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
John E. StoneSenior Research Programmer, University of Illinois at Urbana-ChampaignVerified email at ks.uiuc.edu
Emad Tajkhorshid, PhDProfessor of Biochemistry and Biophysics, University of IllinoisVerified email at illinois.edu
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
Gengbin ZhengIntelVerified email at intel.com
Benoit RouxProfessor of Biochemistry, The university of ChicagoVerified email at uchicago.edu
Attila GursoyProfessor of Computer Science, Koc UniversityVerified email at ku.edu.tr
Brian RadakRoivant SciencesVerified email at roivant.com
João Vieira RibeiroRoivant DiscoveryVerified email at roivant.com
Zaida (Zan) Luthey-SchultenUniversity of Illinois at Urbana-ChampaignVerified email at illinois.edu
Abhishek SingharoyAssistant professorVerified email at asu.edu
Peter L. FreddolinoAssociate ProfessorVerified email at umich.edu
Sameer KumarGoogle Inc.Verified email at google.com
Ronak BuchUniversity of Illinois at Urbana-ChampaignVerified email at illinois.edu
Rafael C BernardiAssistant Professor - Department of Physics at Auburn UniversityVerified email at auburn.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	16614	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	2808	1999
GPU computing JD Owens, M Houston, D Luebke, S Green, JE Stone, JC Phillips Proceedings of the IEEE 96 (5), 879-899, 2008	2655	2008
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	889	2007
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), 044130, 2020	578	2020
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	339	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	314	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	242	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	232	2008
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	190	1997
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	155	2005
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	132	2008
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	128	2011
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	127	2001
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), 1-14, 2016	124	2016
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	120	2014
Overcoming scaling challenges in biomolecular simulations across multiple platforms A Bhatele, S Kumar, C Mei, JC Phillips, G Zheng, LV Kale 2008 IEEE International Symposium on Parallel and Distributed Processing, 1-12, 2008	113	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	110	2018
Quantum dynamics of the femtosecond photoisomerization of retinal in bacteriorhodopsin M Ben-Nun, F Molnar, H Lu, JC Phillips, TJ Martínez, K Schulten Faraday Discussions 110, 447-462, 1998	106	1998
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	98	2017

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