRS and UCLA Institute for Digital Research and Education’s Research Technology Group (Hoffman2).” (Gamble et al., 2020, p. 10)
Gao, Lei; Cong Su; Xiaoxia Du; Ruishan Wang; Shuming Chen; Yu Zhou; Chengwei Liu; Xiaojing Liu; Runze Tian; Liyun Zhang; Kebo Xie; She Chen; Qianqian Guo; Lanping Guo; Yoshio Hano; Manabu Shimazaki; Atsushi Minami; Hideaki Oikawa; Niu Huang; K. N. Houk; Luqi Huang; Jungui Dai, and Xiaoguang Lei. “FAD-dependent enzyme-catalysed intermolecular [4+2] cycloaddition in natural product biosynthesis.” Nature Chemistry 12 no. 7 (2020): 620-628. 10.1038/s41557-020-0467-7.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (grant OCI-1053575).” (Gao et al., 2020, p. 632) PMID: 32451436
Gao, Shang; Meng Duan; Kendall N. Houk, and Ming Chen. “Chiral Phosphoric Acid Dual-Function Catalysis: Asymmetric Allylation with α-Vinyl Allylboron Reagents.” Angewandte Chemie International Edition 59 no. 26 (2020): 10540-10548. 10.1002/anie.202000039.
“Calculations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported bythe National Science Foundation (OCI1053575).” (Gao et al., 2020, p. 10546)
Gao, Shang; Meng Duan; Qianzhen Shao; K. N. Houk, and Ming Chen. “Development of α,α-Disubstituted Crotylboronate Reagents and Stereoselective Crotylation via Brønsted or Lewis Acid Catalysis.” Journal of the American Chemical Society 142 no. 43 (2020): 18355-18368. 10.1021/jacs.0c04107.
“Calculations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI1053575).” (Gao et al., 2020, p. 18364)
Garlets, ZJ; JN Sanders; H Malik; C Gampe; KN Houk, and HML Davies. “Enantioselective C-H functionalization of bicyclo[1.1.1]pentanes.” NATURE CATALYSIS 3 no. 4 (2020): 351-357. 10.1038/s41929-019-0417-1.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE).” (Garlets et al., 2020, p. 357)
Ge, Yijun and Timothy S. Fisher. “Photoconductivity calculations of bilayer graphene from first principles and deformation-potential approach.” Physical Review B 101 no. 23 (2020): 235429. 10.1103/PhysRevB.101.235429.
“This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the US National Science Foundation, Grant No. DMR170128 and computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Ge and Fisher, 2020, p. 8)
Gieuw, Matthew H.; Shuming Chen; Zhihai Ke; K. N. Houk, and Ying-Yeung Yeung. “Boron tribromide as a reagent for anti-Markovnikov addition of HBr to cyclopropanes.” Chemical Science 11 no. 35 (2020): 9426-9433. 10.1039/D0SC02567D.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI-1053575).” (Gieuw et al., 2020, p. 9432)
Gilman, D.; S. Birrer, and T. Treu. “TDCOSMO - III. Dark matter substructure meets dark energy. The effects of (sub)halos on strong-lensing measurements of H0.” Astronomy & Astrophysics 642 (2020): A194. 10.1051/0004-6361/202038829.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Gilman et al., 2020, p. 11)
Gilman, Daniel; Simon Birrer; Anna Nierenberg; Tommaso Treu; Xiaolong Du, and Andrew Benson. “Warm dark matter chills out: constraints on the halo mass function and the free-streaming length of dark matter with eight quadruple-image strong gravitational lenses.” Monthly Notices of the Royal Astronomical Society 491 no. 4 (2020): 6077-6101. 10.1093/mnras/stz3480.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Gilman et al., 2020, p. 6096)
Hennefarth, MR and AN Alexandrova. “Direct Look at the Electric Field in Ketosteroid Isomerase and Its Variants.” ACS CATALYSIS 10 no. 17 (2020): 9915-9924. 10.1021/acscatal.0c02795.
“We also acknowledge the UCLA-IDRE cluster Hoffman2 computational resources.” (Hennefarth and Alexandrova, 2020, p. 20)
Hill, Pamela S.; Edwin A. Schauble, and Aradhna Tripati. “Theoretical constraints on the effects of added cations on clumped, oxygen, and carbon isotope signatures of dissolved inorganic carbon species and minerals.” Geochimica et Cosmochimica Acta 269 (2020): 496-539. 10.1016/j.gca.2019.10.016.
“Calculations on the inner, moveable atoms were performed by the B3LYP method and the Pople basis sets 6-311++G (2d, 2p), 6-311G*, and 6-31G*, using Gaussian 09, Revision D.01 (Gaussian 09, 2013) on the UCLA Hoffman2 computer cluster.” (Hill et al., 2020, p. 500)
Huang, Brian Z; Alexandra M Binder; Catherine A Sugar; Chun R Chao; Veronica Wendy Setiawan, and Zuo-Feng Zhang. “Methylation of immune-regulatory cytokine genes and pancreatic cancer outcomes.” Epigenomics 12 no. 15 (2020): 1273-1285. 10.2217/epi-2019-0335.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Huang et al., 2020, p. 1283) PMID: 32867538 PMCID: PMC7546161
Huang, Hui; Lingsen Meng; Roland Bürgmann; Wei Wang, and Kang Wang. “Spatio-temporal foreshock evolution of the 2019 M 6.4 and M 7.1 Ridgecrest, California earthquakes.” Earth and Planetary Science Letters 551 (2020): 116582. 10.1016/j.epsl.2020.116582.
“This work relies on the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Huang et al., 2020, p. 10)
Huffman, Benjamin J.; Shuming Chen; J. Luca Schwarz; R. Erik Plata; Emily N. Chin; Luke L. Lairson; K. N. Houk, and Ryan A. Shenvi. “Electronic complementarity permits hindered butenolide heterodimerization and discovery of novel cGAS/STING pathway antagonists.” Nature Chemistry 12 no. 3 (2020): 310-317. 10.1038/s41557-019-0413-8.
“All calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles and the Extreme Science and Engineering Discovery Environment (XSEDE) supported by the NSF (OCI-1053575).” (Huffman et al., 2020, p. 318)
Jimenez, Amy M; Junghee Lee; Eric A Reavis; Jonathan K Wynn, and Michael F Green. “Neural Correlates of True and False Recognition Memory for Socially Relevant Information in Schizophrenia.” Schizophrenia Bulletin Open 1 no. 1 (2020): sgaa029. 10.1093/schizbullopen/sgaa029.
“fMRI data analysis for this study used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Jimenez et al., 2020, p. 7)
Kalligeris, N.; P. B. Smit; B. C. Ludka; R. T. Guza, and T. W. Gallien. “Calibration and assessment of process-based numerical models for beach profile evolution in southern California.” Coastal Engineering 158 (2020): 103650. 10.1016/j.coastaleng.2020.103650.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Educations Research Technology Group.” (Kalligeris et al., 2020, p. 26)
Khan, Arshad H.; Andy Lin; Richard T. Wang; Joshua S. Bloom; Kenneth Lange, and Desmond J. Smith. “Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells.” Genome Research 30 no. 10 (2020): 1458-1467. 10.1101/gr.262204.120.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education Research Technology Group.” (Khan et al., 2020, p. 1465) PMID: 32878976 PMCID: PMC7605260
Kiel, Gavin R.; Katherine L. Bay; Adrian E. Samkian; Nathaniel J. Schuster; Janice B. Lin; Rex C. Handford; Colin Nuckolls; K. N. Houk, and T. Don Tilley. “Expanded Helicenes as Synthons for Chiral Macrocyclic Nanocarbons.” Journal of the American Chemical Society 142 no. 25 (2020): 11084-11091. 10.1021/jacs.0c03177.
“Computations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI1053575).” (Kiel et al., 2020, p. 11089)
Li, Xingguang; Meng Duan; Zhiqin Deng; Qianzhen Shao; Min Chen; Guangyu Zhu; K. N. Houk, and Jianwei Sun. “Catalytic enantioselective synthesis of chiral tetraarylmethanes.” Nature Catalysis 3 no. 12 (2020): 1010-1019. 10.1038/s41929-020-00535-4.
“Calculations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575).” (Li et al., 2020, p. 1019)
Li, Yolanda L.; Chih-Te Zee; Janice B. Lin; Victoria M. Basile; Mit Muni; Maria D. Flores; Julen Munárriz; Richard B. Kaner; Anastassia N. Alexandrova; K. N. Houk; Sarah H. Tolbert, and Yves Rubin. “Fjord-Edge Graphene Nanoribbons with Site-Specific Nitrogen Substitution.” Journal of the American Chemical Society 142 no. 42 (2020): 18093-18102. 10.1021/jacs.0c07657.
“This work used computational and storage services associated with the Hoffman2 cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group, the NSF-supported Extreme Science and Engineering Discovery Environment (XSEDE) (NSF-OCI−1054575 and TG-CHE160054), and high-performance research computing resources by Texas A&M University (http://hprc.tamu.edu).” (Li et al., 2020, p. 18100)
Liepuoniute, Ieva; Chau Minh Huynh; Salvador Perez-Estrada; Yangyang Wang; Saeed Khan; K. N. Houk, and Miguel A. Garcia-Garibay. “Enhanced Rotation by Ground State Destabilization in Amphidynamic Crystals of a Dipolar 2,3-Difluorophenylene Rotator as Established by Solid State 2H NMR and Dielectric Spectroscopy.” The Journal of Physical Chemistry C 124 no. 28 (2020): 15391-15398. 10.1021/acs.jpcc.0c05314.
“Computations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575). C.M.H.’s research was supported by the UCLA-DOE Center for Global Mentoring.” (Liepuoniute et al., 2020, p. 15397)
Liepuoniute, Ieva; Jacob N. Sanders; Miguel A. Garcia-Garibay, and K. N. Houk. “Computational Investigation into Ligand Effects on Correlated Geared Dynamics in Dirhodium Supramolecular Gears—Insights Beyond the NMR Experimental Window.” The Journal of Organic Chemistry 85 no. 13 (2020): 8695-8701. 10.1021/acs.joc.0c01230.
“Computations were performed on the Hoffman2 cluster at the UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Liepuoniute et al., 2020, p. 8700)
Liu, JY; XQ Gong; RX Li; HT Shi; SB Cronin, and AN Alexandrova. “(Photo)Electrocatalytic CO2 Reduction at the Defective Anatase TiO2 (101) Surface.” ACS CATALYSIS 10 no. 7 (2020): 4048-4058. 10.1021/acscatal.0c00947.
“We also acknowledge the UCLA-IDRE cluster Hoffman2 and XSEDE for computational resources.” (Liu et al., 2020, p. 16)
Liu, Luping; Yike Zou; Ahanjit Bhattacharya; Dongyang Zhang; Susan Q. Lang; K. N. Houk, and Neal K. Devaraj. “Enzyme-free synthesis of natural phospholipids in water.” Nature Chemistry 12 no. 11 (2020): 1029-1034. 10.1038/s41557-020-00559-0.
“Computation time was provided by the UCLA Institute for Digital Research and Education (IDRE).” (Liu et al., 2020, p. 1035) Number: 11
Madson, Austin and Yongwei Sheng. “Reservoir induced deformation analysis for several filling and operational scenarios at the grand Ethiopian renaissance dam impoundment.” Remote Sensing 12 no. 11 (2020): 1886.
“Reservoir induced deformation analysis for several filling and operational scenarios at the grand Ethiopian renaissance dam impoundment
McCraney, W. Tyler; Christine E. Thacker, and Michael E. Alfaro. “Supermatrix phylogeny resolves goby lineages and reveals unstable root of Gobiaria.” Molecular Phylogenetics and Evolution 151 (2020): 106862. 10.1016/j.ympev.2020.106862.
“Computational and storage services associated with the Hoffman2 Shared Cluster were provided by UCLA Institute for Digital Research and Education Research Technology Group.” (McCraney et al., 2020, p. 12)
Miao, Yu; Nicholas W. Johnson; Thien Phan; Kimberly Heck; Phillip B. Gedalanga; Xiaoru Zheng; David Adamson; Charles Newell; Michael S. Wong, and Shaily Mahendra. “Monitoring, assessment, and prediction of microbial shifts in coupled catalysis and biodegradation of 1,4-dioxane and co-contaminants.” Water Research 173 (2020): 115540. 10.1016/j.watres.2020.115540.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Miao et al., 2020, p. 11)
Munarriz, Julen; Paul J. Robinson, and Anastassia N. Alexandrova. “Towards a Single Chemical Model for Understanding Lanthanide Hexaborides.” Angewandte Chemie 132 no. 50 (2020): 22873-22878. 10.1002/ange.202010638.
“We thank the Institute for Digital Research and Education at UCLA and the Extreme Science and Engineering Discovery Environment for supercomputer time.” (Munarriz et al., 2020, p. 22877)
Murray, James I.; Jacob N. Sanders; Paul F. Richardson; K. N. Houk, and Donna G. Blackmond. “Isotopically Directed Symmetry Breaking and Enantioenrichment in Attrition-Enhanced Deracemization.” Journal of the American Chemical Society 142 no. 8 (2020): 3873-3879. 10.1021/jacs.9b11422.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE).” (Murray et al., 2020, p. 3879)
Neiser, Tom F. and this link will open in a new tab Link to external site. “Fermi Degenerate Antineutrino Star Model of Dark Energy.” Advances in Astronomy 2020 (2020). 10.1155/2020/8654307.
“This work used computational resources associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education.” (Neiser and Link to external site, 2020, p. 10) Num Pages: 11 Place: New York, United Kingdom
Ni, Dongshun; Brittany P. Witherspoon; Hong Zhang; Chen Zhou; K. N. Houk, and M. Kevin Brown. “Stereoselective [4+2]-Cycloaddition with Chiral Alkenylboranes.” Angewandte Chemie International Edition 59 no. 28 (2020): 11432-11439. 10.1002/anie.202000652.
“Computations were performed on the Hoffman2 cluster at UCLA.” (Ni et al., 2020, p. 11438)
O’Connor, Christopher R.; Kaining Duanmu; Dipna A. Patel; Eri Muramoto; Matthijs A. van Spronsen; Dario Stacchiola; E. Charles H. Sykes; Philippe Sautet; Robert J. Madix, and Cynthia M. Friend. “Facilitating hydrogen atom migration via a dense phase on palladium islands to a surrounding silver surface.” Proceedings of the National Academy of Sciences 117 no. 37 (2020): 22657-22664. 10.1073/pnas.2010413117.
“The DFT calculations were performed on the HOFFMAN2 cluster at the University of California, Los Angeles, Institute for Digital Research and Education, on the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported under Contract No. DE-AC02-05CH11231, through allocation m3275, and on computing resources at Extreme Science and Engineering Discovery Environment (XSEDE) through the allocation CHE170060.” (O’Connor et al., 2020, p. 22663)
Peng, L.; Z. Wei; C. Wan; J. Li; Z. Chen, and D. Zhu. “A fundamental look at electrocatalytic sulfur reduction reaction.” Nature Catalysis 3 no. 9 (2020): 762-770. 10.1038/s41929-020-0498-x.
“The calculations were performed on the Hoffman2 cluster at UCLA Institute for Digital Research and Education (IDRE), The National Energy Research Scientific Computing Center (NERSC), and the Extreme Science and Engineering Discovery Environment (XSEDE)52, which is supported by National Science Foundation grant number ACI-1548562, through allocation TG-CHE170060.” (Peng et al., 2020, p. 770)
Quintela-Varela, Hugo; Cooper S. Jamieson; Qianzhen Shao; K. N. Houk, and Dirk Trauner. “Bioinspired Synthesis of (−)-PF-1018.” Angewandte Chemie International Edition 59 no. 13 (2020): 5263-5267. 10.1002/anie.201912452.
“All computational resources were provided by the Institute for Digital Research and Education.” (Quintela-Varela et al., 2020, p. 5266)
Ramirez, Melissa; Wenfei Li; Yu-hong Lam; Léon Ghosez, and K. N. Houk. “Mechanisms and Conformational Control of (4 + 2) and (2 + 2) Cycloadditions of Dienes to Keteniminium Cations.” The Journal of Organic Chemistry 85 no. 4 (2020): 2597-2606. 10.1021/acs.joc.9b03340.
“This study used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Ramirez et al., 2020, p. 2605)
Reavis, Eric A; Junghee Lee; Lori L Altshuler; Mark S Cohen; Stephen A Engel; David C Glahn; Amy M Jimenez; Katherine L Narr; Keith H Nuechterlein; Philipp Riedel; Jonathan K Wynn, and Michael F Green. “Structural and Functional Connectivity of Visual Cortex in Schizophrenia and Bipolar Disorder: A Graph-Theoretic Analysis.” Schizophrenia Bulletin Open 1 no. 1 (2020): sgaa056. 10.1093/schizbullopen/sgaa056.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Reavis et al., 2020, p. 10)
Sanders, Jacob N.; HyunJune Jun; Roland A. Yu; James L. Gleason, and K. N. Houk. “Mechanism of an Organocatalytic Cope Rearrangement Involving Iminium Intermediates: Elucidating the Role of Catalyst Ring Size.” Journal of the American Chemical Society 142 no. 39 (2020): 16877-16886. 10.1021/jacs.0c08427.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and by the San Diego Supercomputing Center (SDSC) through XSEDE (ACI-1548562).” (Sanders et al., 2020, p. 16885)
Sang, X; YT Xia; P Sautet, and JEP Chang. “Atomic layer etching of metals with anisotropy, specificity, and selectivity.” JOURNAL OF VACUUM SCIENCE & TECHNOLOGY A 38 no. 4 (2020). 10.1116/6.0000225.
“Yantao Xia and Philippe Sautet acknowledge UCLA IDRE for computational resources on the Hoffman2 cluster.” (Sang et al., 2020, p. 10) Publication Title: Journal of Vacuum Science & …
Shang, Rui; Stephan N. Steinmann; Bo-Qing Xu, and Philippe Sautet. “Mononuclear Fe in N-doped carbon: computational elucidation of active sites for electrochemical oxygen reduction and oxygen evolution reactions.” Catalysis Science & Technology 10 no. 4 (2020): 1006-1014. 10.1039/C9CY01935A.
“This work used computational and storage services associated with the Hoffman2 shared cluster provided by UCLA Institute for Digital Research and Education Group.” (Shang et al., 2020, p. 1013)
Shende, VV; Y Khatri; SA Newmister; JN Sanders; P Lindovska; FG Yu; TJ Doyon; J Kim; KN Houk; M Movassaghi, and DH Sherman. “Structure and Function of NzeB, a Versatile C-C and C-N Bond-Forming Diketopiperazine Dimerase.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 142 no. 41 (2020): 17413-17424. 10.1021/jacs.0c06312.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and by the San Diego Supercomputing Center (SDSC) through XSEDE (ACI-1548562).” (Shende et al., 2020, p. 12)
Sumaria, Vaidish; Luan Nguyen; Franklin Feng Tao, and Philippe Sautet. “Optimal Packing of CO at a High Coverage on Pt(100) and Pt(111) Surfaces.” ACS Catalysis 10 no. 16 (2020): 9533-9544. 10.1021/acscatal.0c01971.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Sumaria et al., 2020, p. 9543)
Sun, Geng; Anastassia N. Alexandrova, and Philippe Sautet. “Structural Rearrangements of Subnanometer Cu Oxide Clusters Govern Catalytic Oxidation.” ACS Catalysis 10 no. 9 (2020): 5309-5317. 10.1021/acscatal.0c00824.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Sun et al., 2020, p. 5315)
Svatunek, Dennis; Ryan P. Pemberton; Joel L. Mackey; Peng Liu, and K. N. Houk. “Concerted [4 + 2] and Stepwise (2 + 2) Cycloadditions of Tetrafluoroethylene with Butadiene: DFT and DLPNO-UCCSD(T) Explorations.” The Journal of Organic Chemistry 85 no. 5 (2020): 3858-3864. 10.1021/acs.joc.0c00222.
“Computations were performed using the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation grant number ACI-1548562 and by the UCLA Institute for Digital Research and Education (IDRE).” (Svatunek et al., 2020, p. 3863)
Tan, Yuqi; Shuming Chen; Zijun Zhou; Yubiao Hong; Sergei Ivlev; K. N. Houk, and Eric Meggers. “Intramolecular C(sp3)–H Bond Oxygenation by Transition-Metal Acylnitrenoids.” Angewandte Chemie International Edition 59 no. 48 (2020): 21706-21710. 10.1002/anie.202009335.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles ,and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI-1053575).” (Tan et al., 2020, p. 21710)
Thompson, N. F.; E. C. Anderson, and A. J. Clemento. “A complex phenotype in salmon controlled by a simple change in migratory timing.” Science 370 no. 6516 (2020): 609-613. 10.1126/science.aba9059.
“We thank the field biologists that sampled fish; C. Davis and M. Banks for Siletz River samples; E. Campbell, C. Columbus, and E. Correa for laboratory aid; R. Corbett-Detig for computational aid; E. Bjorkstedt and C. Edwards for temperature data; E. Palkovacs for helpful comments on the manuscript; and the UCLA IDRE for the Hoffman2 Shared Cluster.” (Thompson et al., 2020, p. 5)
Vong, A.; D. R. Widmer, and B. J. Schwartz. “Nonequilibrium Solvent Effects during Photodissociation in Liquids: Dynamical Energy Surfaces, Caging, and Chemical Identity.” The Journal of Physical … 11 no. 21 (2020): 9230−9238. 10.1021/acs.jpclett.0c02515.
“We gratefully acknowledge the Institute for Digital Research and Education (IDRE) at UCLA for use of the hoffman2 computing cluster.” (Vong et al., 2020, p. 9236)
Walker, Morgan M.; Brian Koronkiewicz; Shuming Chen; K. N. Houk; James M. Mayer, and Jonathan A. Ellman. “Highly Diastereoselective Functionalization of Piperidines by Photoredox-Catalyzed α-Amino C–H Arylation and Epimerization.” Journal of the American Chemical Society 142 no. 18 (2020): 8194-8202. 10.1021/jacs.9b13165.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI1053575).” (Walker et al., 2020, p. 8201)
Widmer, D. R. and B. J. Schwartz. “The Role of the Solvent in the Condensed-Phase Dynamics and Identity of Chemical Bonds: The Case of the Sodium Dimer Cation in THF.” The Journal of Physical Chemistry B 124 no. 30 (2020): 6603-6616. 10.1021/acs.jpcb.0c03298.
“The authors also thank the Institute for Digital Research and Education (IDRE) at UCLA for use of the hoffman2 computing cluster.” (Widmer and Schwartz, 2020, p. 6615)
Xu, Yan; Jonathan J. Wong; Adrian E. Samkian; Jeong Hoon Ko; Shuming Chen; K. N. Houk, and Robert H. Grubbs. “Efficient Z-Selective Olefin-Acrylamide Cross-Metathesis Enabled by Sterically Demanding Cyclometalated Ruthenium Catalysts.” Journal of the American Chemical Society 142 no. 50 (2020): 20987-20993. 10.1021/jacs.0c11334.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI-1053575).” (Xu et al., 2020, p. 20991)
Yamano, MM; AV Kelleghan; QN Shao; M Giroud; BJ Simmons; B Li; SM Chen; KN Houk, and NK Garg. “Intercepting fleeting cyclic allenes with asymmetric nickel catalysis.” NATURE 586 no. 7828 (2020): 242-+. 10.1038/s41586-020-2701-2.
“Calculations were performed on the Hoffman2 cluster and the UCLA Institute of Digital Research and Education (IDRE) at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575).” (Yamano et al., 2020, p. 248)
Ye, Chen-Xi; Shuming Chen; Feng Han; Xiulan Xie; Sergei Ivlev; K. N. Houk, and Eric Meggers. “Atroposelective Synthesis of Axially Chiral N-Arylpyrroles by Chiral-at-Rhodium Catalysis.” Angewandte Chemie International Edition 59 no. 32 (2020): 13552-13556. 10.1002/anie.202004799.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI-1053575).” (Ye et al., 2020, p. 13555)
Yeung, Christopher; Ju-Ming Tsai; Brian King; Yusaku Kawagoe; David Ho; Mark W. Knight, and Aaswath P. Raman. “Elucidating the Behavior of Nanophotonic Structures through Explainable Machine Learning Algorithms.” ACS Photonics 7 no. 8 (2020): 2309-2318. 10.1021/acsphotonics.0c01067.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Yeung et al., 2020, p. 2317)
Yi, Xiyu and Shimon Weiss. “Cusp-artifacts in high order superresolution optical fluctuation imaging.” Biomedical Optics Express 11 no. 2 (2020): 554-570. 10.1364/BOE.382296.
“Finally, we acknowledge the computational and storage services provided by the Hoffman2 Shared Cluster maintained by the Research Technology Group of the UCLA Institute for Digital Research and Education.” (Yi and Weiss, 2020, p. 569) PMID: 32206387 PMCID: PMC7041480
Yu, Q.; M. J. Simmonds; R. Doerner, and G. R. Tynan. “Understanding hydrogen retention in damaged tungsten using experimentally-guided models of complex multispecies evolution.” Nuclear Fusion 60 no. 9 (2020): 096003. 10.1088/1741-4326/ab9b3c.
“Computer time allocations at UCLA’s IDRE Hoffman2 supercomputer are gratefully acknowledged.” (Yu et al., 2020, p. 19)
Yu, Qianran; Michael Reyes; Nachiket Shah, and Jaime Marian. “Kinetic Model of Incipient Hydride Formation in Zr Clad under Dynamic Oxide Growth Conditions.” Materials 13 no. 5 (2020): 1088. 10.3390/ma13051088.
“This work was done using computer time allocations at UCLA’s IDRE Hoffman2 supercomputer.” (Yu et al., 2020, p. 15) PMID: 32121442 PMCID: PMC7084820
Zah, Eugenia; Eunwoo Nam; Vinya Bhuvan; Uyen Tran; Brenda Y. Ji; Stanley B. Gosliner; Xiuli Wang; Christine E. Brown, and Yvonne Y. Chen. “Systematically optimized BCMA/CS1 bispecific CAR-T cells robustly control heterogeneous multiple myeloma.” Nature Communications 11 no. 1 (2020): 2283. 10.1038/s41467-020-16160-5.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Zah et al., 2020, p. 13) Number: 1
Zeng, Tieqiang; Geng Sun; Changxi Miao; George Yan; Yingchun Ye; Weimin Yang, and Philippe Sautet. “Stabilizing Oxidative Dehydrogenation Active Sites at High Temperature with Steam: ZnFe2O4-Catalyzed Oxidative Dehydrogenation of 1-Butene to 1,3-Butadiene.” ACS Catalysis 10 no. 21 (2020): 12888-12897. 10.1021/acscatal.0c03405.
“The DFT calculations were performed on the HOFFMAN2 cluster at the UCLA Institute for Digital Research and Education (IDRE).” (Zeng et al., 2020, p. 17)
Zhang, Yichi; Yangyao Ding, and Panagiotis D. Christofides. “Multiscale computational fluid dynamics modeling and reactor design of plasma-enhanced atomic layer deposition.” Computers & Chemical Engineering 142 (2020): 107066. 10.1016/j.compchemeng.2020.107066.
“For the macroscopic domain, because of the high computational demand of the fine mesh and the volumetric reactions, 84 computing cores each equipped with 8 GB or 16 GB RAM on the UCLA hoffman2 cluster are used.” (Zhang et al., 2020, p. 10)
Zhang, Yichi; Yangyao Ding, and Panagiotis D. Christofides. “Integrating Feedback Control and Run-to-Run Control in Multi-Wafer Thermal Atomic Layer Deposition of Thin Films.” Processes 8 no. 1 (2020): 18. 10.3390/pr8010018.
“On the UCLA Hoffman2 Cluster, the parallel computation of the multiscale CFD model is implemented with the Message Passing Interface (MPI) [29].” (Zhang et al., 2020, p. 6)
Zhang, Zizhao; Weng Kee Wong, and Kay Chen Tan. “Competitive Swarm Optimizer with Mutated Agents for Finding Optimal Designs for Nonlinear Regression Models with Multiple Interacting Factors.” Memetic Computing 12 no. 3 (2020): 219-233. 10.1007/s12293-020-00305-6.
“All experiments were run on Hoffman2 shared cluster housed at the University of California at Los Angeles.” (Zhang et al., 2020, p. 8) PMID: 33747240 PMCID: PMC7968042
Zhao, Yue; Lucile Dezerald; Marta Pozuelo; Xinran Zhou, and Jaime Marian. “Simulating the mechanisms of serrated flow in interstitial alloys with atomic resolution over diffusive timescales.” Nature Communications 11 no. 1 (2020): 1227. 10.1038/s41467-020-15085-3.
“Computer time allocations at UCLA’s IDRE Hoffman2 supercomputer are acknowledged.” (Zhao et al., 2020, p. 7)
Zhao, Yujian; Weiming An; Xinlu Xu; Fei Li; Lance Hildebrand; Mark J. Hogan; Vitaly Yakimenko; Chan Joshi, and Warren B. Mori. “Emittance preservation through density ramp matching sections in a plasma wakefield accelerator.” Physical Review Accelerators and Beams 23 no. 1 (2020): 011302. 10.1103/PhysRevAccelBeams.23.011302.
