John E. Stone

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.

Research Interests
Research Articles
Book Chapters
Google Scholar
Presentations
Service
Press Articles
Education
Consulting
Honors
Linked-In
Personal Site
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:

Venus Transit 2012 Sunrise on Haleakala, Maui

Book Chapters:

"Stochastic Simulations of Cellular Processes: From Single Cells to Colonies"
John Cole, Michael J. Hallock, Piyush Labhsetwar, Joseph R. Peterson, John E. Stone, and Zaida Luthey-Schulten.
In, Andres Kriete, editor, Computational Systems Biology, Second Edition, Chapter 13, pp. 277-293, 2013.
Book home pages: Amazon | Elsevier
"GPU-Accelerated Computation and Interactive Display of Molecular Orbitals"
John E. Stone, David J. Hardy, Jan Saam, Kirby L. Vandivort, and Klaus Schulten.
In, Wen-Mei Hwu, editor, GPU Computing Gems, Chapter 1, pp. 5-18, 2011.
Book home pages: Amazon | Elsevier
"Fast Molecular Electrostatics Algorithms on GPUs"
David J. Hardy, John E. Stone, Kirby L. Vandivort, David Gohara, Christopher Rodrigues, and Klaus Schulten.
In, Wen-Mei Hwu, editor, GPU Computing Gems, Chapter 4, pp. 43-58, 2011.
Book home pages: Amazon | Elsevier
"GPU Algorithms for Molecular Modeling"
John E. Stone, David J. Hardy, Barry Isralewitz, and Klaus Schulten.
In Jack Dongarra, David A. Bader, and Jakub Kurzak editors, Scientific Computing with Multicore and Accelerators, Chapman & Hall / CRC Press, Chapter 16, pp. 351-371, 2010.
Book home pages: Amazon | CRC Press

Research Articles:

"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.
Submitted, 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

"Unlocking the Full Potential of the Cray XK7 Accelerator"
Mark D. Klein and John E. Stone.
Cray Users Group, Lugano Switzerland, 2014. (In press)

"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 Discussion 169, 2014. (In press)
Online full text available at http://dx.doi.org/10.1039/C4FD00005F

"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 Discussion 169, 2014. (In press)
Online full text available at http://dx.doi.org/10.1039/C3FD00145H

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

"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

Short Articles and Whitepapers:

"Random Numbers, Efficiency, and Other Things"
John Stone
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

"Workstation Clusters for Parallel Computing"
John Stone, Fikret Ercal
IEEE Potentials pages 31-33, April/May 2001
IEEE Home page

"The Ups and Downs of Multithreaded Ray Tracing and Optimization"
John Stone
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

Presentations:

Service:

    National Science Foundation "Passionate on Parallel" REU Mentorships:
  • 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

Press Articles and Interviews:

Consulting Activities:

I serve as a consultant to Delcross Technologies LLC for the GPU and MPI-based parallel computing aspects of the projects:
  • "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.

I serve as a consultant to Verachem LLC for the GPU parallel computing aspects of the project:
  • "Multilevel Parallelization of Software for Accurate Protein-Ligand Affinities", SBIR 1R44GM088867, funded by the National Institutes of Health, 2010-present.

I served as a consultant to Production Data Services, developing tools for 3-D stereoscopic movie production. I developed and maintained a sophisticated software module for synchronized 3-D stereoscopic display of asynchronous, parallel-decoded video streams that formed the basis of the RushPlay 3D digital dailies system used in producing the Lionsgate 3-D movie My Bloody Valentine 3-D, released in January 2009.

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

Bachelor of Science in Computer Science
University of Missouri-Rolla

Honors and Other Accomplishments:

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, IEEE, and the Royal Society of Chemistry.

I hold an FCC Amateur Extra Class radio license 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