John E. Stone
- Senior Research Programmer, Theoretical and Computational Biophysics Group and NIH Center for Macromolecular Modeling and Bioinformatics
- Associate Director, CUDA Center of Excellence at University of Illinois at Urbana-Champaign
- Co-PI, "The Computational Microscope", NSF Petascale Resource Allocation (PRAC), NSF 14-518, 2014-2017
- NVIDIA CUDA Fellow, 2010 to Present: NVIDIA 2010 CUDA Fellows Press Release, UIUC CUDA Center Announcement
Mr. Stone is the lead developer of VMD, a high performance molecular visualization tool used by researchers all over the world. His research interests include molecular visualization, GPU computing, parallel processing, ray tracing, haptics, and virtual environments. Mr. Stone was inducted as an NVIDIA CUDA Fellow in 2010. He also provides consulting services for projects involving computer graphics, GPU computing, and high performance computing.
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Research Interests
Research Articles Book Chapters Google Scholar Presentations Service Press Articles Education Consulting Honors Linked-In Personal Site |
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Contact:
Ph: 217-244-3349 johns@ks.uiuc.edu |
All-atom HIV-1 capsid
rendered with the VMD QuickSurf representation and the Tachyon parallel ray tracing engine |
Crux, the Southern Cross, the smallest constellation.
The Coalsack dark nebula is visible at the lower right. Canon EOS 6D 135mm f/2L @ f2.8, 30 sec exposure. Langdam in Koo guest farm, two hours from Cape Town. South Africa, April 20, 2014 |
Research Interests:
VMD:
High performance visualization of biomolecular complexes,
interactive molecular dynamics simulations,
programmable shading
GPU Computing:
Accelerating scientific applications using graphics processing units
Tachyon:
Parallel ray tracing on shared memory and
distributed memory architectures, molecular visualization
Immersive Visualization, Virtual Environments, and Haptic Feedback: CAVE, FreeVR, VRPN
Published Journal and Book Cover Images, Photographs:
Book Chapters:
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Research Articles:
- "Multilevel Summation Method for Electrostatic Force Evaluation"
- David J. Hardy, Zhe Wu, James C. Phillips John E. Stone,
Robert D. Skeel, and Klaus Schulten.
- Journal of Chemical Theory and Computation, 11:766-779, 2015.
- Online full text available at http://pubs.acs.org/doi/abs/10.1021/ct5009075
- Journal of Chemical Theory and Computation, 11:766-779, 2015.
- "Visualization of Energy Conversion Processes in a Light Harvesting Organelle at Atomic Detail"
- Melih Sener, John E. Stone, Angela Barragan, Abhishek Singharoy,
Ivan Teo, Kirby L. Vandivort, Barry Isralewitz, Bo Liu,
Boon Chong Goh, James C. Phillips,
Lena F. Kourkoutis, C. Neil Hunter, and Klaus Schulten
- SC'14 Visualization and Data Analytics Showcase, 2014. (In press)
- Winner of the SC'14 Visualization and Data Analytics Showcase
- Online full text available at SC'14 site
- SC'14 Visualization and Data Analytics Showcase, 2014. (In press)
- "Petascale Tcl with NAMD, VMD, and Swift/T"
- James C. Phillips, John E. Stone, Kirby L. Vandivort,
Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde,
and Klaus Schulten.
- Proceedings of the First Workshop for High Performance Technical Computing in Dynamic Languages, pp. 6-17, 2014.
- Online full text available at ACM digital library
- Online full text available at http://dx.doi.org/10.1109/HPTCDL.2014.7
- Proceedings of the First Workshop for High Performance Technical Computing in Dynamic Languages, pp. 6-17, 2014.
- "Stable Small Quantum Dots for Synaptic Receptor Tracking on Live Neurons"
- En Cai, Pinghua Ge, Sang Hak Lee, Okunola Jeyifous, Yong Wang,
Yanxin Liu, Katie M. Wilson, Sung Jun Lim, Michele A. Baird,
John E. Stone, Kwan Young Lee, David G. Fernig, Michael W. Davidson,
Hee Jung Chung, Klaus Schulten, Andrew M. Smith, William N. Green,
and Paul R. Selvin.
- Angewandte Chemie - International Edition in English, 53(46):12484-12488, 2014.