“The simulations were run on Bluewaters, NERSC, and the UCLA Hoffman2 clusters.” (Zhao et al., 2020, p. 10)
Zink, Jon K.; Konstantin Batygin, and Fred C. Adams. “The Great Inequality and the Dynamical Disintegration of the Outer Solar System.” The Astronomical Journal 160 no. 5 (2020): 232. 10.3847/1538-3881/abb8de.
“The simulations described here were performed on the UCLA Hoffman2 shared computing cluster and used resources provided by the Bhaumik Institute.” (Zink et al., 2020, p. 9)
Zink, Jon K.; Kevin K. Hardegree-Ullman; Jessie L. Christiansen; Courtney D. Dressing; Ian J. M. Crossfield; Erik A. Petigura; Joshua E. Schlieder, and David R. Ciardi. “Scaling K2. II. Assembly of a Fully Automated C5 Planet Candidate Catalog Using EDI-Vetter.” The Astronomical Journal 159 no. 4 (2020): 154. 10.3847/1538-3881/ab7448.
“The simulations described here were performed on the UCLA Hoffman2 shared computing cluster and using the resources provided by the Bhaumik Institute.” (Zink et al., 2020, p. 21)
Zink, Jon K.; Kevin K. Hardegree-Ullman; Jessie L. Christiansen; Erik A. Petigura; Courtney D. Dressing; Joshua E. Schlieder; David R. Ciardi, and Ian J. M. Crossfield. “Scaling K2. III. Comparable Planet Occurrence in the FGK Samples of Campaign 5 and Kepler.” The Astronomical Journal 160 no. 2 (2020): 94. 10.3847/1538-3881/aba123.
“The simulations described here were performed on the UCLA Hoffman2 shared computing cluster and using the resources provided by the Bhaumik Institute.” (Zink et al., 2020, p. 12)
Zou, Yike; Jonathan J. Wong, and K. N. Houk. “Computational Exploration of a Redox-Neutral Organocatalytic Mitsunobu Reaction.” Journal of the American Chemical Society 142 no. 38 (2020): 16403-16408. 10.1021/jacs.0c07487.
“All calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI-1053575).” (Zou et al., 2020, p. 16407)
Zou, Yike; Song Yang; Jacob N. Sanders; Wei Li; Peiyuan Yu; Hongbo Wang; Zhijun Tang; Wen Liu, and K. N. Houk. “Computational Investigation of the Mechanism of Diels–Alderase PyrI4.” Journal of the American Chemical Society 142 no. 47 (2020): 20232-20239. 10.1021/jacs.0c10813.
“All calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI-1053575). ” (Zou et al., 2020, p. 20237)
Theses for 2020¶
Beichman, Annabel Carroll. “Aquatic Adaptation and Fur Trade Devastation: A Deep Dive into the Genomic History of the Sea Otter.” Ph.D. Thesis, University of California, Los Angeles, 2020. ProQuest, https://www.proquest.com/docview/2415863038.
“To the Hoffman2 team and Ray Yamauchi for technical expertise.” (Beichman, 2020, p. 14)
Madson, Austin. “Magnitudes, Mechanisms, and Effects from Large-Scale Lacustrine Changes.” Ph.D. Thesis, University of California, Los Angeles, 2020. ProQuest, https://www.proquest.com/docview/2488242228.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Madson, 2020, p. 69)
Nadel, Brian Benjamin. “Utilizing Gene Expression Data to Estimate Cell Type Abundances.” Ph.D. Thesis, University of California, Los Angeles, 2020. ProQuest, https://www.proquest.com/docview/2460759927.
“We installed and ran GEDIT, CIBERSORT, DeconRNASeq and dtangle on the hoffman2 computational cluster at UCLA.” (Nadel, 2020, p. 41)
Stephan, Alexander Patrick. “Stellar Evolution in Hierarchical Triples: Applications for Supermassive Black Holes and Exoplanets.” Ph.D. Thesis, University of California, Los Angeles, 2020. ProQuest, https://www.proquest.com/docview/2450182369.
“Calculations for this project were performed on the UCLA cluster Hoffman2.” (Stephan, 2020, p. 25)
Widmer, Devon Rose. “Local Solvent Environment Can Define Solute Chemical Identity, Dynamics, and Reactivity.” Thesis, UCLA, 2020. escholarship.org, https://escholarship.org/uc/item/6k11q2sc.
“I also gratefully acknowledge the Institute for Digital Research and Education (IDRE) at UCLA for use of the hoffman2 computing cluster.” (Widmer, 2020, p. xvii)
Xia, Yantao. “Thermodynamic Screening of Reaction Chemistries for Atomic Layer Etching of Metals.” M.S. Thesis, University of California, Los Angeles, 2020. ProQuest, https://www.proquest.com/docview/2419079346.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Gilman et al., 2020, p. 11)
Zhang, Zizhao. “Using Competitive Swarm Optimizer with Mutated Agents to Find Optimal Experimental Designs.” Ph.D. Thesis, University of California, Los Angeles, 2020. ProQuest, https://www.proquest.com/docview/2471484210.
“All tests are run on Hoffman2 shared cluster housed at the University of California, Los Angeles.” (Zhang, 2020, p. 44)
Reports for 2020¶
Ong, Paul; Andre Comandom; Nicholas DiRago, and Lauren Harper. “COVID-19 Impacts on Minority Businesses and Systemic Inequality.” UCLA: Center for Neighborhood Knowledge, 2020. https://escholarship.org/uc/item/5jz7c4vd.
“Computational and storage services associated with the Hoffman2 Shared Cluster were provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Ong et al., 2020, p. 3)
Newspaper Articles for 2020¶
Starr, Michelle. “Our Solar System Is Going to Totally Disintegrate Sooner Than We Thought.” 2020. https://www.sciencealert.com/our-solar-system-is-going-to-totally-disintegrate-sooner-than-we-thought.
With these additional influences accounted for in their calculations, the team ran 10 N-body simulations for the outer planets (leaving out Mars to save on computation costs, since its influence should be negligible), using the powerful Shared Hoffman2 Cluster.” (Starr, 2020) Section: space
Conference Papers for 2020¶
Zhang, Yichi; Yangyao Ding; Zhe Wu, and Panagiotis D. Christofides. “Run-to-Run Control of Thermal Atomic Layer Deposition.” In 2020 28th Mediterranean Conference on Control and Automation (MED): 2020 28th Mediterranean Conference on Control and Automation (MED) 2020: 1080-1086. 10.1109/MED48518.2020.9183059.
“to improve the computational efficiency, multiscale CFD computations are parallelized on the UCLA Hoffman2 Cluster with the Message Passing Interface (MPI)” (Zhang et al., 2020, p. 1082) ISSN: 2473-3504
2019¶
- 71 publications for 2019
Journal Articles for 2019¶
Alvarado, Andrew; Hsing-Yin Chang; Warren Nadvornick; Nasr Ghoniem, and Jaime Marian. “Monte Carlo raytracing method for calculating secondary electron emission from micro-architected surfaces.” Applied Surface Science 478 (2019): 142-149. 10.1016/j.apsusc.2019.01.089.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Alvarado et al., 2019, p. 149)
Aseev, N. A.; Y. Y. Shprits; D. Wang; J. Wygant; A. Y. Drozdov; A. C. Kellerman, and G. D. Reeves. “Transport and Loss of Ring Current Electrons Inside Geosynchronous Orbit During the 17 March 2013 Storm.” Journal of Geophysical Research: Space Physics 124 no. 2 (2019): 915-933. 10.1029/2018JA026031.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Aseev et al., 2019, p. 930)
Bertuzzi, Giulio; Mathias Kirk Thøgersen; Maxime Giardinetti; Andreu Vidal-Albalat; Adam Simon; K. N. Houk, and Karl Anker Jørgensen. “Catalytic Enantioselective Hetero-[6+4] and -[6+2] Cycloadditions for the Construction of Condensed Polycyclic Pyrroles, Imidazoles, and Pyrazoles.” Journal of the American Chemical Society 141 no. 7 (2019): 3288-3297. 10.1021/jacs.8b13659.
“This work used computational and storage resources associated with the Hoffman2 Shared Cluster provided by the UCLA Institute of Digital Research and Education (IDRE).” (Bertuzzi et al., 2019, p. 3296)
Cai, Yujuan; Yang Hai; Masao Ohashi; Cooper S. Jamieson; Marc Garcia-Borras; K. N. Houk; Jiahai Zhou, and Yi Tang. “Structural basis for stereoselective dehydration and hydrogen-bonding catalysis by the SAM-dependent pericyclase LepI.” Nature Chemistry 11 no. 9 (2019): 812-820. 10.1038/s41557-019-0294-x.
“The computational resources from the UCLA Institute of Digital Research and Education (IDRE) are acknowledged.” (Cai et al., 2019, p. 820)
Chen, Geoff C-F; Christopher D Fassnacht; Sherry H Suyu; Cristian E Rusu; James H H Chan; Kenneth C Wong; Matthew W Auger; Stefan Hilbert; Vivien Bonvin; Simon Birrer; Martin Millon; Léon V E Koopmans; David J Lagattuta; John P McKean; Simona Vegetti; Frederic Courbin; Xuheng Ding; Aleksi Halkola; Inh Jee; Anowar J Shajib; Dominique Sluse; Alessandro Sonnenfeld, and Tommaso Treu. “A SHARP view of H0LiCOW: H0 from three time-delay gravitational lens systems with adaptive optics imaging.” Monthly Notices of the Royal Astronomical Society 490 no. 2 (2019): 1743-1773. 10.1093/mnras/stz2547.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Chen et al., 2019, p. 1767)
Chen, Maggie; Cyndi Qixin He, and K. N. Houk. “Mechanism and Regioselectivity of an Unsymmetrical Hexadehydro-Diels–Alder (HDDA) Reaction.” The Journal of Organic Chemistry 84 no. 4 (2019): 1959-1963. 10.1021/acs.joc.8b02865.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Chen et al., 2019, p. 1962)
Chen, Qibin; Jie Gao; Cooper Jamieson; Jiawang Liu; Masao Ohashi; Jian Bai; Daojian Yan; Bingyu Liu; Yongsheng Che; Yanan Wang; K. N. Houk, and Youcai Hu. “Enzymatic Intermolecular Hetero-Diels–Alder Reaction in the Biosynthesis of Tropolonic Sesquiterpenes.” Journal of the American Chemical Society 141 no. 36 (2019): 14052-14056. 10.1021/jacs.9b06592.
“The UCLA Institute of Digital Research and Education (IDRE) provided computational resources for all calculations.” (Chen et al., 2019, p. 14055)
Chen, Shuming; Amy Y. Chan; Morgan M. Walker; Jonathan A. Ellman, and K. N. Houk. “π-Facial Selectivities in Hydride Reductions of Hindered Endocyclic Iminium Ions.” The Journal of Organic Chemistry 84 no. 1 (2019): 273-281. 10.1021/acs.joc.8b02603.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI1053575).” (Chen et al., 2019, p. 280)
Dan, Qingyun; Sean A. Newmister; Kimberly R. Klas; Amy E. Fraley; Timothy J. McAfoos; Amber D. Somoza; James D. Sunderhaus; Ying Ye; Vikram V. Shende; Fengan Yu; Jacob N. Sanders; W. Clay Brown; Le Zhao; Robert S. Paton; K. N. Houk; Janet L. Smith; David H. Sherman, and Robert M. Williams. “Fungal indole alkaloid biogenesis through evolution of a bifunctional reductase/Diels–Alderase.” Nature Chemistry 11 no. 11 (2019): 972-980. 10.1038/s41557-019-0326-6.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575)” (Dan et al., 2019, p. 980)
Darzi, Evan R.; Joyann S. Barber, and Neil K. Garg. “Cyclic Alkyne Approach to Heteroatom-Containing Polycyclic Aromatic Hydrocarbon Scaffolds.” Angewandte Chemie 131 no. 28 (2019): 9519-9524. 10.1002/ange.201903060.
“This work used computational and storage services associated with theHoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Educations Research Technology Group.” (Darzi et al., 2019, p. 9523)
Dobynde, M. I.; F. Effenberger; D. A. Kartashov; Y. Y. Shprits, and V. A. Shurshakov. “Ray-tracing simulation of the radiation dose distribution on the surface of the spherical phantom of the MATROSHKA-R experiment onboard the ISS.” Life Sciences in Space Research 21 (2019): 65-72. 10.1016/j.lssr.2019.04.001.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA’s Institute for Digital Research and Education’s Research Technology Group.” (Dobynde et al., 2019, p. 71)
Fan, Hang; Huan Wu; Lucas Lindsay, and Yongjie Hu. “Ab initio investigation of single-layer high thermal conductivity boron compounds.” Physical Review B 100 no. 8 (2019): 085420. 10.1103/PhysRevB.100.085420.
“This work used computational and storage services associated with the Hoffman 2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by NSF Grant No. ACI1548562.” (Fan et al., 2019, p. 10)
Fuller, J; TR Wilson; ME Eberhart, and AN Alexandrova. “Charge Density in Enzyme Active Site as a Descriptor of Electrostatic Preorganization.” JOURNAL OF CHEMICAL INFORMATION AND MODELING 59 no. 5 (2019): 2367-2373. 10.1021/acs.jcim.8b00958.
“We also acknowledge the UCLA-IDRE cluster Hoffman2 for computational resources.” (Fuller et al., 2019, p. 16)
Gilman, Daniel; Simon Birrer; Tommaso Treu; Anna Nierenberg, and Andrew Benson. “Probing dark matter structure down to 107 solar masses: flux ratio statistics in gravitational lenses with line-of-sight haloes.” Monthly Notices of the Royal Astronomical Society 487 no. 4 (2019): 5721-5738. 10.1093/mnras/stz1593.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Gilman et al., 2019, p. 5734)
Hamlin, Trevor A.; Brian J. Levandowski; Ayush K. Narsaria; Kendall N. Houk, and F. Matthias Bickelhaupt. “Structural Distortion of Cycloalkynes Influences Cycloaddition Rates both by Strain and Interaction Energies.” Chemistry – A European Journal 25 no. 25 (2019): 6342-6348. 10.1002/chem.201900295.
“We thank SURFsara for use of the Cartesius supercomputer and UCLA Institute for Digital Research and Education (IDRE) for use of the Hoffman2 supercomputer.” (Hamlin et al., 2019, p. 6347)
Hardy, Anthony J.; Erin Angel; Maryam Bostani; Chris Cagnon, and Michael McNitt-Gray. “Estimating fetal dose from tube current-modulated (TCM) and fixed tube current (FTC) abdominal/pelvis CT examinations.” Medical Physics 46 no. 6 (2019): 2729-2743. 10.1002/mp.13499.
“This work used the computational and storage services of the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Hardy et al., 2019, p. 2731)
Hardy, Anthony J.; Maryam Bostani; Andrew M. Hernandez; Maria Zankl; Cynthia McCollough; Chris Cagnon; John M. Boone, and Michael McNitt-Gray. “Estimating a size-specific dose for helical head CT examinations using Monte Carlo simulation methods.” Medical Physics 46 no. 2 (2019): 902-912. 10.1002/mp.13301.
“This study used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Hardy et al., 2019, p. 905)
He, S.; E. Overly; V. Bulatov; J. Marian, and D. Cereceda. “Coupling 2D atomistic information to 3D kink-pair enthalpy models of screw dislocations in bcc metals.” Physical Review Materials 3 no. 10 (2019): 103603. 10.1103/PhysRevMaterials.3.103603.
“Computer time allocations at UCLA’s IDRE Hoffman2 supercomputer are acknowledged.” (He et al., 2019, p. 12)
Huang, Shu and Jaime Marian. “Rates of diffusion controlled reactions for one-dimensionally-moving species in 3D space.” Philosophical Magazine 99 no. 20 (2019): 2562-2583. 10.1080/14786435.2019.1635721.
“Computer time allocations at UCLA’s IDRE Hoffman2 supercomputer are acknowledged.” (Huang and Marian, 2019, p. 2579)
Huang, Xiongyi; Marc Garcia-Borràs; Kun Miao; S. B. Jennifer Kan; Arjun Zutshi; K. N. Houk, and Frances H. Arnold. “A Biocatalytic Platform for Synthesis of Chiral α-Trifluoromethylated Organoborons.” ACS Central Science 5 no. 2 (2019): 270-276. 10.1021/acscentsci.8b00679.
“Computational resources were provided by the University of California, Los Angeles Institute for Digital Research and Education and the Extreme Science and Engineering Discovery Environment, which is supported by National Science Foundation Grant OCI-1053575.” (Huang et al., 2019, p. 274)
Jimenez, Amy M.; Philipp Riedel; Junghee Lee; Eric A. Reavis, and Michael F. Green. “Linking resting-state networks and social cognition in schizophrenia and bipolar disorder.” Human Brain Mapping 40 no. 16 (2019): 4703-4715. 10.1002/hbm.24731.
“fMRI data analysis for this study used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Jimenez et al., 2019, p. 4712)
Kang, K; J Fuller; AH Reath; J Ziller; A Alexandrova, and JY Yang. “Installation of internal electric fields by non-redox active cations in transition metal complexes.” CHEMICAL SCIENCE 10 no. 43 (2019): 10135-10142. 10.1039/c9sc02870f.
“Calculations were performed on the UCLA IDRE shared computer cluster, Hoffman2.” (Kang et al., 2019, p. 7) Publication Title: Chemical …
Krysan, Kostyantyn; Linh M. Tran; Brandon S. Grimes; Gregory A. Fishbein; Atsuko Seki; Brian K. Gardner; Tonya C. Walser; Ramin Salehi-Rad; Jane Yanagawa; Jay M. Lee; Sherven Sharma; Denise R. Aberle; Arum E. Spira; David A. Elashoff; William D. Wallace; Michael C. Fishbein, and Steven M. Dubinett. “The Immune Contexture Associates with the Genomic Landscape in Lung Adenomatous Premalignancy.” Cancer Research 79 no. 19 (2019): 5022-5033. 10.1158/0008-5472.CAN-19-0153.
“The authors thank Drs. Antoni Ribas and Siwen Hu-Lieskovan for assistance with the HALO system, Lauren Winter for administrative support, Francis Rosen for clinical coordination, the UCLA Jonsson Comprehensive Cancer Center for shared resources, the UCLA CNSI Advanced Light Microscopy/Spectroscopy Facility, and the UCLA Institute for Digital Research and Education for providing the Hoffman2 Cluster.” (Krysan et al., 2019, p. 5032)
Lee, Junghee; Amy M. Jimenez; William P. Horan, and Michael F. Green. “fMRI biomarkers of social cognitive skills training in psychosis: Extrinsic and intrinsic functional connectivity.” PLOS ONE 14 no. 5 (2019): e0214303. 10.1371/journal.pone.0214303.
“fMRI data analysis for this study used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group” (Lee et al., 2019, p. 2)
Lee, Junghee; Eric A. Reavis; Stephen A. Engel; Lori L. Altshuler; Mark S. Cohen; David C. Glahn; Keith H. Nuechterlein; Jonathan K. Wynn, and Michael F. Green. “fMRI evidence of aberrant neural adaptation for objects in schizophrenia and bipolar disorder.” Human Brain Mapping 40 no. 5 (2019): 1608-1617. 10.1002/hbm.24472.
“fMRI data analysis for this study used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Lee et al., 2019, p. 1615)
Levandowski, Brian J.; Nile S. Abularrage; K. N. Houk, and Ronald T. Raines. “Hyperconjugative Antiaromaticity Activates 4H-Pyrazoles as Inverse-Electron-Demand Diels–Alder Dienes.” Organic Letters 21 no. 20 (2019): 8492-8495. 10.1021/acs.orglett.9b03351.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE)” (Levandowski et al., 2019, p. 3)
Levandowski, Brian J.; Trevor A. Hamlin; Hannah J. Eckvahl; F. Matthias Bickelhaupt, and K. N. Houk. “Diels-Alder reactivities of cycloalkenediones with tetrazine.” Journal of Molecular Modeling 25 no. 2 (2019): 33. 10.1007/s00894-018-3909-z.
“Computer time was provided by the UCLA Institute for Digital Research and Education (IDRE) on the Hoffman2 supercomputer.” (Levandowski et al., 2019, p. 5)
Levandowski, Brian J.; Ronald T. Raines, and K. N. Houk. “Hyperconjugative π → σ*CF Interactions Stabilize the Enol Form of Perfluorinated Cyclic Keto–Enol Systems.” The Journal of Organic Chemistry 84 no. 10 (2019): 6432-6436. 10.1021/acs.joc.9b00825.
“The computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE).” (Levandowski et al., 2019, p. 6436)
Levandowski, Brian J.; Dennis Svatunek; Barbara Sohr; Hannes Mikula, and K. N. Houk. “Secondary Orbital Interactions Enhance the Reactivity of Alkynes in Diels–Alder Cycloadditions.” Journal of the American Chemical Society 141 no. 6 (2019): 2224-2227. 10.1021/jacs.8b13088.
“Computer time was provided by the UCLA Institute for Digital Research and Education (IDRE).” (Levandowski et al., 2019, p. 2226)
Li, Mufan; Kaining Duanmu; Chengzhang Wan; Tao Cheng; Liang Zhang; Sheng Dai; Wenxin Chen; Zipeng Zhao; Peng Li; Huilong Fei; Yuanming Zhu; Rong Yu; Jun Luo; Ketao Zang; Zhaoyang Lin; Mengning Ding; Jin Huang; Hongtao Sun; Jinghua Guo; Xiaoqing Pan; William A. Goddard; Philippe Sautet; Yu Huang, and Xiangfeng Duan. “Single-atom tailoring of platinum nanocatalysts for high-performance multifunctional electrocatalysis.” Nature Catalysis 2 no. 6 (2019): 495-503. 10.1038/s41929-019-0279-6.
“The calculations were performed on the Hoffman2 cluster at UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (grant no. ACI‐1053575).” (Li et al., 2019, p. 503)
Lin, Janice B.; Evan R. Darzi; Ramesh Jasti; Ilhan Yavuz, and K. N. Houk. “Solid-State Order and Charge Mobility in [5]- to [12]Cycloparaphenylenes.” Journal of the American Chemical Society 141 no. 2 (2019): 952-960. 10.1021/jacs.8b10699.
“Calculations were performed on the Hoffman2 cluster provided by the UCLA Institute of Digital Research and Education’s Research Technology Group and SIMULAB in the Physics Department of Marmara University and also on the NSF-supported Extreme Science and Engineering Discovery Environment (XSEDE)’s Gordon supercomputer (OCI1053575) at the San Diego Supercomputing Center.” (Lin et al., 2019, p. 958)
Liu, Ji-Yuan; Xue-Qing Gong, and Anastassia N. Alexandrova. “Mechanism of CO2 Photocatalytic Reduction to Methane and Methanol on Defected Anatase TiO2 (101): A Density Functional Theory Study.” The Journal of Physical Chemistry C 123 no. 6 (2019): 3505-3511. 10.1021/acs.jpcc.8b09539.
“Computer time was provided by the UCLA Institute for Digital Research and Education (IDRE).” (Wheeler and Houk, 2010, p. 8664)
Machovina, Melodie M.; Sam J. B. Mallinson; Brandon C. Knott; Alexander W. Meyers; Marc Garcia-Borràs; Lintao Bu; Japheth E. Gado; April Oliver; Graham P. Schmidt; Daniel J. Hinchen; Michael F. Crowley; Christopher W. Johnson; Ellen L. Neidle; Christina M. Payne; Kendall N. Houk; Gregg T. Beckham; John E. McGeehan, and Jennifer L. DuBois. “Enabling microbial syringol conversion through structure-guided protein engineering.” Proceedings of the National Academy of Sciences 116 no. 28 (2019): 13970-13976. 10.1073/pnas.1820001116.
“Computer time was provided by Extreme Science and Engineering Discovery Environment, supported by NSF Grant ACI-1548562 via allocation MCB-090159 to G.T.B. at the Pittsburgh Supercomputing Center (Bridges) and the Texas Advanced Computing Center (Stampede2), by the National Renewable Energy Laboratory Computational Sciences Center supported by the DOE Office of EERE under Contract DE-AC36-08GO28308, and by the UCLA Institute for Digital Research and Education.” (Machovina et al., 2019, p. 13976)
Miao, Yu; Nicholas W. Johnson; Phillip B. Gedalanga; David Adamson; Charles Newell, and Shaily Mahendra. “Response and recovery of microbial communities subjected to oxidative and biological treatments of 1,4-dioxane and co-contaminants.” Water Research 149 (2019): 74-85. 10.1016/j.watres.2018.10.070.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Miao et al., 2019, p. 83)
Mirocha, Jordan and Steven R Furlanetto. “What does the first highly redshifted 21-cm detection tell us about early galaxies?.” Monthly Notices of the Royal Astronomical Society 483 no. 2 (2019): 1980-1992. 10.1093/mnras/sty3260.
“This work used computational and storage services associated with the HOFFMAN2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group, and relied on the Python packages NUMPY12 (Oliphant 2007)andMATPLOTLIB13 (Hunter 2007).” (Mirocha and Furlanetto, 2019, p. 1991)
Montoya, Dennis J.; Priscila Andrade; Bruno J. A. Silva; Rosane M. B. Teles; Feiyang Ma; Bryan Bryson; Saheli Sadanand; Teia Noel; Jing Lu; Euzenir Sarno; Kristine B. Arnvig; Douglas Young; Ramanuj Lahiri; Diana L. Williams; Sarah Fortune; Barry R. Bloom; Matteo Pellegrini, and Robert L. Modlin. “Dual RNA-Seq of Human Leprosy Lesions Identifies Bacterial Determinants Linked to Host Immune Response.” Cell Reports 26 no. 13 (2019): 3574-3585.e3. 10.1016/j.celrep.2019.02.109.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Montoya et al., 2019, p. 3583) PMID: 30917313 PMCID: PMC6508871
Moore, Lucas C.; Anna Lo; Jason S. Fell; Matthew R. Duong; Jose A. Moreno; Barry E. Rich; Martin Bravo; James C. Fettinger; Lucas W. Souza; Marilyn M. Olmstead; Kendall N. Houk, and Jared T. Shaw. “Acyclic Stereocontrol in the Additions of Nucleophilic Alkenes to α-Chiral N-Sulfonyl Imines.” Chemistry – A European Journal 25 no. 52 (2019): 12214-12220. 10.1002/chem.201902790.
“J.S.F. acknowledges the computational resources provided by UCLA Institute for Digital Research and Education and the National Science Foundation through XSEDE Science Gateways Program(TG-CHE0 40013N).” (Moore et al., 2019, p. 12219)
Ni, Feng; Arunika Ekanayake; Bianca Espinosa; Caiqun Yu; Jacob N. Sanders; John Perino; K. N. Houk, and Chao Zhang. “Synthesis and Target Identification of a Novel Electrophilic Warhead, 2-Chloromethylquinoline.” Biochemistry 58 no. 24 (2019): 2715-2719. 10.1021/acs.biochem.9b00359.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE).” (Ni et al., 2019, p. 2718)
Reilley, David J.; Konstantin I. Popov; Nikolay V. Dokholyan, and Anastassia N. Alexandrova. “Uncovered Dynamic Coupling Resolves the Ambiguous Mechanism of Phenylalanine Hydroxylase Oxygen Binding.” The Journal of Physical Chemistry B 123 no. 21 (2019): 4534-4539. 10.1021/acs.jpcb.9b02893.
“The authors thank the Institute for Digital Research and Education at UCLA for supercomputer time and NSF CAREER grant NSF-CHE-1351968 to A.N.A..” (Reilley et al., 2019, p. 4539)
Riedel, Benedikt; Lincoln Bryant; John Carlstrom; Thomas Crawford; Robert W. Gardner; Nicholas Harrington; Nicholas Huang; Alexandra Rahlin; Judith Stephen, and Nathan Whitehorn. “SPT-3G Computing.” EPJ Web of Conferences 214 (2019): 03051. 10.1051/epjconf/201921403051.
“In production, we have connected the Hoffman2 [20] cluster at University of California, Los Angeles to the SPT resource pool.” (Riedel et al., 2019, p. 5)
Rivera, Jared; Jonathan Berjikian; R. Ravinder; Hariprasad Kodamana; Sumanta Das; Naresh Bhatnagar; Mathieu Bauchy, and N. M. Anoop Krishnan. “Glass Fracture Upon Ballistic Impact: New Insights From Peridynamics Simulations.” Frontiers in Materials 6 (2019). 10.3389/fmats.2019.00239.
“The authors thank the UCLA Institute for Digital Research and Education’s Research Technology Group and the IIT Delhi HPC facility for providing the computational and storage resources.” (Rivera et al., 2019, p. 10)
Salas, Jesus M; Smadar Naoz; Mark R Morris, and Alexander P Stephan. “Unseen companions of V Hya inferred from periodic ejections.” Monthly Notices of the Royal Astronomical Society 487 no. 3 (2019): 3029-3036. 10.1093/mnras/stz1515.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Salas et al., 2019, p. 3036)
Sun, Geng; Anastassia N. Alexandrova, and Philippe Sautet. “Pt8 cluster on alumina under a pressure of hydrogen: Support-dependent reconstruction from first-principles global optimization.” The Journal of Chemical Physics 151 no. 19 (2019): 194703. 10.1063/1.5129296.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Sun et al., 2019, p. 14)
Sun, Geng and Philippe Sautet. “Toward Fast and Reliable Potential Energy Surfaces for Metallic Pt Clusters by Hierarchical Delta Neural Networks.” Journal of Chemical Theory and Computation 15 no. 10 (2019): 5614-5627. 10.1021/acs.jctc.9b00465.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Sun and Sautet, 2019, p. 29) PMID: 31465216
Svatunek, D and KN Houk. “autoDIAS: a python tool for an automated distortion/interaction activation strain analysis.” JOURNAL OF COMPUTATIONAL CHEMISTRY 40 no. 28 (2019): 2509-2515. 10.1002/jcc.26023.
