John E. Stone
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Contact:Tel: (217) 244-3349johns@ks.uiuc.edu |
| Comet McNaught
C/2006 P1, Jan 2007 Champaign, Illinois |
Veil Nebula complex in Cygnus (supernova remnant)
SBIG ST-8XE w/ Canon 200mm f/2.8L-II @ f2.8, 112 mins exposure (14x8min) w/ 6nm H-α filter, Illinois Dark Skies Star Party, September 27, 2008 |
Research interests:
VMD:
High performance visualization of biomolecular complexes,
haptic feedback, interactive molecular dynamics simulations,
programmable shading
GPU Computing:
Accelerating scientific applications using graphics processing units
Tachyon:
Multiprocessor ray tracing on shared memory and
distributed memory architectures, molecular visualization,
visualization of large models
FreeVR:
A free multi-platform alternative to the CAVE library.
Research Publications:
Follow this link to the Publications Page where you can read abstractacts as well as download PDF copies of many group publications.- "Visualization of Cyclic and Multi-branched Molecules with VMD"
- Simon Cross, Michelle M. Kuttell, John E. Stone, and James E. Gain.
- Journal of Molecular Graphics and Modelling. (In press)
- Online full text of paper
- Journal of Molecular Graphics and Modelling. (In press)
- "Long time-scale simulations of in vivo diffusion using GPU hardware"
- Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-mei W. Hwu, and Zaida Luthey-Schulten.
- Eighth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2009). (In press)
- Eighth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2009). (In press)
- "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, and Klaus Schulten.
- In Proceedings of the 2nd Workshop on General-Purpose Processing on Graphics Processing Units, ACM International Conference Proceeding Series, volume 383, pp. 9-18, 2009.
- Online full text of paper
- In Proceedings of the 2nd Workshop on General-Purpose Processing on Graphics Processing Units, ACM International Conference Proceeding Series, volume 383, pp. 9-18, 2009.
- "Multilevel Summation of Electrostatic Potentials Using Graphics Processing Units"
- David J. Hardy, John E. Stone, and Klaus Schulten.
- Parallel Computing, 28:164-177, 2009.
- Online full text of paper
- Parallel Computing, 28:164-177, 2009.
- "Adapting a Message-driven Parallel Application to GPU-Accelerated Clusters"
- James C. Phillips, John E. Stone, and Klaus Schulten.
- In SC '08: Proceedings of the 2008 ACM/IEEE Conference on Supercomputing, pp. 1-9, Piscataway, NJ, USA, 2008. IEEE Press.
- Online full text of paper
- In SC '08: Proceedings of the 2008 ACM/IEEE Conference on Supercomputing, pp. 1-9, Piscataway, NJ, USA, 2008. IEEE Press.
- "Using VMD - An Introductory Tutorial"
- Jen Hsin, Anton Arkhipov, Ying Yin, John E. Stone, and Klaus Schulten.
- Current Protocols - Bioinformatics, 5:Unit 5.7, 2008
- Online full text of paper
- Current Protocols - Bioinformatics, 5:Unit 5.7, 2008
- "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
- In CF'08: Proceedings of the 2008 conference on Computing frontiers, pp. 273-282, New York, NY, USA, 2008. ACM.
- Online full text of paper
- In CF'08: Proceedings of the 2008 conference on Computing frontiers, pp. 273-282, New York, NY, USA, 2008. ACM.
- "GPU Computing"
- John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, James C. Phillips
- Proceedings of the IEEE, 96:879-899, 2008.
- Online full text of paper
- Proceedings of the IEEE, 96:879-899, 2008.
- "Accelerating Molecular Modeling Applications with Graphics Processors"
- John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten
- Journal of Computational Chemistry, 28:2618-2640, 2007.
- Online full text of paper
- Journal Web Site
- Journal of Computational Chemistry, 28:2618-2640, 2007.