- Online full text available at http://dx.doi.org/10.1002/anie.201405735
- Angewandte Chemie - International Edition in English, 53(46):12484-12488, 2014.
- "Runtime and Architecture Support for Efficient Data Exchange in Multi-Accelerator Applications"
- Javier Cabezas, Isaac Gelado, John E. Stone,
Nacho Navarro, David B. Kirk, and Wen-mei Hwu.
- IEEE Transactions on Parallel and Distributed Systems, 2014. (In press)
- Online full text available at http://dx.doi.org/10.1109/TPDS.2014.2316825
- IEEE Transactions on Parallel and Distributed Systems, 2014. (In press)
- "Unlocking the Full Potential of the Cray XK7 Accelerator"
- Mark D. Klein and John E. Stone.
- Cray Users Group, Lugano Switzerland, May 2014.
- Online full text in CUG 2014 Proceedings
- Cray Users Group, Lugano Switzerland, May 2014.
- "GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting"
- John E. Stone, Ryan McGreevy, Barry Isralewitz, and Klaus Schulten.
- Faraday Discussions, 169:265-283, 2014.
- Online full text available at http://dx.doi.org/10.1039/C4FD00005F
- Faraday Discussions, 169:265-283, 2014.
- "Methodologies for the Analysis of Instantaneous Lipid Diffusion in MD Simulations of Large Membrane Systems"
- Matthieu Chavent, Tyler Reddy, Joseph Goose, Anna Caroline E. Dahl,
John E. Stone, Bruno Jobard, and Mark S.P. Sansom.
- Faraday Discussions, 169:455-475, 2014.
- Online full text available at http://dx.doi.org/10.1039/C3FD00145H
- Faraday Discussions, 169:455-475, 2014.
- "Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations"
- Michael J. Hallock, John E. Stone, Elijah Roberts,
Corey Fry, and Zaida Luthey-Schulten.
- Journal of Parallel Computing, 40:86-99, 2014.
- Online full text available at http://dx.doi.org/10.1016/j.parco.2014.03.009
- Journal of Parallel Computing, 40:86-99, 2014.
- "Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating"
- Ramya Gamini, Wei Han, John E. Stone, and Klaus Schulten.
- PLoS Computational Biology, 10(3): e1003488, 2014.
- Online full text available at http://dx.doi.org/10.1371/journal.pcbi.1003488
- PLoS Computational Biology, 10(3): e1003488, 2014.
- "GPU-Accelerated Molecular Visualization on Petascale Supercomputing Platforms"
- John E. Stone, Kirby L. Vandivort, and Klaus Schulten.
- UltraVis'13: Proceedings of the 8th International Workshop on Ultrascale Visualization, pp. 6:1-6:8, 2013.
- Online full text available at http://dx.doi.org/10.1145/2535571.2535595
- UltraVis'13: Proceedings of the 8th International Workshop on Ultrascale Visualization, pp. 6:1-6:8, 2013.
- "Early Experiences Scaling VMD Molecular Visualization and Analysis Jobs on Blue Waters"
- John E. Stone, Barry Isralewitz, and Klaus Schulten.
- Extreme Scaling Workshop (XSW), pp. 43-50, 2013.
- Online full text available at http://dx.doi.org/10.1109/XSW.2013.10
- Extreme Scaling Workshop (XSW), pp. 43-50, 2013.
- "Lattice microbes: High-Performance stochastic simulation method for the reaction-diffusion master equation"
- Elijah Roberts, John E. Stone, and Zaida Luthey-Schulten.
- Journal of Computational Chemistry, 34(3):245-255, 2013.
- Online full text: http://dx.doi.org/10.1002/jcc.23130
- Journal of Computational Chemistry, 34(3):245-255, 2013.
- "Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories"
- Michael Krone, John E. Stone, Thomas Ertl, and Klaus Schulten.
- EuroVis - Short Papers, pp. 67-71, 2012.
- Online full text: http://dx.doi.org/10.2312/PE/EuroVisShort/EuroVisShort2012/067-071
- EuroVis - Short Papers, pp. 67-71, 2012.
- "Optimization of a Broadband Discone Antenna Design and Platform Installed Radiation Patterns Using a GPU-Accelerated Savant/WIPL-D Hybrid Approach"
- Tod Courtney, Matthew C. Miller, John E. Stone, and Robert A. Kipp.