“Computer time at Hoffman2 was provided by the UCLA Institute for Digital Research and Education (IDRE).” (Svatunek and Houk, 2019, p. 2514)
Tan, Dan; Cooper S. Jamieson; Masao Ohashi; Man-Cheng Tang; K. N. Houk, and Yi Tang. “Genome-Mined Diels–Alderase Catalyzes Formation of the cis-Octahydrodecalins of Varicidin A and B.” Journal of the American Chemical Society 141 no. 2 (2019): 769-773. 10.1021/jacs.8b12010.
“The computational resources from the UCLA Institute of Digital Research and Education (IDRE) are gratefully acknowledged.” (Tan et al., 2019, p. 772)
Tang, Yan; Chithra Asokan; Mingjie Xu; George W. Graham; Xiaoqing Pan; Phillip Christopher; Jun Li, and Philippe Sautet. “Rh single atoms on TiO2 dynamically respond to reaction conditions by adapting their site.” Nature Communications 10 no. 1 (2019): 4488. 10.1038/s41467-019-12461-6.
“The calculations were performed at the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group as well as partially at Tsinghua National Laboratory for Information Science and Technology.” (Tang et al., 2019, p. 9)
Vafaei-Najafabadi, N.; L. D. Amorim; E. Adli; W. An; C. I. Clarke; C. E. Clayton; S. Corde; S. Gessner; S. Z. Green; M. J. Hogan; C. Joshi; O. Kononenko; C. A. Lindstrøm; M. Litos; W. Lu; K. A. Marsh; W. B. Mori; P. San Miguel Claveria; B. O’Shea; G. Raj; D. Storey; G. White; Xinlu Xu, and V. Yakimenko. “Producing multi-coloured bunches through beam-induced ionization injection in plasma wakefield accelerator.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 377 no. 2151 (2019): 20180184. 10.1098/rsta.2018.0184.
“Simulations were performed on the UCLA Hoffman2 cluster through NSF OCI-1036224.” (Vafaei-Najafabadi et al., 2019, p. 12)
van Spronsen, Matthijs A.; Kaining Daunmu; Christopher R. O’Connor; Tobias Egle; Heath Kersell; Judit Oliver-Meseguer; Miquel B. Salmeron; Robert J. Madix; Philippe Sautet, and Cynthia M. Friend. “Dynamics of Surface Alloys: Rearrangement of Pd/Ag(111) Induced by CO and O2.” The Journal of Physical Chemistry C 123 no. 13 (2019): 8312-8323. 10.1021/acs.jpcc.8b08849.
“The DFT calculations were performed on the HOFFMAN2 cluster at the UCLA Institute for Digital Research and Education (IDRE), and computing resources at Extreme Science and Engineering Discovery Environment (XSEDE) through the allocation CHE170060.” (Spronsen et al., 2019, p. 8321)
Wang, Rui; Jingjing Xue; Kai-Li Wang; Zhao-Kui Wang; Yanqi Luo; David Fenning; Guangwei Xu; Selbi Nuryyeva; Tianyi Huang; Yepin Zhao; Jonathan Lee Yang; Jiahui Zhu; Minhuan Wang; Shaun Tan; Ilhan Yavuz; Kendall N. Houk, and Yang Yang. “Constructive molecular configurations for surface-defect passivation of perovskite photovoltaics.” Science 366 no. 6472 (2019): 1509-1513. 10.1126/science.aay9698.
“Computer time was provided by the UCLA Institute for Digital Research and Education (IDRE).” (Wang et al., 2019, p. 5)
Wang, YB; PY Yu; ZP Zhou; J Zhang; J Wang; SH Luo; QS Gu; KN Houk, and B Tan. “Rational design, enantioselective synthesis and catalytic applications of axially chiral EBINOLs.” NATURE CATALYSIS 2 no. 6 (2019): 504-513. 10.1038/s41929-019-0278-7.
“P.Y. and K.N.H. acknowledge computational resources provided by the Institute of Digital Research and Education (IDRE) at UCLA and by the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Wang et al., 2019, p. 513)
Weidl, Martin S.; Dan Winske, and Christoph Niemann. “Three Regimes and Four Modes for the Resonant Saturation of Parallel Ion-beam Instabilities.” The Astrophysical Journal 873 no. 1 (2019): 57. 10.3847/1538-4357/ab0462.
“Several computations were performed on the Hoffman2 cluster at UCLA and made possible by the BhaumikCenter for Theoretical Physics;” (Weidl et al., 2019, p. 16)
Yamano, Michael M.; Rachel R. Knapp; Aurapat Ngamnithiporn; Melissa Ramirez; Kendall N. Houk; Brian M. Stoltz, and Neil K. Garg. “Cycloadditions of Oxacyclic Allenes and a Catalytic Asymmetric Entryway to Enantioenriched Cyclic Allenes.” Angewandte Chemie 131 no. 17 (2019): 5709-5713. 10.1002/ange.201900503.
“This study used computational and storage services associated with theHoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Educations Research Technology Group.” (Yamano et al., 2019, p. 5712)
Yan, G and P Sautet. “Surface Structure of Co3O4 (111) under Reactive Gas-Phase Environments.” ACS CATALYSIS 9 no. 7 (2019): 6380-6392. 10.1021/acscatal.9b01485.
“The calculations in this work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA’s Institute for Digital Research and Education Group (IDRE).” (Yan and Sautet, 2019, p. 36)
Yan, G; T Wähler; R Schuster; M Schwarz; C Hohner; K Werner; J Libuda, and P Sautet. “Water on Oxide Surfaces: A Triaqua Surface Coordination Complex on Co3O4(111).” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 141 no. 14 (2019): 5623-5627. 10.1021/jacs.9b00898.
“The calculations in this work used computational and storage services associated with the Hoffman2 shared computational cluster located at UCLA, provided by UCLA’s Institute for Digital Research and Education Group (IDRE).” (Yan et al., 2019, p. 6)
Yavuz, Ilhan; Janice B. Lin, and K. N. Houk. “Impact of morphology, side-chains, and crystallinity on charge-transport properties of π-extended double helicenes.” Physical Chemistry Chemical Physics 21 no. 2 (2019): 901-914. 10.1039/C8CP06982D.
“Calculations were performed on the Hoffman2 cluster provided by the UCLA Institute of Digital Research and Education’s Research Technology Group and on the NSF-supported Extreme Science and Engineering Discovery Environment (XSEDE)’s Gordon supercomputer (OCI-1053575) at the San Diego Supercomputing Center.” (Yavuz et al., 2019, p. 14)
Young, Maria-Elena De Trinidad; Gabriela Leon-Perez; Christine R. Wells, and Steven P. Wallace. “Inclusive state immigrant policies and health insurance among Latino, Asian/Pacific Islander, Black, and White noncitizens in the United States.” Ethnicity & Health 24 no. 8 (2019): 960-972. 10.1080/13557858.2017.1390074.
“We conducted analysis with Stata 14 software, using the commands for survey design, through the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group and the California Center for Population Research.” (Young et al., 2019, p. 965)
Yu, Yanmin; Zhongyue Yang, and K. N. Houk. “Molecular dynamics of the intramolecular 1, 3-dipolar ene reaction of a nitrile oxide and an alkene: non-statistical behavior of a reaction involving a diradical intermediate*.” Molecular Physics 117 no. 9-12 (2019): 1360-1366. 10.1080/00268976.2018.1549338.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Yu et al., 2019, p. 1365)
Zhang, Bin; Geng Sun; Shipeng Ding; Hiroyuki Asakura; Jia Zhang; Philippe Sautet, and Ning Yan. “Atomically Dispersed Pt1–Polyoxometalate Catalysts: How Does Metal–Support Interaction Affect Stability and Hydrogenation Activity?.” Journal of the American Chemical Society 141 no. 20 (2019): 8185-8197. 10.1021/jacs.9b00486.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Zhang et al., 2019, p. 8195)
Zhang, Zhuan; Cooper S. Jamieson; Yi-Lei Zhao; Dehai Li; Masao Ohashi; K. N. Houk, and Yi Tang. “Enzyme-Catalyzed Inverse-Electron Demand Diels–Alder Reaction in the Biosynthesis of Antifungal Ilicicolin H.” Journal of the American Chemical Society 141 no. 14 (2019): 5659-5663. 10.1021/jacs.9b02204.
“The UCLA Institute of Digital Research and Education (IDRE) provided computational resources for all calculations.” (Zhang et al., 2019, p. 5662)
Zhao, Yue; Lucile Dezerald, and Jaime Marian. “Electronic Structure Calculations of Oxygen Atom Transport Energetics in the Presence of Screw Dislocations in Tungsten.” Metals 9 no. 2 (2019): 252. 10.3390/met9020252.
“Computer time allocations at UCLA’s IDRE Hoffman2 supercomputer are acknowledged.” (Zhao et al., 2019, p. 11) Number: 2
Zou, Yike; Xiao-Song Xue; Yifan Deng; Amos B. III Smith, and K. N. Houk. “Factors Controlling Reactivity in the Hydrogen Atom Transfer and Radical Addition Steps of a Radical Relay Cascade.” Organic Letters 21 no. 15 (2019): 5894-5897. 10.1021/acs.orglett.9b02023.
“Computation time was provided by the UCLA Institute for Digital Research and Education (IDRE).” (Zou et al., 2019, p. 5897)
Theses for 2019¶
Arneson, Douglas Victor. “Development and Application of Systems Genomics Approaches to Dissect Complex Diseases.” Ph.D. Thesis, University of California, Los Angeles, 2019. ProQuest, https://www.proquest.com/docview/2320971412.
“The Mergeomics web server is hosted within UCLA’s Hoffman2 High Performance Cluster as part of the Institute for Digital Research and Education (IDRE), and jobs are submitted using the Sun Grid Engine queuing system.” (Arneson, 2019, p. 30)
Chang, Hsing-Yin. “Computational Modeling of Plasma-Induced Secondary Electron Emission from Micro-Architected Surfaces.” Ph.D. Thesis, University of California, Los Angeles, 2019. ProQuest, https://www.proquest.com/docview/2203048309.
“This is for Intel Xeon E5-2650v4 CPUs installed on the hoffman2 cluster at UCLA” (Chang, p. 78)
Mccraney, William Tyler. “Phylogeny and Divergence Times of Gobiarian Fishes.” Thesis, UCLA, 2019. escholarship.org, https://escholarship.org/uc/item/19m3p095.
“We are grateful to Jonathan Chang and Francesco Santini for providing technical advice. Computational and storage services associated with the Hoffman2 Shared Cluster were provided by UCLA Institute for Digital Research and Education Research Technology Group.” (Mccraney, 2019, p. 44)
Messina, Marco Stefano. “Developing Inorganic Approaches to Polymerization and Bioconjugation.” Ph.D. Thesis, University of California, Los Angeles, 2019. ProQuest, https://www.proquest.com/docview/2307785577.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Messina, 2019, p. 67)
Rhodes, Tyler James. “Numerical Study of 3D Magnetohydrodynamic Flows Towards Liquid Metal Blankets, Including Complex Geometry and Buoyancy Effects.” Ph.D. Thesis, University of California, Los Angeles, 2019. ProQuest, https://www.proquest.com/docview/2288064777.
“The numerical efforts in Part I of this research used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Rhodes, 2019, p. 34)
Tableman, Adam Ryan. “Kinetic Plasma Simulation: Meeting the Demands of Increased Complexity.” Ph.D. Thesis, University of California, Los Angeles, 2019. ProQuest, https://www.proquest.com/docview/2203022826.
“Simulations were performed at the Hoffman2 cluster in UCLA. We also acknowledge useful discussions with Dr. B. Reville.” (Tableman, 2019, p. 18)
Zhai, Huanchen. “Potential Energy Surface Exploration of Metal Catalytic Clusters.” Ph.D. Thesis, University of California, Los Angeles, 2019. ProQuest, https://www.proquest.com/docview/2341560801.
“My research would be impossible without the funding from Air Force Office of Scientific Research, the computational resources from Department of Defense High Performance Computing Modernization Program (HPCMP), Extreme Science and Engineering Discovery Environment (XSEDE), and UCLA IDRE.” (Zhai, 2019, pp. -)
Zhao, Yue. “Modeling Solute-Dislocation Interactions in Body-Centered Cubic Alloys Using Kinetic Monte Carlo Simulations.” Thesis, UCLA, 2019. escholarship.org, https://escholarship.org/uc/item/6c03j98n.
“Computer time allocations at UCLAs IDRE Hoffman2 supercomputer are acknowledged.” (Zhao, 2019, p. xv)
Conference Papers for 2019¶
Yi, Xiyu; Rafael Piestun, and Shimon Weiss. “3D super-resolution imaging using a generalized and scalable progressive refinement method on sparse recovery (PRIS).” In Single Molecule Spectroscopy and Superresolution Imaging XII: Single Molecule Spectroscopy and Superresolution Imaging XII San Francisco, California, United States, 2019: 1088406. 10.1117/12.2506827.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Yi et al., 2019, p. 11)
2018¶
Journal Articles for 2018¶
Admal, N. C.; G. Po, and J. Marian. “A unified framework for polycrystal plasticity with grain boundary evolution.” International Journal of Plasticity 106 no. 1 (2018): 1-30. 10.1016/j.ijplas.2018.01.014.
“Computer time allocations at UCLA’s IDRE Hoffman2 supercomputer are acknowledged.” (Admal et al., 2018, p. 24)
Ahmed, Tonia S.; Jessica M. Grandner; Buck L. H. Taylor; Myles B. Herbert; K. N. Houk, and Robert H. Grubbs. “Metathesis and Decomposition of Fischer Carbenes of Cyclometalated Z-Selective Ruthenium Metathesis Catalysts.” Organometallics 37 no. 14 (2018): 2212-2216. 10.1021/acs.organomet.8b00150.
“Calculations were performed using the NSF funded (OCI-1053575) Extreme Science and Engineering Discovery Environment (XSEDE), the UCLA IDRE Hoffman2 Cluster, and the ONR supported Copper Cluster.” (Ahmed et al., 2018, p. 2215)
Baldo, Elisabeth and Steven A. Margulis. “Assessment of a multiresolution snow reanalysis framework: a multidecadal reanalysis case over the upper Yampa River basin, Colorado.” Hydrology and Earth System Sciences 22 no. 7 (2018): 3575-3587. 10.5194/hess-22-3575-2018.
“All simulations were performed by using computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Baldo and Margulis, 2018, p. 3585)
Barber, JS; MM Yamano; M Ramirez; ER Darzi; RR Knapp; F Liu; KN Houk, and NK Garg. “Diels-Alder cycloadditions of strained azacyclic allenes.” NATURE CHEMISTRY 10 no. 9 (2018): 953-960. 10.1038/s41557-018-0080-1.
“Computations were performed with resources made available from the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575), as well as the UCLA Institute of Digital Research and Education (IDRE).” (Barber et al., 2018, p. 959)
Bay, Katherine L.; Yun-Fang Yang, and K. N. Houk. “Computational Exploration of a Pd(II)-Catalyzed γ-C–H Arylation Where Stereoselectivity Arises from Attractive Aryl–Aryl Interactions.” The Journal of Organic Chemistry 83 no. 23 (2018): 14786-14790. 10.1021/acs.joc.8b02416.
“Computations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Bay et al., 2018, p. 14789)
Chen, Shuming and K. N. Houk. “Origins of Stereoselectivity in Mannich Reactions Catalyzed by Chiral Vicinal Diamines.” The Journal of Organic Chemistry 83 no. 6 (2018): 3171-3176. 10.1021/acs.joc.8b00037.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI1053575).” (Chen and Houk, 2018, p. 3175)
Chen, Shuming; Peiyuan Yu, and K. N. Houk. “Ambimodal Dipolar/Diels–Alder Cycloaddition Transition States Involving Proton Transfers.” Journal of the American Chemical Society 140 no. 51 (2018): 18124-18131. 10.1021/jacs.8b11080.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI1053575).” (Chen et al., 2018, p. 18130)
Chen, Shuming; Yu Zheng; Tianjiao Cui; Eric Meggers, and K. N. Houk. “Arylketone π-Conjugation Controls Enantioselectivity in Asymmetric Alkynylations Catalyzed by Centrochiral Ruthenium Complexes.” Journal of the American Chemical Society 140 no. 15 (2018): 5146-5152. 10.1021/jacs.8b00485.
“Calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (Grant OCI1053575).” (Chen et al., 2018, p. 5151)
Chogii, Isaac; Pradipta Das; Jason S. Fell; Kevin A. Scott; Mark N. Crawford; K. N. Houk, and Jon T. Njardarson. “Correction to “New Class of Anion-Accelerated Amino-Cope Rearrangements as Gateway to Diverse Chiral Structures”.” Journal of the American Chemical Society 140 no. 29 (2018): 9314-9314. 10.1021/jacs.8b06895.
“We are grateful for the computational resources provided by UCLA Institute for Digital Research and Education and the National Science Foundation through XSEDE Science Gateways Program (TG-CHE040013N).” (Chogii et al., 2018, p. 1)
Enders, Craig K.. “A Comparison of Multilevel Imputation Schemes for Random Coefficient Models: Fully Conditional Specification and Joint Model Imputation with Random Covariance Matrices.” 53 no. 5 (2018). 10.1080/00273171.2018.1477040.
“All computational tasks were executed on UCLA’s Shared Hoffman2 Cluster, and we used a Linux shell script to coordinate the simulation components.” (Enders, 2018, p. 703)
Engebretson, M. J.; J. L. Posch; D. J. Braun; W. Li; Q. Ma; A. C. Kellerman; C.-L. Huang; S. G. Kanekal; C. A. Kletzing; J. R. Wygant; H. E. Spence; D. N. Baker; J. F. Fennell; V. Angelopoulos; H. J. Singer; M. R. Lessard; R. B. Horne; T. Raita; K. Shiokawa; R. Rakhmatulin; E. Dmitriev, and E. Ermakova. “EMIC Wave Events During the Four GEM QARBM Challenge Intervals.” Journal of Geophysical Research: Space Physics 123 no. 8 (2018): 6394-6423. 10.1029/2018JA025505.
“PSD and adiabatic invariant computations were made using code developed by A. C K., the IRBEM library, and the UCLA Hoffman2 cluster.” (Engebretson et al., 2018, p. 6422)
Fereyduni, E; JN Sanders; G Gonzalez; KN Houk, and AJ Grenning. “Transient [3,3] Cope rearrangement of 3,3-dicyano-1,5-dienes: computational analysis and 2-step synthesis of arylcycloheptanes.” CHEMICAL SCIENCE 9 no. 46 (2018): 8760-8764. 10.1039/c8sc03057j.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE).” (Fereyduni et al., 2018, p. 8764)
Fortunel, Claire; Jesse R. Lasky; María Uriarte; Renato Valencia; S. Joseph Wright; Nancy C. Garwood, and Nathan J. B. Kraft. “Topography and neighborhood crowding can interact to shape species growth and distribution in a diverse Amazonian forest.” Ecology 99 no. 10 (2018): 2272-2283. 10.1002/ecy.2441.
“We fit models on the Hoffman2 High-Performance Computing cluster at the University of California, Los Angeles.” (Fortunel et al., 2018, p. 5)
Gao, SS; T Zhang; M Garcia-Borràs; YS Hung; JM Billingsley; KN Houk; YC Hu, and Y Tang. “Biosynthesis of Heptacyclic Duclauxins Requires Extensive Redox Modifications of the Phenalenone Aromatic Polyketide.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 140 no. 22 (2018): 6991-6997. 10.1021/jacs.8b03705.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Gao et al., 2018, p. 8)
Gilman, Daniel; Simon Birrer; Tommaso Treu; Charles R Keeton, and Anna Nierenberg. “Probing the nature of dark matter by forward modelling flux ratios in strong gravitational lenses.” Monthly Notices of the Royal Astronomical Society 481 no. 1 (2018): 819-834. 10.1093/mnras/sty2261.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Gilman et al., 2018, p. 830)
Goh, Shermin S.; Pier Alexandre Champagne; Sureshbabu Guduguntla; Takashi Kikuchi; Makoto Fujita; K. N. Houk, and Ben L. Feringa. “Stereospecific Ring Contraction of Bromocycloheptenes through Dyotropic Rearrangements via Nonclassical Carbocation–Anion Pairs.” Journal of the American Chemical Society 140 no. 15 (2018): 4986-4990. 10.1021/jacs.8b00821.
“Computations were performed on the Hoffman2 cluster at UCLA.” (Goh et al., 2018, p. 4989)
Hansen, Bradley M S. “A dynamical context for the origin of Phobos and Deimos.” Monthly Notices of the Royal Astronomical Society 475 no. 2 (2018): 2452-2466. 10.1093/mnras/stx3361.
“The simulations described here were performed on the UCLA Hoffman2 Shared computing cluster and using the resources provided by the Bhaumik Institute.” (Hansen, 2018, p. 2465)
Hatamizadeh, Ali; Yuanping Song, and Jonathan B. Hopkins. “Optimizing the Geometry of Flexure System Topologies Using the Boundary Learning Optimization Tool.” Mathematical Problems in Engineering 2018 no. 1 (2018): 1058732. 10.1155/2018/1058732.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Hatamizadeh et al., 2018, p. 13)
Huang, C. H.; M. R. Gilbert, and J. Marian. “Simulating irradiation hardening in tungsten under fast neutron irradiation including Re production by transmutation.” Journal of Nuclear Materials 499 (2018): 204-215. 10.1016/j.jnucmat.2017.11.026.
“Computer time allocations at UCLA’s IDRE Hoffman2 supercomputer are also acknowledged.” (Huang et al., 2018, p. 214)
Huang, Hui and Lingsen Meng. “Slow Unlocking Processes Preceding the 2015 Mw 8.4 Illapel, Chile, Earthquake.” Geophysical Research Letters 45 no. 9 (2018): 3914-3922. 10.1029/2018GL077060.
“This work relies on the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Huang and Meng, 2018, p. 3921)
Jalal, Siavash and Peter M. Bentler. “Using Monte Carlo Normal Distributions to Evaluate Structural Models With Nonnormal Data.” Structural Equation Modeling: A Multidisciplinary Journal 25 no. 4 (2018): 541-557. 10.1080/10705511.2017.1390753.
“To expedite the computation process a cluster computation from the Hoffman2 shared cluster1 was used.” (Jalal and Bentler, 2018, p. 547)
Joglekar, Archis S.; Benjamin J. Winjum; Adam Tableman; Han Wen; Michail Tzoufras, and Warren B. Mori. “Validation of OSHUN against collisionless and collisional plasma physics.” Plasma Physics and Controlled Fusion 60 no. 6 (2018): 064010. 10.1088/1361-6587/aab978.
“The modeling was performed using computational resources and services provided by the Hoffman2 and Dawson2 Computing Clusters at UCLA.” (Joglekar et al., 2018, p. 7)
Joshi, C.; E. Adli; W. An; C. E. Clayton; S. Corde; S. Gessner; M. J. Hogan; M. Litos; W. Lu; K. A. Marsh; W. B. Mori; N. Vafaei-Najafabadi; B. O’shea; Xinlu Xu; G. White, and V. Yakimenko. “Plasma wakefield acceleration experiments at FACET II.” Plasma Physics and Controlled Fusion 60 no. 3 (2018): 034001. 10.1088/1361-6587/aaa2e3.
“Simulations were performed on the UCLA Hoffman2 and Dawson2 computers and on Blue Waters through NSF OCI-1036224.” (Joshi et al., 2018, p. 13)
Kishimoto, Shinji; Kodai Hara; Hiroshi Hashimoto; Yuichiro Hirayama; Pier Alexandre Champagne; Kendall N. Houk; Yi Tang, and Kenji Watanabe. “Enzymatic one-step ring contraction for quinolone biosynthesis.” Nature Communications 9 no. 1 (2018): 2826. 10.1038/s41467-018-05221-5.
“Computations were performed on the Hoffman2 cluster at UCLA.” (Kishimoto et al., 2018, p. 7)
Lee, You-Hsun; Li-Min Huang; You-Seng Zou; Shao-Ching Huang, and Chao-An Lin. “Simulations of turbulent duct flow with lattice Boltzmann method on GPU cluster.” Computers & Fluids 168 (2018): 14-20. 10.1016/j.compfluid.2018.03.064.
“The authors gratefully acknowledge the supports by the computational facilities provided by NCHC and UCLA Hoffman2 Cluster.” (Lee et al., 2018, p. 20)
Levandowski, BJ; D Herath; NM Gallup, and KN Houk. “Origin of π-Facial Stereoselectivity in Thiophene 1-Oxide Cycloadditions.” JOURNAL OF ORGANIC CHEMISTRY 83 no. 5 (2018): 2611-2616. 10.1021/acs.joc.7b03016.
“Computer time was provided by the UCLA Institute for Digital Research and Education (IDRE).” (Levandowski et al., 2018, p. 5)
Li, GY; M Garcia-Borràs; MJLJ Fürst; A Ilie; MW Fraaije; KN Houk, and MT Reetz. “Overriding Traditional Electronic Effects in Biocatalytic Baeyer-Villiger Reactions by Directed Evolution.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 140 no. 33 (2018): 10464-10472. 10.1021/jacs.8b04742.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Li et al., 2018, p. 10471)
Lindstrøm, C. A.; E. Adli; J. M. Allen; W. An; C. Beekman; C. I. Clarke; C. E. Clayton; S. Corde; A. Doche; J. Frederico; S. J. Gessner; S. Z. Green; M. J. Hogan; C. Joshi; M. Litos; W. Lu; K. A. Marsh; W. B. Mori; B. D. O’Shea; N. Vafaei-Najafabadi, and V. Yakimenko. “Measurement of Transverse Wakefields Induced by a Misaligned Positron Bunch in a Hollow Channel Plasma Accelerator.” Physical Review Letters 120 no. 12 (2018): 124802. 10.1103/PhysRevLett.120.124802.
“Simulations were performed on the UCLA Hoffman2 cluster through NSF OCI-1036224.” (Lindstrøm et al., 2018, p. 5)
Listgarten, Jennifer; Michael Weinstein; Benjamin P. Kleinstiver; Alexander A. Sousa; J. Keith Joung; Jake Crawford; Kevin Gao; Luong Hoang; Melih Elibol; John G. Doench, and Nicolo Fusi. “Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs.” Nature Biomedical Engineering 2 no. 1 (2018): 38-47. 10.1038/s41551-017-0178-6.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group, and also an Azure-for-Research grant to UCLA.” (Listgarten et al., 2018, p. 47)
Martins, Karina; Paul F. Gugger; Jesus Llanderal-Mendoza; Antonio González-Rodríguez; Sorel T. Fitz-Gibbon; Jian-Li Zhao; Hernando Rodríguez-Correa; Ken Oyama, and Victoria L. Sork. “Landscape genomics provides evidence of climate-associated genetic variation in Mexican populations of Quercus rugosa.” Evolutionary Applications 11 no. 10 (2018): 1842-1858. 10.1111/eva.12684.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Martins et al., 2018, p. 1854)
Mei, Bing-Ang; Jonathan Lau; Terri Lin; Sarah H. Tolbert; Bruce S. Dunn, and Laurent Pilon. “Physical Interpretations of Electrochemical Impedance Spectroscopy of Redox Active Electrodes for Electrical Energy Storage.” The Journal of Physical Chemistry C 122 no. 43 (2018): 24499-24511. 10.1021/acs.jpcc.8b05241.
“The computation for this study was performed on the Hoffman2 cluster hosted by the Academic Technology Services (ATS) at the University of California, Los Angeles, USA.” (Mei et al., 2018, p. 24508)
Mei, Bing-Ang; Obaidallah Munteshari; Jonathan Lau; Bruce Dunn, and Laurent Pilon. “Physical Interpretations of Nyquist Plots for EDLC Electrodes and Devices.” The Journal of Physical Chemistry C 122 no. 1 (2018): 194-206. 10.1021/acs.jpcc.7b10582.
“The computation for this study was performed on the Hoffman2 cluster hosted by the Academic Technology Services (ATS) at the University of California, Los Angeles, U.S.A.” (Mei et al., 2018, p. 204)
Mirocha, Jordan; Richard H Mebane; Steven R Furlanetto; Krishma Singal, and Donald Trinh. “Unique signatures of Population III stars in the global 21-cm signal.” Monthly Notices of the Royal Astronomical Society 478 no. 4 (2018): 5591-5606. 10.1093/mnras/sty1388.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Mirocha et al., 2018, p. 5605)
Newmister, SA; SS Li; M Garcia-Borràs; JN Sanders; S Yang; AN Lowell; FG Yu; JL Smith; RM Williams; KN Houk, and DH Sherman. “Structural basis of the Cope rearrangement and cyclization in hapalindole biogenesis.” NATURE CHEMICAL BIOLOGY 14 no. 4 (2018): 345-+. 10.1038/s41589-018-0003-x.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Newmister et al., 2018, p. 351)
Patel, Anita; Gautam Pulugundla; Sergey Smolentsev; Mohamed Abdou, and Rajendraprasad Bhattacharyay. “Validation of numerical solvers for liquid metal flow in a complex geometry in the presence of a strong magnetic field.” Theoretical and Computational Fluid Dynamics 32 no. 2 (2018): 165-178. 10.1007/s00162-017-0446-9.
