John E. Stone - RankMe

50 papers A* 2A 2C 1Journal 26Unranked 17

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