A system for interactive molecular dynamics simulation. - John E. Stone; Justin Gullingsrud; Klaus Schulten (SI3D, 2001)

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)

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 (Conf. Computing Frontiers, 2008)

Adapting a message-driven parallel application to GPU-accelerated clusters. - James C. Phillips; John E. Stone; Klaus Schulten (SC, 2008)

GPU Computing. - John D. Owens; Mike Houston; David Luebke; Simon Green; John E. Stone; James C. Phillips (Proc. IEEE, 2008)

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 (GPGPU, 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 (CLUSTER, 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 (IPDPS, 2009)

Multilevel summation of electrostatic potentials using graphics processing units. - David J. Hardy; John E. Stone; Klaus Schulten (Parallel Comput., 2009)

Probing Biomolecular Machines with Graphics Processors. - James C. Phillips; John E. Stone (ACM Queue, 2009)

GPU Algorithms for Molecular Modeling. - John E. Stone; David J. Hardy; Barry Isralewitz; Klaus Schulten (Scientific Computing with Multicore and Accelerators, 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 (ASPLOS, 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 (Green Computing Conference, 2010)

Immersive Molecular Visualization and Interactive Modeling with Commodity Hardware. - John E. Stone; Axel Kohlmeyer; Kirby L. Vandivort; Klaus Schulten (ISVC (2), 2010)

OpenCL: A Parallel Programming Standard for Heterogeneous Computing Systems. - John E. Stone; David Gohara; Guochun Shi (Comput. Sci. Eng., 2010)

Immersive Out-of-Core Visualization of Large-Size and Long-Timescale Molecular Dynamics Trajectories. - John E. Stone; Kirby L. Vandivort; Klaus Schulten (ISVC (2), 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)

Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories. - Michael Krone; John E. Stone; Thomas Ertl; Klaus Schulten (EuroVis (Short Papers), 2012)

GPU-accelerated molecular visualization on petascale supercomputing platforms. - John E. Stone; Kirby L. Vandivort; Klaus Schulten (UltraVis@SC, 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)

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 (HPTCDL@SC, 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)

Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating. - Ramya Gamini; Wei Han; John E. Stone; Klaus Schulten (PLoS Comput. Biol., 2014)

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)

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 (IPDPS Workshops, 2016)

High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL. - John E. Stone; Peter Messmer; Robert Sisneros; Klaus Schulten (IPDPS Workshops, 2016)

Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering. - John E. Stone; William R. Sherman; Klaus Schulten (IPDPS Workshops, 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 (ISC Workshops, 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)

Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing. - John E. Stone; Melih Sener; Kirby L. Vandivort; Angela M. Barragan; Abhishek Singharoy; Ivan Teo; João V. Ribeiro 003; Barry Isralewitz; Bo Liu; Boon Chong Goh; James C. Phillips; Craig MacGregor-Chatwin; et al. (Parallel Comput., 2016)

Communicating science through visualization in an age of alternative facts. - Kalina Borkiewicz; A. J. Christensen 001; John E. Stone (SIGGRAPH Courses, 2017)

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)

Scalable molecular dynamics with NAMD on the Summit system. - Bilge Acun; David J. Hardy; Laxmikant V. Kalé; Keqin Li 001; James C. Phillips; John E. Stone (IBM J. Res. Dev., 2018)

Omnidirectional Stereoscopic Projections for VR. - John E. Stone (VR Developer Gems, 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)

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)

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)

Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus. - David J. Hardy; John E. Stone; Barry Isralewitz; Emad Tajkhorshid (UrgentHPC@SC, 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; et al. (Int. J. High Perform. Comput. Appl., 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 001; Barry Isralewitz; Robert Patterson; Kalina Borkiewicz; Jeffrey Carpenter; C. Neil Hunter; Zaida Luthey-Schulten; Donna J. Cox (Parallel Comput., 2021)

ANARI: ANAlytic Rendering Interface. - Kevin S. Griffin; Jefferson Amstutz; David E. DeMarle; Johannes Günther 001; Jakob Progsch; William R. Sherman; John E. Stone; Will Usher 001; Kees van Kooten (EuroVis (Posters), 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; et al. (CoRR, 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)

ANARI: A 3-D Rendering API Standard. - John E. Stone; Kevin S. Griffin; Jefferson Amstutz; David E. DeMarle; William R. Sherman; Johannes Günther 001 (Comput. Sci. Eng., 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 019; et al. (Int. J. High Perform. Comput. Appl., 2022)

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; et al. (HPC Asia Workshops, 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 003; A. Sofia F. Oliveira; Clare Morris; Anthony T. Bogetti; Anda Trifan; Alexander Brace; et al. (Int. J. High Perform. Comput. Appl., 2023)

VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations. - Mariano Spivak; John E. Stone; João Ribeiro 003; Jan Saam; Peter L. Freddolino; Rafael C. Bernardi; Emad Tajkhorshid (J. Chem. Inf. Model., 2023)