“All HIMAG simulations used the computational resources of Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Patel et al., 2018, p. 177)
Picazo, Elias; Sarah M. Anthony; Maude Giroud; Adam Simon; Margeaux A. Miller; K. N. Houk, and Neil K. Garg. “Arynes and Cyclic Alkynes as Synthetic Building Blocks for Stereodefined Quaternary Centers.” Journal of the American Chemical Society 140 no. 24 (2018): 7605-7610. 10.1021/jacs.8b02875.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Picazo et al., 2018, p. 7609)
Popov, Ivan A.; Elisa Jimenez-Izal; Anastassia N. Alexandrova, and Alexander I. Boldyrev. “Multicenter Bonding Effects in Oxygen Vacancy in the Bulk and on the Surface of MgO.” The Journal of Physical Chemistry C 122 no. 22 (2018): 11933-11937. 10.1021/acs.jpcc.8b03118.
“Calculations were performed on the UCLA shared cluster Hoffman2.” (Popov et al., 2018, p. 11936)
Rhodes, Tyler J.; Sergey Smolentsev, and Mohamed Abdou. “Magnetohydrodynamic pressure drop and flow balancing of liquid metal flow in a prototypic fusion blanket manifold.” Physics of Fluids 30 no. 5 (2018): 057101. 10.1063/1.5026404.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Rhodes et al., 2018, p. 15)
Rhodes, Tyler J.; Sergey Smolentsev, and Mohamed Abdou. “Effect of the length of the poloidal ducts on flow balancing in a liquid metal blanket.” Fusion Engineering and Design 136 (2018): 847-851. 10.1016/j.fusengdes.2018.04.019.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Rhodes et al., 2018, p. 851)
Scholl, Katie; John Dillashaw; Evan Timpy; Yu-hong Lam; Lindsey DeRatt; Tyler R. Benton; Jacqueline P. Powell; K. N. Houk, and Jeremy B. Morgan. “Quinine-Promoted, Enantioselective Boron-Tethered Diels–Alder Reaction by Anomeric Control of Transition-State Conformation.” The Journal of Organic Chemistry 83 no. 10 (2018): 5756-5765. 10.1021/acs.joc.8b00938.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant No. ACI-1053575.” (Scholl et al., 2018, p. 5764)
Scott, SK; JN Sanders; KE White; RA Yu; KN Houk, and AJ Grenning. “Controlling, Understanding, and Redirecting the Thermal Rearrangement of 3,3-Dicyano-1,5-enynes.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 140 no. 47 (2018): 16134-16139. 10.1021/jacs.8b08553.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE).” (Scott et al., 2018, p. 6)
Shajib, Anowar J.; Tommaso Treu, and Adriano Agnello. “Improving time-delay cosmography with spatially resolved kinematics.” Monthly Notices of the Royal Astronomical Society 473 no. 1 (2018): 210-226. 10.1093/mnras/stx2302.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Shajib et al., 2018, p. 225)
Stephan, Alexander P.; Smadar Naoz, and B. Scott Gaudi. “A-type Stars, the Destroyers of Worlds: The Lives and Deaths of Jupiters in Evolving Stellar Binaries.” The Astronomical Journal 156 no. 3 (2018): 128. 10.3847/1538-3881/aad6e5.
“Calculations for this project were performed on the UCLA cluster Hoffman2.” (Stephan et al., 2018, p. 10)
Sun, Geng and Philippe Sautet. “Metastable Structures in Cluster Catalysis from First-Principles: Structural Ensemble in Reaction Conditions and Metastability Triggered Reactivity.” Journal of the American Chemical Society 140 no. 8 (2018): 2812-2820. 10.1021/jacs.7b11239.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Sun and Sautet, 2018, p. 2819)
T. Ly, Jack; Steven A. Lopez; Janice B. Lin; Jae Joon Kim; Hyunbok Lee; Edmund K. Burnett; Lei Zhang; Alán Aspuru-Guzik; K. N. Houk, and Alejandro L. Briseno. “Oxidation of rubrene , and implications for device stability.” Journal of Materials Chemistry C 6 no. 14 (2018): 3757-3761. 10.1039/C7TC05775J.
“This work used computational and storage services associated with the Hoffman2 cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group and the NSF-supported Extreme Science and Engineering Discovery Environment (XSEDE)’s Gordon supercomputer (OCI-1053575) at the San Diego Supercomputing Center.” (T. Ly et al., 2018, p. 8)
Tran, Anh; Madeleine Pont; Andres Aguirre; Helen Durand; Marquis Crose, and Panagiotis D. Christofides. “Bayesian model averaging for estimating the spatial temperature distribution in a steam methane reforming furnace.” Chemical Engineering Research and Design 131 (2018): 465-487. 10.1016/j.cherd.2017.09.027.
“The proposed integrated model identification scheme is executed on the Hoffman2 cluster at UCLA to construct the data-driven model for the OTWT distribution from the training data, and the results from the goodness-of-fit and out-of-sample prediction tests of the data-driven model are used to demonstrate the effectiveness of the scheme proposed in this work.” (Tran et al., 2018, p. 465)
Tran, Anh; Madeleine Pont; Marquis Crose, and Panagiotis D. Christofides. “Real-time furnace balancing of steam methane reforming furnaces.” Chemical Engineering Research and Design 134 (2018): 238-256. 10.1016/j.cherd.2018.03.032.
“As a result, all simulations of the reformer CFD model and the derivation of M are executed on the Hoffman2 computing cluster at UCLA.” (Tran et al., 2018, p. 247)
Walker, Morgan M.; Shuming Chen; Brandon Q. Mercado; K. N. Houk, and Jonathan A. Ellman. “Formation of Aminocyclopentadienes from Silyldihydropyridines: Ring Contractions Driven by Anion Stabilization.” Angewandte Chemie International Edition 57 no. 22 (2018): 6605-6609. 10.1002/anie.201800596.
“Density functional theory (DFT) calculations were performed on the Hoffman2 cluster at the University of California, Los Angeles, and the Extreme Science and Engineering Discovery Environment (XSEDE),” (Walker et al., 2018, p. 5)
Wan, Y.; J. F. Hua; C.-H. Pai; F. Li; Y. P. Wu; W. Lu; C. J. Zhang; X. L. Xu; C. Joshi, and W. B. Mori. “Phase locked multiple rings in the radiation pressure ion acceleration process.” Plasma Physics and Controlled Fusion 60 no. 4 (2018): 044016. 10.1088/1361-6587/aaae36.
“Simulations were performed on the HOFFMAN2 clusters at UCLA and Sunway TaihuLight cluster at the National Supercomputing Center in Wuxi (NSCCWX).” (Wan et al., 2018, p. 6)
Wan, Y.; C.-H. Pai; J. F. Hua; Y. P. Wu; W. Lu; F. Li; C. J. Zhang; X. L. Xu; C. Joshi, and W. B. Mori. “Tri-stage quasimonoenergetic proton acceleration from a multi-species thick target.” Physics of Plasmas 25 no. 7 (2018): 073105. 10.1063/1.5029556.
“Simulations were performed on the HOFFMAN2 clusters at UCLA and the Sunway TaihuLight cluster at National Supercomputing Center in Wuxi (NSCCWX).” (Wan et al., 2018, p. 7)
Wang, Hong; Xiaolin Chen, and Gang Li. “Survival Forests with R-Squared Splitting Rules.” Journal of Computational Biology 25 no. 4 (2018): 388-395. 10.1089/cmb.2017.0107.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Wang et al., 2018, p. 394)
Widmer, Devon R. and Benjamin J. Schwartz. “Solvents can control solute molecular identity.” Nature Chemistry 10 no. 9 (2018): 910-916. 10.1038/s41557-018-0066-z.
“The authors acknowledge the Institute for Digital Research and Education (IDRE) at UCLA for use of the hoffman2 computing cluster, B. Taggart for assistance setting up the simulations, and W. Glover and C.-C. Zhou for discussions.” (Widmer and Schwartz, 2018, p. 916)
Winjum, B. J.; F. S. Tsung, and W. B. Mori. “Mitigation of stimulated Raman scattering in the kinetic regime by external magnetic fields.” Physical Review E 98 no. 4 (2018): 043208. 10.1103/PhysRevE.98.043208.
“Simulations were performed on the UCLA Dawson2 (NSF PHY-0960344) and UCLA Hoffman2 Clusters, NSF’s BlueWaters (NSF-1614949), and ALCF’s Mira under an INCITE allocation.” (Winjum et al., 2018, p. 4)
Witzel, G.; G. Martinez; J. Hora; S. P. Willner; M. R. Morris; C. Gammie; E. E. Becklin; M. L. N. Ashby; F. Baganoff; S. Carey; T. Do; G. G. Fazio; A. Ghez; W. J. Glaccum; D. Haggard; R. Herrero-Illana; J. Ingalls; R. Narayan, and H. A. Smith. “Variability Timescale and Spectral Index of Sgr A* in the Near Infrared: Approximate Bayesian Computation Analysis of the Variability of the Closest Supermassive Black Hole.” The Astrophysical Journal 863 no. 1 (2018): 15. 10.3847/1538-4357/aace62.
Xie, Yazhou; Jian Zhang, and Yili Huo. “Simplified Drift Demand Prediction of Bridges under Liquefaction-Induced Lateral Spreading.” Journal of Bridge Engineering 23 no. 8 (2018): 04018053. 10.1061/(ASCE)BE.1943-5592.0001266.
“The research utilized the Hoffman2 cluster of Academic Technology Services at the University of California, Los Angeles, to conduct the numerical simulations presented in this paper.” (Xie et al., 2018, p. 12)
Xue, Xiao-Song; Brian J. Levandowski; Cyndi Qixin He, and K. N. Houk. “Origins of Selectivities in the Stork Diels–Alder Cycloaddition for the Synthesis of (±)-4-Methylenegermine.” Organic Letters 20 no. 19 (2018): 6108-6111. 10.1021/acs.orglett.8b02548.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Xue et al., 2018, p. 6110)
Yang, Zhongyue; Xiaofei Dong; Yanmin Yu; Peiyuan Yu; Yingzi Li; Cooper Jamieson, and K. N. Houk. “Relationships between Product Ratios in Ambimodal Pericyclic Reactions and Bond Lengths in Transition Structures.” Journal of the American Chemical Society 140 no. 8 (2018): 3061-3067. 10.1021/jacs.7b13562.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Yang et al., 2018, p. 3066)
Yang, Zhongyue and K. N. Houk. “The Dynamics of Chemical Reactions: Atomistic Visualizations of Organic Reactions, and Homage to van ’t Hoff.” Chemistry – A European Journal 24 no. 16 (2018): 3916-3924. 10.1002/chem.201706032.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE ),which is supported by the NSF (OCI1053575).” (Yang and Houk, 2018, p. 3922)
Yang, ZY; LY Zou; YM Yu; FJ Liu; XF Dong, and KN Houk. “Molecular dynamics of the two-stage mechanism of cyclopentadiene dimerization: concerted or stepwise?.” CHEMICAL PHYSICS 514 (2018): 120-125. 10.1016/j.chemphys.2018.02.020.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Yang et al., 2018, p. 124)
Yu, Peiyuan; Cyndi Qixin He; Adam Simon; Wei Li; Rasmus Mose; Mathias Kirk Thøgersen; Karl Anker Jørgensen, and K. N. Houk. “Organocatalytic [6+4] Cycloadditions via Zwitterionic Intermediates: Chemo-, Regio-, and Stereoselectivities.” Journal of the American Chemical Society 140 no. 42 (2018): 13726-13735. 10.1021/jacs.8b07575.
“Calculations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575).” (Yu et al., 2018, p. 13735)
Zhang, Jian; Peiyuan Yu; Shao-Yu Li; He Sun; Shao-Hua Xiang; Jun (Joelle) Wang; Kendall N. Houk, and Bin Tan. “Asymmetric phosphoric acid–catalyzed four-component Ugi reaction.” Science 361 no. 6407 (2018): eaas8707. 10.1126/science.aas8707.
“P.Y. and K.N.H. acknowledge the computational resources provided by the Institute of Digital Research and Education (IDRE) at UCLA, and by the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Zhang et al., 2018, p. 9)
Zhang, K; LC Cai; ZY Yang; KN Houk, and O Kwon. “Bridged [2.2.1] bicyclic phosphine oxide facilitates catalytic γ-umpolung addition-Wittig olefination.” CHEMICAL SCIENCE 9 no. 7 (2018): 1867-1872. 10.1039/c7sc04381c.
“CombiFlash and HPLC. Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575)” (Zhang et al., 2018, p. 4)
Zhao, Yue and Jaime Marian. “Direct prediction of the solute softening-to-hardening transition in W–Re alloys using stochastic simulations of screw dislocation motion.” Modelling and Simulation in Materials Science and Engineering 26 no. 4 (2018): 045002. 10.1088/1361-651X/aaaecf.
“Computer time allocations at UCLA’s IDRE Hoffman2 supercomputer are also acknowledged.” (Zhao and Marian, 2018, p. 14)
Theses for 2018¶
Fell, Jason Scott. “Computational Exploration of Reactivities and Catalysis of Pericyclic Reactions.” Ph.D. Thesis, University of California, Los Angeles, 2018. ProQuest, https://www.proquest.com/docview/2131454710.
“High performance computing resources were provided by the UCLA Hoffman2 cluster and the NSF Extreme Science and Engineering Discovery Environment (TG-CHE040013N).” (Fell, p. 39)
Haghnegahdar, Mojhgan. “Theoretical Study of Tellurium Isotope Fractionations in Ore-Forming Systems, and Studies of Doubly Substituted Isotopologues of Methane.” Thesis, UCLA, 2018. escholarship.org, https://escholarship.org/uc/item/7bd5c85d.
“All electronic structure calculations in this thesis are made using the Gaussian09 software package (Gaussian 09: AM6 4 L-G09RevB.01 12 August 2010) on the UCLA Hoffman2 cluster.” (Haghnegahdar, 2018, p. 30)
Huang, Alden Yen-Wen. “Copy Number Variation in Neuropsychiatric Disorders.” Thesis, UCLA, 2018. escholarship.org, https://escholarship.org/uc/item/94p9m4k7.
“The variant calling was performed in the high performance cluster at UCLA called the Hoffman2 cluster.” (Huang, 2018, p. 110)
Jones, Talmage Harnish. “Mechanical Design of Graphene Nanoribbon Compliant Mechanisms for Electrostatic Discharge.” M.S. Thesis, University of California, Los Angeles, 2018. ProQuest, https://www.proquest.com/docview/2061082090.
“This portion of the work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Jones, p. 44)
Lin, Janice Biay. “Computational Studies of Organic Electronic Materials.” Ph.D. Thesis, University of California, Los Angeles, 2018. ProQuest, https://www.proquest.com/docview/2162884798.
“his work used computational and storage services associated with the Hoffman2 cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group, the NSFU supported Extreme Science and Engineering Discovery Environment (XSEDE)’s Gordon and Comet supercomputers (OCIU1053575) at the San Diego Supercomputing Center.” (Lin, p. 20)
Mei, Bing-Ang. “Physical Interpretations and Electrode Design Guidelines for Electrochemical Capacitors.” Ph.D. Thesis, University of California, Los Angeles, 2018. ProQuest, https://www.proquest.com/docview/2053996725.
“The computation for this study was performed on the Hoffman2 cluster hosted by the Academic Technology Services (ATS) at the University of California, Los Angeles, USA.” (Mei, p. 29)
Sahakyan, Anna. “Mechanisms of X-chromosome Regulation During Mammalian Development.” Ph.D. Thesis, University of California, Los Angeles, 2018. ProQuest, https://www.proquest.com/docview/2054001497.
“DNA Methyla- tion calling was performed using BS-Seeker2 (2.0.32) using Bowtie (0.12.9) for read alignment on the UCLA Hoffman2 computer cluster [55]” (Sahakyan, p. 80)
Singh, Amit Rajnarayan. “Study of Zero and Finite Temperature Response of Discrete Deformable Surfaces.” Ph.D. Thesis, University of California, Los Angeles, 2018. ProQuest, https://www.proquest.com/docview/2131641528.
“I thank IDRE for providing Hoffman2 cluster for computer simulations reported in this work.” (Singh, p. xiii)
Tran, Anh Tuan. “Computational Fluid Dynamics and Machine Learning Modeling, Operation and Control of Steam Methane Reforming Reactors and Furnaces.” Ph.D. Thesis, University of California, Los Angeles, 2018. ProQuest, https://www.proquest.com/docview/2151416649.
“I would like to thank Prakashan Korambath from the Institute for Digital Research and Education for his help on managing the Hoffman2 computing cluster.” (Tran, p. 20)
Vasista Srinivasan Ranganathan, Sudarsan. “Advances in Protograph-Based LDPC Codes and a Rate Allocation Problem.” Thesis, UCLA, 2018. escholarship.org, https://escholarship.org/uc/item/2419j1rh.
“The work in this dissertation was possible, in large part, due to the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Vasista Srinivasan Ranganathan, 2018, p. 19)
Conference Papers for 2018¶
Anh Tran, Madeleine Pont, Marquis Crose and Panagiotis D. Christofides. “Steam Methane Reforming Furnace Temperature Balancing Using Bayesian Model Identification | IEEE Conference Publication | IEEE Xplore.” 2018 Annual American Control Conference (ACC) Wisconsin Center, Milwaukee, USA, 2018. https://ieeexplore.ieee.org/abstract/document/8431519.
“The furnace-balancing scheme is executed on a shared computing cluster at UCLA (i.e., the Hoffman2 cluster) using 4 high performance compute nodes of 16 cores, which generates the empirical model for the OTWT distribution, the optimized total FSF flow rate, the respective optimized FSF distribution and the corresponding reformer CFD data over the course of 48 hours.” (“Steam Methane Reforming Furnace Temperature Balancing Using Bayesian Model Identification | IEEE Conference Publication | IEEE Xplore”, p. 4904)
Ranganathan, Sudarsan V.S.; Richard D. Wesel, and Dariush Divsalar. “Linear Rate-Compatible Codes with Degree-1 Extending Variable Nodes Under Iterative Decoding.” In 2018 IEEE International Symposium on Information Theory (ISIT): 2018 IEEE International Symposium on Information Theory (ISIT) 2018: 1166-1170. 10.1109/ISIT.2018.8437332.
“This work used computational and storage services of the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Ranganathan et al., 2018, p. 1170) ISSN: 2157-8117
Tran, Anh; Madeleine Pont; Marquis Crose, and Panagiotis D. Christofides. “Steam Methane Reforming Furnace Temperature Balancing Using Bayesian Model Identification.” In 2018 Annual American Control Conference (ACC): 2018 Annual American Control Conference (ACC) 2018: 4899-4905. 10.23919/ACC.2018.8431519.
The furnace-balancing scheme is executed on a shared computing cluster at UCLA (i.e., the Hoffman2 cluster) using 4 high performance compute nodes of 16 cores, which generates the empirical model for the OTWT distribution, the optimized total FSF flow rate, the respective optimized FSF distribution and the corresponding reformer CFD data over the course of 48 hours.” (Tran et al., 2018, p. 4904). ISSN: 2378-5861
Winjum, Benjamin J. and Warren B. Mori. “APS -60th Annual Meeting of the APS Division of Plasma Physics - Event - PIC simulations of the damping of nonlinear electron plasma waves propagating in magnetic fields.” In Bulletin of the American Physical Society: 60th Annual Meeting of the APS Division of Plasma Physics 2018. https://meetings.aps.org/Meeting/DPP18/Event/337086.
“Simulations were performed on the UCLA Dawson2 (NSF PHY 0960344) and UCLA Hoffman2 Clusters, NSF’s BlueWaters, and ALCF’s Mira.”
Reports for 2018¶
Edgar, Thomas F.; Michael Baldea; Ofodike Ezekoye; Hari Ganesh; Ankur Kumar; Dan Wanegar; Vincent M. Torres; Jim Davis; Panagiotis Christofides; Prakashan Korambath; Vasilios Manousiouthakis; Robert Graybill; Brian Schott; Larry Megan; Jesus Flores-Cerillo; Gangshi Hu; Tushar Vispute; Joseph Chup; Todd Albertson; Stephen Cannizzaro; Darlene Schuster; Phil Callahan, and Denise Swink. “Industrial Scale Demonstration of Smart Manufacturing, Achieving Transformational Energy Productivity Gains.” The University of Texas at Austin, Austin, TX (United States), 2018. https://www.osti.gov/biblio/1454266.
“The ANSYS Fluent calculation itself requires 80 cores of compute CPUs, 1 TB RAM and a high-speed network for MPI job communications running on an HPC resource like the Hoffman2 cluster at UCLA.” (Edgar et al., 2018, p. 31) DOI: 10.2172/1454266
Lleras-Muney, Adriana and Flavien Moreau. “A Unified Law of Mortality: Implications for the Long Run Effects of Early Conditions.” UCLA, 2018.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Lleras-Muney and Moreau, p. 1)
Book Sections for 2018¶
Tran, Anh; Madeleine Pont; Marquis Crose, and Panagiotis D. Christofides. “Estimating the Spatial Temperature Distribution in a Steam Methane Reforming Furnace Using Bayesian Modelling.” Elsevier, 2018. https://www.sciencedirect.com/science/article/pii/B9780444642417503311.
“The Bayesian model identification is executed on the Hoffman2 cluster at UCLA to construct the data-driven model for the ORTWT distribution from the training data set, and the results from the resubstitution and forecast tests of the data-driven model are used to demonstrate the effectiveness of the proposed approach.” (Tran et al., 2018, p. 2017) DOI: 10.1016/B978-0-444-64241-7.50331-1
2017¶
- 39 publications for 2017
Journal Articles for 2017¶
Aseev, N. A.; Y. Y. Shprits; A. Y. Drozdov; A. C. Kellerman; M. E. Usanova; D. Wang, and I. S. Zhelavskaya. “Signatures of Ultrarelativistic Electron Loss in the Heart of the Outer Radiation Belt Measured by Van Allen Probes.” Journal of Geophysical Research: Space Physics 122 no. 10 (2017): 10,102-10,111. 10.1002/2017JA024485.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Aseev et al., 2017, p. 10110)
Badr, Yasmine; Andres Torres, and Puneet Gupta. “Mask Assignment and DSA Grouping for DSA-MP Hybrid Lithography for Sub-7 nm Contact/Via Holes.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 36 no. 6 (2017): 913-926. 10.1109/TCAD.2016.2614262.
“All the experiments were run on a shared cluster [27], using four cores and using up to 70 GB of memory.” (Badr et al., 2017, p. 921) “[27] Ucla Hoffman2 Cluster. accessed on Oct. 5, 2016. [Online]. Available: https://idre.ucla.edu/hoffman2” (Badr et al., 2017, p. 926) Conference Name: IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems
Carnevali, Davide; Anastasia Conti; Matteo Pellegrini, and Giorgio Dieci. “Whole-genome expression analysis of mammalian-wide interspersed repeat elements in human cell lines.” DNA Research 24 no. 1 (2017): 59-69. 10.1093/dnares/dsw048.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Carnevali et al., 2017, p. 69)
Carnevali, Davide and Giorgio Dieci. “Identification of RNA Polymerase III-Transcribed SINEs at Single-Locus Resolution from RNA Sequencing Data.” Non-Coding RNA 3 no. 1 (2017): 15. 10.3390/ncrna3010015.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Carnevali and Dieci, 2017, p. 7) Number: 1
Cortés, G and S Margulis. “Impacts of El Nino and La Nina on interannual snow accumulation in the Andes: Results from a high-resolution 31 year reanalysis.” GEOPHYSICAL RESEARCH LETTERS 44 no. 13 (2017): 6859-6867. 10.1002/2017GL073826.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA IDRE Research Technology Group.” (Cortés and Margulis, 2017, p. 6866)
Drozdov, A. Y.; Y. Y. Shprits; M. E. Usanova; N. A. Aseev; A. C. Kellerman, and H. Zhu. “EMIC wave parameterization in the long-term VERB code simulation.” Journal of Geophysical Research: Space Physics 122 no. 8 (2017): 8488-8501. 10.1002/2017JA024389.
“The authors would like to acknowledge high-performance computing support from Yellowstone (ark:/85065/ d7wd3xhc) provided by UCAR’s Computational and Information System Laboratory, sponsored by the National Science Foundation and other agencies and computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Drozdov et al., 2017, p. 8500)
Fang, LZ; TG Saint-Denis; BLH Taylor; S Ahlquist; K Hong; SS Liu; LL Han; KN Houk, and JQ Yu. “Experimental and Computational Development of a Conformationally Flexible Template for the meta-C-H Functionalization of Benzoic Acids.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 139 no. 31 (2017): 10702-10714. 10.1021/jacs.7b03296.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF. L.F., S.S.L., and L.H. were supported by the National Natural Science Foundation of China (81172952).” (Fang et al., 2017, p. 10713)
Fell, Jason S.; Steven A. Lopez; Cody J. Higginson; M. G. Finn, and K. N. Houk. “Theoretical Analysis of the Retro-Diels–Alder Reactivity of Oxanorbornadiene Thiol and Amine Adducts.” Organic Letters 19 no. 17 (2017): 4504-4507. 10.1021/acs.orglett.7b02064.
“We are grateful for the computational resources provided by UCLA Institute for Digital Research and Education and the National Science Foundation through XSEDE Science Gateways Program (TG-CHE040013N).” (Fell et al., 2017, p. 4506)
Fraley, AE; M Garcia-Borràs; A Tripathi; D Khare; EV Mercado-Marin; H Tran; QY Dan; GP Webb; KR Watts; P Crews; R Sarpong; RM Williams; JL Smith; KN Houk, and DH Sherman. “Function and Structure of MaIA/MaIA′, Iterative Halogenases for Late-Stage C-H Functionalization of Indole Alkaloids.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 139 no. 34 (2017): 12060-12068. 10.1021/jacs.7b06773.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Fraley et al., 2017, p. 10)
Garcia-Borràs, Marc; Kendall N. Houk, and Gonzalo Jiménez-Osés. “Computational Design of Protein Function.” (2017). 10.1039/9781788010139-00087.
“Computing resources were provided by CESGA, UR (Beronia cluster), UCLA Academic Technology Services/Institute for Digital Research and Education and IDRE and XSEDE (NSF OCI-1053575).” (Garcia-Borràs et al., 2017, p. 102)
Ghahari, S F; H Ebrahimian, and E Taciroglu. “INVESTIGATION OF THE SPATIAL VARIABILITY OF SEISMIC INPUT MOTIONS FOR CSMIP-INSTRUMENTED BRIDGES DURING THE 2014 SOUTH NAPA EARTHQUAKE—THE CASE OF GOLDEN GATE BRIDGE.” (2017).
“Also, Dr. D’Auria from UCLA Institute for Digital Research and Education helped us to carry out analyses on UCLA Hoffman cluster, which is appreciated.” (Ghahari et al., p. 88)
Grandner, JM; HL Shao; RH Grubbs; P Liu, and KN Houk. “Origins of the Stereoretentive Mechanism of Olefin Metathesis with Ru-Dithiolate Catalysts.” JOURNAL OF ORGANIC CHEMISTRY 82 no. 19 (2017): 10595-10600. 10.1021/acs.joc.7b02129.
“This work used computational resources for projects TG-CHE040013N and TG-CHE140139 in the Extreme Science and Engineering Discovery Environment (XSEDE),19 which is supported by National Science Foundation grant number ACI-1548562, and computational resources provided by the UCLA IDRE Hoffman2 cluster.” (Grandner et al., 2017, p. 10600)
Grayson, MN; ZY Yang, and KN Houk. “Chronology of CH•••O Hydrogen Bonding from Molecular Dynamics Studies of the Phosphoric Acid-Catalyzed Allylboration of Benzaldehyde.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 139 no. 23 (2017): 7717-7720. 10.1021/jacs.7b03847.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI1053575).” (Grayson et al., 2017, p. 4)
Gugger, P. F.; J. M. Peñaloza-Ramírez, and J. W. Wright. “Whole-transcriptome response to water stress in a California endemic oak, Quercus lobata.” Tree … (2017).
“the computational services available through the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Gugger et al., 2017, p. 642)
Han, Xu; Jiyong Park; Wei Wu; Andres Malagon; Lingyu Wang; Edgar Vargas; Athula Wikramanayake; K. N. Houk, and Roger M. Leblanc. “A resorcinarene for inhibition of Aβ fibrillation.” Chemical Science 8 no. 3 (2017): 2003-2009. 10.1039/C6SC04854D.