- "A System for Interactive Molecular Dynamics Simulation"
- John E. Stone, Justin Gullingsrud, Klaus Schulten, Paul Grayson
- In 2001 ACM Symposium on Interactive 3D Graphics,
- John F. Hughes and Carlo H. Sequin, editors, pages 191-194, New York, 2001, ACM SIGGRAPH
- ACM Digital Library, citations, online full text, etc
- Online full text of paper
- I3D 2001 Conference Home Page
- In 2001 ACM Symposium on Interactive 3D Graphics,
- "An Efficient Library for Parallel Ray Tracing and Animation"
- John E. Stone
- Master's Thesis, University of Missouri-Rolla, Department of Computer Science, April 1998
- Master's Thesis, University of Missouri-Rolla, Department of Computer Science, April 1998
- "Accelerating Software-based MPEG Encoding Using the VIS Instruction Set"
- John Stone, Ahmad Zandi
- 1997 NAB Interactive Insights: A Multimedia Compendium
- 1997 National Association of Broadcasters Convention
- Las Vegas, Nevada
- 1997 NAB Interactive Insights: A Multimedia Compendium
- "Rendering of Numerical Flow Simulations Using MPI"
- John Stone, Mark Underwood
- 1996 MPI Developers Conference
- University of Notre Dame, IN
- 1996 MPI Developers Conference
- "Numerical Flow Simulation and Rendering Using MPI"
- John Stone, Mark Underwood
- 1996 Intel Supercomputer Users Group Conference
- Oak Ridge National Laboratory, Knoxville TN
- 1996 Intel Supercomputer Users Group Conference
- "An Efficient Library for Parallel Ray Tracing and Animation"
- John Stone
- 1995 Intel Supercomputer Users Group Conference
- Sandia National Laboratory, Albequerque NM
- 1995 Intel Supercomputer Users Group Conference
Short articles:
Presentations, talks, and demonstrations:
- GPU Accelerated Visualization and Analysis in VMD
- Center for Molecular Modeling, University of Pennsylvania, 6/9/2009
- Keynote: Accelerating Molecular Modeling Applications with GPU Computing
- Second Sharcnet Symposium on GPU and Cell Computing, University of Waterloo, 5/20/2009
- Experiences with Multi-GPU Acceleration in VMD
- Path to Petascale: Adapting GEO/CHEM/ASTRO Applications for Accelerators and Accelerator Clusters, NCSA, 4/2/2009
- High Performance Computation and Interactive Display of Molecular Orbitals on GPUs and Multi-core CPUs
- Second Workshop on General-Purpose Processing on Graphics Processing Units, Washington D.C., 3/8/2009
- High Performance Computation and Interactive Display of Molecular Orbitals on GPUs and Multi-core CPUs
- IACAT Accelerator Workshop, NCSA, 1/23/2009
- GPU Computing Case Study: Molecular Modeling Applications
- ECE 598SP: Massively Parallel Processors, University of Illinois, 11/11/2008
- GPU Computing,
- Cape Linux Users Group, South Africa, 10/28/2008
- Visualizing Biomolecular Complexes with VMD,
- Centre for High Performance Computing,
CSIR Rosebank Campus, Cape Town, South Africa, 10/27/2008
- An Introduction to Molecular Visualization with VMD,
- Centre for High Performance Computing,
CSIR Rosebank Campus, Cape Town, South Africa, 10/27/2008
- Accelerating Molecular Modeling Applications with Graphics Processors,
- Computer Science Department, University of Cape Town, South Africa, 10/23/2008
- Accelerating Computational Biology by 100x Using CUDA,
- NVISION 08, San Jose Convention Center, San Jose, CA, 8/26/2008
- Case Study - Accelerating Molecular Dynamics Experimentation,
- VSCSE: Accelerators for Science and Engineering Applications: GPUs and Multicore, NCSA, 8/21/2008
- Accelerating Scientific Applications with GPUs,
- Workshop on Programming Massively Parallel Processors, NCSA, 7/10/2008
- Accelerating Molecular Modeling Applications with Graphics Processors
- SIAM conference on Parallel Processing for Scientific Computing, Atlanta, GA 3/12/2008
- Case Study: Molecular Visualization and Analysis
- Supercomputing 2007 Tutorial: High Performance Computing with CUDA, Reno, NV, 11/11/2007
- GPU Acceleration of Scientific Applications Using CUDA
- AstroGPU 2007, Institute for Advanced Study, Princeton University, 11/09/2007
- ECE498AL CUDA Performance Case Studies: Ion Placement Tool, VMD
- University of Illinois at Urbana-Champaign, 10/15/2007
- ECE498AL CUDA Performance Case Studies: Ion Placement Tool, VMD
