John E. Stone

According to our database, John E. Stone authored at least 48 papers between 2001 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations.

Mariano Spivak, John E. Stone, João Ribeiro, Jan Saam, Peter L. Freddolino, Rafael C. Bernardi, Emad Tajkhorshid

J. Chem. Inf. Model., August, 2023

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol.

Abigail C. Dommer, Lorenzo Casalino, Fiona L. Kearns, Mia A. Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John Russo, A. Sofia F. Oliveira, Clare Morris, Anthony T. Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, S. Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders S. Christensen, Daniel G. A. Smith, Zhuoran Qiao, Sai K. Sirumalla, Michael O'Connor, Frederick R. Manby, Anima Anandkumar, David J. Hardy, James C. Phillips, Abraham C. Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John D. McCalpin, Christopher J. Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John E. Stone, Daniel M. Zuckerman, Adrian J. Mulholland, Thomas F. Miller III, Shantenu Jha, Arvind Ramanathan, Lillian T. Chong, Rommie E. Amaro

Int. J. High Perform. Comput. Appl., 2023

Application Experiences on a GPU-Accelerated Arm-based HPC Testbed.

Wael R. Elwasif, William F. Godoy, Nick Hagerty, James Austin Harris, Oscar R. Hernandez, Bálint Joó, Paul R. C. Kent, Damien Lebrun-Grandié, Elijah A. MacCarthy, Verónica G. Melesse Vergara, Bronson Messer, Ross Miller, Sarp Oral, Sergei I. Bastrakov, Michael Bussmann, Alexander Debus, Klaus Steiniger, Jan Stephan, René Widera, Spencer H. Bryngelson, Henry Le Berre, Anand Radhakrishnan, Jeffrey Young, Sunita Chandrasekaran, Florina M. Ciorba, Osman Simsek, Kate Clark, Filippo Spiga, Jeff R. Hammond, John E. Stone, David J. Hardy, Sebastian Keller, Jean-Guillaume Piccinali, Christian Trott

Proceedings of the HPC Asia 2023 Workshops, 2023

2022

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.

Anda Trifan, Defne Gorgun, Michael Salim, Zongyi Li, Alexander Brace, Maxim Zvyagin, Heng Ma, Austin Clyde, David Clark, David J. Hardy, Tom Burnley, Lei Huang, John D. McCalpin, Murali Emani, Hyenseung Yoo, Junqi Yin, Aristeidis Tsaris, Vishal Subbiah, Tanveer Raza, Jessica Liu, Noah Trebesch, Geoffrey Wells, Venkatesh Mysore, Tom Gibbs, James C. Phillips, S. Chakra Chennubhotla, Ian T. Foster, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, John E. Stone, Emad Tajkhorshid, Sarah A. Harris, Arvind Ramanathan

Int. J. High Perform. Comput. Appl., 2022

ANARI: A 3-D Rendering API Standard.

John E. Stone, Kevin S. Griffin, Jefferson Amstutz, David E. DeMarle, William R. Sherman, Johannes Günther

Comput. Sci. Eng., 2022

Analytic Rendering and Hardware-Accelerated Simulation for Scientific Applications.

Paul A. Navrátil, Christiaan P. Gribble, Pascal Grosset, John E. Stone

Comput. Sci. Eng., 2022

Early Application Experiences on a Modern GPU-Accelerated Arm-based HPC Platform.

Wael R. Elwasif, Sergei I. Bastrakov, Spencer H. Bryngelson, Michael Bussmann, Sunita Chandrasekaran, Florina M. Ciorba, Michael A. Clark, Alexander Debus, William F. Godoy, Nick Hagerty, Jeff R. Hammond, David J. Hardy, James Austin Harris, Oscar R. Hernandez, Bálint Joó, Sebastian Keller, Paul R. C. Kent, Henry Le Berre, Damien Lebrun-Grandié, Elijah A. MacCarthy, Verónica G. Melesse Vergara, Bronson Messer, Ross Miller, Sarp Oral, Jean-Guillaume Piccinali, Anand Radhakrishnan, Osman Simsek, Filippo Spiga, Klaus Steiniger, Jan Stephan, John E. Stone, Christian Trott, René Widera, Jeffrey Young

CoRR, 2022

ANARI: ANAlytic Rendering Interface.

