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James C. Phillips
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2020 – today
- 2024
- [j19]Santiago Antolínez
, Peter Eugene Jones
AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD. J. Chem. Inf. Model. 64(2): 543-554 (2024) - 2023
- [j18]Abigail C. Dommer, Lorenzo Casalino
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. Int. J. High Perform. Comput. Appl. 37(1): 28-44 (2023) - 2022
- [j17]Anda Trifan, Defne Gorgun, Michael Salim, Zongyi Li
Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action. Int. J. High Perform. Comput. Appl. 36(5-6): 603-623 (2022) - 2021
- [j16]Lorenzo Casalino
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. Int. J. High Perform. Comput. Appl. 35(5) (2021) - 2020
- [i2]Caroline Jay
The challenges of theory-software translation. F1000Research 9: 1192 (2020)
2010 – 2019
- 2019
- [i1]Caroline Jay, Robert Haines, Daniel S. Katz, Jeffrey C. Carver, James C. Phillips, Anshu Dubey, Sandra Gesing, Matthew J. Turk, Hui Wan
Theory-Software Translation: Research Challenges and Future Directions. CoRR abs/1910.09902 (2019) - 2018
- [j15]Bilge Acun
Scalable molecular dynamics with NAMD on the Summit system. IBM J. Res. Dev. 62(6): 4:1-4:9 (2018) - [c17]James C. Phillips
What You Should Know About NAMD and Charm++ But Were Hoping to Ignore. PEARC 2018: 55:1-55:6 - 2016
- [j14]John E. Stone
Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing. Parallel Comput. 55: 17-27 (2016) - [c16]John E. Stone
Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads. IPDPS Workshops 2016: 89-100 - [c15]John E. Stone
Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms. ISC Workshops 2016: 188-206 - 2014
- [j13]Wei Jiang, James C. Phillips
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. Comput. Phys. Commun. 185(3): 908-916 (2014) - [c14]James C. Phillips
Petascale Tcl with NAMD, VMD, and Swift/T. HPTCDL@SC 2014: 6-17 - [c13]James C. Phillips
Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation. SC 2014: 81-91 - 2013
- [p2]James C. Phillips, Klaus Schulten, Abhinav Bhatele, Chao Mei, Yanhua Sun, Eric J. Bohm, Laxmikant V. Kalé:
Scalable Molecular Dynamics with NAMD. Parallel Science and Engineering Applications 2013: 61-78 - 2012
- [c12]Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Bohm, James C. Phillips
Optimizing fine-grained communication in a biomolecular simulation application on Cray XK6. SC 2012: 55 - 2011
- [c11]Chao Mei, Yanhua Sun, Gengbin Zheng, Eric J. Bohm, Laxmikant V. Kalé, James C. Phillips
Enabling and scaling biomolecular simulations of 100 million atoms on petascale machines with a multicore-optimized message-driven runtime. SC 2011: 61:1-61:11 - [r1]Laxmikant V. Kalé, Abhinav Bhatele, Eric J. Bohm, James C. Phillips:
NAMD (NAnoscale Molecular Dynamics). Encyclopedia of Parallel Computing 2011: 1249-1254 - 2010
- [c10]Jeremy Enos
Quantifying the impact of GPUs on performance and energy efficiency in HPC clusters. Green Computing Conference 2010: 317-324
2000 – 2009
- 2009
- [j12]James C. Phillips
Probing biomolecular machines with graphics processors. Commun. ACM 52(10): 34-41 (2009) - [j11]Praveen K. Chandrasekharan
Beta-sandwich - beta-barrel transformation may serve as a model of a conversion of 'normal' soluble proteins into amyloid aggregates. Int. J. Medical Eng. Informatics 1(4): 473-489 (2009) - [j10]James C. Phillips
Probing Biomolecular Machines with Graphics Processors. ACM Queue 7(9): 30 (2009) - [j9]Guochun Shi, Volodymyr V. Kindratenko, Ivan S. Ufimtsev, Todd J. Martínez
Implementation of scientific computing applications on the Cell Broadband Engine. Sci. Program. 17(1-2): 135-151 (2009) - [c9]Volodymyr V. Kindratenko
GPU clusters for high-performance computing. CLUSTER 2009: 1-8 - 2008
- [j8]Sameer Kumar, Chao Huang, Gengbin Zheng, Eric J. Bohm, Abhinav Bhatele, James C. Phillips
Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system. IBM J. Res. Dev. 52(1-2): 177-188 (2008) - [j7]John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone
GPU Computing. Proc. IEEE 96(5): 879-899 (2008) - [c8]Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. Phillips
Overcoming scaling challenges in biomolecular simulations across multiple platforms. IPDPS 2008: 1-12 - [c7]James C. Phillips
Adapting a message-driven parallel application to GPU-accelerated clusters. SC 2008: 8 - 2007
- [j6]John E. Stone
Accelerating molecular modeling applications with graphics processors. J. Comput. Chem. 28(16): 2618-2640 (2007) - [j5]Robert D. Skeel, David J. Hardy, James C. Phillips
Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations. J. Comput. Phys. 225(1): 1-5 (2007) - 2006
- [c6]David M. Kunzman, Gengbin Zheng, Eric J. Bohm, James C. Phillips
Poster reception - Charm++ simplifies coding for the cell processor. SC 2006: 135 - 2005
- [j4]James C. Phillips
Scalable molecular dynamics with NAMD. J. Comput. Chem. 26(16): 1781-1802 (2005) - [j3]Gerald Lucovsky, James C. Phillips:
Bond strain and defects at interfaces in high-k gate stacks. Microelectron. Reliab. 45(5-6): 770-778 (2005) - 2002
- [c5]James C. Phillips
NAMD: biomolecular simulation on thousands of processors. SC 2002: 53:1-53:18 - 2000
- [j2]Rajeev Sharma, Michael Zeller, Vladimir Pavlovic
Speech/Gesture Interface to a Visual-Computing Environment. IEEE Computer Graphics and Applications 20(2): 29-37 (2000) - [c4]Robert Brunner, James C. Phillips
Scalable Molecular Dynamics for Large Biomolecular Systems. SC 2000: 45
1990 – 1999
- 1999
- [c3]Laxmikant V. Kalé, Robert Brunner, James C. Phillips
Application Performance of a Linux Cluster Using Converse. IPPS/SPDP Workshops 1999: 483-495 - [p1]James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind A. Bhandarkar, Neal Krawetz, Attila Gürsoy, Laxmikant V. Kalé, Robert D. Skeel, Klaus Schulten:
Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code. Computational Molecular Dynamics 1999: 472-482 - 1998
- [j1]James C. Phillips:
Algebraic Constructs for the Graphical and Computational Solution to Balancing Chemical Equations. Comput. Chem. 22(4): 295-308 (1998) - 1997
- [c2]Michael Zeller, James C. Phillips, Andrew Dalke, William Humphrey, Klaus Schulten, Thomas S. Huang, Vladimir Pavlovic
A Visual Computing Environment for Very Large Scale Biomolecular Modeling. ASAP 1997: 3- - [c1]Laxmikant V. Kalé, Milind A. Bhandarkar, Robert Brunner, Neal Krawetz, James C. Phillips
NAMD: A Case Study in Multilingual Parallel Programming. LCPC 1997: 367-381
Coauthor Index
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