“J. P. and K. N. H. are grateful for utilizing the computational resources of Hoffman2 cluster from UCLA Institute for Digital Research and Education and XSEDE program (TGCHE040013N).” (Han et al., 2017, p. 6)
Harrison, Theresa M.; Donald G. McLaren; Teena D. Moody; Jamie D. Feusner, and Susan Y. Bookheimer. “Generalized Psychophysiological Interaction (PPI) Analysis of Memory Related Connectivity in Individuals at Genetic Risk for Alzheimer’s Disease.” Journal of Visualized Experiments: JoVE no. 129 (2017): 55394. 10.3791/55394.
“The authors used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Harrison et al., 2017, p. 8) PMID: 29286444 PMCID: PMC5755367
He, Cyndi Qixin; Adam Simon; Yu-hong Lam; Andrew P. J. Brunskill; Nobuyoshi Yasuda; Jiajing Tan; Alan M. Hyde; Edward C. Sherer, and K. N. Houk. “Model for the Enantioselectivity of Asymmetric Intramolecular Alkylations by Bis-Quaternized Cinchona Alkaloid-Derived Catalysts.” The Journal of Organic Chemistry 82 no. 16 (2017): 8645-8650. 10.1021/acs.joc.7b01577.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (He et al., 2017, p. 8649)
He, Cyndi Qixin; Peiyuan Yu; Yu-hong Lam, and K. N. Houk. “Origins of Stereoselectivity in Chiral Aminoalcohol Catalysis of Oxyallyl Cation–Indole Reactions.” Organic Letters 19 no. 20 (2017): 5685-5688. 10.1021/acs.orglett.7b02851.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (He et al., 2017, p. 5688)
Huang, Chen-Hsi; Leili Gharaee; Yue Zhao; Paul Erhart, and Jaime Marian. “Mechanism of nucleation and incipient growth of Re clusters in irradiated W-Re alloys from kinetic Monte Carlo simulations.” Physical Review B 96 no. 9 (2017): 094108. 10.1103/PhysRevB.96.094108.
“Computer time allocations at UCLA’s IDRE Hoffman2 supercomputer are also acknowledged.” (Huang et al., 2017, p. 16)
Huang, Hui; Wenbin Xu; Lingsen Meng; Roland Bürgmann, and Juan Carlos Baez. “Early aftershocks and afterslip surrounding the 2015 Mw 8.4 Illapel rupture.” Earth and Planetary Science Letters 457 (2017): 282-291. 10.1016/j.epsl.2016.09.055.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Huang et al., 2017, p. 26)
Jordan, Robert S.; Yolanda L. Li; Cheng-Wei Lin; Ryan D. McCurdy; Janice B. Lin; Jonathan L. Brosmer; Kristofer L. Marsh; Saeed I. Khan; K. N. Houk; Richard B. Kaner, and Yves Rubin. “Synthesis of N = 8 Armchair Graphene Nanoribbons from Four Distinct Polydiacetylenes.” Journal of the American Chemical Society 139 no. 44 (2017): 15878-15890. 10.1021/jacs.7b08800.
“This work used computational and storage services associated with the Hoffman2 cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group, the NSF-supported Extreme Science and Engineering Discovery Environment (XSEDE) (OCI-1053575), and high-performance research computing resources provided by Texas A&M University (http://hprc.tamu.edu).” (Jordan et al., 2017, p. 15889)
Koch, Aaron A.; Douglas A. Hansen; Vikram V. Shende; Lawrence R. Furan; K. N. Houk; Gonzalo Jiménez-Osés, and David H. Sherman. “A Single Active Site Mutation in the Pikromycin Thioesterase Generates a More Effective Macrocyclization Catalyst.” Journal of the American Chemical Society 139 no. 38 (2017): 13456-13465. 10.1021/jacs.7b06436.
“Calculations were performed using the Extreme Science and Engineering Discovery Environment (XSEDE), which is funded by the NSF (OCI-1053575), UR (Beronia cluster), and the UCLA Institute of Digital Research and Education (IDRE).” (Koch et al., 2017, p. 13464)
Krishnan, NMA; B Wang; G Sant; JC Phillips, and M Bauchy. “Revealing the Effect of Irradiation on Cement Hydrates: Evidence of a Topological Self-Organization.” ACS APPLIED MATERIALS & INTERFACES 9 no. 37 (2017): 32377-32385. 10.1021/acsami.7b09405.
Lin, Janice B.; Yu Jin; Steven A. Lopez; Nathaniel Druckerman; Steven E. Wheeler, and K. N. Houk. “Torsional Barriers to Rotation and Planarization in Heterocyclic Oligomers of Value in Organic Electronics.” Journal of Chemical Theory and Computation 13 no. 11 (2017): 5624-5638. 10.1021/acs.jctc.7b00709.
“This work used computational and storage services associated with the Hoffman2 cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group, the NSF-supported Extreme Science and Engineering Discovery Environment (XSEDE)’s Gordon supercomputer (OCI1053575) at the San Diego Supercomputing Center, and high performance research computing resources provided by Texas A&M University (http://hprc.tamu.edu).” (Lin et al., 2017, p. 5634)
Lin, Janice B.; Tejas K. Shah; Adam E. Goetz; Neil K. Garg, and K. N. Houk. “Conjugated Trimeric Scaffolds Accessible from Indolyne Cyclotrimerizations: Synthesis, Structures, and Electronic Properties.” Journal of the American Chemical Society 139 no. 30 (2017): 10447-10455. 10.1021/jacs.7b05317.
“This work used computational and storage services associated with the Hoffman2 cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group and the NSF-supported Extreme Science and Engineering Discovery Environment (XSEDE)’s Gordon supercomputer (OCI1053575) at the San Diego Supercomputing Center.” (Lin et al., 2017, p. 10453)
Messina, MS; JH Ko; ZY Yang; MJ Strouse; KN Houk, and HD Maynard. “Effect of trehalose polymer regioisomers on protein stabilization.” POLYMER CHEMISTRY 8 no. 33 (2017): 4781-4788. 10.1039/c7py00700k.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Messina et al., 2017, p. 4787)
Park, Jiyong; Sunny Chun; Thomas A. Bobik; Kendall N. Houk, and Todd O. Yeates. “Molecular Dynamics Simulations of Selective Metabolite Transport across the Propanediol Bacterial Microcompartment Shell.” The Journal of Physical Chemistry B 121 no. 34 (2017): 8149-8154. 10.1021/acs.jpcb.7b07232.
“Computations from this work were run and analyzed on the UCLA IDRE Hoffman2 cluster, the Keeneland and Stampede supercomputers through the XSEDE program (TG-CHE040013N), and the UCLA-DOE Cassini cluster, supported by the BER program of the DOE Office of Science under Award No. DE-FC02-2ER63421.” (Park et al., 2017, p. 8153)
Reavis, Eric A.; Junghee Lee; Jonathan K. Wynn; Stephen A. Engel; Mark S. Cohen; Keith H. Nuechterlein; David C. Glahn; Lori L. Altshuler, and Michael F. Green. “Assessing neural tuning for object perception in schizophrenia and bipolar disorder with multivariate pattern analysis of fMRI data.” NeuroImage: Clinical 16 (2017): 491-497. 10.1016/j.nicl.2017.08.023.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Reavis et al., 2017, p. 496)
Robinson, P. J.; X. Zhang, and T. McQueen. “SmB6– Cluster Anion: Covalency Involving f Orbitals.” The Journal of … (2017).
“UCLA IDRE cluster Hoffman2 was used for all calculations.” (Robinson et al., 2017, p. 1853)
Robinson, Paul J.; Gaoxiang Liu; Sandra Ciborowski; Chalynette Martinez-Martinez; Juan R. Chamorro; Xinxing Zhang; Tyrel M. McQueen; Kit H. Bowen, and Anastassia N. Alexandrova. “Mystery of Three Borides: Differential Metal–Boron Bonding Governing Superhard Structures.” Chemistry of Materials 29 no. 23 (2017): 9892-9896. 10.1021/acs.chemmater.7b04378.
“UCLA IDRE cluster Hoffman2 was used for all calculations.” (Robinson et al., 2017, p. 9895)
Simon, A; YH Lam, and KN Houk. “Origins of Stereoselectivity of Enamine-Iminium-Activated Nazarov Cyclizations by Vicinal Diamines.” JOURNAL OF ORGANIC CHEMISTRY 82 no. 15 (2017): 8186-8190. 10.1021/acs.joc.7b01606.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s (IDRE) Research Technology Group.” (Simon et al., 2017, p. 8189)
Sudarsan V. S. Ranganathan; Tong Mu, and Richard D. Wesel. “Allocating Redundancy Between Erasure Coding and Channel Coding When Fading Channel Diversity Grows With Codeword Length | IEEE Journals & Magazine | IEEE Xplore.” (2017).
” The work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Sudarsan V. S. Ranganathan; Tong Mu; Richard D. Wesel, 2017, p. 3236)
Ugur, Ilke; Sesil Agopcan Cinar; Burcu Dedeoglu; Viktorya Aviyente; M. Frederick Hawthorne; Peng Liu; Fang Liu; K. N. Houk, and Gonzalo Jiménez-Osés. “1,3-Dipolar Cycloaddition Reactions of Low-Valent Rhodium and Iridium Complexes with Arylnitrile N-Oxides.” The Journal of Organic Chemistry 82 no. 10 (2017): 5096-5101. 10.1021/acs.joc.7b00282.
“Computing resources used in this work were provided by the TUBITAK ULAKBIM High Performance and Grid Computing Center, the National Center for High Performance Computing (UHeM) under grant number 11062010, CESGA, UR (Beronia cluster), and UCLA Academic Technology Services/Institute for Digital Research and Education.” (Ugur et al., 2017, p. 5101)
Zhou, CC; MF Hawthorne; KN Houk, and G Jiménez-Osés. “Multiple Mechanisms for the Thermal Decomposition of Metallaisoxazolin-5-ones from Computational Investigations.” JOURNAL OF ORGANIC CHEMISTRY 82 no. 16 (2017): 8438-8443. 10.1021/acs.joc.7b01169.
“Computing resources used in this work were provided by CESGA, UR (Beronia cluster), UCLA Academic Technology Services/Institute for Digital Research and Education, and IDRE and XSEDE (NSF OCI-1053575).” (Zhou et al., 2017, p. 8443)
Zou, Y; M Garcia-Borràs; MC Tang; Y Hirayama; DH Li; L Li; K Watanabe; KN Houk, and Y Tang. “Enzyme-catalyzed cationic epoxide rearrangements in quinolone alkaloid biosynthesis.” NATURE CHEMICAL BIOLOGY 13 no. 3 (2017): 325-+. 10.1038/NCHEMBIO.2283.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Zou et al., 2017, p. 332)
Theses for 2017¶
Huang, Chien-Jung. “Numerical Tool Development of Fluid-Structure Interactions in Upper Airway for Investigation of Obstructive Sleep Apnea.” Ph.D. Thesis, University of California, Los Angeles, 2017. ProQuest, https://www.proquest.com/docview/1989042248.
“Three kinds of size of test problems are listed in the table 4.2. The tests are conducted on the Hoffman2 Cluster in UCLA Institute for Digital Research and Education (IDRE) with intel E5-2670 processors.” (Huang, 2017, p. 85)
Jalal, Siavash. “Using Monte Carlo Normal Distributions to Evaluate Structural Models with Nonnormal Data.” Ph.D. Thesis, University of California, Los Angeles, 2017. ProQuest, https://www.proquest.com/docview/1914650890.
“I would like to thank Raffaella D’Auria from UCLA Hoffman2 IDRE for technical support.” (Jalal, 2017, pp. -) “To expedite the computation process a cluster computation from the Hoffman2 shared cluster1 has been used.” (Jalal, 2017, p. 23) “The Hoffman2 cluster is a campus computing resource at UCLA, maintain by the Institute for Digital Research and Education (IDRE).” (Jalal, 2017, p. 23)
Conference Papers for 2017¶
Hatamizadeh, Ali; Yuanping Song, and Jonathan B. Hopkins. “Geometry Optimization of Flexure System Topologies Using the Boundary Learning Optimization Tool (BLOT).” In Volume 5A: 41st Mechanisms and Robotics Conference: ASME 2017 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference Cleveland, Ohio, USA, 2017: V05AT08A009. 10.1115/DETC2017-67465.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Hatamizadeh et al., 2017, p. 10)
Ranganathan, Sudarsan V. S.; Dariush Divsalar, and Richard D. Wesel. “Design of improved quasi-cyclic protograph-based Raptor-like LDPC codes for short block-lengths.” In 2017 IEEE International Symposium on Information Theory (ISIT): 2017 IEEE International Symposium on Information Theory (ISIT) 2017: 1207-1211. 10.1109/ISIT.2017.8006720.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Ranganathan et al., 2017, p. 1207) ISSN: 2157-8117
2016¶
- 20 publications for 2016
Journal Articles for 2016¶
Arneson, D; A Bhattacharya; L Shu; VP Mäkinen, and X Yang. “Mergeomics: a web server for identifying pathological pathways, networks, and key regulators via multidimensional data integration.” BMC GENOMICS 17 (2016). 10.1186/s12864-016-3057-8.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Arneson et al., 2016, p. 8) Publication Title: BMC genomics Type: 10.1186/s12864-016-3057-8
Freedman, Adam H.; Rena M. Schweizer; Diego Ortega-Del Vecchyo; Eunjung Han; Brian W. Davis; Ilan Gronau; Pedro M. Silva; Marco Galaverni; Zhenxin Fan; Peter Marx; Belen Lorente-Galdos; Oscar Ramirez; Farhad Hormozdiari; Can Alkan; Carles Vilà; Kevin Squire; Eli Geffen; Josip Kusak; Adam R. Boyko; Heidi G. Parker; Clarence Lee; Vasisht Tadigotla; Adam Siepel; Carlos D. Bustamante; Timothy T. Harkins; Stanley F. Nelson; Tomas Marques-Bonet; Elaine A. Ostrander; Robert K. Wayne, and John Novembre. “Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs.” PLOS Genetics 12 no. 3 (2016): e1005851. 10.1371/journal.pgen.1005851.
“The computations in this paper were run on the Hoffmann2 cluster supported by the IDRE Research Technology Group at the University of California, Los Angeles, and the Odyssey cluster supported by the FAS Division of Science, Research Computing Group at Harvard University.” (Freedman et al., 2016, p. 19)
Gao, SS; AB Duan; W Xu; PY Yu; L Hang; KN Houk, and Y Tang. “Phenalenone Polyketide Cyclization Catalyzed by Fungal Polyketide Synthase and Flavin-Dependent Monooxygenase.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 138 no. 12 (2016): 4249-4259. 10.1021/jacs.6b01528.
“Computational re-sources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Gao et al., 2016, p. 15)
Grandner, JM; RA Cacho; Y Tang, and KN Houk. “Mechanism of the P450-Catalyzed Oxidative Cyclization in the Biosynthesis of Griseofulvin.” ACS CATALYSIS 6 no. 7 (2016): 4506-4511. 10.1021/acscatal.6b01068.
“We are thankful to the NSF funded XSEDE supercomputer resources (OCI-1053575) and the UCLA IDRE Hoffman2 cluster for the computational resources.” (Grandner et al., 2016, p. 5)
Grayson, MN and KN Houk. “Cinchona Alkaloid-Catalyzed Asymmetric Conjugate Additions: The Bifunctional Bronsted Acid-Hydrogen Bonding Model.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 138 no. 4 (2016): 1170-1173. 10.1021/jacs.5b13275.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI1053575).” (Grayson and Houk, 2016, p. 3)
Grayson, MN and KN Houk. “Cinchona Urea-Catalyzed Asymmetric Sulfa-Michael Reactions: The Bronsted Acid-Hydrogen Bonding Model.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 138 no. 29 (2016): 9041-9044. 10.1021/jacs.6b05074.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Grayson and Houk, 2016, p. 9044)
Guo, Peng; Bu Wang; Mathieu Bauchy, and Gaurav Sant. “Misfit Stresses Caused by Atomic Size Mismatch: The Origin of Doping-Induced Destabilization of Dicalcium Silicate.” Crystal Growth & Design 16 no. 6 (2016): 3124-3132. 10.1021/acs.cgd.5b01740.
“Access to computational resources was provisioned by (a) Laboratory for the Chemistry of Construction Materials (LC2), (b) Institute for Digital Research and Education (IDRE) at UCLA, and (c) Extreme Science and Engineering Discovery Environment (XSEDE) supported by the National Science Foundation (OCI-1053575 and DMR-130039)” (Guo et al., 2016, p. 3130)
Ha, MA and AN Alexandrova. “Oxygen Vacancies of Anatase(101): Extreme Sensitivity to the Density Functional Theory Method.” JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12 no. 6 (2016): 2889-2895. 10.1021/acs.jctc.6b00095.
“Computational resources were provided 329 by the UCLA-IDRE cluster and the Air Force Research 330 Laboratory’s Spirit cluster.” (Ha and Alexandrova, 2016, p. 7)
Jimenez-Izal, E and AN Alexandrova. “σ-Aromaticity in polyhydride complexes of Ru, Ir, Os, and Pt.” PHYSICAL CHEMISTRY CHEMICAL PHYSICS 18 no. 17 (2016): 11644-11652. 10.1039/c5cp04330a.
“Computational resources were provided by the UCLA-IDRE cluster.” (Jimenez-Izal and Alexandrova, 2016, p. 11651)
Lin, HC; TC McMahon; A Patel; M Corsello; A Simon; W Xu; MX Zhao; KN Houk; NK Garg, and Y Tang. “P450-Mediated Coupling of Indole Fragments To Forge Communesin and Unnatural Isomers.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 138 no. 12 (2016): 4002-4005. 10.1021/jacs.6b01413.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Lin et al., 2016, p. 6)
Lotfollahi, M.; M. M. Alinia, and E. Taciroglu. “Validated finite element techniques for quasi-static cyclic response analyses of braced frames at sub-member scales.” Engineering Structures 106 (2016): 222-242. 10.1016/j.engstruct.2015.07.049.
“This research was initiated while the first author’s was a visiting Ph.D. student at the University of California, Los Angeles (UCLA). He gratefully acknowledges the UCLA’s financial support and for allowing the use of the Hoffman2 Cluster for analyses.” (Lotfollahi et al., 2016, p. 241)
Nechay, MR; NM Gallup; A Morgenstern; QA Smith; ME Eberhart, and AN Alexandrova. “Histone Deacetylase 8: Characterization of Physiological Divalent Metal Catalysis.” JOURNAL OF PHYSICAL CHEMISTRY B 120 no. 26 (2016): 5884-5895. 10.1021/acs.jpcb.6b00997.
“Computational resources were provided by the UCLA-IDRE cluster.” (Nechay et al., 2016, p. 5893)
Pignatelli, I; A Kumar; R Alizadeh; Y Le Pape; M Bauchy, and G Sant. “A dissolution-precipitation mechanism is at the origin of concrete creep in moist environments.” JOURNAL OF CHEMICAL PHYSICS 145 no. 5 (2016). 10.1063/1.4955429.
“Access to computational resources was provisioned by the Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), the Laboratory for the Chemistry of Construction Materials (LC2), and the Institute for Digital Research and Education (IDRE) at UCLA.” (Pignatelli et al., 2016, p. 10)
Pignatelli, I; A Kumar; M Bauchy, and G Sant. “Topological Control on Silicates’ Dissolution Kinetics.” LANGMUIR 32 no. 18 (2016): 4434-4439. 10.1021/acs.langmuir.6b00359.
“Access to computational resources was provisioned by the Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), the Laboratory for the Chemistry of Construction Materials (LC2) and the Institute for Digital Research and Education (IDRE) at UCLA.” (Pignatelli et al., 2016, p. 5)
Rodríguez, Elsa; Matthew N. Grayson; Amparo Asensio; Pablo Barrio; K. N. Houk, and Santos Fustero. “Chiral Brønsted Acid-Catalyzed Asymmetric Allyl(propargyl)boration Reaction of ortho-Alkynyl Benzaldehydes: Synthetic Applications and Factors Governing the Enantioselectivity.” ACS Catalysis 6 no. 4 (2016): 2506-2514. 10.1021/acscatal.6b00209.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Rodríguez et al., 2016, p. 2512)
Rose, TE; BH Curtin; KV Lawson; A Simon; KN Houk, and PG Harran. “On the prevalence of bridged macrocyclic pyrroloindolines formed in regiodivergent alkylations of tryptophan.” CHEMICAL SCIENCE 7 no. 7 (2016): 4158-4166. 10.1039/c5sc04612b.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE).” (Rose et al., 2016, p. 4164)
Simon, Adam; Alexander J. Yeh; Yu-hong Lam, and K. N. Houk. “Origins of Stereoselectivity of Chiral Vicinal Diamine-Catalyzed Aldol Reactions.” The Journal of Organic Chemistry 81 no. 24 (2016): 12408-12415. 10.1021/acs.joc.6b02542.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s (IDRE) Research Technology Group.” (Simon et al., 2016, p. 12414)
Theses for 2016¶
Cooper, Aaron. “Integration site-based clonality analyses of potency of stem and progenitor cells and safety in human gene and cell therapy.” Ph.D. Thesis, University of California, Los Angeles, 2016. ProQuest, https://www.proquest.com/docview/1771706416.
“I also thank the staff of the UCLA Institute for Digital Research and Education (IDRE) who maintain the Hoffman2 cluster, which has been an essential resource in my research.” (Cooper, 2016, p. 14)
Lu, Xiang. “Handling Incomplete High-Dimensional Multivariate Longitudinal Data with Mixed Data Types by Multiple Imputation Using a Longitudinal Factor Analysis Model.” Ph.D. Thesis, University of California, Los Angeles, 2016. ProQuest, https://www.proquest.com/docview/1775739671.
“We use a script “R.q” to build a command file (.cmd) for the R program. A complete list of available scientific computing software and corresponding instructions is available in the document “Hoffman 2 software” available at http://www.hoffman2.idre.ucla.edu/software/ .” (Lu, 2016, p. 53) “The ensemble of R as a programming interface, C++ as a low-level language, the Scythe Statistical Library as an efficient toolkit for familiar statistically-relevant computational tasks, and the Hoffman 2 parallel computing environment thus provided a powerful engine for carrying at multiple imputation for high-dimensional multivariate incomplete data sets with mixed data types and longitudinal structure.” (Lu, 2016, p. 58)
Conference Papers for 2016¶
Ita, Harald; Fernando Febres Cordero, and Philipp Hofmann. “Di-vector Boson Production in Association with Multiple Jets at the LHC.” In Proceedings of The European Physical Society Conference on High Energy Physics — PoS(EPS-HEP2015): The European Physical Society Conference on High Energy Physics Vienna, Austria, 2016: 493. 10.22323/1.234.0493.
“This work was performed on the bwUniCluster funded by the Ministry of Science, Research and the Arts Baden-Württemberg and the Universities of the State of BadenWürttemberg, Germany, within the framework program bwHP, as well as using the computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Ita et al., 2016, p. 7)
2015¶
- 40 publications for 2015
10 Theses
Journal Articles for 2015¶
Boeser, CL; JC Holder; BLH Taylor; KN Houk; BM Stoltz, and RN Zare. “Mechanistic analysis of an asymmetric palladium-catalyzed conjugate addition of arylboronic acids to β-substituted cyclic enones.” CHEMICAL SCIENCE 6 no. 3 (2015): 1917-1922. 10.1039/c4sc03337j.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF.” (Boeser et al., 2015, p. 5)
Cokus, Shawn J.; Paul F. Gugger, and Victoria L. Sork. “Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks.” BMC Genomics 16 no. 1 (2015): 552. 10.1186/s12864-015-1761-4.
“We also acknowledge the University of California Reserve System and the California Department of Parks and Recreation for access to some sample sites; the Neuroscience Genomics Core at UCLA for its sequencing facilities; and the computational services available through the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Cokus et al., 2015, p. 15)
Dadras, J; E Jimenez-Izal, and AN Alexandrova. “Alloying Pt Sub-nano-clusters with Boron: Sintering Preventative and Coke Antagonist?.” ACS CATALYSIS 5 no. 10 (2015): 5719-5727. 10.1021/acscatal.5b01513.
“Computational resources were provided by the UCLA IDRE cluster.” (Dadras et al., 2015, p. 5726)
Dadras, J; L Shen, and A Alexandrova. “Pt-Zn Clusters on Stoichiometric MgO(100) and TiO2(110): Dramatically Different Sintering Behavior.” JOURNAL OF PHYSICAL CHEMISTRY C 119 no. 11 (2015): 6047-6055. 10.1021/jp512277x.
“Computational resources were provided by the UCLA-IDRE cluster.” (Dadras et al., 2015, p. 6053)
Decyk, Viktor K.. “Skeleton Particle-in-Cell Codes on Emerging Computer Architectures.” Computing in Science & Engineering 17 no. 2 (2015): 47-52. 10.1109/MCSE.2014.131.
“This work was supported by the US Department of Energy, the National Science Foundation, and the UCLA Institute for Digital Research and Education (IDRE).” (Decyk, 2015, p. 5) Conference Name: Computing in Science & Engineering
Grayson, MN; MJ Krische, and KN Houk. “Ruthenium-Catalyzed Asymmetric Hydrohydroxyalkylation of Butadiene: The Role of the Formyl Hydrogen Bond in Stereochemical Control.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 137 no. 27 (2015): 8838-8850. 10.1021/jacs.5b04844.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Grayson et al., 2015, p. 8)
Hie, Liana; Noah F. Fine Nathel; Tejas K. Shah; Emma L. Baker; Xin Hong; Yun-Fang Yang; Peng Liu; K. N. Houk, and Neil K. Garg. “Conversion of amides to esters by the nickel-catalysed activation of amide C–N bonds.” Nature 524 no. 7563 (2015): 79-83. 10.1038/nature14615.
“Computations were performed with resources made available by the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (grant number OCI-1053575), as well as the UCLA Institute of Digital Research and Education (IDRE).” (Hie et al., 2015, p. 83)
Hog, DT; FME Huber; G Jiménez-Osés; P Mayer; KN Houk, and D Trauner. “Evolution of a Unified Strategy for Complex Sesterterpenoids: Progress toward Astellatol and the Total Synthesis of (-)-Nitidasin.” CHEMISTRY-A EUROPEAN JOURNAL 21 no. 39 (2015): 13646-13665. 10.1002/chem.201501423.
“This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575) along with the UCLA Institute of Digital Research and Education (IDRE).” (Hog et al., 2015, p. 20)
Huang, J; L Valenzano, and G Sant. “Framework and Channel Modifications in Mayenite (12CaO•7Al2O3) Nanocages By Cationic Doping.” CHEMISTRY OF MATERIALS 27 no. 13 (2015): 4731-4741. 10.1021/acs.chemmater.5b01360.
“Access to computational resources was provided by (a) the Laboratory for the Chemistry of Construction Materials (LC2), (b) the Institute for Digital Research and Education (IDRE) at UCLA, and (c) the Extreme Science and Engineering Discovery Environment (XSEDE), which was supported by the National Science Foundation (Nos. OCI-1053575 and DMR-130039).” (Huang et al., 2015, p. 4740)
Huang, Jian; Bu Wang; Yingtian Yu; Loredana Valenzano; Mathieu Bauchy, and Gaurav Sant. “Electronic Origin of Doping-Induced Enhancements of Reactivity: Case Study of Tricalcium Silicate.” The Journal of Physical Chemistry C 119 no. 46 (2015): 25991-25999. 10.1021/acs.jpcc.5b08286.
“Access to parallel computational resources was provisioned by the Laboratory for the Chemistry of Construction Materials (LC2), the Physics of AmoRphous and Inorganic Solids Laboratory (PARISlab), the Institute for Digital Research and Education (IDRE) at UCLA, and the Extreme Science and Engineering Discovery Environment (XSEDE) supported by the U.S. National Science Foundation (OCI-1053575 and DMR-130039).” (Huang et al., 2015, p. 25998)
Jackson, T. S.; Gunnar Möller, and Rahul Roy. “Geometric stability of topological lattice phases.” Nature Communications 6 no. 1 (2015): 8629. 10.1038/ncomms9629.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.”(Jackson et al., 2015, p. 11)
Kellerman, A. C.; Y. Y. Shprits; R. A. Makarevich; E. Spanswick; E. Donovan, and G. Reeves. “Characterization of the energy-dependent response of riometer absorption.” Journal of Geophysical Research: Space Physics 120 no. 1 (2015): 615-631. 10.1002/2014JA020027.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Kellerman et al., 2015, p. 629)
Lam, Yu-hong and K. N. Houk. “Origins of Stereoselectivity in Intramolecular Aldol Reactions Catalyzed by Cinchona Amines.” Journal of the American Chemical Society 137 no. 5 (2015): 2116-2127. 10.1021/ja513096x.
“The computational resources from UCLA Institute for Digital Research and Education and the National Science Foundation through XSEDE resources provided by the XSEDE Science Gateways Program (TG-CHE040013N) are gratefully acknowledged.” (Lam and Houk, 2015, p. 2125)
Liao, Wei; Gwen Jordaan; Phillipp Nham; Ryan T. Phan; Matteo Pelegrini, and Sanjai Sharma. “Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.” BMC Cancer 15 no. 1 (2015): 714. 10.1186/s12885-015-1708-9.