Kevin S. Griffin, Jefferson Amstutz, David E. DeMarle, Johannes Günther, Jakob Progsch, William R. Sherman, John E. Stone, Will Usher, Kees van Kooten

Proceedings of the 24th Eurographics Conference on Visualization, 2022

2021

Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales.

Melih Sener, Stuart Levy, John E. Stone, A. J. Christensen, Barry Isralewitz, Robert Patterson, Kalina Borkiewicz, Jeffrey Carpenter, C. Neil Hunter, Zaida Luthey-Schulten, Donna J. Cox

Parallel Comput., 2021

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics.

Lorenzo Casalino, Abigail C. Dommer, Zied Gaieb, Emília P. Barros, Terra Sztain, Surl-Hee Ahn, Anda Trifan, Alexander Brace, Anthony T. Bogetti, Austin Clyde, Heng Ma, Hyungro Lee, Matteo Turilli, Syma Khalid, Lillian T. Chong, Carlos Simmerling, David J. Hardy, Julio D. C. Maia, James C. Phillips, Thorsten Kurth, Abraham C. Stern, Lei Huang, John D. McCalpin, Mahidhar Tatineni, Tom Gibbs, John E. Stone, Shantenu Jha, Arvind Ramanathan, Rommie E. Amaro

Int. J. High Perform. Comput. Appl., 2021

Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus.

David J. Hardy, John E. Stone, Barry Isralewitz, Emad Tajkhorshid

Proceedings of the IEEE/ACM HPC for Urgent Decision Making, 2021

2020

Scalable Analysis of Authentic Viral Envelopes on FRONTERA.

Fabio González-Arias, Tyler Reddy, John E. Stone, Jodi A. Hadden-Perilla, Juan R. Perilla

Comput. Sci. Eng., 2020

2019

High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities.

Alexander J. Bryer, Jodi A. Hadden-Perilla, John E. Stone, Juan R. Perilla

J. Chem. Inf. Model., 2019

NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems.

Sergio Decherchi, Andrea Spitaleri, John E. Stone, Walter Rocchia

Bioinform., 2019

Omnidirectional Stereoscopic Projections for VR.

John E. Stone

Proceedings of the VR Developer Gems, 1st Edition, 2019

2018

Scalable molecular dynamics with NAMD on the Summit system.

Bilge Acun, David J. Hardy, Laxmikant V. Kalé, Keqin Li, James C. Phillips, John E. Stone

IBM J. Res. Dev., 2018

Best Practices in Running Collaborative GPU Hackathons: Advancing Scientific Applications with a Sustained Impact.

Sunita Chandrasekaran, Guido Juckeland, Meifeng Lin, Matthew Otten, Dirk Pleiter, John E. Stone, Juan Lucio-Vega, Michael Zingale, Fernanda S. Foertter

Comput. Sci. Eng., 2018

2017

Communicating science through visualization in an age of alternative facts.

Kalina Borkiewicz, A. J. Christensen, John E. Stone

Proceedings of the Special Interest Group on Computer Graphics and Interactive Techniques Conference, 2017

2016

Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing.

John E. Stone, Melih Sener, Kirby L. Vandivort, Angela Barragan, Abhishek Singharoy, Ivan Teo, João V. Ribeiro, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Craig MacGregor-Chatwin, Matthew P. Johnson, Lena F. Kourkoutis, C. Neil Hunter, Klaus Schulten

Parallel Comput., 2016

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

Josh Vincent Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, Axel Kohlmeyer

J. Chem. Inf. Model., 2016

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

Proceedings of the High Performance Computing, 2016

Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering.

John E. Stone, William R. Sherman, Klaus Schulten

Proceedings of the 2016 IEEE International Parallel and Distributed Processing Symposium Workshops, 2016

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

John E. Stone, Peter Messmer, Robert Sisneros, Klaus Schulten

Proceedings of the 2016 IEEE International Parallel and Distributed Processing Symposium Workshops, 2016

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, Klaus Schulten

Proceedings of the 2016 IEEE International Parallel and Distributed Processing Symposium Workshops, 2016

2015

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

Javier Cabezas, Isaac Gelado, John E. Stone, Nacho Navarro, David Blair Kirk, Wen-mei W. Hwu

IEEE Trans. Parallel Distributed Syst., 2015

2014

Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating.

