John E. Stone

Mr. Stone is the lead developer of VMD, a high performance tool for preparation, analysis, and visualization of biomolecular simulations used by over 100,000 researchers all over the world. Our research papers describing VMD and its algorithms have been cited by more than 33,000 peer-reviewed research papers, both by users of VMD itself and by researchers developing related software and algorithms. Mr. Stone's research interests include molecular visualization, GPU computing, parallel computing, ray tracing, haptics, virtual environments, and immersive visualization. Mr. Stone is a frequent presenter and mentor in HPC and exascale computing training workshops and related "Hackathon" events that aim to give computational scientists both the knowledge of theory and the practical experience they need to successfully develop high performance scientific software for next-generation parallel computing systems. Mr. Stone was inducted as an NVIDIA CUDA Fellow in 2010. In 2015 Mr. Stone joined the Khronos Group Advisory Panel for the Vulkan Graphics API. In 2017, 2018, and 2019 Mr. Stone was awarded as an IBM Champion for Power, for innovative thought leadership in the technical community. In 2020, Mr. Stone joined the Khronos working group for ANARI, a new analytic rendering standard for high-fidelity scientific and technical visualization. Mr. Stone and coathors won the ACM Gordon Bell Special Prize for High Performance Computing-Based COVID-19 Research at Supercomputing 2020. He also provides consulting services for projects involving computer graphics, GPU computing, and high performance computing.

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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 		NGC6888 Crescent Nebula in Cygnus
313 min H-α exposure: 209x90sec subexposures
Takahashi FSQ106N refractor, QHY163M camera,
Astro-Physics AP1200GTO equatorial mount
Urbana, IL, July 29, 2017

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 Movies and Visualizations:

An Accessible Visual Narrative for the Primary Energy Source of Life from the Fulldome Show Birth of Planet Earth
1st Place, SC'19 Visualization and Data Analytics Showcase

Paper (PDF)

Abstract:
Conversion of sunlight into chemical energy, namely photosynthesis, is the primary energy source of life on Earth. An explanatory visualization depicting this process is presented in the form of an excerpt from the fulldome show Birth of Planet Earth. This accessible visual narrative shows a lay audience, especially children, how the energy of sunlight is captured, converted, and stored through a chain of proteins to power living cells. The visualization is the result of a multi-year collaboration among biophysicists, visualization scientists, and artists, which, in turn, is based on a decade-long experimental-computational collaboration on structural and functional modeling that produced an atomic detail description of a bacterial bioenergetic organelle, the chromatophore. The energy conversion steps depicted feature an integration of function from electronic to cell levels, spanning nearly 12 orders of magnitude in time scales modeled with multi-scale computational approaches. This atomic detail description uniquely enables a modern retelling of one of humanity's earliest stories---the interplay between light and life.

Authors: Melih Sener, Stuart Levy, AJ Chistensen, Robert Patterson, Kalina Borkiewicz, John E. Stone, Barry Isralewitz, Jeffrey Carpenter, Donna Cox. (University of Illinois at Urbana-Champaign)

Birth of Planet Earth fulldome excerpt: Photosynthesis in a chromatophore

"Photosynthesis in a Chromotaosphere," a sequence in the Spitz fulldome show Birth of Planet Earth, was selected to screen at SIGGRAPH's Electronic Theater, Monday, July 29, 2019. Hundreds of short films are submitted to this prestigious program each year, with only a handful selected for the event. It was also an official selection at Siggraph Asia, 2019, and was shown in the The SIGGRAPH Computer Animation Festival celebrates computer graphics as a medium for storytelling in animation, visual effects, games, and more. The event is recognized as a qualifying festival by the Academy of Motion Picture Arts and Sciences, and several works that were originally presented in this program have received Best Animated Short Academy Awards. Birth of Planet Earth is a joint production of Spitz Creative Media, NCSA's Advanced Visualization Lab, and Thomas Lucas Productions, Inc., in association with Tellus Science Museum.