- In Proceedings of the Applied Computational Electromagnetics Symposium (ACES 2012), Columbus, Ohio, April 2012.
- Online full text
- In Proceedings of the Applied Computational Electromagnetics Symposium (ACES 2012), Columbus, Ohio, April 2012.
- "Immersive Out-of-Core Visualization of Large-Size and Long-Timescale Molecular Dynamics Trajectories"
- John E. Stone, Kirby L. Vandivort, and Klaus Schulten.
- G. Bebis et al. (Eds.): 7th International Symposium on Visual Computing (ISVC 2011), LNCS 6939, pp. 1-12, 2011.
- Online full text: http://dx.doi.org/10.1007/978-3-642-24031-7_1
- G. Bebis et al. (Eds.): 7th International Symposium on Visual Computing (ISVC 2011), LNCS 6939, pp. 1-12, 2011.
- "Using GPUs to Accelerate Installed Antenna Performance Simulations"
- Tod Courtney, John E. Stone, and Bob Kipp.
- In Proceedings of the 2011 Antenna Applications Symposium, Allerton Park, Monticello IL, September 2011.
- Online full text
- In Proceedings of the 2011 Antenna Applications Symposium, Allerton Park, Monticello IL, September 2011.
- "Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units — Radial Distribution Function Histogramming"
- Benjamin G. Levine, John E. Stone, and Axel Kohlmeyer.
- Journal of Computational Physics, 230(9):3556-3569, 2011.
- Online full text: http://dx.doi.org/10.1016/j.jcp.2011.01.048
- Journal of Computational Physics, 230(9):3556-3569, 2011.
- "Immersive Molecular Visualization and Interactive Modeling with Commodity Hardware"
- John E. Stone, Axel Kohlmeyer, Kirby L. Vandivort, and Klaus Schulten.
- G. Bebis et al. (Eds.): ISVC 2010, Part II, LNCS 6454, pp. 382-393, 2010.
- Online full text: http://dx.doi.org/10.1007/978-3-642-17274-8_38
- G. Bebis et al. (Eds.): ISVC 2010, Part II, LNCS 6454, pp. 382-393, 2010.
- "Quantifying the Impact of GPUs on Performance and Energy Efficiency in HPC Clusters"
- Jeremy Enos, Craig Steffen, Joshi Fullop, Michael Showerman,
Guochun Shi, Kenneth Esler, Volodymyr Kindratenko,
John E. Stone, and James C. Phillips.
- International Conference on Green Computing, pp. 317-324, 2010.
- Online full text: http://dx.doi.org/10.1109/GREENCOMP.2010.5598297
- International Conference on Green Computing, pp. 317-324, 2010.
- "GPU-Accelerated Molecular Modeling Coming Of Age"
- John E. Stone, David J. Hardy, Ivan S. Ufimtsev, and Klaus Schulten.
- Journal of Molecular Graphics and Modelling, 29(2):116-125, 2010.
- Online full text: http://dx.doi.org/10.1016/j.jmgm.2010.06.010
- Journal of Molecular Graphics and Modelling, 29(2):116-125, 2010.
- "OpenCL: A Parallel Programming Standard for Heterogeneous Computing Systems"
- John E. Stone, David Gohara, and Guochun Shi.
- Computing in Science and Engineering, 12(3):66-73, 2010.
- Online full text: http://dx.doi.org/10.1109/MCSE.2010.69
- Computing in Science and Engineering, 12(3):66-73, 2010.
- "An Asymmetric Distributed Shared Memory Model for Heterogeneous Parallel Systems"
- Isaac Gelado, John E. Stone, Javier Cabezas, Sanjay Patel, Nacho Navarro, and Wen-mei W. Hwu.
- ASPLOS '10: Proceedings of the 15th International Conference on Architectural Support for Programming Languages and Operating Systems, pp. 347-358, 2010.
- Online full text: http://doi.acm.org/10.1145/1736020.1736059
- ASPLOS '10: Proceedings of the 15th International Conference on Architectural Support for Programming Languages and Operating Systems, pp. 347-358, 2010.
- "Probing Biomolecular Machines with Graphics Processors"
- James C. Phillips and John E. Stone.
- Communications of the ACM 52(10):34-41, 2009.
- Online full text: http://doi.acm.org/10.1145/1562764.1562780
- Communications of the ACM 52(10):34-41, 2009.
