Publications by authors named "James C Phillips"

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Scalable molecular dynamics on CPU and GPU architectures with NAMD.
James C Phillips, David J Hardy, Julio D C Maia, John E Stone, João V Ribeiro, Rafael C Bernardi, Ronak Buch, Giacomo Fiorin, Jérôme Hénin, Wei Jiang

J Chem Phys· July 2020

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AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD.
Santiago Antolínez, Peter Eugene Jones, James C Phillips, Jodi A Hadden-Perilla

J Chem Inf Model· January 2024

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AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics.
Lorenzo Casalino, Abigail C Dommer, Zied Gaieb, Emilia P Barros, Terra Sztain, James C Phillips

Int J High Perform Comput Appl· September 2021

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The challenges of theory-software translation.
Caroline Jay, Robert Haines, Daniel S Katz, Jeffrey C Carver, Sandra Gesing, James C Phillips

F1000Res· April 2021

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AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics.
Lorenzo Casalino, Abigail Dommer, Zied Gaieb, Emilia P Barros, Terra Sztain, James C Phillips

bioRxiv· November 2020

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Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism.
Abhishek Singharoy, Christopher Maffeo, Karelia H Delgado-Magnero, David J K Swainsbury, Melih Sener, James C Phillips

Cell· November 2019

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Why Aβ42 Is Much More Toxic than Aβ40.
James C Phillips

ACS Chem Neurosci· June 2019

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Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.
Brian K Radak, Christophe Chipot, Donghyuk Suh, Sunhwan Jo, Wei Jiang, James C Phillips

J Chem Theory Comput· December 2018

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NAMD goes quantum: an integrative suite for hybrid simulations.
Marcelo C R Melo, Rafael C Bernardi, Till Rudack, Maximilian Scheurer, Christoph Riplinger, James C Phillips

Nat Methods· May 2018

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Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.
Brian K Radak, Christophe Chipot, Donghyuk Suh, Sunhwan Jo, Wei Jiang, James C Phillips

J Chem Theory Comput· December 2017

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Revealing the Effect of Irradiation on Cement Hydrates: Evidence of a Topological Self-Organization.
N M Anoop Krishnan, Bu Wang, Gaurav Sant, James C Phillips, Mathieu Bauchy

ACS Appl Mater Interfaces· September 2017

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Why Ubiquitin Has Not Evolved.
Douglas C Allan, James C Phillips

Int J Mol Sci· September 2017

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Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome.
Fuxing Zeng, Yanbo Chen, Jonathan Remis, Mrinal Shekhar, James C Phillips

Nature· January 2017

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Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing.
John E Stone, Melih Sener, Kirby L Vandivort, Angela Barragan, Abhishek Singharoy, James C Phillips

Parallel Comput· July 2016

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Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms.
John E Stone, Antti-Pekka Hynninen, James C Phillips, Klaus Schulten

High Perform Comput (2016)· June 2016

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QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts.
João V Ribeiro, Rafael C Bernardi, Till Rudack, John E Stone, James C Phillips

Sci Rep· May 2016

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Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads.
John E Stone, Michael J Hallock, James C Phillips, Joseph R Peterson, Zaida Luthey-Schulten

IEEE Int Symp Parallel Distrib Process Workshops Phd Forum· May 2016

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Multilevel summation method for electrostatic force evaluation.
David J Hardy, Zhe Wu, James C Phillips, John E Stone, Robert D Skeel

J Chem Theory Comput· February 2015

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Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules.
Jeffrey Comer, James C Phillips, Klaus Schulten, Christophe Chipot

J Chem Theory Comput· December 2014

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Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD.
Wei Jiang, James C Phillips, Lei Huang, Mikolai Fajer, Yilin Meng

Comput Phys Commun· March 2014

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Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation.
James C Phillips, Yanhua Sun, Nikhil Jain, Eric J Bohm, Laxmikant V Kalé

SC Conf Proc· January 2014

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GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations.
David E Tanner, James C Phillips, Klaus Schulten

J Chem Theory Comput· July 2012

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Parallel Generalized Born Implicit Solvent Calculations with NAMD.
David E Tanner, Kwok-Yan Chan, James C Phillips, Klaus Schulten

J Chem Theory Comput· November 2011

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Getting boozy in books: substance use in adolescent literature.
Sarah M Coyne, Mark Callister, James C Phillips

Health Commun· September 2011

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High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD.
Wei Jiang, David J Hardy, James C Phillips, Alexander D Mackerell, Klaus Schulten

J Phys Chem Lett· January 2011

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