John E. Stone

Publication Activity (10 Years)

Years Active: 2001-2023
Publications (10 Years): 25

Top Topics

Diffusion Process

Severe Acute Respiratory Syndrome

Top Venues

Comput. Sci. Eng.

IPDPS Workshops

Int. J. High Perform. Comput. Appl.

J. Chem. Inf. Model.

Publications

Mariano Spivak, John E. Stone, João Ribeiro, Jan Saam, Peter L. Freddolino, Rafael C. Bernardi, Emad Tajkhorshid
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations. J. Chem. Inf. Model. 63 (15) (2023)
Abigail C. Dommer, Lorenzo Casalino, Fiona L. Kearns, Mia 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 Miller, Shantenu Jha, Arvind Ramanathan, Lillian T. Chong, Rommie E. Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. Int. J. High Perform. Comput. Appl. 37 (1) (2023)
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
Application Experiences on a GPU-Accelerated Arm-based HPC Testbed. HPC Asia Workshops (2023)
Kevin S. Griffin, Jefferson Amstutz, David E. DeMarle, Johannes Günther, Jakob Progsch, William R. Sherman, John E. Stone, Will Usher, Kees van Kooten
ANARI: ANAlytic Rendering Interface. EuroVis (Posters) (2022)
John E. Stone, Kevin S. Griffin, Jefferson Amstutz, David E. DeMarle, William R. Sherman, Johannes Günther
ANARI: A 3-D Rendering API Standard. Comput. Sci. Eng. 24 (2) (2022)
Wael R. Elwasif, Sergei I. Bastrakov, Spencer H. Bryngelson, Michael Bussmann, Sunita Chandrasekaran, Florina 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
Early Application Experiences on a Modern GPU-Accelerated Arm-based HPC Platform. CoRR (2022)
Paul A. Navrátil, Christiaan P. Gribble, Pascal Grosset, John E. Stone
Analytic Rendering and Hardware-Accelerated Simulation for Scientific Applications. Comput. Sci. Eng. 24 (2) (2022)
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
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) (2022)
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
Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales. Parallel Comput. 102 (2021)
David J. Hardy, John E. Stone, Barry Isralewitz, Emad Tajkhorshid
Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus. UrgentHPC@SC (2021)
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
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. Int. J. High Perform. Comput. Appl. 35 (5) (2021)
Fabio González-Arias, Tyler Reddy, John E. Stone, Jodi A. Hadden-Perilla, Juan R. Perilla
Scalable Analysis of Authentic Viral Envelopes on FRONTERA. Comput. Sci. Eng. 22 (6) (2020)
Sergio Decherchi, Andrea Spitaleri, John E. Stone, Walter Rocchia
NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems. Bioinform. 35 (7) (2019)
Alexander J. Bryer, Jodi A. Hadden-Perilla, John E. Stone, Juan R. Perilla
High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities. J. Chem. Inf. Model. 59 (10) (2019)
Sunita Chandrasekaran, Guido Juckeland, Meifeng Lin, Matthew Otten, Dirk Pleiter, John E. Stone, Juan Lucio-Vega, Michael Zingale, Fernanda S. Foertter
Best Practices in Running Collaborative GPU Hackathons: Advancing Scientific Applications with a Sustained Impact. Comput. Sci. Eng. 20 (4) (2018)
Bilge Acun, David J. Hardy, Laxmikant V. Kalé, Keqin Li, James C. Phillips, John E. Stone
Scalable molecular dynamics with NAMD on the Summit system. IBM J. Res. Dev. 62 (6) (2018)
Kalina Borkiewicz, A. J. Christensen, John E. Stone
Communicating science through visualization in an age of alternative facts. SIGGRAPH Courses (2017)
Kalina Borkiewicz, A. J. Christensen, John E. Stone
Communicating science through visualization in an age of alternative facts. SIGGRAPH ASIA (Courses) (2017)
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
Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing. Parallel Comput. 55 (2016)
John E. Stone, Peter Messmer, Robert Sisneros, Klaus Schulten
High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL. IPDPS Workshops (2016)
John E. Stone, Antti-Pekka Hynninen, James C. Phillips, Klaus Schulten
Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms. ISC Workshops (2016)
Josh Vincent Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, Axel Kohlmeyer
TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD. J. Chem. Inf. Model. 56 (6) (2016)