Abstract:
This visualization of the quantum-mechanical process of photosynthesis involved combining structural models from atomic, protein, organelle, and cell scales. We descend into a prehistoric hot spring, revealing primitive bacteria which use an early form of photosynthesis to turn sunlight into chemical energy in structures called chromatophores. This fulldome animation follows the energy through progressively more stable forms: a captured photon, electronic excitation, pumped protons, and finally, synthesis of ATP molecules. The team used VMD, a GPU-accelerated molecular visualization tool, to create geometric abstractions from a 5-million-atom static snapshot of the scientific research model. To achieve an organic flight path through the 3D data, they adapted their Virtual Director camera choreography software to interface with VMD. In Houdini, they choreographed particle effects which were then exported to VMD for rendering of the hero chromatophore. Nine more layers were rendered in Houdini's Mantra, including 500,000 instanced chromatophores and particle effects, 300 high-resolution cell membranes, and depth passes to control luminance and depth effects. The visualization treatments from Houdini and VMD were combined in Nuke for a seamless flight through this dynamic microscopic light show.

Siggraph 2019: ACM SIGGRAPH 2019 Computer Animation Festival, July 2019, Article No.: 1, Pages 1.
https://doi.org/10.1145/3302502.3321346

Siggraph Asia 2019: ACM SIGGRAPH ASIA Computer Animation Festival, November 2019, Article No.: 14, Pages 1.
https://doi.org/10.1145/3354919.3365061

Authors: Donna Cox, Robert Patterson, Stuart Levy, AJ Christensen, Kalina Borkiewicz, Jeff Carpenter, Melih Sener, John Stone, Barry Isralewitz. (University of Illinois at Urbana-Champaign)

Birth of Planet Earth, Fulldome Movie
Birth of Planet Earth tells the twisted tale of our planet's origins.

Scientists now believe that our galaxy is filled with solar systems, including up to a billion planets roughly the size of our own. The film employs advanced, data-driven, cinematic-quality visualizations to explore some of the greatest questions in science today: How did Earth become a living planet in the wake of our solar system's violent birth? What does its history tell us about our chances of finding other worlds that are truly Earth-like?

Produced by Spitz Creative Media, NCSA's Advanced Visualization Lab, Thomas Lucas Productions, Inc., in association with Tellus Science Museum. This project has been made possible with support from the Commonwealth of Pennsylvania and the Greater Philadelphia Film Office; funded in part by the National Science Foundation.

Chemical Visualization of Human Pathogens : The Retroviral Capsids,
Finalist, SC'15 Visualization and Data Analytics Showcase

Paper (PDF)

Abstract:
Retroviruses are pathogens characterized by their ability to incorporate viral DNA into a host cell's genome. Retroviruses like Rous Sarcoma Virus (RSV) infect cells during mitosis, when the chromatin is exposed to the cytoplasm. Conversely, the genus of lentiviruses, like the human immunodeficiency virus (HIV), have evolved to infect non-dividing cells. Despite infecting cells at different stages of their life cycles, RSV and HIV share a similar late stage replication cycle that is highly dependent on the group actin polyprotein precursor (Gag), which contains the matrix (MA), capsid (CA) and nucleocapsid (NC) proteins. Both HIV's CA and Gag are considered unexploited targets for pharmaceutical intervention. We describe the techniques that were used to build, simulate, analyze and visualize the structures of both Gag and CA, as well as we discuss scientific visualization needs that spurred development of an interactive GPU-accelerated ray tracing engine and the use of remote visualization technologies.

Authors: Juan R. Perilla, Boon Chong Goh, John E. Stone, Klaus Schulten (University of Illinois at Urbana-Champaign)

Visualization of Energy Conversion Processes in a Light Harvesting Organelle at Atomic Detail,
1st Place, SC'14 Visualization and Data Analytics Showcase

Paper (PDF)

Abstract:
The cellular process responsible for providing energy for most life on Earth, namely, photosynthetic light-harvesting, requires the cooperation of hundreds of proteins across an organelle, involving length and time scales spanning several orders of magnitude over quantum and classical regimes. Simulation and visualization of this fundamental energy conversion process pose many unique methodological and computational challenges. We present, in an accompanying movie, light-harvesting in the photosynthetic apparatus found in purple bacteria, the so-called chromatophore. The movie is the culmination of three decades of modeling efforts, featuring the collaboration of theoretical, experimental, and computational scientists. We describe the techniques that were used to build, simulate, analyze, and visualize the structures shown in the movie, and we highlight cases where scientific needs spurred the development of new parallel algorithms that efficiently harness GPU accelerators and petascale computers.