“RNA-seq data were analyzed using the UCLA Galaxy server (galaxy.hoffman2.idre.ucla.edu).” (Liao et al., 2015, p. 2)
Mao, Xu-Ming; Zha-Jun Zhan; Matthew N. Grayson; Man-Cheng Tang; Wei Xu; Yong-Quan Li; Wen-Bing Yin; Hsiao-Ching Lin; Yit-Heng Chooi; K. N. Houk, and Yi Tang. “Efficient Biosynthesis of Fungal Polyketides Containing the Dioxabicyclo-octane Ring System.” Journal of the American Chemical Society 137 no. 37 (2015): 11904-11907. 10.1021/jacs.5b07816.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI1053575).” (Mao et al., 2015, p. 11907)
McMahon, TC; JM Medina; YF Yang; BJ Simmons; KN Houk, and NK Garg. “Generation and Regioselective Trapping of a 3,4-Piperidyne for the Synthesis of Functionalized Heterocycles.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 137 no. 12 (2015): 4082-4085. 10.1021/jacs.5b01589.
“This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575) along with the UCLA Institute of Digital Research and Education (IDRE).” (McMahon et al., 2015, p. 4)
Narayan, Alison R. H.; Gonzalo Jiménez-Osés; Peng Liu; Solymar Negretti; Wanxiang Zhao; Michael M. Gilbert; Raghunath O. Ramabhadran; Yun-Fang Yang; Lawrence R. Furan; Zhe Li; Larissa M. Podust; John Montgomery; K. N. Houk, and David H. Sherman. “Enzymatic hydroxylation of an unactivated methylene C–H bond guided by molecular dynamics simulations.” Nature Chemistry 7 no. 8 (2015): 653-660. 10.1038/nchem.2285.
“Calculations were performed using the Extreme Science and Engineering Discovery Environment (XSEDE), which is funded by the NSF (OCI-1053575), and the UCLA Institute of Digital Research and Education (IDRE).” (Narayan et al., 2015, p. 660)
Nedd, S. and A. N. Alexandrova. “The mechanism of the Pd-catalyzed formation of coumarins: a theoretical study.” Physical Chemistry Chemical Physics 17 no. 2 (2015): 1347-1353. 10.1039/C4CP03418J.
“The calculations were carried out on the computers of the Hoffman2 cluster at the Institute for Digital Research and Education (IDRE) located in the University of California, Los Angeles.” (Nedd and N. Alexandrova, 2015, p. 8)
Noey, Elizabeth L.; Nidhi Tibrewal; Gonzalo Jiménez-Osés; Sílvia Osuna; Jiyong Park; Carly M. Bond; Duilio Cascio; Jack Liang; Xiyun Zhang; Gjalt W. Huisman; Yi Tang, and Kendall N. Houk. “Origins of stereoselectivity in evolved ketoreductases.” Proceedings of the National Academy of Sciences 112 no. 51 (2015): E7065-E7072. 10.1073/pnas.1507910112.
“This work was performed using the Extreme Science and Engineering Discovery Environment, which is supported by the National Science Foundation (Grant OCI-1053575) and the University of California, Los Angeles (UCLA) Institute for Digital Research and Education’s Hoffman2 computer cluster.” (Noey et al., 2015, p. 7071)
Numajiri, Yoshitaka; Gonzalo Jiménez-Osés; Bo Wang; K. N. Houk, and Brian M. Stoltz. “Enantioselective Synthesis of Dialkylated N-Heterocycles by Palladium-Catalyzed Allylic Alkylation.” Organic Letters 17 no. 5 (2015): 1082-1085. 10.1021/ol503425t.
“G.J.O. and K.N.H. used the Extreme Science and Engineering Discovery Environment (XSEDE) supported by a grant (OCI1053575) along with the UCLA Institute of Digital Research and Education (IDRE).” (Numajiri et al., 2015, p. 1084)
Pan, Andrew and Chi On Chui. “Gate-Induced Source Tunneling FET (GISTFET).” IEEE Transactions on Electron Devices 62 no. 8 (2015): 2390-2395. 10.1109/TED.2015.2445343.
“This work used computational and storage services associated with the California NanoSystems Institute and the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Pan and Chui, 2015, p. 2394) Conference Name: IEEE Transactions on Electron Devices
Pan, Andrew; Greg Leung, and Chi On Chui. “Junctionless Silicon and In0.53Ga0.47As Transistors—Part I: Nominal Device Evaluation With Quantum Simulations.” IEEE Transactions on Electron Devices 62 no. 10 (2015): 3199-3207. 10.1109/TED.2015.2464291.
“This work used computational and storage services associated with the California NanoSystems Institute and the Hoffman2 Shared Cluster provided by the UCLA Institute for Digital Research and Education’s Research Technology Group.” (Pan et al., 2015, p. 8) Conference Name: IEEE Transactions on Electron Devices
Patel, Ashay; Joseph R. Vella; Zhi-Xiong Ma; R. P. Hsung, and K. N. Houk. “Transition State Gauche Effects Control the Torquoselectivities of the Electrocyclizations of Chiral 1-Azatrienes.” The Journal of Organic Chemistry 80 no. 23 (2015): 11888-11894. 10.1021/acs.joc.5b02085.
“‘This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group in addition to the NSF-supported Extreme Science and Engineering Discovery Environment (XSEDE)’s Trestles and Gordon supercomputers (OCI-1053575) at the San Diego Supercomputing Center.” (Patel et al., 2015, p. 11893)
Pulugundla, Gautam; Sergey Smolentsev; Tyler Rhodes; Charlie Kawczynski, and Mohamed Abdou. “Transition to a Quasi-Fully Developed MHD Flow in an Electrically Conducting Pipe under a Transverse Non-Uniform Magnetic Field.” Fusion Science and Technology 68 no. 3 (2015): 684–689. 10.13182/FST14-983.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Pulugundla et al., 2015, p. 689)
Pérez-Estrada, Salvador; Braulio Rodrı́guez-Molina; Leilei Xiao; Rosa Santillan; Gonzalo Jiménez-Osés; K. N. Houk, and Miguel A. Garcia-Garibay. “Thermodynamic Evaluation of Aromatic CH/π Interactions and Rotational Entropy in a Molecular Rotor.” Journal of the American Chemical Society 137 no. 6 (2015): 2175-2178. 10.1021/ja512053t.
“This work was supported by the National Science Foundation (Grant DMR1402682 to M.G.-G. and CHE-1361104 to K.N.H.) and used the Extreme Science and Engineering Discovery Environment (XSEDE) supported by Grant OCI1053575 along with the UCLA Institute of Digital Research and Education (IDRE).” (Pérez-Estrada et al., 2015, p. 2178)
Richmond, Edward; Kenneth B. Ling; Nicolas Duguet; Lois B. Manton; Nihan Çelebi-Ölçüm; Yu-Hong Lam; Sezen Alsancak; Alexandra M. Z. Slawin; K. N. Houk, and Andrew D. Smith. “An asymmetric pericyclic cascade approach to 3-alkyl-3-aryloxindoles: generality, applications and mechanistic investigations.” Organic & Biomolecular Chemistry 13 no. 6 (2015): 1807-1817. 10.1039/C4OB02526A.
“We also thank the UCLA Institute for Digital Research and Education (IDRE), the XSEDE resources provided by the XSEDE Science Gateways Program (TG-CHE040013N) of the National Science Foundation (USA), and TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA, Turkey) for generous computer time.” (Richmond et al., 2015, p. 1815)
Robinson, PJ and AN Alexandrova. “Assessing the Bonding Properties of Individual Molecular Orbitals.” JOURNAL OF PHYSICAL CHEMISTRY A 119 no. 51 (2015): 12862-12867. 10.1021/acs.jpca.5b09687.
“Computational resources were provided by the UCLA-IDRE cluster.” (Robinson and Alexandrova, 2015, p. 12866)
Zhai, HC; MA Ha, and AN Alexandrova. “AFFCK: Adaptive Force-Field-Assisted ab Initio Coalescence Kick Method for Global Minimum Search.” JOURNAL OF CHEMICAL THEORY AND COMPUTATION 11 no. 5 (2015): 2385-2393. 10.1021/acs.jctc.5b00065.
“Computational resources were provided by the UCLA-IDRE cluster.” (Zhai et al., 2015, p. 2393)
Zhang, XX; PJ Robinson; G Ganteför; A Alexandrova, and KH Bowen. “Photoelectron spectroscopic and theoretical study of the [HPd(η2-H2)]-cluster anion.” JOURNAL OF CHEMICAL PHYSICS 143 no. 9 (2015). 10.1063/1.4929998.
“Computational resources were provided by the UCLA-IDRE Cluster.” (Zhang et al., 2015, p. 6)
Theses for 2015¶
Asensio, Omar Isaac. “Human Behavior and Intelligent Energy Metering Systems: Experimental Approaches.” D.Env. Thesis, University of California, Los Angeles, 2015. ProQuest, https://www.proquest.com/docview/1696076374.
“Overarching the statistical models in this dissertation, I would also like to acknowledge the Hoffman2 high performance computing facilities managed by the IDRE Research Technology group, which were invaluable throughout this time for statistical computing with large data sets.” (Asensio, 2015, p. 16)
Boyce, Scott Elliott. “Model Reduction via Proper Orthogonal Decomposition of Transient Confined and Unconfined Groundwater-Flow.” Ph.D. Thesis, University of California, Los Angeles, 2015. ProQuest, https://www.proquest.com/docview/1732406259.
“This research also was supported in part by the Institute of Digital Research and Education at the University of California, Los Angeles through the Hoffman2 shared computing resources.” (Boyce, 2015, p. 54)
Frewen, Shane Franklin Nishi. “Eccentric planets around evolved stars.” Ph.D. Thesis, University of California, Los Angeles, 2015. ProQuest, https://www.proquest.com/docview/1698504854.
“We ran the simulation, as well as those in Sections 2.4 and 2.6, on the UCLA Institute for Digital Research and Education (IDRE) Hoffman2 cluster using the Mercury integrator package (Chambers, 1999).” (Frewen, p. 26)
Lao, Liangfeng. “Economic Model Predictive Control: Handling Preventive Actuator and Sensor Maintenance and Application to Transport-Reaction Processes.” Ph.D. Thesis, University of California, Los Angeles, 2015. ProQuest, https://www.proquest.com/docview/1722488946.
“To conduct the CFD simulation of this small-scale reformer model, we used three computational nodes in UCLA’s Hoffman2 Cluster.” (Lao, 2015, p. 334)
Mackey, Joel Loren. “Quantum Mechanics and Molecular Dynamic Investigations of Organic Reactions.” Ph.D. Thesis, University of California, Los Angeles, 2015. ProQuest, https://www.proquest.com/docview/1739017545.
“Funding for my graduate studies was provided by the National Science Foundation (CHE-0548209) and computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Hoffman2 cluster along with the Extreme Science and Engineering Discovery Environment (XSEDE) (CHE040014).” (Mackey, p. 14)
Noey, Elizabeth Lynn. “Computational Studies of Organic, Organometallic, and Enzyme Catalysis.” Ph.D. Thesis, University of California, Los Angeles, 2015. ProQuest, https://www.proquest.com/docview/1664840592.
“I am grateful for the computing resources: UCLA IDRE Hoffman2 computing cluster, the San Diego Supercomputing Center, the Pittsburgh Supercomputing Center and the use of ANTON, and the KNH computing cluster.” (Noey, 2015, pp. -)
Pan, Andrew Samuel. “Physics and Modeling of Tunneling in Low Power Transistors.” Ph.D. Thesis, University of California, Los Angeles, 2015. ProQuest, https://www.proquest.com/docview/1722048563.
“Many of the Green’s function calculations performed throughout this work were carried out using the Hoffman2 shared cluster provided by the UCLA Institute for Digital Research and Education (IDRE)’s Research Technology Group.” (Pan, p. 22)
Pan, Qingjiang. “Charged Particle Energization and Transport in the Magnetotail during Substorms.” Ph.D. Thesis, University of California, Los Angeles, 2015. ProQuest, https://www.proquest.com/docview/1709243674.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Pan, p. 17)
Park, Hyun Wook. “A Numerical Study of the Effects of Superhydrophobic Surfaces on Skin-Friction Drag Reduction in Wall-Bounded Shear Flows.” Ph.D. Thesis, University of California, Los Angeles, 2015. ProQuest, https://www.proquest.com/docview/1694579737.
“This research was supported by the ONR (Grant No. N000141110503 and N000141410291), NSF through XSEDE resources provided by SDSC and TACC, and Hoffman2 Cluster of the UCLA IDRE.” (Park, p. 18)
Patel, Ashay. “Understanding the Kinetics, Stereoselectivity, and Catalysis of Pericyclic Reactions in Chemistry and Biology through Quantum Mechanical Computations.” Ph.D. Thesis, University of California, Los Angeles, 2015. ProQuest, https://www.proquest.com/docview/1748046275.
“The following computational resources were used in this study: the Hoffman2 cluster at UCLA (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE)’s Trestles and Gordon supercomputers (OCI1053575) at the San Diego Supercomputing Center.” (Patel, 2015, p. 144)
Conference Papers for 2015¶
Park, Juw Won; Julia Chariker, and Yi Xing. “Strand specific RNA-seq data for higher specificity.” In Proceedings of the 2015 Conference on research in adaptive and convergent systems: New York, NY, USA, 2015: 123–124. 10.1145/2811411.2814709.
“This work used computational and storage services associated with the Hoffman2 Shared Cluster provided by UCLA Institute for Digital Research and Education’s Research Technology Group.” (Park et al., 2015, p. 2)
2014¶
- 17 publications for 2014
2 Theses
Journal Articles for 2014¶
Ascenzi, Maria-Grazia; Andre Lutz; Xia Du; Laureen Klimecky; Neal Kawas; Talia Hourany; Joelle Jahng; Jesse Chin; Yin Tintut; Udo Nackenhors, and Joyce Keyak. “Hyperlipidemia affects multiscale structure and strength of murine femur.” Journal of Biomechanics 47 no. 10 (2014): 2436-2443. 10.1016/j.jbiomech.2014.04.006.
“This research was supported by XSEDE (NSF Grant # OCI-1053575), UCLA’s Hoffman2 Cluster; and Orthopedic Hospital Research Center. The authors thank Active Life Scientific for microindentation, Alexandre Lomovtsev for image preparation, Josh Kimmel for manuscript preparation, and Mahidas Tatenani (XSEDE Extended Collaborative Support Service) and Tajendra Singh (UCLA’s Institute for Digital Research) for computing assistance.” (Ascenzi et al., 2014, p. 2442)
Breugst, Martin and K. N. Houk. “Computational Analysis of Cyclophane-Based Bisthiourea-Catalyzed Henry Reactions.” The Journal of Organic Chemistry 79 no. 13 (2014): 6302-6309. 10.1021/jo501227m.
“This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant OCI-1053575, resources from the UCLA Institute for Digital Research and Education (IDRE), and the Cologne High Efficiency Operating Platform for Sciences (CHEOPS).” (Breugst and Houk, 2014, p. 6308)
Choi, SR; M Breugst; KN Houk, and CD Poulter. “δ-Deuterium Isotope Effects as Probes for Transition-State Structures of lsoprenoid Substrates.” JOURNAL OF ORGANIC CHEMISTRY 79 no. 8 (2014): 3572-3580. 10.1021/jo500394u.
“This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant No. OCI1053575 and resources from the UCLA Institute for Digital Research and Education (IDRE).” (Choi et al., 2014, p. 3579)
Dornan, PK; KGM Kou; KN Houk, and VM Dong. “Dynamic Kinetic Resolution of Allylic Sulfoxides by Rh-Catalyzed Hydrogenation: A Combined Theoretical and Experimental Mechanistic Study.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 136 no. 1 (2014): 291-298. 10.1021/ja409824b.
“Computations were performed on the IDRE Hoffman2 cluster at UCLA and the HPCVL cluster at Queen’s University, Kingston.” (Dornan et al., 2014, p. 7)
Ha, Mai-Anh; Jonny Dadras, and Anastassia Alexandrova. “Rutile-Deposited Pt–Pd clusters: A Hypothesis Regarding the Stability at 50/50 Ratio.” ACS Catalysis 4 no. 10 (2014): 3570-3580. 10.1021/cs5011426.
“Computational resources were provided by the UCLA-IDRE cluster.” (Ha et al., 2014, p. 3579)
Huang, J; L Valenzano; TV Singh; R Pandey, and G Sant. “Influence of (Al, Fe, Mg) Impurities on Triclinic Ca3SiO5: Interpretations from DFT Calculations.” CRYSTAL GROWTH & DESIGN 14 no. 5 (2014): 2158-2171. 10.1021/cg401647f.
“Access to computational resources was provisioned by (a) the Laboratory for the Chemistry of Construction Materials (LC2), (b) the Institute for Digital Research and Education (IDRE) at UCLA, and (c) the Extreme Science and Engineering Discovery Environment (XSEDE) supported by the National Science Foundation (OCI-1053575 and DMR130039).” (Huang et al., 2014, p. 2170)
Jarvis, CL; MT Richers; M Breugst; KN Houk, and D Seidel. “Redox-Neutral α-Sulfenylation of Secondary Amines: Ring-Fused N,S-Acetals.” ORGANIC LETTERS 16 no. 13 (2014): 3556-3559. 10.1021/ol501509b.
“This work used resources from the UCLA Institute for Digital Research and Education (IDRE) and the Cologne High Efficiency Operating Platform for Sciences (CHEOPS).” (Jarvis et al., 2014, p. 3558)
Malik, HA; BLH Taylor; JR Kerrigan; JE Grob; KN Houk; J Du Bois; LG Hamann, and AW Patterson. “Non-directed allylic C-H acetoxylation in the presence of Lewis basic heterocycles.” CHEMICAL SCIENCE 5 no. 6 (2014): 2352-2361. 10.1039/c3sc53414f.
“Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF.” (Malik et al., 2014, p. 2360)
Matute, Ricardo A.; Miguel A. Garcia-Garibay, and K. N. Houk. “Theory of Substituent Effects on the Regioselectivity of Di-π-methane Rearrangements of Dibenzobarrelenes.” Organic Letters 16 no. 19 (2014): 5232-5234. 10.1021/ol5024823.
“Computer time was also provided by the UCLA Institute for Digital Research and Education (IDRE).” (Matute et al., 2014, p. 5234)
Medina, JM; JL Mackey; NK Garg, and KN Houk. “The Role of Aryne Distortions, Steric Effects, and Charges in Regioselectivities of Aryne Reactions.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 136 no. 44 (2014): 15798-15805. 10.1021/ja5099935.
“This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575) along with the UCLA Institute of Digital Research and Education (IDRE).” (Medina et al., 2014, p. 15803)
Medina, JM; TC McMahon; G Jiménez-Osés; KN Houk, and NK Garg. “Cycloadditions of Cyclohexynes and Cyclopentyne.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 136 no. 42 (2014): 14706-14709. 10.1021/ja508635v.
“This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575) along with the UCLA Institute of Digital Research and Education (IDRE).” (Medina et al., 2014, p. 14708)
Neufeldt, Sharon R.; Gonzalo Jiménez-Osés; Daniel L. Comins, and K. N. Houk. “A Twist on Facial Selectivity of Hydride Reductions of Cyclic Ketones: Twist-Boat Conformers in Cyclohexanone, Piperidone, and Tropinone Reactions.” The Journal of Organic Chemistry 79 no. 23 (2014): 11609-11618. 10.1021/jo5022635.
“This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation grant number ACI-1053575 along with the UCLA Institute of Digital Research and Education (IDRE).” (Neufeldt et al., 2014, p. 11617)
Prasad, G; AA Joshi; A Feng; AW Toga; PM Thompson, and D Terzopoulos. “Skull-stripping with machine learning deformable organisms.” JOURNAL OF NEUROSCIENCE METHODS 236 (2014): 114-124. 10.1016/j.jneumeth.2014.07.023.
“Additional support was from the UCLA I2-IDRE Research Informatics and Computational Data Development Grant to PT and GP.” (Prasad et al., 2014, p. 15)
Richers, MT; M Breugst; AY Platonova; A Ullrich; A Dieckmann; KN Houk, and D Seidel. “Redox-Neutral α-Oxygenation of Amines: Reaction Development and Elucidation of the Mechanism.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 136 no. 16 (2014): 6123-6135. 10.1021/ja501988b.
“This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant OCI-1053575, resources from the UCLA Institute for Digital Research and Education (IDRE), and the Cologne High Efficiency Operating Platform for Sciences (CHEOPS).” (Richers et al., 2014, p. 6133)
Simkin, M. V. and V. P. Roychowdhury. “Stochastic modeling of a serial killer.” Journal of Theoretical Biology 355 (2014): 111-116. 10.1016/j.jtbi.2014.03.039.
“Computations were performed at the UCLA IDRE Hoffman2 cluster.” (Simkin and Roychowdhury, 2014, p. 116)
Theses for 2014¶
Hong, Xin. “The Mechanism and Origins of Reactivities and Selectivities in Transition-metal-catalyzed and Organocatalyzed Cycloadditions.” Ph.D. Thesis, University of California, Los Angeles, 2014. ProQuest, https://www.proquest.com/docview/1541541378.
“Computer time was provided in part by the UCLA Institute for Digital Research and Education (IDRE) Hoffman2 cluster, and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Hong, 2014, pp. -)
Liu, Fang. “Theory of Gated Hemicarcerands and Diels-Alder Reactions of Tetrazines.” Ph.D. Thesis, University of California, Los Angeles, 2014. ProQuest, https://www.proquest.com/docview/1545890148.
“Computations were performed on the Extreme Science and Engineering Discovery Environment (XSEDE) and the UCLA IDRE Hoffman2 cluster.” (Liu, 2014, pp. -)
2013¶
- 20 publications for 2013
Journal Articles for 2013¶
Balu, Radhakrishnan; Prakashan Korambath; Ravindra Pandey, and Shashi P. Karna. “<i>Ab initio</i> study of nonlinear optical properties of aromatic fused rings.” Chemical Physics Letters 590 (2013): 58-62. 10.1016/j.cplett.2013.10.078.
“Calculations were performed on the Hoffman2 cluster at University of California, Los Angeles and DOD Supercomputing Resource Centers (DSRCs) located at the U.S. Army Research Laboratory.” (Balu et al., 2013, p. 62)
Bjelic, S; LG Nivón; N Çelebi-Ölçüm; G Kiss; CF Rosewall; HM Lovick; EL Ingalls; JL Gallaher; J Seetharaman; S Lew; GT Montelione; JF Hunt; FE Michael; KN Houk, and D Baker. “Computational Design of Enone-Binding Proteins with Catalytic Activity for the Morita-Baylis-Hillman Reaction.” ACS Chemical Biology 8 no. 4 (2013): 749-757. 10.1021/cb3006227.
“K.N.H. thanks the National Institute of General Medical Sciences, National Institutes of Health (GM075962) for financial support and acknowledges computer time on DESRES’s Anton special purpose supercomputer at the National Resource for Biomedical Supercomputing (NRBSC) at the Pittsburgh Supercomputing Center, and on the UCLA Institute for Digital Research and Education (IDRE) Hoffman 2 and Dawson 2 clusters.” (Bjelic et al., 2013, p. 9)
Breugst, M; A Eschenmoser, and KN Houk. “Theoretical Exploration of the Mechanism of Riboflavin Formation from 6,7-Dimethyl-8-ribityllumazine: Nucleophilic Catalysis, Hydride Transfer, Hydrogen Atom Transfer, or Nucleophilic Addition?.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 135 no. 17 (2013): 6658-6668. 10.1021/ja402099f.
“This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant No. OCI1053575, and resources from the UCLA Institute for Digital Research and Education (IDRE).” (Breugst et al., 2013, p. 6668)
Breugst, Martin; René Grée, and K. N. Houk. “Synergistic Effects between Lewis and Brønsted Acids: Application to the Prins Cyclization.” The Journal of Organic Chemistry 78 no. 19 (2013): 9892-9897. 10.1021/jo401628e.
“This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant OCI1053575, and resources from the UCLA Institute for Digital Research and Education (IDRE).” (Breugst et al., 2013, p. 9897)
Dieckmann, Arne; Martin Breugst, and K. N. Houk. “Zwitterions and Unobserved Intermediates in Organocatalytic Diels–Alder Reactions of Linear and Cross-Conjugated Trienamines.” Journal of the American Chemical Society 135 no. 8 (2013): 3237-3242. 10.1021/ja312043g.
“This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant Number OCI-1053575 and resources from the UCLA Institute for Digital Research and Education (IDRE).” (Dieckmann et al., 2013, p. 3241)
James, NC; JM Um; AB Padias; HK Hall, and KN Houk. “Computational Investigation of the Competition between the Concerted Diels-Alder Reaction and Formation of Diradicals in Reactions of Acrylonitrile with Nonpolar Dienes.” The Journal of Organic Chemistry 78 no. 13 (2013): 6582-6592. 10.1021/jo400900x.
“Computations were performed using the Extreme Science and Engineering Discovery Environment (XSEDE) resources supported by NSF (OCI-1053575) and the UCLA Institute for Digital Research and Education (IDRE) Hoffman2 cluster.” (James et al., 2013, p. 6591)
Kahros, A and BJ Schwartz. “Going beyond the frozen core approximation: Development of coordinate-dependent pseudopotentials and application to Na2+.” JOURNAL OF CHEMICAL PHYSICS 138 no. 5 (2013). 10.1063/1.4789425.
“We gratefully acknowledge the Institute for Digital Research and Education (IDRE) at UCLA for use of the hoffman2 computing cluster and William Glover and Jennifer Casey for helpful discussion.” (Kahros and Schwartz, 2013, p. 10)
Kahros, Argyris and Benjamin J. Schwartz. “Erratum: “Going beyond the frozen core approximation: Development of coordinate-dependent pseudopotentials and application to ${rm Na}_2^+ $ Na 2+” [J. Chem. Phys. 138, 054110 (2013)].” The Journal of Chemical Physics 139 no. 14 (2013): 149901. 10.1063/1.4823770.
“We gratefully acknowledge the Institute for Digital Research and Education (IDRE) at UCLA for use of the hoffman2 computing cluster and William Glover for helpful discussion.” (Kahros and Schwartz, 2013, p. 3)
Krenske, Elizabeth H.; Shuzhong He; Jian Huang; Yunfei Du; K. N. Houk, and Richard P. Hsung. “Intramolecular Oxyallyl–Carbonyl (3 + 2) Cycloadditions.” Journal of the American Chemical Society 135 no. 14 (2013): 5242-5245. 10.1021/ja312459b.
“We thank the NIH (GM-66055 to R.P.H), NSF (CHE0548209 to K.N.H.), Australian Research Council (FT120100632 and DP0985623 to E.H.K.), and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology (funding to E.H.K.) for generous financial support and the NCSA, UCLA ATS, UCLA IDRE, NCI NF (Australia), University of Queensland Research Computing Centre, and University of Melbourne for computer resources.” (Krenske et al., 2013, p. 5244)
Lee, Euntaek and Laurent Pilon. “Absorption and scattering by long and randomly oriented linear chains of spheres.” JOSA A 30 no. 9 (2013): 1892-1900. 10.1364/JOSAA.30.001892.
“The computation for this study was performed on the Hoffman2 cluster hosted by the Academic Technology Services (ATS) at the University of California, Los Angeles.” (Lee and Pilon, 2013, p. 1899)
Lopez, Steven A. and K. N. Houk. “Alkene Distortion Energies and Torsional Effects Control Reactivities, and Stereoselectivities of Azide Cycloadditions to Norbornene and Substituted Norbornenes.” The Journal of Organic Chemistry 78 no. 5 (2013): 1778-1783. 10.1021/jo301267b.
“The computations were performed on the UCLA IDRE Hoffman2 cluster.” (Lopez and Houk, 2013, p. 1782)
Ryazantsev, Sergey; Vladimir Tischenko; Christopher Nguyen; Vyacheslav Abramov, and Vladimir Zav’yalov. “Three-Dimensional Structure of the Human Myeloma IgG2.” PLOS ONE 8 no. 6 (2013): e64076. 10.1371/journal.pone.0064076.
“This research was supported in part by Institute of Digital Research and Education, University of California Los Angeles through Hoffman2 computing resources.” (Ryazantsev et al., 2013, p. 1)
Wang, Hao; Fang Liu; Roger C. Helgeson, and Kendall N. Houk. “Reversible Photochemically Gated Transformation of a Hemicarcerand to a Carcerand.” Angewandte Chemie International Edition 52 no. 2 (2013): 655-659. 10.1002/anie.201205376.
“Computations were performed on the Extreme Science and Engineering Discovery Environment (XSEDE), and on the UCLA IDRE Hoffman2 cluster.” (Wang et al., 2013, p. 655)
Theses for 2013¶
Arlen, Timothy Christian. “Constraining the Intergalactic Magnetic Field Through its Imprint on Gamma Ray Data from Distant Sources.” Ph.D. Thesis, University of California, Los Angeles, 2013. ProQuest, https://www.proquest.com/docview/1459459715.
“I wish to thank the funding agency that has supported this work, the National Science Foundation under grant award number 0969948, and acknowledge that the many simulations in my thesis were performed on the UCLA hoffman2 cluster.” (Arlen, p. xxi)
Athakitkarnka, Pavitra. “Gene Annotation in Rice Genome Using Homology.” M.S. Thesis, University of California, Los Angeles, 2013. ProQuest, https://www.proquest.com/docview/1420366991.