John E. Stone, Michael J. Hallock, James C. Phillips, Joseph R. Peterson, Zaida Luthey-Schulten, Klaus Schulten
Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads. IPDPS Workshops (2016)
John E. Stone, William R. Sherman, Klaus Schulten
Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering. IPDPS Workshops (2016)
Javier Cabezas, Isaac Gelado, John E. Stone, Nacho Navarro, David Blair Kirk, Wen-mei W. Hwu
Runtime and Architecture Support for Efficient Data Exchange in Multi-Accelerator Applications. IEEE Trans. Parallel Distributed Syst. 26 (5) (2015)
Ramya Gamini, Wei Han, John E. Stone, Klaus Schulten
Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating. PLoS Comput. Biol. 10 (3) (2014)
James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, Klaus Schulten
Petascale Tcl with NAMD, VMD, and Swift/T. HPTCDL@SC (2014)
Michael J. Hallock, John E. Stone, Elijah Roberts, Corey Fry, Zaida Luthey-Schulten
Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations. Parallel Comput. 40 (5-6) (2014)
John E. Stone, Kirby L. Vandivort, Klaus Schulten
GPU-accelerated molecular visualization on petascale supercomputing platforms. UltraVis@SC (2013)
Elijah Roberts, John E. Stone, Zaida Luthey-Schulten
Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation. J. Comput. Chem. 34 (3) (2013)
Michael Krone, John E. Stone, Thomas Ertl, Klaus Schulten
Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories. EuroVis (Short Papers) (2012)
Benjamin G. Levine, John E. Stone, Axel Kohlmeyer
Fast analysis of molecular dynamics trajectories with graphics processing units - Radial distribution function histogramming. J. Comput. Phys. 230 (9) (2011)
John E. Stone, Kirby L. Vandivort, Klaus Schulten
Immersive Out-of-Core Visualization of Large-Size and Long-Timescale Molecular Dynamics Trajectories. ISVC (2) (2011)
Jeremy Enos, Craig P. Steffen, Joshi Fullop, Michael T. Showerman, Guochun Shi, Kenneth Esler, Volodymyr V. Kindratenko, John E. Stone, James C. Phillips
Quantifying the impact of GPUs on performance and energy efficiency in HPC clusters. Green Computing Conference (2010)
John E. Stone, Axel Kohlmeyer, Kirby L. Vandivort, Klaus Schulten
Immersive Molecular Visualization and Interactive Modeling with Commodity Hardware. ISVC (2) (2010)
Isaac Gelado, Javier Cabezas, Nacho Navarro, John E. Stone, Sanjay J. Patel, Wen-mei W. Hwu
An asymmetric distributed shared memory model for heterogeneous parallel systems. ASPLOS (2010)
John E. Stone, David Gohara, Guochun Shi
OpenCL: A Parallel Programming Standard for Heterogeneous Computing Systems. Comput. Sci. Eng. 12 (3) (2010)
John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wen-mei W. Hwu, Klaus Schulten
High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs. GPGPU (2009)
James C. Phillips, John E. Stone
Probing biomolecular machines with graphics processors. Commun. ACM 52 (10) (2009)
James C. Phillips, John E. Stone
Probing Biomolecular Machines with Graphics Processors. ACM Queue 7 (9) (2009)
Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-mei W. Hwu, Zaida Luthey-Schulten
Long time-scale simulations of in vivo diffusion using GPU hardware. IPDPS (2009)
Volodymyr V. Kindratenko, Jeremy Enos, Guochun Shi, Michael T. Showerman, Galen Wesley Arnold, John E. Stone, James C. Phillips, Wen-mei W. Hwu
GPU clusters for high-performance computing. CLUSTER (2009)
David J. Hardy, John E. Stone, Klaus Schulten
Multilevel summation of electrostatic potentials using graphics processing units. Parallel Comput. 35 (3) (2009)
John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, James C. Phillips
GPU Computing. Proc. IEEE 96 (5) (2008)
Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, Wen-mei W. Hwu
GPU acceleration of cutoff pair potentials for molecular modeling applications. Conf. Computing Frontiers (2008)
James C. Phillips, John E. Stone, Klaus Schulten
Adapting a message-driven parallel application to GPU-accelerated clusters. SC (2008)
John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten
Accelerating molecular modeling applications with graphics processors. J. Comput. Chem. 28 (16) (2007)
John E. Stone, Justin Gullingsrud, Klaus Schulten
A system for interactive molecular dynamics simulation. SI3D (2001)