Authors: 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 (Cornell University), C. Neil Hunter (University of Sheffield), Klaus Schulten (University of Illinois at Urbana-Champaign)

Published Journal and Book Cover Images, Photographs:

Venus Transit 2012 Sunrise on Haleakala, Maui

Book Chapters:

"Interactive Ray Tracing Techniques for High-Fidelity Scientific Visualization"
John E. Stone.
In, Eric Haines and Tomas Akenine-Möller, editors, Ray Tracing Gems, Apress, Chapter 27, pp. 493-515, 2019.
Book home pages: Apress | Raytracinggems.com
"A Planetarium Dome Master Camera"
John E. Stone.
In, Eric Haines and Tomas Akenine-Möller, editors, Ray Tracing Gems, Apress, Chapter 4, pp. 49-60, 2019.
Book home pages: Apress | Raytracinggems.com
"Omnidirectional Stereoscopic Projections for VR"
John E. Stone.
In, William R. Sherman, editor, VR Developer Gems, Taylor and Francis / CRC Press, Chapter 24, pp. 423-436, 2019.
Book home pages: Amazon
"Application Case Study — Molecular Visualization and Analysis"
John E. Stone.
In, David Kirk, Wen-mei Hwu, Programming Massively Parallel Processors: A Hands-on Approach (Third Edition), Morgan Kaufmann, Chapter 15, pp. 331-344, Cambridge, MA, 2017.
Book home pages: Amazon | Elsevier | Online full text at ScienceDirect
"GPU-Accelerated Molecular Dynamics Clustering Analysis with OpenACC"
John E. Stone, Juan R. Perilla, C. Keith Cassidy, and Klaus Schulten.
In, Robert Farber, editor, Parallel Programming with OpenACC, Morgan Kaufmann, Chapter 11, pp. 215-240, Cambridge, MA, 2016.
Book home pages: Amazon | Elsevier | Online full text at ScienceDirect
"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, Roland Eils and Andres Kriete, editors, 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 | Online full text at ScienceDirect
"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 | Online full text at ScienceDirect
"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:

"VMD as a Platform for Interactive Small Molecule Preparation and Visualization for Quantum and Classical Simulations"
In Preparation

"Molecular Simulation Analysiswith Ray Tracing Methods"
In Preparation

"py-MCMD: Python Software for Performing Hybrid Monte Carlo -- Molecular Dynamics Simulations with GOMC and NAMD"
M. Soroush, B. Crawford, G. Schwing D. Hardy, J. E. Stone, L. Schwiebert, J. Potoff, E. Tajkhorshid.
Submitted

"ANARI: A 3D Rendering Interface Standard"
J. E. Stone, K. Griffin, J. Amstutz, D. DeMarle, W. Sherman, J. Gunther.
Submitted

"Early Experiences Using GPU-Direct I/O for Molecular Simulation Analysis and Visualization in VMD"
J. E. Stone.
Submitted

"AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics"
Lorenzo Casalino, Abigail Dommer, Zied Gaieb, Emilia P. Barros, Terra Sztain, Surl-Hee Ahn, Anda Trifan, Alexander Brace, Anthony Bogetti, Heng Ma, Hyungro Lee, Matteo Turilli, Syma Khalid, Lillian Chong, Carlos Simmerling, David J. Hardy, Julio D. C. Maia, James C. Phillips, Thorsten Kurth, Abraham Stern, Lei Huang, John McCalpin, Mahidhar Tatineni, Tom Gibbs, John E. Stone, Shantenu Jha, Arvind Ramanathan, Rommie E. Amaro.
International Journal of High Performance Computing Applications (IJHPCA), April 2021.
Winner of the ACM Gordon Bell Special Prize for High Performance Computing-Based COVID-19 Research
Overview of our Gordon Bell team's research
Online full text https://dx.doi.org/10.1177/10943420211006452
Online full text pre-print available at bioRxiv: https://www.biorxiv.org/content/10.1101/2020.11.19.390187v1

"Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales"
Melih Sener, Stuart Levy, John E. Stone, AJ Christensen, Barry Isralewitz, Robert Patterson, Kalina Borkiewicz, Jeffrey Carpenter, C. Neil Hunter, Zaida Luthey-Schulten, Donna Cox
J. Parallel Computing, 102, pp. 102698, 2020.
Online full text available at https://doi.org/10.1016/j.parco.2020.102698

"Scalable molecular dynamics on CPU and GPU architectures with NAMD"
James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone, João V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin, Jérôme Hénin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo, Brian K. Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoit Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kalé, Klaus Schulten, Christophe Chipot, Emad Tajkhorshid.
J. Chemical Physics, 153(4), 2020.
Online full text available at https://dx.doi.org/10.1063/5.0014475

"Scalable Analysis of Authentic Viral Envelopes on FRONTERA"
Fabio Gonzalez-Arias, Tyler Reddy, John E. Stone, Jodi A. Hadden-Perilla, and Juan R. Perilla.
Computing in Science and Engineering, 22(6):11-20, 2020.
Online full text available at https://dx.doi.org/10.1109/MCSE.2020.3020508

"An accessible visual narrative for the primary energy source of life from the fulldome show Birth of Planet Earth"
Melih Sener, Stuart Levy, AJ Chistensen, Robert Patterson, Kalina Borkiewicz, John E. Stone, Barry Isralewitz, Jeffrey Carpenter, Donna Cox.
SC'19 Visualization and Data Analytics Showcase, 2019.
SC'19 Visualization and Data Analytics Showcase Proceedings
SC'19 Visualization and Data Analytics Showcase

"Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism"
A. Singharoy, C. Maffeo, K. H. Delgado-Magnero, D. J. K. Swainsbury, M. Sener, U. Kleinekathöfer, B. Isralewitz, I. Teo, D. Chandler, J. E. Stone, J. Phillips, T. V. Pogorelov, M. I. Mallus, C. Chipot, Z. Luthey-Schulten, P. Tieleman, C. N. Hunter, E. Tajkhorshid, A. Aksimentiev, K. Schulten.
Cell 179(5), pp. 1098-1111.e23, November 14, 2019.
Online full text available at https://doi.org/10.1016/j.cell.2019.10.021

"High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities"
Alexander J. Bryer, Jodi A. Hadden, John E. Stone, Juan R. Perilla.
J. Chemical Information and Modeling, 59(10), 4328-4338, 2019.
Online full text available at http://dx.doi.org/10.1021/acs.jcim.9b00324

"NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems"
Sergio Decherchi, Andrea Spitaleri, John Stone, and Walter Rocchia.
Bioinformatics 35(7): 1241-1243, 2019.
Online full text available at http://dx.doi.org/10.1093/bioinformatics/bty761

"Scalable Molecular Dynamics with NAMD on the Summit System"
Bilge Acun, David J. Hardy, Laxmikant V. Kale, Ke Li, James C. Phillips, and John E. Stone.
IBM Journal of Research and Development, 62(6):4:1-4:9, 2018.
Online full text available at http://dx.doi.org/10.1147/JRD.2018.2888986

"Best Practices in Running Collaborative GPU Hackathons: Advancing Scientific Applications with a Sustained Impact"
Sunita Chandrasekaran, Guido Juckeland, Meifeng Ling, Matthew Otten, Dirk Pleiter, John E. Stone, Juan Lucio-Vega, Michael Zingale, and Fernanda Foertter.
Computing in Science and Engineering 20(4):95-106, 2018.
Online full text available at http://dx.doi.org/10.1109/MCSE.2018.042781332

"NAMD goes quantum: an integrative suite for hybrid simulations"
Marcelo C. R. Melo, Rafael C. Bernardi, Till Rudack, Maximilian Scheurer, Christoph Riplinger, James C. Phillips, Julio D. C. Maia, Gerd B. Rocha, João V. Ribeiro, John E. Stone, Frank Neese, Klaus Schulten, and Zaida Luthey-Schulten.
Nature Methods, 15: 351-354, 2018.
Online full text available at https://www.nature.com/articles/nmeth.4638

