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2020 – today
- 2020
[j17]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
- [j16]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) - [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 V. 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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