- "GPU Clusters for High Performance Computing"
- Volodymyr Kindratenko, Jeremy Enos, Guochun Shi, Michael Showerman,
Galen Arnold, John E. Stone, James Phillips, and Wen-mei Hwu.
- Cluster Computing and Workshops, 2009. CLUSTER '09. IEEE International Conference on. pp. 1-8, Aug. 2009.
- Online full text: http://dx.doi.org/10.1109/CLUSTR.2009.5289128
- Cluster Computing and Workshops, 2009. CLUSTER '09. IEEE International Conference on. pp. 1-8, Aug. 2009.
- "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. 28:131-139, 2009.
- Online full text: http://dx.doi.org/10.1016/j.jmgm.2009.04.010
- Journal of Molecular Graphics and Modelling. 28:131-139, 2009.
- "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.
- IPDPS '09: Proceedings of the 2009 IEEE International Symposium on Parallel & Distributed Processing, pp. 1-8, 2009
- Online full text: http://dx.doi.org/10.1109/IPDPS.2009.5160930
- IPDPS '09: Proceedings of the 2009 IEEE International Symposium on Parallel & Distributed Processing, pp. 1-8, 2009
- "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: http://doi.acm.org/10.1145/1513895.1513897
- 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: http://dx.doi.org/10.1016/j.parco.2008.12.005
- 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: http://dx.doi.org/10.1109/SC.2008.5214716
- 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: http://dx.doi.org/10.1002/0471250953.bi0507s24
- 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, and 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: http://doi.acm.org/10.1145/1366230.1366277
- 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, and James C. Phillips.
- Proceedings of the IEEE, 96:879-899, 2008.
- Online full text: http://dx.doi.org/10.1109/JPROC.2008.917757
- 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, and Klaus Schulten.
- Journal of Computational Chemistry, 28:2618-2640, 2007.
- Online full text of paper
- Online full text (JCC web site): http://dx.doi.org/10.1002/jcc.20829
- Journal of Computational Chemistry, 28:2618-2640, 2007.
- "A System for Interactive Molecular Dynamics Simulation"
- John E. Stone, Justin Gullingsrud, Klaus Schulten, and 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: http://doi.acm.org/10.1145/364338.364398
- 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
- "Rendering of Numerical Flow Simulations Using MPI"
- John Stone and Mark Underwood.
- Second MPI Developers Conference, pages 138-141, 1996.
- Online full text: http://dx.doi.org/10.1109/MPIDC.1996.534105
- Second MPI Developers Conference, pages 138-141, 1996.
- "Numerical Flow Simulation and Rendering Using MPI"
- John Stone, Mark Underwood
- In Proceedings of the 1996 Intel Supercomputer Users Group Conference
- Oak Ridge National Laboratory, Knoxville TN
- In Proceedings of the 1996 Intel Supercomputer Users Group Conference
- "An Efficient Library for Parallel Ray Tracing and Animation"
- John Stone
- In Proceedings of the 1995 Intel Supercomputer Users Group Conference
- Sandia National Laboratory, Albequerque NM
- In Proceedings of the 1995 Intel Supercomputer Users Group Conference
Short Articles and Whitepapers:
- "Random Numbers, Efficiency, and Other Things"
- John Stone
- Ray Tracing News, Volume 20, Number 1, May 19, 2007
- Ray Tracing News, Volume 20, Number 1, May 19, 2007
- "Real-Time GPU Spheres"
- John Stone
- Ray Tracing News, Volume 18, Number 1, December 12, 2005
- Ray Tracing News, Volume 18, Number 1, December 12, 2005
- "Workstation Clusters for Parallel Computing"
- John Stone, Fikret Ercal
- IEEE Potentials pages 31-33, April/May 2001
- IEEE Home page
- IEEE Potentials pages 31-33, April/May 2001
- "The Ups and Downs of Multithreaded Ray Tracing and Optimization"
- John Stone
- Ray Tracing News, Volume 12, Number 2, December 21, 1999