“In this project, I was able to search 67,393 rice amino acid query sequences against the protein sequence database of 49,966 rice-specific protein sequences using the computing power of the Hoffman2 cluster.” (Athakitkarnka, 2013, p. 27)
Wang, Hao. “Design and Synthesis of a Photoswitchable Gated Hemicarcerand and Computational Investigations of Stereoselective Organic Reactions.” Ph.D. Thesis, University of California, Los Angeles, 2013. ProQuest, https://www.proquest.com/docview/1442591532.
“Computations were performed on the Extreme Science and Engineering Discovery Environment (XSEDE), and on the UCLA IDRE Hoffman2 cluster.” (Wang, 2013, p. 16)
Zou, Lufeng. “Quantum Chemistry in Organic Reactions: Investigations of Mechanism and Stereoselectivity in C-H Bond Functionalizations and Cycloaddition Reactions.” Ph.D. Thesis, University of California, Los Angeles, 2013. ProQuest, https://www.proquest.com/docview/1459462800.
“Computer time was provided in part by the UCLA Institute for Digital Research and Education (IDRE) Hoffman2 cluster, and the Extreme Science and Engineering Discovery Environment (XSEDE).” (Zou, 2013, p. 16)
Conference Papers for 2013¶
Adli, E.; M. Hogan; J. Frederico; M. D. Litos; W. An, and W. Mori. “Transverse effects in plasma wakefield acceleration at FACET - Simulation studies.” ADVANCED ACCELERATOR CONCEPTS: 15th Advanced Accelerator Concepts Workshop Austin, Texas, USA, 2013: 541-546. 10.1063/1.4773755.
“We acknowledge gratefully useful discussions with Alex Chao and Jean-Pierre Delahaye for stimulating discussions. QuickPIC simulations are performed on the Hoffman2 Cluster at UCLA.” (Adli et al., 2013, p. 545)
Hidding, B.; J. B. Rosenzweig; Y. Xi; B. O’Shea; G. Andonian; D. Schiller; S. Barber; O. Williams; G. Pretzler; T. Königstein; F. Kleeschulte; M. J. Hogan; M. Litos; S. Corde; W. W. White; P. Muggli; D. L. Bruhwiler, and K. Lotov. “Beyond injection: Trojan horse underdense photocathode plasma wakefield acceleration.” ADVANCED ACCELERATOR CONCEPTS: 15th Advanced Accelerator Concepts Workshop Austin, Texas, USA, 2013: 570-575. 10.1063/1.4773760.
“We gratefully used computational resources at UCLA’s Hoffman2 cluster, on JUROPA at Research Centre Jülich, and at the National Energy Research Scientific Computing Center, which is supported by DOE Grant No. DE-AC02-05CH11231.” (Hidding et al., 2013, p. 575)
Book Sections for 2013¶
Kiss, Gert; Vijay S. Pande, and K. N. Houk. “Chapter Seven - Molecular Dynamics Simulations for the Ranking, Evaluation, and Refinement of Computationally Designed Proteins.” Academic Press, 2013. https://doi.org/10.1016/B978-0-12-394292-0.00007-2.
“Computational resources at ERDC, AFRL, LLNL, and IDRE were essential to this work and are gratefully acknowledged.” (Kiss et al., 2013, p. 168) DOI: 10.1016/B978-0-12-394292-0.00007-2
2012¶
- 34 publications for 2012
Journal Articles for 2012¶
Bogdan, Andrew R.; Steven V. Jerome; K. N. Houk, and Keith James. “Strained Cyclophane Macrocycles: Impact of Progressive Ring Size Reduction on Synthesis and Structure.” Journal of the American Chemical Society 134 no. 4 (2012): 2127-2138. 10.1021/ja208503y.
“We are grateful to the National Institutes of General Medical Sciences, the National Institutes of Health and Pfizer Worldwide R&D for their support, and Academic Technology Services (ATS) at UCLA for access to the Hoffman2 cluster.” (Bogdan et al., 2012, p. 11)
Bronner, Sarah M.; Joel L. Mackey; K. N. Houk, and Neil K. Garg. “Steric Effects Compete with Aryne Distortion To Control Regioselectivities of Nucleophilic Additions to 3-Silylarynes.” Journal of the American Chemical Society 134 no. 34 (2012): 13966-13969. 10.1021/ja306723r.
“Computer time was provided in part by the UCLA Institute for Digital Research and Education (IDRE) and the XSEDE supercomputers Trestles and Gordon at San Diego Supercomputer Center.” (Bronner et al., 2012, p. 13968)
Cacho, Ralph A.; Wei Jiang; Yit-Heng Chooi; Christopher T. Walsh, and Yi Tang. “Identification and Characterization of the Echinocandin B Biosynthetic Gene Cluster from Emericella rugulosa NRRL 11440.” Journal of the American Chemical Society 134 no. 40 (2012): 16781-16790. 10.1021/ja307220z.
“Genome assembly of E.rugulosaNRRL 11440 was performed on the UCLA Academic Technological Services (ATS) Hoffman2 cluster. We would like to thank Qiyang Hu for his assistance in the use of the UCLA Hoffman cluster,” (Cacho et al., 2012, p. 11)
DiRocco, DA; EL Noey; KN Houk, and T Rovis. “Catalytic Asymmetric Intermolecular Stetter Reactions of Enolizable Aldehydes with Nitrostyrenes: Computational Study Provides Insight into the Success of the Catalyst.” ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 51 no. 10 (2012): 2391-2394. 10.1002/anie.201107597.
“KNH is grateful to the National Institute of Health Chemistry-Biology Interface Training Program Grant (T32GM008496) and the National Science Foundation (CHE-0548209) for financial support, TeraGrid resources provided by NCSA (CHE-0400414) and the UCLA Academic Technology Services (ATS) Hoffman2 and IDRE clusters for computational resources.” (DiRocco et al., 2012, p. 1)
Fang, Jin and Laurent Pilon. “Tuning thermal conductivity of nanoporous crystalline silicon by surface passivation: A molecular dynamics study.” Applied Physics Letters 101 no. 1 (2012): 011909. 10.1063/1.4733352.
“The simulations were implemented using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) on the Hoffman2 cluster at the University of California-Los Angeles.” (Fang and Pilon, 2012, p. 5)
Giri, Ramesh; Yu Lan; Peng Liu; K. N. Houk, and Jin-Quan Yu. “Understanding Reactivity and Stereoselectivity in Palladium-Catalyzed Diastereoselective sp3 C–H Bond Activation: Intermediate Characterization and Computational Studies.” Journal of the American Chemical Society 134 no. 34 (2012): 14118-14126. 10.1021/ja304643e.
“We gratefully acknowledge TSRI and NSF Center for Stereoselective C−H Functionalization (CHE-0943980) and the National Science Foundation (CHE-1059084, KNH) for financial support of this research. Calculations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF.” (Giri et al., 2012, p. 14125)
Gordon, CG; JL Mackey; JC Jewett; EM Sletten; KN Houk, and CR Bertozzi. “Reactivity of Biarylazacyclooctynones in Copper-Free Click Chemistry.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 134 no. 22 (2012): 9199-9208. 10.1021/ja3000936.
“Computer time was provided in part by the UCLA Institute for Digital Research and Education (IDRE) and the UC Shared Research Cluster Services South at San Diego Supercomputer Center, supported by the UC Office of the President.” (Gordon et al., 2012, p. 9207)
Herbert, Myles B.; Yu Lan; Benjamin K. Keitz; Peng Liu; Koji Endo; Michael W. Day; K. N. Houk, and Robert H. Grubbs. “Decomposition Pathways of <i>Z</i> -Selective Ruthenium Metathesis Catalysts.” Journal of the American Chemical Society 134 no. 18 (2012): 7861-7866. 10.1021/ja301108m.
“Calculations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575).” (Herbert et al., 2012, p. 5)
Hillesheim, J. C.; C. Holland; L. Schmitz; S. Kubota; T. L. Rhodes, and T. A. Carter. “2D full wave modeling for a synthetic Doppler backscattering diagnostic.” Review of Scientific Instruments 83 no. 10 (2012): 10E331. 10.1063/1.4733549.
“Simulations were run on nodes of the Hoffman2 cluster at the University of California, Los Angeles equipped with Nvidia Tesla GPU cards and required ∼5min each.” (Hillesheim et al., 2012, p. 3)
Kheirabadi, Mahboubeh; Nihan Çelebi-Ölçüm; Matthew F. L. Parker; Qingquan Zhao; Gert Kiss; K. N. Houk, and Christian E. Schafmeister. “Spiroligozymes for Transesterifications: Design and Relationship of Structure to Activity.” Journal of the American Chemical Society 134 no. 44 (2012): 18345-18353. 10.1021/ja3069648.
“We thank the UCLA Institute for Digital Research and Education (IDRE), the Shared Research Computing Services (ShaRCS) Pilot Project for the University of California Systems, and the Extreme Science and Engineering Discovery Environment (XSEDE) for computer time.” (Kheirabadi et al., 2012, p. 18352)
Krenske, EH; EW Perry; SV Jerome; TJ Maimone; PS Baran, and KN Houk. “Why a Proximity-Induced Diels-Alder Reaction Is So Fast.” ORGANIC LETTERS 14 no. 12 (2012): 3016-3019. 10.1021/ol301083q.
“We thank the National Institute of General Medical Sciences, National Institutes of Health (GM-36700 to K.N.H.), Australian Research Council (DP0985623 to E.H.K.), ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, and University of Melbourne School of Chemistry for financial support, and the UCLA IDRE, University of Melbourne School of Chemistry, and NCI NF (Australia) for computational resources.” (Krenske et al., 2012, p. 3)
Krenske, Elizabeth H.; Sesil Agopcan; Viktorya Aviyente; K. N. Houk; Brian A. Johnson, and Andrew B. Holmes. “Causation in a Cascade: The Origins of Selectivities in Intramolecular Nitrone Cycloadditions.” Journal of the American Chemical Society 134 no. 29 (2012): 12010-12015. 10.1021/ja300002k.
“Computing resources used in this work were provided by the National Center for High Performance Computing of Turkey UYBHM (Grants 20452008 and 11062010), UCLA Academic Technology Services/Institute for Digital Research and Education, the National Computational Infrastructure National Facility (Australia), and the University of Melbourne School of Chemistry.” (Krenske et al., 2012, p. 12015)
Lam, Yu-hong; K. N. Houk; Ulf Scheffler, and Rainer Mahrwald. “Stereoselectivities of Histidine-Catalyzed Asymmetric Aldol Additions and Contrasts with Proline Catalysis: A Quantum Mechanical Analysis.” Journal of the American Chemical Society 134 no. 14 (2012): 6286-6295. 10.1021/ja2118392.
“We also thank UCLA Institute for Digital Research and Education, and the Shared Research Computing Services Pilot Project for the UC systems.” (Lam et al., 2012, p. 6294)
Lam, Yu-hong; Kendall N. Houk; Janine Cossy; Domingo Gomez Pardo, and Anne Cochi. “Fluorine as a Regiocontrol Element in the Ring Opening of Bicyclic Aziridiniums.” Helvetica Chimica Acta 95 no. 11 (2012): 2265-2277. 10.1002/hlca.201200461.
“We also thank UCLA Institute for Digital Research and Education and the Extreme Science and Engineering Discovery Environment (XSEDE), supported by National Science Foundation grant number OCI-1053575, for computational resources.” (Lam et al., 2012, p. 2275)
Lan, Y; RL Danheiser, and KN Houk. “Why Nature Eschews the Concerted [2+2+2] Cycloaddition of a Nonconjugated Cyanodiyne. Computational Study of a Pyridine Synthesis Involving an Ene-Diels-Alder-Bimolecular Hydrogen-Transfer Mechanism.” JOURNAL OF ORGANIC CHEMISTRY 77 no. 3 (2012): 1533-1538. 10.1021/jo202424n.
“Computations were performed on the National Science Foundation Terascale Computing System at the National Center for Supercomputing Applications (NCSA), on the California NanoSystems Institute clusters, and the UCLA Hofman2 cluster at IDRE.” (Lan et al., 2012, p. 5)
Lan, Yu; Peng Liu; Stephen G. Newman; Mark Lautens, and K. N. Houk. “Theoretical study of Pd(0)-catalyzed carbohalogenation of alkenes: mechanism and origins of reactivities and selectivities in alkyl halide reductive elimination from Pd(ii) species.” Chemical Science 3 no. 6 (2012): 1987. 10.1039/c2sc20103h.
“Computations were performed on the National Science Foundation Terascale Computing System at the National Center for Supercomputing Applications (NCSA), on the California NanoSystems Institute clusters and UCLA Hoffman2 cluster at IDRE.” (Lan et al., 2012, p. 8)
Liang, Yong; Joel L. Mackey; Steven A. Lopez; Fang Liu, and K. N. Houk. “Control and Design of Mutual Orthogonality in Bioorthogonal Cycloadditions.” Journal of the American Chemical Society 134 no. 43 (2012): 17904-17907. 10.1021/ja309241e.
“Calculations were performed on the Hoffman2 Cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575).” (Liang et al., 2012, p. 17907)
Liu, Peng; Xiufang Xu; Xiaofei Dong; Benjamin K. Keitz; Myles B. Herbert; Robert H. Grubbs, and K. N. Houk. “Z-Selectivity in Olefin Metathesis with Chelated Ru Catalysts: Computational Studies of Mechanism and Selectivity.” Journal of the American Chemical Society 134 no. 3 (2012): 1464-1467. 10.1021/ja2108728.
“Calculations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF.” (Liu et al., 2012, p. 1467)
Liu, Peng; Xing Yang; Vladimir B. Birman, and K. N. Houk. “Origin of Enantioselectivity in Benzotetramisole-Catalyzed Dynamic Kinetic Resolution of Azlactones.” Organic Letters 14 no. 13 (2012): 3288-3291. 10.1021/ol301243f.
“Calculations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI-1053575).” (Liu et al., 2012, p. 4)
Matute, Ricardo A. and Kendall N. Houk. “The Triplet Surface of the Zimmerman Di-π-Methane Rearrangement of Dibenzobarrelene.” Angewandte Chemie International Edition 51 no. 52 (2012): 13097-13100. 10.1002/anie.201208002.
“Computer time was also provided by the UCLA Institute for Digital Research and Education (IDRE).” (Matute and Houk, 2012, p. 13097)
Noey, EL; YD Luo; LM Zhang, and KN Houk. “Mechanism of Gold(I)-Catalyzed Rearrangements of Acetylenic Amine-N-Oxides: Computational Investigations Lead to a New Mechanism Confirmed by Experiment.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 134 no. 2 (2012): 1078-1084. 10.1021/ja208860x.
“ELN is grateful to the National Institute of Health Chemistry-Biology Interface Training Program Grant (T32GM008496), and KNH is grateful to the National Science Foundation (CHE-0548209) for financial support of this research and for TeraGrid resources provided by NCSA (CHE-0400414) and the UCLA Academic Technology Services (ATS) Hoffman2 and IDRE clusters for computational resources, and to Peng Liu for helpful discussions.” (Noey et al., 2012, p. 7)
Schnermann, Martin J.; Nicholas L. Untiedt; Gonzalo Jiménez-Osés; Kendall N. Houk, and Larry E. Overman. “Forming Tertiary Organolithiums and Organocuprates from Nitrile Precursors and their Bimolecular Reactions with Carbon Electrophiles to Form Quaternary Carbon Stereocenters.” Angewandte Chemie International Edition 51 no. 38 (2012): 9581-9586. 10.1002/anie.201205001.
“Computations were performed on the National Science Foundation Terascale Computing System at the National Center for Supercomputing Applications (NCSA), San Diego Supercomputing Center (SDSC), the California NanoSystems Institute clusters, and the UCLA Hofman2 cluster at IDRE.” (Schnermann et al., 2012, p. 1)
Wang, H; P Kohler; LE Overman, and KN Houk. “Origins of Stereoselectivities of Dihydroxylations of cis-Bicyclo[3.3.0]octenes.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 134 no. 38 (2012): 16054-16058. 10.1021/ja3075538.
“Computations were performed on the National Science Foundation Terascale Computing System at the National Center for Supercomputing Applications (NCSA), and on the IDRE Hoffman2 cluster at UCLA.” (Wang et al., 2012, p. 5)
Xu, Xiufang; Peng Liu; Adam Lesser; Lauren E. Sirois; Paul A. Wender, and K. N. Houk. “Ligand Effects on Rates and Regioselectivities of Rh(I)-Catalyzed (5 + 2) Cycloadditions: A Computational Study of Cyclooctadiene and Dinaphthocyclooctatetraene as Ligands.” Journal of the American Chemical Society 134 no. 26 (2012): 11012-11025. 10.1021/ja3041724.
“Calculations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF.” (Xu et al., 2012, p. 11024)
Yang, Xing; Valentina D. Bumbu; Peng Liu; Ximin Li; Hui Jiang; Eric W. Uffman; Lei Guo; Wei Zhang; Xuntian Jiang; K. N. Houk, and Vladimir B. Birman. “Catalytic, Enantioselective N-Acylation of Lactams and Thiolactams Using Amidine-Based Catalysts.” Journal of the American Chemical Society 134 no. 42 (2012): 17605-17612. 10.1021/ja306766n.
“Calculations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation (OCI1053575).” (Yang et al., 2012, p. 17611)
Yang, Xing; Peng Liu; K. N. Houk, and Vladimir B. Birman. “Manifestation of Felkin–Anh Control in Enantioselective Acyl Transfer Catalysis: Kinetic Resolution of Carboxylic Acids.” Angewandte Chemie International Edition 51 no. 38 (2012): 9638-9642. 10.1002/anie.201203327.
“Calculations were performed on the Hoffman2 cluster at UCLA and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF.” (Yang et al., 2012, p. 9638)
Zhang, Jin and Anastassia N. Alexandrova. “Double σ-Aromaticity in a Surface-Deposited Cluster: Pd4 on TiO2 (110).” The Journal of Physical Chemistry Letters 3 no. 6 (2012): 751-754. 10.1021/jz300158s.
“Most calculations were performed on the UCLA Hoffman2 shared cluster.” (Zhang and Alexandrova, 2012, p. 753)
Zhao, Qingquan; Yu-hong Lam; Mahboubeh Kheirabadi; Chongsong Xu; K. N. Houk, and Christian E. Schafmeister. “Hydrophobic Substituent Effects on Proline Catalysis of Aldol Reactions in Water.” The Journal of Organic Chemistry 77 no. 10 (2012): 4784-4792. 10.1021/jo300569c.
“We thank UCLA Institute of Digital Research and Education and the Shared Research Computing Services Pilot Project for the UC systems.” (Zhao et al., 2012, p. 4791)
Conference Papers for 2012¶
Amiri, Behzad; Shayan Garani Srinivasa, and Lara Dolecek. “Quantization, absorbing regions and practical message passing decoders.” In 2012 Conference Record of the Forty Sixth Asilomar Conference on Signals, Systems and Computers (ASILOMAR): 2012 Conference Record of the Forty Sixth Asilomar Conference on Signals, Systems and Computers (ASILOMAR) 2012: 1255-1259. 10.1109/ACSSC.2012.6489224.
“The authors wish to acknowledge Dr. Jiadong Wang for his invaluable help with the Hofman2 cluster and Mr. Fredric Sal a, Mr. Chu-Hsiang Huang and Mr. Yizeng Sun for help with simulations.” (Amiri et al., 2012, p. 1259) ISSN: 1058-6393
Arlen, Timothy C. and Vladimir V. Vassiliev. “Hard spectrum TeV blazars and intergalactic magnetic fields.” HIGH ENERGY GAMMA-RAY ASTRONOMY: 5th International Meeting on High Energy Gamma-Ray Astronomy Heidelberg, Germany, 2012: 606-609. 10.1063/1.4772333.
“All simulations were performed on the UCLA hoffman2 cluster.” (Arlen and Vassiliev, 2012, p. 609)
Fang, Jin and Laurent Pilon. “Effect of Hydrogen Passivation on the Thermal Conductivity of Nanoporous Crystalline Silicon: A Molecular Dynamics Study.” In ASME 2012 Third International Conference on Micro/Nanoscale Heat and Mass Transfer: ASME 2012 Third International Conference on Micro/Nanoscale Heat and Mass Transfer Atlanta, Georgia, USA, 2012: 291-296. 10.1115/MNHMT2012-75153.
“The simulations were implemented using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) on Hoffman2 cluster hosted by the Academic Technology Services at the University of California, Los Angeles.” (Fang and Pilon, 2012, p. 5)
Fang, Jin and Laurent Pilon. “Thermal Conductivity of Crystalline Nanoporous Silicon Using Molecular Dynamics Simulations.” ASME 2011 International Mechanical Engineering Congress and Exposition 2012: 377-386. 10.1115/IMECE2011-64785.
“The MD simulations were performed on the Hoffman2 cluster hosted by the Academic Technology Services (ATS) at University of California, Los Angeles.” (Fang and Pilon, 2012, p. 9)
Theses for 2012¶
Nath, Jayshankar. “Electric field induced spin wave generation for beyond CMOS magnonic logic devices.” M.S. Thesis, University of California, Los Angeles, 2012. ProQuest, https://www.proquest.com/docview/1145534171.
“These numerical studies were run on the University of California, Los Angeles (UCLA) Hoffman 2 cluster” (Nath, 2012, p. 17) “I am also grateful to Tajendra Vir Singh and Edson Smith of the Institute of Digital Research and Education (IDRE), UCLA for the help with and the in-depth tour of the Hoffman 2 cluster.” (Nath, 2012, pp. -)
Book Sections for 2012¶
Le, Hai and Jean-Luc Cambier. “Development of a Flow Solver with Complex Kinetics on the Graphic Processing Units.” American Institute of Aeronautics and Astronautics, 2012. https://arc.aiaa.org/doi/10.2514/6.2012-721.
“They would also like to thank Prof. Ann Karagozian of UCLA for support on performing simulation on the Hoffman2 GPU cluster.” (Le and Cambier, 2012, p. 16) DOI: 10.2514/6.2012-721
2011¶
- 27 publications for 2011
Journal Articles for 2011¶
Antoline, Jennifer E.; Elizabeth H. Krenske; Andrew G. Lohse; K. N. Houk, and Richard P. Hsung. “Stereoselectivities and Regioselectivities of (4 + 3) Cycloadditions Between Allenamide-Derived Chiral Oxazolidinone-Stabilized Oxyallyls and Furans: Experiment and Theory.” Journal of the American Chemical Society 133 no. 36 (2011): 14443-14451. 10.1021/ja205700p.
“We thank the NIH (GM36700 to KNH and GM-66055 to R. P.H.) and Australian Research Council (DP0985623 to E.H.K.) for generous financial support, and the NCSA, UCLA ATS, UCLA IDRE, and NCF NI (Australia) for computer resources.” (Antoline et al., 2011, p. 14450)
Brandenberg, Scott J.; Pirooz Kashighandi; Jian Zhang; Yili Huo, and Minxing Zhao. “Fragility Functions for Bridges in Liquefaction-Induced Lateral Spreads.” Earthquake Spectra 27 no. 3 (2011): 683-717. 10.1193/1.3610248.
“The simulations were performed using the Hoffman2 parallel computing cluster at UCLA.” (Brandenberg et al., 2011, p. 698)
Decyk, Viktor K. and Tajendra V. Singh. “Adaptable Particle-in-Cell algorithms for graphical processing units.” Computer Physics Communications 182 no. 3 (2011): 641-648. 10.1016/j.cpc.2010.11.009.
“This work was supported by the USDOE SciDAC program, the Northrop Grumman Corporation, and the UCLA Institute for Digital Research and Education.” (Decyk and Singh, 2011, p. 648)
Fahlen, J. E.; B. J. Winjum; T. Grismayer, and W. B. Mori. “Transverse plasma-wave localization in multiple dimensions.” Physical Review E 83 no. 4 (2011): 045401. 10.1103/PhysRevE.83.045401.
“Simulations were performed on the Dawson and Hoffman2 clusters at UCLA.” (Fahlen et al., 2011, p. 4)
Fang, Jin and Laurent Pilon. “Scaling laws for thermal conductivity of crystalline nanoporous silicon based on molecular dynamics simulations.” Journal of Applied Physics 110 no. 6 (2011): 064305. 10.1063/1.3638054.
“The MD simulations were performed on the Hoffman2 cluster hosted by the Academic Technology Services (ATS) at University of California, Los Angeles.” (Fang and Pilon, 2011, p. 10)
Glover, William J.; Ross E. Larsen, and Benjamin J. Schwartz. “Simulating the Formation of Sodium:Electron Tight-Contact Pairs: Watching the Solvation of Atoms in Liquids One Molecule at a Time.” The Journal of Physical Chemistry A 115 no. 23 (2011): 5887-5894. 10.1021/jp1101434.
“We also gratefully acknowledge the UCLA Institute for Digital Research and Education for allocating computer time for the calculations presented in this paper” (Glover et al., 2011, p. 5893)
Grismayer, T; J E Fahlen; V K Decyk, and W B Mori. “On the time-dependent resonant width for Landau damping: theory and PIC simulation.” Plasma Physics and Controlled Fusion 53 no. 7 (2011): 074011. 10.1088/0741-3335/53/7/074011.
“Simulations were performed on the UCLA Hoffman2 cluster.” (Grismayer et al., 2011, p. 11)
Krenske, Elizabeth H.; Russell C. Petter; Zhendong Zhu, and K. N. Houk. “Transition States and Energetics of Nucleophilic Additions of Thiols to Substituted α,β-Unsaturated Ketones: Substituent Effects Involve Enone Stabilization, Product Branching, and Solvation.” The Journal of Organic Chemistry 76 no. 12 (2011): 5074-5081. 10.1021/jo200761w.
“We thank the National Science Foundation and Australian Research Council for generous financial support (CHE-0548209 to K.N.H. and DP0985623 to E.H.K.), and the NCSA, UCLA ATS, UCLA IDRE, and NCF NI (Australia) for computer resources.” (Krenske et al., 2011, p. 5080)
Lan, Yu and K. N. Houk. “Mechanism of the Palladium-Catalyzed Addition of Arylboronic Acids to Enones: A Computational Study.” The Journal of Organic Chemistry 76 no. 12 (2011): 4905-4909. 10.1021/jo2002903.
“Computations were performed on the National Science Foundation Terascale Computing System at the National Center for Supercomputing Applications (NCSA), on the California NanoSystems Institute clusters and UCLA Hofman2 cluster at IDRE.” (Lan and Houk, 2011, p. 4909)
Lan, Yu; Steven E. Wheeler, and K. N. Houk. “Extraordinary Difference in Reactivity of Ozone (OOO) and Sulfur Dioxide (OSO): A Theoretical Study.” Journal of Chemical Theory and Computation 7 no. 7 (2011): 2104-2111. 10.1021/ct200293w.
“Computations were performed on the National Science Foundation Terascale Computing System at the National Center for Supercomputing Applications (NCSA), on the California Nano Systems Institute clusters and UCLA Hoffman2 cluster, and using resources provided by the Texas A&M Supercomputing Facility.” (Lan et al., 2011, p. 2109)
Lan, Yu; Lufeng Zou; Yang Cao, and K. N. Houk. “Computational Methods To Calculate Accurate Activation and Reaction Energies of 1,3-Dipolar Cycloadditions of 24 1,3-Dipoles.” The Journal of Physical Chemistry A 115 no. 47 (2011): 13906-13920. 10.1021/jp207563h.
“Computations were performed on the National Science Foundation Terascale Computing System at the National Center for Supercomputing Applications (NCSA) and on the California NanoSystems Institute cluster and the UCLA Hofman2 cluster at the UCLA Institute for Digital Research and Education (IDRE).” (Lan et al., 2011, p. 13919)
Liu, Peng; Michael J. Krische, and Kendall N. Houk. “Mechanism and Origins of Regio- and Enantioselectivities in RhI-Catalyzed Hydrogenative Couplings of 1,3-Diynes and Activated Carbonyl Partners: Intervention of a Cumulene Intermediate.” Chemistry – A European Journal 17 no. 14 (2011): 4021-4029. 10.1002/chem.201002741.
“Calculations were performed on the National Science Foundation Terascale Computing System at the NCSA and the UCLA ATS and IDRE clusters.” (Liu et al., 2011, p. 4028)
Liu, Peng; John Montgomery, and K. N. Houk. “Ligand Steric Contours To Understand the Effects of N-Heterocyclic Carbene Ligands on the Reversal of Regioselectivity in Ni-Catalyzed Reductive Couplings of Alkynes and Aldehydes.” Journal of the American Chemical Society 133 no. 18 (2011): 6956-6959. 10.1021/ja202007s.
“Calculations were performed on the National Science Foundation Terascale Computing System at the NCSA and the Hoffman2 cluster at UCLA.” (Liu et al., 2011, p. 6959)
May, J.; J. Tonge; F. Fiuza; R. A. Fonseca; L. O. Silva; C. Ren, and W. B. Mori. “Mechanism of generating fast electrons by an intense laser at a steep overdense interface.” Physical Review E 84 no. 2 (2011): 025401. 10.1103/PhysRevE.84.025401.
