James C Phillips

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Klaus SchultenProfessor of Physics, University of Illinois at Urbana-ChampaignVerified email at ks.uiuc.edu
Laxmikant KaleProfessor or Computer Science, University of IllinoisVerified email at illinois.edu
Emad Tajkhorshid, PhDProfessor of Biochemistry and Biophysics, University of IllinoisVerified email at illinois.edu
John E. StoneDistinguished Engineer, Scientific Visualization DevTech, NVIDIA CorporationVerified email at nvidia.com
Chris ChipotUniversity of Lorraine — University of Illinois, Urbana-ChampaignVerified email at Univ-Lorraine.fr
Elizabeth VillaHHMI and Department of Molecular Biology, University of California San DiegoVerified email at ucsd.edu
Rosemary BraunAssociate Professor - Molecular Biosciences, Applied Math, & Physics - Northwestern UniversityVerified email at northwestern.edu
Robert K BrunnerNCSA, University of IllinoisVerified email at illinois.edu
James C. GumbartGeorgia TechVerified email at physics.gatech.edu
Benoit RouxProfessor of Biochemistry, The university of ChicagoVerified email at uchicago.edu
Gengbin ZhengIntelVerified email at intel.com
Brian RadakTandem AIVerified email at tandemai.com
João Vieira RibeiroModerna TherapeuticsVerified email at modernatx.com
Zaida (Zan) Luthey-SchultenUniversity of Illinois at Urbana-ChampaignVerified email at illinois.edu
Abhishek SingharoyAssociate professorVerified email at asu.edu
Attila GursoyProfessor of Computer Science, Koc UniversityVerified email at ku.edu.tr
Rafael C BernardiAssociate Professor - Department of Physics at Auburn UniversityVerified email at auburn.edu
Aleksei AksimentievUniversity of Illinois at Urbana-ChampaignVerified email at illinois.edu
Ronak BuchUniversity of Illinois at Urbana-ChampaignVerified email at illinois.edu
Marcelo C. R. MeloAssistant ProfessorVerified email at colostate.edu

James C Phillips

Senior Research Programmer, National Center for Supercomputing Applications, University of Illinois

Verified email at illinois.edu - Homepage

high-performance computing molecular dynamics structural biology


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Scalable molecular dynamics with NAMD JC Phillips, R Braun, W Wang, J Gumbart, E Tajkhorshid, E Villa, C Chipot, ... Journal of computational chemistry 26 (16), 1781-1802, 2005	19335	2005
NAMD2: greater scalability for parallel molecular dynamics L Kalé, R Skeel, M Bhandarkar, R Brunner, A Gursoy, N Krawetz, ... Journal of Computational Physics 151 (1), 283-312, 1999	3037	1999
GPU computing JD Owens, M Houston, D Luebke, S Green, JE Stone, JC Phillips Proceedings of the IEEE 96 (5), 879-899, 2008	3034	2008
Scalable molecular dynamics on CPU and GPU architectures with NAMD JC Phillips, DJ Hardy, JDC Maia, JE Stone, JV Ribeiro, RC Bernardi, ... The Journal of chemical physics 153 (4), 2020	2401	2020
Accelerating molecular modeling applications with graphics processors JE Stone, JC Phillips, PL Freddolino, DJ Hardy, LG Trabuco, K Schulten Journal of computational chemistry 28 (16), 2618-2640, 2007	938	2007
NAMD: Biomolecular simulation on thousands of processors JC Phillips, G Zheng, S Kumar, LV Kalé SC'02: Proceedings of the 2002 ACM/IEEE Conference on Supercomputing, 36-36, 2002	372	2002
GPU clusters for high-performance computing VV Kindratenko, JJ Enos, G Shi, MT Showerman, GW Arnold, JE Stone, ... 2009 IEEE International Conference on Cluster Computing and Workshops, 1-8, 2009	333	2009
High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD W Jiang, DJ Hardy, JC Phillips, AD MacKerell Jr, K Schulten, B Roux The journal of physical chemistry letters 2 (2), 87-92, 2011	307	2011
Adapting a message-driven parallel application to GPU-accelerated clusters JC Phillips, JE Stone, K Schulten SC'08: Proceedings of the 2008 ACM/IEEE Conference on Supercomputing, 1-9, 2008	250	2008
NAMD goes quantum: an integrative suite for hybrid simulations MCR Melo, RC Bernardi, T Rudack, M Scheurer, C Riplinger, JC Phillips, ... Nature methods 15 (5), 351-354, 2018	221	2018
QwikMD—integrative molecular dynamics toolkit for novices and experts JV Ribeiro, RC Bernardi, T Rudack, JE Stone, JC Phillips, PL Freddolino, ... Scientific reports 6 (1), 26536, 2016	212	2016
Predicting the structure of apolipoprotein AI in reconstituted high-density lipoprotein disks JC Phillips, W Wriggers, Z Li, A Jonas, K Schulten Biophysical journal 73 (5), 2337-2346, 1997	200	1997
Constant-pH molecular dynamics simulations for large biomolecular systems BK Radak, C Chipot, D Suh, S Jo, W Jiang, JC Phillips, K Schulten, ... Journal of chemical theory and computation 13 (12), 5933-5944, 2017	182	2017
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics L Casalino, AC Dommer, Z Gaieb, EP Barros, T Sztain, SH Ahn, A Trifan, ... The International Journal of High Performance Computing Applications 35 (5 …, 2021	177	2021
Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins AY Shih, IG Denisov, JC Phillips, SG Sligar, K Schulten Biophysical journal 88 (1), 548-556, 2005	168	2005
Atoms to phenotypes: molecular design principles of cellular energy metabolism A Singharoy, C Maffeo, KH Delgado-Magnero, DJK Swainsbury, M Sener, ... Cell 179 (5), 1098-1111. e23, 2019	167	2019
Parallel generalized Born implicit solvent calculations with NAMD DE Tanner, KY Chan, JC Phillips, K Schulten Journal of chemical theory and computation 7 (11), 3635-3642, 2011	162	2011
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD W Jiang, JC Phillips, L Huang, M Fajer, Y Meng, JC Gumbart, Y Luo, ... Computer physics communications 185 (3), 908-916, 2014	145	2014
Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system S Kumar, C Huang, G Zheng, E Bohm, A Bhatele, JC Phillips, H Yu, ... IBM Journal of Research and Development 52 (1.2), 177-188, 2008	136	2008
Molecular dynamics study of bacteriorhodopsin and the purple membrane J Baudry, E Tajkhorshid, F Molnar, J Phillips, K Schulten The Journal of Physical Chemistry B 105 (5), 905-918, 2001	132	2001

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