- Ray Tracing News, Volume 12, Number 2, December 21, 1999
- "Accelerating Software-based MPEG Encoding Using the VIS Instruction Set"
- John Stone, Ahmad Zandi
- Interactive Insights: A Multimedia Compendium, pages 30-34,
- 1997 National Association of Broadcasters Convention
- Las Vegas, Nevada
- Interactive Insights: A Multimedia Compendium, pages 30-34,
Presentations:
- GPU-accelerated Visualization and Analysis of Petascale Molecular Dynamics Simulations, Integrated Imaging Initiative Workshop: Tomography and Ptychography, Argonne National Laboratory (9/30/2014)
- GPU-accelerated Visualization and Analysis of Petascale Molecular Dynamics Simulations, Research and Technology Development Conference, Missouri University of Science and Technology (9/16/2014)
- Programming for Hybrid Architectures Today and in the Future, LSU Third Annual HPC User Symposium, Louisiana State University (6/5/2014)
- GPU-Accelerated Visualization and Analysis of Biomolecular Complexes, Oxford University, United Kingdom (5/12/2014)
- GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting, Faraday Discussion 169: Molecular Simulations and Visualization, University of Nottingham, United Kingdom (5/8/2014)
- GPGPU2 Advanced Methods for Computing with CUDA, University of Cape Town, South Africa (4/22/2014)
- Petascale Molecular Ray Tracing: Accelerating VMD/Tachyon with OptiX, GPU Technology Conference (03/27/2014)
- Fighting HIV with CUDA, CCoE Achievement Award, GPU Technology conference (03/25/2014)
- Visualization and analysis of petascale molecular simulations with VMD, GPU Technology Conference (03/25/2014)
- Using GPUs to Supercharge Visualization and Analysis of Molecular Dynamics Simulations with VMD, NVIDIA GTC Express (02/25/2014)
- Experiences Developing and Maintaining Scientific Applications on GPU-Accelerated Platforms, Indiana University, IUPUI Campus, Indianapolis, IN (01/24/2014)
- Fighting HIV with GPU-Accelerated Petascale Computing, Supercomputing 2013, Denver, CO (11/19/2013)
- GPU-Accelerated Molecular Visualization on Petascale Supercomputing Platforms, UltraVis'13: Eighth Ultrascale Visualization Workshop, Denver, CO (11/17/2013)
- Visualization and Analysis of Petascale Molecular Dynamics Simulations, San Diego Supercomputer Center, University of California San Diego (11/5/2013)
- Experiences Developing and Maintaining Scientific Applications on GPU-Accelerated Platforms, Indiana University, Bloomington, IN (10/2/2013)
- Interactive Molecular Visualization and Analysis with GPU Computing, Fall National Meeting of the American Chemical Society, Indianapolis, IN (9/11/2013)
- Early Experiences Scaling VMD Molecular Visualization and Analysis Jobs on Blue Waters, XSEDE Extreme Scaling Workshop, Boulder, CO (8/15/2013)
- GPU-Accelerated Molecular Visualization and Analysis with VMD, Midwest Theoretical Chemistry Conference, Urbana, IL, (5/31/2013)
- GPGPU Computing with CUDA Workshop, University of Cape Town, South Africa (4/29/2013)
- VMD: GPU-Accelerated Visualization and Analysis of Petascale Molecular Dynamics Simulations, GPU Technology Conference, San Jose, CA (3/20/2013)
- Keynote: Broadening the Use of Scalable Kernels in NAMD/VMD, VSCSE Many-core Processors, NCSA, University of Illinois (8/16/2012)
- GPU-Accelerated Analysis of Petascale Molecular Dynamics Simulations with VMD, Scalable Software for Scientific Computing Workshop, University of Notre Dame (6/11/2012)
- Visualization of petascale molecular dynamics simulations, Imaging at Illinois, The Next Generation: Computational Imaging and Visualization, Beckman Institute, University of Illinois (6/1/2012)
- In-Situ Visualization and Analysis of Petascale Molecular Dynamics Simulations with VMD, Accelerated HPC Symposium, San Jose, CA (5/17/2012)
- High Performance Molecular Visualization and Analysis on GPUs, GPU Technology Conference, San Jose, CA (5/16/2012)