“The simulations were performed on the Hoffman2 cluster at UCLA.” (May et al., 2011, p. 4)
Paton, Robert S.; Seonah Kim; Audrey G. Ross; Samuel J. Danishefsky, and K. N. Houk. “Experimental Diels–Alder Reactivities of Cycloalkenones and Cyclic Dienes Explained through Transition-State Distortion Energies.” Angewandte Chemie 123 no. 44 (2011): 10550-10552. 10.1002/ange.201103998.
“Computer time was provided in part by the UCLA Institute for Digital Research and Education (IDRE), by the Shared Research Computing Services Pilot (ShaRCS) project for the University of California Systems, and by the National Center for Supercomputing Applications on Cobalt, TG-CHE050044N, and Abe, TGCHE090070.” (Paton et al., 2011, p. 1)
Paton, Robert S.; Sarah E. Steinhardt; Christopher D. Vanderwal, and K. N. Houk. “Unraveling the Mechanism of Cascade Reactions of Zincke Aldehydes.” Journal of the American Chemical Society 133 no. 11 (2011): 3895-3905. 10.1021/ja107988b.
“Computations were performed using the UCLA Academic Technology Services Hoffman2 Beowulf cluster and the San Diego Supercomputer Center Thresher cluster.” (Paton et al., 2011, p. 3904)
Tzoufras, M.; A.R. Bell; P.A. Norreys, and F.S. Tsung. “A Vlasov–Fokker–Planck code for high energy density physics.” Journal of Computational Physics 230 no. 17 (2011): 6475-6494. 10.1016/j.jcp.2011.04.034.
“Simulations were performed at the Hoffman2 cluster in UCLA.” (Tzoufras et al., 2011, p. 6492)
Um, Joann M.; Daniel A. DiRocco; Elizabeth L. Noey; Tomislav Rovis, and K. N. Houk. “Quantum Mechanical Investigation of the Effect of Catalyst Fluorination in the Intermolecular Asymmetric Stetter Reaction.” Journal of the American Chemical Society 133 no. 29 (2011): 11249-11254. 10.1021/ja202444g.
“Computations were performed on the TeraGrid resources provided by NCSA (CHE0400414) and the UCLA Academic Technology Services (ATS) Hoffman2 and IDRE clusters.” (Um et al., 2011, p. 11253)
Xu, Lai; Charles E. Doubleday, and K. N. Houk. “Dynamics of Carbene Cycloadditions.” Journal of the American Chemical Society 133 no. 44 (2011): 17848-17854. 10.1021/ja207051b.
“Computer time was provided in part by the National Center for Supercomputing Applications (NCSA) on Abe (TGCHE040013N to K.N.H. and TG-CHE090070 to C.E.D.), and by the UCLA Institute for Digital Research and Education (IDRE).” (Xu et al., 2011, p. 17854)
Zhang, Jin and Anastassia N. Alexandrova. “Structure, stability, and mobility of small Pd clusters on the stoichiometric and defective TiO2 (110) surfaces.” The Journal of Chemical Physics 135 no. 17 (2011): 174702. 10.1063/1.3657833.
“Most calculations were performed on the UCLA Hoffman2 shared cluster.” (Zhang and Alexandrova, 2011, p. 10)
Zhou, Meng; Maha Ashour-Abdalla; Xiaohua Deng; Mostafa El-Alaoui; Robert L. Richard, and Raymond J. Walker. “Modeling substorm ion injection observed by the THEMIS and LANL spacecraft in the near-Earth magnetotail.” Journal of Geophysical Research: Space Physics 116 no. A8 (2011). 10.1029/2010JA016391.
“The computations were performed on NASA’s Columbia Supercomputer, at the San Diego Supercomputer Center, and at UCLA’s Hoffman2 Cluster.” (Zhou et al., 2011, p. 13)
Çelebi-Ölçüm, Nihan; Ben W. Boal; Alexander D. Huters; Neil K. Garg, and K. N. Houk. “Why Do Some Fischer Indolizations Fail?.” Journal of the American Chemical Society 133 no. 15 (2011): 5752-5755. 10.1021/ja201035b.
“Computer time was provided in part by the UCLA Institute for Digital Research and Education (IDRE), by the Shared Research Computing Services (ShaRCS) Pilot Project for the University of California Systems, and by the National Center for Supercomputing Applications on Cobalt (TG-CHE050044N) and Abe (TG-CHE090070).” (Çelebi-Ölçüm et al., 2011, p. 5755)
Çelebi-Ölçüm, Nihan; Yu-hong Lam; Edward Richmond; Kenneth B. Ling; Andrew D. Smith, and Kendall N. Houk. “Pericyclic Cascade with Chirality Transfer: Reaction Pathway and Origin of Enantioselectivity of the Hetero-Claisen Approach to Oxindoles.” Angewandte Chemie International Edition 50 no. 48 (2011): 11478-11482. 10.1002/anie.201105412.
“We thank the UCLA IDRE, the ShaRCS Pilot Project for the UC systems, and the NCSA TeraGrid for computer time.” (Çelebi-Ölçüm et al., 2011, p. 1)
Theses for 2011¶
Huo, Yili and Jian Zhang. “Seismic Response Assessment and Improvement of Highway Bridges Using Fragility Function Method.” Ph.D. Thesis, University of California, Los Angeles, 2011. https://www.proquest.com/docview/1022071093.
“The research utilized the Hoffman2 cluster of Academic Technology Services (ATS) at University of California, Los Angeles to conduct most numerical simulations presented in this dissertation.” (p. xxiii)
Xu, Lai. “Mechanisms and Dynamics of Cycloadditions.” Ph.D. Thesis, University of California, Los Angeles, 2011. ProQuest, https://www.proquest.com/docview/920013990.
“Computations were performed on the NSF TeraGrid resources provided by NCSA (TG-CHE040013N) and the UCLA Institute for Digital Research and Education (IDRE) clusters.” (Xu, 2011, p. 14)
Zhao, Minxing. “Response of Bridges to Lateral Spreading and Earthquake Shaking.” Ph.D. Thesis, University of California, Los Angeles, 2011. ProQuest, https://www.proquest.com/docview/1002360255.
“Some numerical simulations were performed by utilizing the Hoffman2 cluster of the academic technology services (ATS) at UCLA. Mr. Prakashan Korambath at ATS helped compile the OpenSees source code for UNIX. His help is also greatly significant.” (Zhao, 2011, p. 23-24)
Conference Papers for 2011¶
Winjum, BJ; FS Tsung, and WB Mori. “PIC Simulations of Stimulated Raman Scattering for NIF Scale Lengths and Density Profiles.” In Bulletin of the American Physical Society: 53rd Annual Meeting of the APS Division of Plasma Physics 2011: NP9-089. https://meetings.aps.org/Meeting/DPP11/Session/NP9.89.
“simulations were performed on the UCLA Hoffman2 Cluster”
2010¶
- 24 publications for 2010
5 Theses
Journal Articles for 2010¶
Barman, Dipti N.; Peng Liu; Kendall N. Houk, and Kenneth M. Nicholas. “On the Mechanism of Ligand-Assisted, Copper-Catalyzed Benzylic Amination by Chloramine-T.” Organometallics 29 no. 15 (2010): 3404-3412. 10.1021/om100427s.
“Calculations were performed on the National Science Foundation Terascale Computing System at the NCSA and the UCLA ATS and IDRE clusters.” (Barman et al., 2010, p. 3412)
Glover, William J.; Ross E. Larsen, and Benjamin J. Schwartz. “Nature of Sodium Atoms/(Na+, e−) Contact Pairs in Liquid Tetrahydrofuran.” The Journal of Physical Chemistry B 114 no. 35 (2010): 11535-11543. 10.1021/jp103961j.
“We also gratefully acknowledge the UCLA Institute for Digital Research and Education and the California NanoSystems Institute for allocating computer time for the calculations presented in this paper.” (Glover et al., 2010, p. 11542)
Glover, William J.; Ross E. Larsen, and Benjamin J. Schwartz. “First principles multielectron mixed quantum/classical simulations in the condensed phase. I. An efficient Fourier-grid method for solving the many-electron problem.” The Journal of Chemical Physics 132 no. 14 (2010): 144101. 10.1063/1.3352564.
“We also gratefully acknowledge the UCLA Institute for Digital Research and Education for allocating computer time for the calculations presented in this paper.” (Glover et al., 2010, p. 9)
Glover, William J.; Ross E. Larsen, and Benjamin J. Schwartz. “How Does a Solvent Affect Chemical Bonds? Mixed Quantum/Classical Simulations with a Full CI Treatment of the Bonding Electrons.” The Journal of Physical Chemistry Letters 1 no. 1 (2010): 165-169. 10.1021/jz9000938.
“We gratefully acknowledge the California NanoSystems Institute and the UCLA Institute for Digital Research and Education for use of their Beowulf clusters.” (Glover et al., 2010, p. 169)
Gul, Seref; Franziska Schoenebeck; Viktorya Aviyente, and KN Houk. “Computational study of factors controlling the boat and chair transition states of Ireland− Claisen rearrangements.” The Journal of organic chemistry 75 no. 6 (2010): 2115-2118.
“Computations were performed on the UCLA Hoffman2 cluster, and using the TUBITAK-ULAKBIM High Performance Computing Center and the National Center for High Performance Computing in Turkey (UYBHM), under the grant number 20532009.” (Gul et al., 2010, p. 2118)
H. Krenske, Elizabeth; K. N. Houk; Andrew G. Lohse; Jennifer E. Antoline, and Richard P. Hsung. “Stereoselectivity in oxyallyl – furan (4 + 3) cycloadditions : control of intermediate conformations and dispersive stabilisation in cycloadditions involving oxazolidinone auxiliaries.” Chemical Science 1 no. 3 (2010): 387-392. 10.1039/C0SC00280A.
“We thank the NIH, NSF, and Australian–American Fulbright Commission for generous financial support (GM-36700 to KNH, GM66055 to RPH) and the NCSA, UCLA ATS, and UCLA IDRE for computer resources.” (H. Krenske et al., 2010, p. 5)
Hargis, JC; HF Schaefer; KN Houk, and SE Wheeler. “Noncovalent Interactions of a Benzo[a]pyrene Diol Epoxide with DNA Base Pairs: Insight into the Formation of Adducts of (+)-BaP DE-2 with DNA.” JOURNAL OF PHYSICAL CHEMISTRY A 114 no. 4 (2010): 2038-2044. 10.1021/jp911376p.
“Computer time was provided in part by the National Energy Research Scientific Computing Center (NERSC), which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 and the UCLA Institute for Digital Research and Education (IDRE).” (Hargis et al., 2010, p. 2043)
Kiss, Gert; Daniela Röthlisberger; David Baker, and K. N. Houk. “Evaluation and ranking of enzyme designs.” Protein Science 19 no. 9 (2010): 1760-1773. 10.1002/pro.462.
“Supercomputing resources at LLNL, DOD ERDC, and UCLA IDRE were utilized for the computations.” (Kiss et al., 2010, p. 1772)
Krenske, Elizabeth H.; K. N. Houk; Daniel Lim; Sarah E. Wengryniuk, and Don M. Coltart. “Origins of Stereoselectivity in the α-Alkylation of Chiral Hydrazones.” The Journal of Organic Chemistry 75 no. 24 (2010): 8578-8584. 10.1021/jo1019877.
“We thank the National Institues of General Medical Sciences, National Institutes of Health (GM-36700 to K.N.H.), National Science Foundation (CHE-0548209 to K.N.H.), Duke University, and Australian Research Council (DP0985623 to E.H.K.) for generous financial support, the NCSA, UCLA ATS, UCLA IDRE, and NCI NF (Australia) for computer resources, and the NCBC for spectroscopic resources.” (Krenske et al., 2010, p. 8584)
Lan, Yu and KN Houk. “Mechanism and stereoselectivity of the stepwise 1, 3-dipolar cycloadditions between a thiocarbonyl ylide and electron-deficient dipolarophiles: a computational investigation.” Journal of the American Chemical Society 132 no. 50 (2010): 17921-17927.
“Computations were performed on the National Science Foundation Terascale Computing System at the National Center for Supercomputing Applications (NCSA), on the California Nano Systems Institute clusters and UCLA Hoffman2 cluster.” (Lan and Houk, 2010, p. 17927)
Paton, Robert S.; Joel L. Mackey; Woo Han Kim; Jun Hee Lee; Samuel J. Danishefsky, and K. N. Houk. “Origins of Stereoselectivity in the trans Diels−Alder Paradigm.” Journal of the American Chemical Society 132 no. 27 (2010): 9335-9340. 10.1021/ja1009162.
“Computer time was provided in part by the UCLA Institute for Digital Research and Education (IDRE).” (Paton et al., 2010, p. 9340)
Schoenebeck, Franziska and KN Houk. “Ligand-controlled regioselectivity in palladium-catalyzed cross coupling reactions.” Journal of the American Chemical Society 132 no. 8 (2010): 2496-2497.
“Computations were performed on the NSF TeraGrid resources and on the UCLA Hoffman2 cluster.” (Schoenebeck and Houk, 2010, p. 2)
St-Cyr, Daniel J.; Marie S. T. Morin; Francine Bélanger-Gariépy; Bruce A. Arndtsen; Elizabeth H. Krenske, and K. N. Houk. “Phospha-Münchnones: Electronic Structures and 1,3-Dipolar Cycloadditions.” The Journal of Organic Chemistry 75 no. 12 (2010): 4261-4273. 10.1021/jo1008383.
“We thank the NSF, NSERC, FQRNT, DuPont, the CFI, and the Australian-American Fulbright Commission for financial support and the NCSA, UCLA ATS, and UCLA IDRE for computer resources.” (St-Cyr et al., 2010, p. 4273)
Um, Joann M.; Osvaldo Gutierrez; Franziska Schoenebeck; K. N. Houk, and David W. C. MacMillan. “Nature of Intermediates in Organo-SOMO Catalysis of α-Arylation of Aldehydes.” Journal of the American Chemical Society 132 no. 17 (2010): 6001-6005. 10.1021/ja9063074.
“Computations were performed on the NSF TeraGrid resources provided by NCSA (CHE0400414) and the UCLA Academic Technology Services (ATS) Hoffman2 and IDRE clusters.” (Um et al., 2010, p. 6005)
Um, Joann M.; Naeem S. Kaka; David M. Hodgson, and K. N. Houk. “Transition States and Origins of 1,4-Asymmetric Induction in Alkylations of 2,2,6-Trialkylpiperidine Enamines.” Chemistry – A European Journal 16 no. 21 (2010): 6310-6316. 10.1002/chem.201000046.
“Computations were performed on the UCLA Academic Technology Services (ATS) Hoffman2 cluster.” (Um et al., 2010, p. 6316)
Wheeler, Steven E. and K. N. Houk. “Are Anion/π Interactions Actually a Case of Simple Charge−Dipole Interactions?.” The Journal of Physical Chemistry A 114 no. 33 (2010): 8658-8664. 10.1021/jp1010549.
“Computer time was provided by the UCLA Institute for Digital Research and Education (IDRE).” (Wheeler and Houk, 2010, p. 8664)
Wheeler, Steven E. and K. N. Houk. “Integration Grid Errors for Meta-GGA-Predicted Reaction Energies: Origin of Grid Errors for the M06 Suite of Functionals.” Journal of Chemical Theory and Computation 6 no. 2 (2010): 395-404. 10.1021/ct900639j.
“Computer time was provided by the University of California, Los Angeles Institute for Digital Research and Education (IDRE).” (Wheeler and Houk, 2010, p. 403)
Wheeler, Steven E.; Anne J. McNeil; Peter Müller; Timothy M. Swager, and K. N. Houk. “Probing Substituent Effects in Aryl−Aryl Interactions Using Stereoselective Diels−Alder Cycloadditions.” Journal of the American Chemical Society 132 no. 10 (2010): 3304-3311. 10.1021/ja903653j.
“Computer time was provided in part by the UCLA Institute for Digital Research and Education (IDRE) and the National Center for Supercomputer Applications (NCSA).” (Wheeler et al., 2010, p. 3311)
Yang, Jian; Valerie A Kickhoefer; Benny C Ng; Ajaykumar Gopal; Laurent A Bentolila; Scott John; Sarah H Tolbert, and Leonard H Rome. “Vaults are dynamically unconstrained cytoplasmic nanoparticles capable of half vault exchange.” Acs Nano 4 no. 12 (2010): 7229-7240.
“SAXS shape reconstructions and regression analyses were conducted on the Hoffman2 Campus Computing Cluster available through the UCLA Academic Technology Services.” (Yang et al., 2010, p. 7239)
Theses for 2010¶
Craig, Ian Munro. “Linear and nonlinear optical properties of organic semiconductors.” Ph.D. Thesis, University of California, Los Angeles, 2010. ProQuest, https://www.proquest.com/docview/814761219.
“The authors also thank Colin Carver, Bob Taylor, and the UCLA Molecular Instrumentation Facility for their help with the NMR data, and UCLA Academic Technology Services for access to the UCLA Hoffman2 Beowulf cluster used for the GAMESS calculations.” (Craig, p. 15)
Kovalchik, Stephanie Ann. “Individual patient date meta-analysis of intervention studies.” Ph.D. Thesis, University of California, Los Angeles, 2010. ProQuest, https://www.proquest.com/docview/880622636.
“This work would not have been possible without the technicians at UCLA’s Academic Technology Services who oversee the operations of the Hoffman2 cluster. Thank you for maintaining this powerful computing resource.” (Kovalchik, 2010, p. 15)
Um, Joann M.. “Theoretical Studies of Organocatalysis and Stereoselective Organic Reactions.” Ph.D. Thesis, University of California, Los Angeles, 2010. ProQuest, https://www.proquest.com/docview/850519294.
“Computations were performed on the NSF TeraGrid resources provided by NCSA (CHE0400414) and the UCLA Academic Technology Services (ATS) Hoffman2 and IDRE clusters.” (Um, 2010, p. 19)
Wang, Tyan-Lin. “Amplification of Short Laser Pulses via Resonant Energy Transfer in Underdense Thermal Plasmas.” Ph.D. Thesis, University of California, Los Angeles, 2010. ProQuest, https://www.proquest.com/docview/861924387.
“Going on to the rest of my committee, I want to thank Prof. Warren Mori for letting me attend his simulation group meetings and for granting me computational time to run the OSIRIS code on the Dawson and Hoffman2 clusters.” (Wang, p. 20)
Zeineh, Christopher. “Numerical simulation of magnetohydrodynamic thrust augmentation for pulse detonation rocket engines.” Ph.D. Thesis, University of California, Los Angeles, 2010. ProQuest, https://www.proquest.com/docview/822408709.
“We save time and resources by running the two-dimensional simulations on parallel processors from UCLA’s ATS Hoffman 2 cluster.” (Zeineh, p. 66)
2009¶
- 18 publications for 2009
Journal Articles for 2009¶
Chen, Xin; Colleen K. Regan; Stephen L. Craig; Elizabeth H. Krenske; K. N. Houk; William L. Jorgensen, and John I. Brauman. “Steric and Solvation Effects in Ionic SN2 Reactions.” Journal of the American Chemical Society 131 no. 44 (2009): 16162-16170. 10.1021/ja9053459.
“We are grateful to the National Science Foundation (J.I.B., S.L.C., K.N.H., W.L.J.), Stanford University Stanford Graduate Fellowship (X.C.), the Australian-American Fulbright Commission (E.H.K.), and the UCLA IDRE for computer resources (K.N.H.).” (Chen et al., 2009, p. 16170)
Craig, Ian M.; Hieu M. Duong; Fred Wudl, and Benjamin J. Schwartz. “A new route to dual fluorescence: Spectroscopic properties of the valence tautomers of a 3-(2H)-isoquinolinone derivative.” Chemical Physics Letters 477 no. 4 (2009): 319-324. 10.1016/j.cplett.2009.07.041.
“The authors also thank Colin Carver, Bob Taylor, and the UCLA Molecular Instrumentation Facility for their help with the NMR data, and UCLA Academic Technology Services for access to the UCLA Hoffman2 Beowulf cluster used for the GAMESS calculations.” (Craig et al., 2009, p. 323)
Gutierrez, Osvaldo; Robert G. Iafe, and K. N. Houk. “Origin of Stereoselectivity in the Imidazolidinone-Catalyzed Reductions of Cyclic α,β-Unsaturated Ketones.” Organic Letters 11 no. 19 (2009): 4298-4301. 10.1021/ol901586t.
“We are grateful to the National Institute of General Medical Sciences, National Institutes of Health, Ronald S. Gabriel, M.D./Scrubs Unlimited SRF, for funding of the research and the UCLA Institute for Digital Research and Education for computer time.” (Gutierrez et al., 2009, p. 4)
McCarren, P. R.; Peng Liu; Paul Ha-Yeon Cheong; Timothy F. Jamison, and K. N. Houk. “Mechanism and Transition-State Structures for Nickel-Catalyzed Reductive Alkyne−Aldehyde Coupling Reactions.” Journal of the American Chemical Society 131 no. 19 (2009): 6654-6655. 10.1021/ja900701g.
“Calculations were performed on the NSF TeraGrid resources provided by NCSA and the UCLA ATS and IDRE clusters.” (McCarren et al., 2009, p. 2)
Schoenebeck, Franziska; Daniel H. Ess; Gavin O. Jones, and K. N. Houk. “Reactivity and Regioselectivity in 1,3-Dipolar Cycloadditions of Azides to Strained Alkynes and Alkenes: A Computational Study.” Journal of the American Chemical Society 131 no. 23 (2009): 8121-8133. 10.1021/ja9003624.
“Computations were performed using the UCLA Hoffman2 cluster and the California NanoSystems Institute clusters.” (Schoenebeck et al., 2009, p. 8133)
Wheeler, SE; KN Houk; PVR Schleyer, and WD Allen. “A Hierarchy of Homodesmotic Reactions for Thermochemistry.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 131 no. 7 (2009): 2547-2560. 10.1021/ja805843n.
“Computer time was provided in part by the UCLA Institute for Digital Research and Education (IDRE).” (Wheeler et al., 2009, p. 18)
Wheeler, Steven E. and K. N. Houk. “Substituent Effects in Cation/π Interactions and Electrostatic Potentials above the Centers of Substituted Benzenes Are Due Primarily to Through-Space Effects of the Substituents.” Journal of the American Chemical Society 131 no. 9 (2009): 3126-3127. 10.1021/ja809097r.
“Computer resources were provided in part by the UCLA Institute for Digital Research and Education (IDRE).” (Wheeler and Houk, 2009, p. 2)
Wheeler, Steven E. and K. N. Houk. “Through-Space Effects of Substituents Dominate Molecular Electrostatic Potentials of Substituted Arenes.” Journal of Chemical Theory and Computation 5 no. 9 (2009): 2301-2312. 10.1021/ct900344g.
“Computer time was provided in part by the UCLA Institute for Digital Research and Education (IDRE).” (Wheeler and Houk, 2009, p. 2310)
Wheeler, Steven E. and K.N. Houk. “Origin of substituent effects in edge-to-face aryl–aryl interactions.” Molecular Physics 107 no. 8-12 (2009): 749-760. 10.1080/00268970802537614.
“Computational resources were provided in part by the UCLA Institute for Digital Research and Education (IDRE).” (Wheeler and Houk, 2009, p. 758)
Wheeler, Steven E.; Antonio Moran; Susan N. Pieniazek, and K. N. Houk. “Accurate Reaction Enthalpies and Sources of Error in DFT Thermochemistry for Aldol, Mannich, and α-Aminoxylation Reactions.” The Journal of Physical Chemistry A 113 no. 38 (2009): 10376-10384. 10.1021/jp9058565.
“Computer time was partially provided by the UCLA Institute for Digital Research and Education (IDRE).” (Wheeler et al., 2009, p. 10383)
Zhang, Jian and Yili Huo. “Evaluating effectiveness and optimum design of isolation devices for highway bridges using the fragility function method.” Engineering Structures 31 no. 8 (2009): 1648-1660. 10.1016/j.engstruct.2009.02.017.
“The research utilizes the Hoffman2 cluster of Academic Technology Services (ATS) at University of California, Los Angeles to conduct most numerical simulations presented in this paper.” (pg. 1660)
Theses for 2009¶
Han, Buhm. “Effective design and analysis of genetic association studies.” Ph.D. Thesis, University of California, San Diego, 2009. ProQuest, https://www.proquest.com/docview/304851397.
“I thank the National Biomedical Computational Resource (NBCR), the UCSD Fast Wired and Wireless Grid Project (FWGrid), Institute for Digital Research and Education (IDRE) for allowing us to utilize their cluster system.” (Han, p. 12)
Kang, Hyun Min. “Effective design and analysis of systems genetics studies.” Ph.D. Thesis, University of California, San Diego, 2009. ProQuest, https://www.proquest.com/docview/304852119.
“I thank the National Biomedical Computational Resource (NBCR), the UCSD Fast Wired and Wireless Grid Project (FWGrid), Insitutide for Digital Research and Education (IDRE) for allowing us to utilize their cluster system.” (Kang, p. 15)
Kashighandi, Pirooz. “Demand fragility surfaces for bridges in liquefied laterally spreading ground.” Ph.D. Thesis, University of California, Los Angeles, 2009. https://www.proquest.com/docview/276322603.
“Numerical modeling analyses were performed by utilizing the Hoffman2 cluster of the academic technology services (ATS) at UCLA. Mr. Prakashan Korambath at ATS helped compile the OpenSees source code for UNIX and taught me how to utilize the cluster. His help is also greatly valued.” (Kashighandi, p. 21)
Liu, Jian. “Controlling the dynamics of recurrent neural networks with synaptic learning rules.” Ph.D. Thesis, University of California, Los Angeles, 2009. ProQuest, https://www.proquest.com/docview/304851345.
“I thank the mathematics computing group for the excellent Bamboo cluster, and the UCLA IDRE for the Hoffman2 Cluster. Most of simulations in this dissertation can not be done without them.” (Liu, p. 14)
McCarren, Patrick Ryan. “Computational investigations of organometallic and S-nitrosothiol reaction mechanisms.” Ph.D. Thesis, University of California, Los Angeles, 2009. ProQuest, https://www.proquest.com/docview/304852917.
“UCLA Academic Technology Services and the UCLA Institute for Digital Research and Education have provided shared computer resources that were directly used for this research.” (McCarren, p. 24)
Ye, Chun. “Statistical methods for the analysis of expression quantitative traits.” Ph.D. Thesis, University of California, San Diego, 2009. ProQuest, https://www.proquest.com/docview/304850234.
“In addition, I thank the UCSD Fast Wired and Wireless Grid Project (FWGrid), Institute for Digital Research and Education (IDRE) for allowing us to utilize their cluster system.” (Ye, p. 15)
Conference Papers for 2009¶
Decyk, V K; S A Friedman, and T V Singh. “Graphical Processing Unit-Based Particle-In-Cell Simulations.” In ICAP09, the tenth International Computational Accelerator Physics conference,: ICAP09, the tenth International Computational Accelerator Physics conference, San Francisco, 2009.
“Work supported by Northrop Grumman, UCLA IDRE, and USDOE (SciDAC)” (Decyk et al., p. 96)
2008¶
- 5 publications for 2008
Journal Articles for 2008¶
Gunaydin, Hakan and K. N. Houk. “Molecular Dynamics Prediction of the Mechanism of Ester Hydrolysis in Water.” Journal of the American Chemical Society 130 no. 46 (2008): 15232-15233. 10.1021/ja8050525.
“The computations were performed on the UCLA CNSI and Hoffman ATS clusters.” (Gunaydin and Houk, 2008, p. 2)
Jones, Gavin O.; Xuechen Li; Amy E. Hayden; K. N. Houk, and Samuel J. Danishefsky. “The Coupling of Isonitriles and Carboxylic Acids Occurring By Sequential Concerted Rearrangement Mechanisms.” Organic Letters 10 no. 18 (2008): 4093-4096. 10.1021/ol8016287.
“Computational resources from the UCLA ATS are appreciated.” (Jones et al., 2008, p. 4096)
Pieniazek, Susan N.; Fernando R. Clemente, and Kendall N. Houk. “Sources of Error in DFT Computations of C–C Bond Formation Thermochemistries: π→σ Transformations and Error Cancellation by DFT Methods.” Angewandte Chemie International Edition 47 no. 40 (2008): 7746-7749. 10.1002/anie.200801843.
“The computations were performed on the UCLA Academic Technology Services (ATS) Hoffman Beowulf cluster.” (Pieniazek et al., 2008, p. 1)
Wheeler, Steven E. and K. N. Houk. “Substituent Effects in the Benzene Dimer are Due to Direct Interactions of the Substituents with the Unsubstituted Benzene.” Journal of the American Chemical Society 130 no. 33 (2008): 10854-10855. 10.1021/ja802849j.
“Computer resources were provided in part by the UCLA Institute for Digital Research and Education (IDRE).” (Wheeler and Houk, 2008, p. 2)
Zhang, Jian; Yili Huo; Scott J. Brandenberg, and Pirooz Kashighandi. “Effects of structural characterizations on fragility functions of bridges subject to seismic shaking and lateral spreading.” Earthquake Engineering and Engineering Vibration 7 no. 4 (2008): 369-382. 10.1007/s11803-008-1009-2.
“The research utilizes the Hoffman2 cluster of Academic Technology Services (ATS) at University of California, Los Angeles, to conduct most numerical simulations.” (pg. 381)