- University of Illinois at Urbana-Champaign, 3/14/2007
- Visualization of Nano-Scale Structures
- University of Texas Health Science Center at Houston, 4/20/2006
- Universidad Nacional Autónoma de Mexico, DGSCA, 8/11/2006 (Video Conference Presentation)
- Universidad Nacional Autónoma de Mexico, DGSCA, 8/11/2006 (Video Conference Presentation)
- VMD: Algorithms and Methods for Large Scale Biomolecular Visualization
- San Diego Supercomputer Center, 9/12/2005
- Dancing Proteins: 3-D Visualization of Protein Structure and Dynamics on Next-Generation Graphics Hardware
- ITG Forum at University of Illinois at Urbana-Champaign, 2/15/2005
- CS Colloqium at University of Missouri-Rolla, 2/22/2005
- Purdue University Envision Center, 2/25/2005
- CS Colloqium at University of Missouri-Rolla, 2/22/2005
- VMD: Biomolecular Visualization and Analysis
- The Scripps Research Institute, La Jolla CA,
July 31, 2003
- Designing a Cluster for a Small Research Group
- Summer School on Theoretical Biophysics, Beckman Institute UIUC,
June 11, 2003
- Biomolecular Visualization in the CAVE with VMD
- Center for Parallel Computing, Swedish Royal Institute of Technology, Stockholm Sweden,
October 3, 2001
- Cluster-based visualization with VMD on a tiled display wall
- NCSA Terascale Clusters Dedication, September 5, 2001
- Biomolecular Visualization, Interactive Molecular Dynamics
- Siggraph 2001, Sun Microsystems Booth, August 14-16, 2001
- "Low-Cost Linux Clusters for Biomolecular Simulations Using NAMD"
- Beckman Institute UIUC, June 26, 2001
- Software Development Tutorial for Biomedical Research Scientists
- Beckman Institute UIUC, April 3, 2001
- "Linux Clusters"
- Beckman Institute UIUC, November 11, 1999
Service:
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Book reviews:
- GPU Gems 3 (chapter reviewer, published 2007)
- Geometric Tools for Computer Graphics (reviewer, published 2002)
- Real-Time Rendering (reviewer, first edition, published 1999)
- Program Committee Memberships:
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Manuscript reviews:
- Computing in Science and Engineering (2009)
- BMC Structural Biology (2008, 2009)
- Journal of Computational Chemistry (2008)
- Computer Graphics Forum (2008, 2009)
- Journal of Parallel Computing (2008)
- Siggraph 2008
- IEEE VIS 2007
- 2006 IEEE Symposium on Interactive Ray Tracing
- ACM Computing Surveys (2006)
- Virtual Reality, Volume 9 number 1 (2005)
- International Journal of Parallel and Distributed Systems and Networks (2002)
- 2000 IEEE International Parallel & Distributed Processing Symposium
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Advisory Board Memberships:
- Computer Science Advisory Board (2008, 2009), Missouri University of Science and Technology
- Computer Science Advisory Board (2007), University of Missouri-Rolla
Press articles and interviews:
- NVIDIA: "NVIDIA Appoints First CUDA Center of Excellence",
Andrew Humber, June 30, 2008 - Bio-IT World: "Life Scientists Get Their Game Faces On",
by Mike May, April 1, 2008 - Genome Technology: "Not Just for Kids Anymore",
by Matthew Dublin, September, 2007 - BeHardware: "NVIDIA CUDA: practical uses" (English),
by Damien Triolet, August 17, 2007 - Hardware.fr: "NVIDIA CUDA: plus en pratique" (French),
by Damien Triolet, August 9, 2007 - TG Daily: "NCSA: A look inside one of the world's most capable supercomputer facilities",
by Rick C. Hodgin, July 2, 2007 - Beyond3D: "NVIDIA Tesla: GPU computing gets its own brand",
by Tim Murray, June 20, 2007 - TG Daily: "NVIDIA unveils Tesla, moves into supercomputing",
by Wolfgang Gruener, June 20, 2007
Education:
- Master of Science in Computer Science
- Master's Program Advisor: Dr. Fikret Ercal
- University of Missouri-Rolla
- University of Missouri-Rolla
- Bachelor of Science in Computer Science
- University of Missouri-Rolla
Other Accomplishments:
- I was one of the founding members of the University of Missouri-Rolla Solar Car Team
- 17th Place in 21st Annual ACM International Collegiate Programming Contest,
- 1996 World Finals, Philadelphia PA
- 1st Place in 1996 ACM Mid-Central Regional Programming Contest
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