- Immersive Out-of-Core Visualization of Large-Size and Long-Timescale Molecular Dynamics Trajectories, ISVC 2011, Las Vegas, NV (9/26/2011)
- Immersive Molecular Visualization and Interactive Modeling with Commodity Hardware, ISVC 2010, Las Vegas, NV (12/1/2010)
- Faster, Cheaper, Better: Biomolecular Simulation with NAMD, VMD, and CUDA, NVIDIA Booth, Supercomputing 2010, New Orleans, LA (11/16/2010)
- High Performance Computing with CUDA Case Study: Heterogeneous GPU Computing for Molecular Modeling, CUDA Tutorial, Supercomputing 2010, New Orleans, LA (11/14/2010)
- High Performance Molecular Simulation, Visualization, and Analysis on GPUs, GPU Technology Conference (09/22/2010)
- High Performance Molecular Simulation, Visualization, and Analysis on GPUs, Oak Ridge National Laboratory (09/16/2010)
- Faster, Cheaper, and Better Science: Molecular modeling on GPUs, Fall National Meeting of the Americal Chemical Society, Boston, MA (8/22/2010)
- OpenCL: Molecular modeling on heterogeneous computing systems, Fall National Meeting of the Americal Chemical Society, Boston, MA (8/22/2010)
- Lecture 4: Cut-off and Binning for Regular Data Sets, VSCSE Many-core Processors, University of Illinois (8/03/2010)
- The OpenCL Programming Model, Part 1 Illinois UPCRC Summer School (7/23/2010)
- The OpenCL Programming Model, Part 2 Illinois UPCRC Summer School (7/23/2010)
- Molecular Visualization and Analysis on GPUs, Symposium on Application of GPUs in Chemistry and Materials Science, University of Pittsburgh (06/29/2010)
- ECE498AL Application Performance Case Studies: Molecular Visualization and Analysis, University of Illinois at Urbana-Champaign (04/08/2010)
- An Introduction to OpenCL, GPUComputing.net Webinar (12/10/2009)
- OpenCL for Molecular Modeling Applications: Early Experiences, OpenCL BOF, Supercomputing 2009, Portland, OR (11/18/2009)
- Accelerating Molecular Modeling Applications with GPU Computing, Exhibition, Supercomputing 2009, Portland, OR (11/18/2009)
- High Performance Computing with CUDA Case Study: Molecular Modeling Applications,CUDA Tutorial, Supercomputing 2009, Portland, OR (11/15/2009)
- An Introduction to OpenCL, IACAT/CCOE GPU Brown Bag Forum, University of Illinois (10/21/2009)
- High Performance Molecular Visualization and Analysis with GPU Computing, Beckman Institute Forum for Imaging and Visualization, University of Illinois (10/20/2009)
- GPU Accelerated Visualization and Analysis in VMD and Recent NAMD Developments, GPU Technology Conference, San Jose, CA (10/1/2009)
- Case Study - Accelerating Molecular Dynamics Experimentation, VSCSE: Many-Core Processors for Science and Engineering Applications, NCSA (8/13/2009)
- Multidisciplinary Panel, VSCSE: Many-Core Processors for Science and Engineering Applications, NCSA (8/10/2009)
- Accelerating Molecular Dynamics on a GPU, Careers in High-Performance Systems Mentoring Workshop, National Center for Supercomputing Applications (7/25/2009)
- 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)
- ECE498AL Application Performance Case Studies: Molecular Visualization and Analysis, University of Illinois at Urbana-Champaign (04/09/2009)
- 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 NJ (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)
- 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)
- VMD: Biomolecular Visualization and Analysis, The Scripps Research Institute, La Jolla CA (7/31/2003)
- Designing a Cluster for a Small Research Group, Summer School on Theoretical Biophysics, Beckman Institute UIUC, 6/11/2003
- Biomolecular Visualization in the CAVE with VMD, Center for Parallel Computing, Swedish Royal Institute of Technology, Stockholm Sweden (10/3/2001)
- Cluster-based visualization with VMD on a tiled display wall, NCSA Terascale Clusters Dedication (9/5/2001)
