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2020 – today
- 2023
[j25]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 F. Miller III, 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): 28-44 (2023)- [j24]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): 4664-4678 (2023) - [c22]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: 35-49 - 2022
- [j23]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): 4-6 (2022) - [j22]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): 7-18 (2022) - [j21]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): 603-623 (2022) - [c21]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: 83-85 - [i1]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:
Early Application Experiences on a Modern GPU-Accelerated Arm-based HPC Platform. CoRR abs/2209.09731 (2022) - 2021
- [j20]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) - [j19]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: 102698 (2021) - [c20]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: 1-10 - 2020
- [j18]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): 11-20 (2020)
2010 – 2019
- 2019
- [j17]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): 1241-1243 (2019) - [j16]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): 4328-4338 (2019) - [p2]John E. Stone:
Omnidirectional Stereoscopic Projections for VR. VR Developer Gems 2019: 423-435 - 2018
- [j15]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): 95-106 (2018) - [j14]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): 4:1-4:9 (2018) - 2017
- [c19]Kalina Borkiewicz, A. J. Christensen, John E. Stone:
Communicating science through visualization in an age of alternative facts. SIGGRAPH Courses 2017: 8:1-8:204 - [c18]Kalina Borkiewicz, A. J. Christensen, John E. Stone:
Communicating science through visualization in an age of alternative facts. SIGGRAPH ASIA (Courses) 2017: 3:1-3:122 - 2016
- [j13]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): 1112-1116 (2016) - [j12]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: 17-27 (2016) - [c17]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: 89-100 - [c16]John E. Stone, Peter Messmer, Robert Sisneros, Klaus Schulten:
High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL. IPDPS Workshops 2016: 1014-1023 - [c15]John E. Stone, William R. Sherman, Klaus Schulten:
Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering. IPDPS Workshops 2016: 1048-1057 - [c14]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: 188-206 - 2015
- [j11]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): 1405-1418 (2015) - 2014
- [j10]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): 86-99 (2014) - [j9]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) - [c13]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: 6-17 - 2013
- [j8]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): 245-255 (2013) - [c12]John E. Stone, Kirby L. Vandivort, Klaus Schulten:
GPU-accelerated molecular visualization on petascale supercomputing platforms. UltraVis@SC 2013: 6:1-6:8 - 2012
- [c11]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 - 2011
- [j7]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): 3556-3569 (2011) - [c10]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: 1-12 - 2010
- [j6]John E. Stone, David Gohara, Guochun Shi:
OpenCL: A Parallel Programming Standard for Heterogeneous Computing Systems. Comput. Sci. Eng. 12(3): 66-73 (2010) - [c9]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: 347-358 - [c8]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: 317-324 - [c7]John E. Stone, Axel Kohlmeyer, Kirby L. Vandivort, Klaus Schulten:
Immersive Molecular Visualization and Interactive Modeling with Commodity Hardware. ISVC (2) 2010: 382-393 - [p1]John E. Stone, David J. Hardy, Barry Isralewitz, Klaus Schulten:
GPU Algorithms for Molecular Modeling. Scientific Computing with Multicore and Accelerators 2010: 351-371
2000 – 2009
- 2009
- [j5]James C. Phillips, John E. Stone:
Probing biomolecular machines with graphics processors. Commun. ACM 52(10): 34-41 (2009) - [j4]David J. Hardy, John E. Stone, Klaus Schulten:
Multilevel summation of electrostatic potentials using graphics processing units. Parallel Comput. 35(3): 164-177 (2009) - [j3]James C. Phillips, John E. Stone:
Probing Biomolecular Machines with Graphics Processors. ACM Queue 7(9): 30 (2009) - [c6]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: 9-18 - [c5]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: 1-8 - [c4]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: 1-8 - 2008
- [j2]John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, James C. Phillips:
GPU Computing. Proc. IEEE 96(5): 879-899 (2008) - [c3]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: 273-282 - [c2]James C. Phillips, John E. Stone, Klaus Schulten:
Adapting a message-driven parallel application to GPU-accelerated clusters. SC 2008: 8 - 2007
- [j1]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): 2618-2640 (2007) - 2001
- [c1]John E. Stone, Justin Gullingsrud, Klaus Schulten:
A system for interactive molecular dynamics simulation. SI3D 2001: 191-194
Coauthor Index
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