OpenCL: A Parallel Programming Standard for Heterogeneous Computing Systems

Por Stone, John E., Gohara, David, Shi, Guochun
Publicado em 2010

Multilevel Summation of Electrostatic Potentials Using Graphics Processing Units

Por Hardy, David J., Stone, John E., Schulten, Klaus
Publicado em 2009

Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units—Radial Distribution Function Histogramming

Por Levine, Benjamin G., Stone, John E., Kohlmeyer, Axel
Publicado em 2011

Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation

Por Roberts, Elijah, Stone, John E., Luthey-Schulten, Zaida
Publicado em 2012

Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering

Por Stone, John E., Sherman, William R., Schulten, Klaus
Publicado no IEEE Int Symp Parallel Distrib Process Workshops Phd Forum (2016)

Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating

Por Gamini, Ramya, Han, Wei, Stone, John E., Schulten, Klaus
Publicado em 2014

High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL

Por Stone, John E., Messmer, Peter, Sisneros, Robert, Schulten, Klaus
Publicado no IEEE Int Symp Parallel Distrib Process Workshops Phd Forum (2016)

GPU-Accelerated Molecular Modeling Coming Of Age

Por Stone, John E., Hardy, David J., Ufimtsev, Ivan S., Schulten, Klaus
Publicado em 2010

GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting

Por Stone, John E., McGreevy, Ryan, Isralewitz, Barry, Schulten, Klaus
Publicado em 2014

Using VMD - An Introductory Tutorial

Por Hsin, Jen, Arkhipov, Anton, Yin, Ying, Stone, John E., Schulten, Klaus
Publicado em 2008

Visualisation of Cyclic and Multi-Branched Molecules with VMD

Por Cross, Simon, Kuttel, Michelle M., Stone, John E., Gain, James E.
Publicado em 2009

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms

Por Stone, John E., Hynninen, Antti-Pekka, Phillips, James C., Schulten, Klaus
Publicado no High Perform Comput (2016) (2016)

Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations

Por Hallock, Michael J., Stone, John E., Roberts, Elijah, Fry, Corey, Luthey-Schulten, Zaida
Publicado em 2014

Topogromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD

Por Vermaas, Josh V, Hardy, David J, Stone, John E, Tajkhorshid, Emad, Kohlmeyer, Axel
Publicado no J Chem Inf Model (2016)

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

Por Singharoy, Abhishek, Teo, Ivan, McGreevy, Ryan, Stone, John E, Zhao, Jianhua, Schulten, Klaus
Publicado no eLife (2016)

Runtime and Architecture Support for Efficient Data Exchange in Multi-Accelerator Applications

Por Cabezas, Javier, Gelado, Isaac, Stone, John E., Navarro, Nacho, Kirk, David B., Hwu, Wen-mei
Publicado no IEEE Trans Parallel Distrib Syst (2014)

Multilevel Summation Method for Electrostatic Force Evaluation

Por Hardy, David J., Wu, Zhe, Phillips, James C., Stone, John E., Skeel, Robert D., Schulten, Klaus
Publicado no J Chem Theory Comput (2014)

Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads

Por Stone, John E., Hallock, Michael J., Phillips, James C., Peterson, Joseph R., Luthey-Schulten, Zaida, Schulten, Klaus
Publicado no IEEE Int Symp Parallel Distrib Process Workshops Phd Forum (2016)

Challenges of Integrating Stochastic Dynamics and Cryo-electron Tomograms in Whole-cell Simulations

Por Earnest, Tyler M., Watanabe, Reika, Stone, John E., Mahamid, Julia, Baumeister, Wolfgang, Villa, Elizabeth, Luthey-Schulten, Zaida
Publicado no J Phys Chem B (2017)

Methodologies for the Analysis of Instantaneous Lipid Diffusion in MD Simulations of Large Membrane Systems

Por Chavent, Matthieu, Reddy, Tyler, Goose, Joseph, Dahl, Anna Caroline E., Stone, John E., Jobard, Bruno, Sansom, Mark S.P.
Publicado em 2014