- Biomolecular Visualization, Interactive Molecular Dynamics, Siggraph 2001, Sun Microsystems Booth (8/14/2001)
- 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:
- Editorial Board Member, Journal of Molecular Graphics and Modelling (2010-2013)
- Guest Editorial Board Member, IEEE TPDS Special Issue on High Performance Computing with Accelerators
- International workshop on OpenCL (IWOCL) (2013, 2014, 2015)
- Sixth Workshop on General Purpose Processing on Graphics Processing Units (2013)
- Workshop on Programmability Issues for Heterogeneous Multicores (MULTIPROG 2011, 2012, 2013)
- Symposium on Application Accelerators in High Performance Computing (SAAHPC 2009, 2010, 2011, 2012)
- 2011 IEEE International Parallel & Distributed Processing Symposium (IPDPS 2011)
- International Symposium on Visual Computing (ST3 2011)
- IEEE International Workshop on High Performance Computational Biology (HiCOMB 2009, 2010)
- 2010 Workshop on Language, Compiler, and Architecture support for GPGPU
- NCSA/IACAT Workshop on Programming Massively Parallel Processors (PMPP 2008)
- GPU Computing Gems Emerald Edition (chapter reviewer, published 2011)
- GPU Gems 3 (chapter reviewer, published 2007)
- Geometric Tools for Computer Graphics (reviewer, published 2002)
- Real-Time Rendering (reviewer, first edition, published 1999)
- IEEE Pacific Visualization (2015)
- Eurovis (2014)
- IEEE Transactions on Parallel and Distributed Systems (2014)
- International Workshop on OpenCL (2013, 2014)
- Journal of Molecular Graphics and Modelling (2013)
- Workshop on General Purpose Processing on GPUs (2013)
- EuroPar (2012)
- Computing in Science and Engineering (2009, 2011, 2012)
- PLOS ONE (2012)
- Supercomputing (2009, 2011)
- Parallel Computing, (2010, 2011)
- Computing Frontiers (2011)
- High Performance Graphics (2010)
- Computer Physics Communications (2010)
- Journal of Computational Chemistry (2008, 2009, 2010)
- Computers and Graphics (2010)
- Visualization in Medicine and Life Sciences (2009)
- PPAM 2009 Eighth International Conference on Parallel Processing and Applied Mathematics (2009)
- BMC Structural Biology (2008, 2009)
- 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)
- IEEE International Parallel & Distributed Processing Symposium (2000)
- Computer Science Advisory Board, Missouri University of Science and Technology (2008-2013)
- Biomedical Analysis and Simulation Supercomputer Advisory Board, NIH Resource for Computer-Integrated Systems for Microscopy and Manipulation (CISMM), University of North Carolina at Chapel Hill (2009, 2010)
- Computer Science Advisory Board, University of Missouri-Rolla (2007)
- Utilizing Wide Vector Instructions with NAMD (2014),
Craig Disselkoen and Jordan Jorgensen - GPU-accelerated Brownian Dynamics (2013),
Justin Dufresne and Terrance Howard - GPU-accelerated Secondary Structure Analysis (2013),
Alex Knaust and John McCann - GPU-accelerated Molecular Dynamics Simulation Analysis (2012),
Jason Hutcheson and Michael Musson - GPU-accelerated Molecular Dynamics Simulation Analysis (2011),
Sean Karlage and Michael Robson
- Arjun Radhakrishnan, M.Sc. Electrical Engineering, "Accelerating Pulsar Dedispersion for MeerKAT on Graphics Processing Units", University of Cape Town, South Africa, 2010
- Juan-Pierre Longmore, M.Sc. Computer Science, "Towards Realistic Interactive Sand: A GPU-based Framework", University of Cape Town, South Africa, 2009
- Judging panel for SCS Science Image Challenge competitions (2011, 2012, 2013, 2014)
Press Articles and Interviews:
- Scientific Computing World: "Does HPC's future lie in remote visualization, by Tom Wilkie, Scientific Computing World, February/March, 2015.
- InsideHPC: "HPC's Future Lies in Remote Visualization, by Tom Wilkie, InsideHPC, February 11, 2015.
- NVIDIA: "CUDA for ARM Platforms is Now Available, by Mark Harris, NVIDIA, June 18, 2013.