Ramya Gamini, Wei Han, John E. Stone, Klaus Schulten

PLoS Comput. Biol., 2014

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

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

Parallel Comput., 2014

Petascale Tcl with NAMD, VMD, and Swift/T.

James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, Klaus Schulten

Proceedings of the 1st First Workshop for High Performance Technical Computing in Dynamic Languages, 2014

2013

Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation.

Elijah Roberts, John E. Stone, Zaida Luthey-Schulten

J. Comput. Chem., 2013

GPU-accelerated molecular visualization on petascale supercomputing platforms.

John E. Stone, Kirby L. Vandivort, Klaus Schulten

Proceedings of the 8th International Workshop on Ultrascale Visualization, 2013

2012

Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories.

Michael Krone, John E. Stone, Thomas Ertl, Klaus Schulten

Proceedings of the 14th Eurographics Conference on Visualization, 2012

2011

Fast analysis of molecular dynamics trajectories with graphics processing units - Radial distribution function histogramming.

Benjamin G. Levine, John E. Stone, Axel Kohlmeyer

J. Comput. Phys., 2011

Immersive Out-of-Core Visualization of Large-Size and Long-Timescale Molecular Dynamics Trajectories.

John E. Stone, Kirby L. Vandivort, Klaus Schulten

Proceedings of the Advances in Visual Computing - 7th International Symposium, 2011

2010

OpenCL: A Parallel Programming Standard for Heterogeneous Computing Systems.

John E. Stone, David Gohara, Guochun Shi

Comput. Sci. Eng., 2010

Immersive Molecular Visualization and Interactive Modeling with Commodity Hardware.

John E. Stone, Axel Kohlmeyer, Kirby L. Vandivort, Klaus Schulten

Proceedings of the Advances in Visual Computing - 6th International Symposium, 2010

Quantifying the impact of GPUs on performance and energy efficiency in HPC clusters.

Jeremy Enos, Craig P. Steffen, Joshi Fullop, Michael T. Showerman, Guochun Shi, Kenneth Esler, Volodymyr V. Kindratenko, John E. Stone, James C. Phillips

Proceedings of the International Green Computing Conference 2010, 2010

An asymmetric distributed shared memory model for heterogeneous parallel systems.

Isaac Gelado, Javier Cabezas, Nacho Navarro, John E. Stone, Sanjay J. Patel, Wen-mei W. Hwu

Proceedings of the 15th International Conference on Architectural Support for Programming Languages and Operating Systems, 2010

GPU Algorithms for Molecular Modeling.

John E. Stone, David J. Hardy, Barry Isralewitz, Klaus Schulten

Proceedings of the Scientific Computing with Multicore and Accelerators., 2010

2009

Probing Biomolecular Machines with Graphics Processors.

James C. Phillips, John E. Stone

ACM Queue, 2009

Multilevel summation of electrostatic potentials using graphics processing units.

David J. Hardy, John E. Stone, Klaus Schulten

Parallel Comput., 2009

Long time-scale simulations of in vivo diffusion using GPU hardware.

Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-mei W. Hwu, Zaida Luthey-Schulten

Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009

GPU clusters for high-performance computing.

Volodymyr V. Kindratenko, Jeremy Enos, Guochun Shi, Michael T. Showerman, Galen Wesley Arnold, John E. Stone, James C. Phillips, Wen-mei W. Hwu

Proceedings of the 2009 IEEE International Conference on Cluster Computing, August 31, 2009

High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs.

John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wen-mei W. Hwu, Klaus Schulten

Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, 2009

2008

GPU Computing.

John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, James C. Phillips

Proc. IEEE, 2008

Adapting a message-driven parallel application to GPU-accelerated clusters.

James C. Phillips, John E. Stone, Klaus Schulten

Proceedings of the ACM/IEEE Conference on High Performance Computing, 2008

GPU acceleration of cutoff pair potentials for molecular modeling applications.

Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, Wen-mei W. Hwu

Proceedings of the 5th Conference on Computing Frontiers, 2008

2007

Accelerating molecular modeling applications with graphics processors.

John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten

J. Comput. Chem., 2007

2001

A system for interactive molecular dynamics simulation.

John E. Stone, Justin Gullingsrud, Klaus Schulten

Proceedings of the 2001 Symposium on Interactive 3D Graphics, 2001