- National Science Foundation: "Cracking the Code of HIV; Providing An Up-Close View of the Enemy", by Diana Yates, UIUC, and Lisa-Joy Zgorski NSF, May 29, 2013
- Inside HPC: "GPUs Helps Researchers Uncover New Approach to Combating HIV Virus", by Rich Brueckner, May 29, 2013
- PC Magazine: "Nvidia GPUs Assist in Battling HIV Virus", by Damon Poeter, May 29, 2013
- Bio-IT World: "Researchers Characterize Chemical Structure of HIV Capsid, by Allison Proffitt, May 29, 2013
- NVIDIA: "Breakthrough in HIV Research Enabled by NVIDIA GPU Accelerators", by George Millington, May 29, 2013
- Tech News Daily: "Supercomputer Tackles Mystery of HIV's Structure", by Jillian Scharr, May 29, 2013
- HPCwire: NVIDIA Releases CUDA 4.0 Toolkit, February 28, 2011
- University of Illinois: "Illinois Researcher Named 2010 CUDA Fellow by NVIDIA", by Laurie Talkington, December 13, 2010
- Scientific Computing: "Speeding Up Science", by Mike May, November 20, 2010
- NVIDIA: "NVIDIA Names Three New 2010 CUDA Fellows", November 10, 2010
- Chemical and Engineering News: "The GPU Revolution, by Lauren Wolf, November 1, 2010
- GenomeWeb: "Eyeing a Growing Market, Nvidia Launches Portal to Aggregate GPU-Enabled Life Science Applications", by Vivien Marx, January 15, 2010
- CNN/Money: "Tesla Bio Workbench Enables Scientists to Achieve New Breakthroughs in Biosciences", January 14, 2010
- SciDAC Review: "Hardware: Core Strength", Number 15, Winter 2009
- TG Daily: "NVIDIA teams up with Microsoft for HPC", by Andrew Thomas, September 28, 2009
- Wired: "Personal Supercomputers Promise Teraflops on Your Desk", by Priya Ganapati, August 3, 2009
- 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
Consulting Activities:
- "Graphics Processing Unit (GPU) Acceleration for Cosite Interference Prediction Tools", SBIR N131-008, funded by NAVAIR, U.S. Navy, 2013-present.
- "Antenna Placement Optimization on Large, Airborne, Naval Platforms", SBIR N101-022, funded by NAVAIR, U.S. Navy, 2010-2013.
- "Multilevel Parallelization of Software for Accurate Protein-Ligand Affinities", SBIR PAR-07-160, 1R44GM088867, funded by the National Institutes of Health, 2010-2014.
Previous Employment:
- I was previously a Senior Programmer/Analyst at Heuris/Pulitzer, and later Heuris Logic, developing commercial video encoding and transcoding software used in service bureaus, the standalone commercial MPEG Power Professional software, and plug-ins for the leading non-linear video editing systems. My work in this era was noteworthy mainly for my early use of parallel processing and SIMD instruction set extensions for acceleration of the routines for color space conversions, image filtering and de-noising, and motion estimation within the video encoder subsystem.
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
Honors and Other Accomplishments:
- Winner of the SC'14 Visualization and Data Analytics Showcase
for the movie and accompanying paper entitled:
"Visualization of Energy Conversion Processes in a Light Harvesting Organelle at Atomic Detail"
- Most Cited Article Since 2009, Journal of Molecular Graphics and Modelling
- 2014 CUDA Center of Excellence Achievement Award: Fighting HIV with CUDA
- NVIDIA CUDA Fellow: NVIDIA 2010 CUDA Fellows Announcement, UIUC Press Release
- 2010 HiPEAC Paper Award for the paper "An Asymmetric Distributed Shared Memory Model for Heterogeneous Parallel Systems" presented at ASPLOS 2010.
- Tachyon, the ray tracing package I originally wrote for my Master's Thesis and continue to maintain today, was selected as a finalist for the SPEC MPI benchmark and is now part of the SPEC MPI2007 benchmark suite.
- I'm a member in good standing of ACM and IEEE.
- I hold an FCC Amateur Extra Class radio license KC9VGG, and a GMRS radio license.
- I have served the Champaign-Urbana Astronomical Society (CUAS) as Vice President (2008, 2009, 2010), and Fifth Director (2013).
- 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
- First Place Prize Winner: Intelligent Systems Center Graduate Research Paper Presentation Contest, University of Missouri-Rolla, April 20, 1996
- Prize Winner: Intelligent Systems Center Graduate Research Paper Presentation Contest, University of Missouri-Rolla, March 30, 1995
- I was a member of the Upsilon Pi Epsilon international computer science honorary society while a graduate student at University of Missouri-Rolla. I served as the treasurer for the local chapter in 1995.
- I was a member of the Kappa Kappa Psi national honorary band fraternity while a graduate student at University of Missouri-Rolla.
- I was one of the founding members of the University of Missouri-Rolla Solar Car Team while an undergraduate student.
- I was a member of six man team (itself part of the ISRA junior team) that won the 1990 National Trophy Rifle Team match at the National Trophy Rifle Matches at Camp Perry, Ohio