"The OLCF GPU Hackathon Series: The Story Behind Advancing Scientific Applications with a Sustained Impact"
Sunita Chandrasekaran, Guido Juckeland, Meifeng Ling, Matthew Otten, Dirk Pleiter, John E. Stone, Juan Lucio-Vega, Michael Zingale, and Fernanda Foertter.
The 2017 Workshop on Education for High Performance Computing (EduHPC'17), 2017.

"Challenges of Integrating Stochastic Dynamics and Cryo-electron Tomograms in Whole-cell Simulations"
Tyler M. Earnest, Reika Watanabe, John E. Stone, Julia Mahamid, Wolfgang Baumeister, Elizabeth Villa, and Zaida Luthey-Schulten.
J. Physical Chemistry B, 121(15): 3871-3881, 2017.
Online full text available at http://pubs.acs.org/doi/10.1021/acs.jpcb.7b00672

"Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms"
John E. Stone, Antti-Pekka Hynninen, James C. Phillips, and Klaus Schulten.
International Workshop on OpenPOWER for HPC (IWOPH'16), LNCS 9945, pp. 188-206, 2016.
Online full text available at http://dx.doi.org/10.1007/978-3-319-46079-6_14

"Molecular dynamics-based refinement and validation for sub-5Å cryo-electron microscopy maps"
Abhishek Singharoy, Ivan Teo, Ryan McGreevy, John E. Stone, Jianhua Zhao, and Klaus Schulten.
eLife 2016;10.7554/eLife.16105.
Online full text available at http://dx.doi.org/10.7554/eLife.16105
Access the recommendation on F1000Prime

"TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD"
Josh V. Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, and Axel Kohlmeyer.
J. Chemical Information and Modeling, 56(6):1112-1116, 2016.
Online full text available at http://dx.doi.org/10.1021/acs.jcim.6b00103

"QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts"
João V. Ribeiro, Rafael C. Bernardi, Till Rudack, John E. Stone, James C. Phillips, Peter L. Freddolino, and Klaus Schulten.
Scientific Reports, 6:2653, 2016.
Online full text available at http://dx.doi.org/10.1038/srep26536

"Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering"
John E. Stone, William R. Sherman, and Klaus Schulten.
High Performance Data Analysis and Visualization Workshop, 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), pp. 1048-1057, 2016.
Online full text available at http://dx.doi.org/10.1109/IPDPSW.2016.121

"High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL"
John E. Stone, Peter Messmer, Robert Sisneros, and Klaus Schulten.
High Performance Data Analysis and Visualization Workshop, 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), pp. 1014-1023, 2016.
Online full text available at http://dx.doi.org/10.1109/IPDPSW.2016.127

"Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads"
John E. Stone, Michael J. Hallock, James C. Phillips, Joseph R. Peterson, Zaida Luthey-Schulten, and Klaus Schulten.
25th International Heterogeneity in Computing Workshop, 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), pp. 89-100, 2016.
Online full text available at http://dx.doi.org/10.1109/IPDPSW.2016.130

"Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing"
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, and Klaus Schulten
J. Parallel Computing, 55:17-27, 2016.
Online full text available at http://dx.doi.org/10.1016/j.parco.2015.10.015

"Chemical Visualization of Human Pathogens: the Retroviral Capsids"
Juan R. Perilla, Boon Chong Goh, John E. Stone, and Klaus Schulten
SC'15 Visualization and Data Analytics Showcase, 2015.
Finalist, SC'15 Visualization and Data Analytics Showcase
Online full text available at SC'15 site

"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, 26(5):1405-1418, 2015.
Online full text available at http://dx.doi.org/10.1109/TPDS.2014.2316825

"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

"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.
Winner of the SC'14 Visualization and Data Analytics Showcase
Online full text available at SC'14 site

"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

"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

"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

"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

"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

"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
Online full text available at http://www.xsede.org/web/xscale/agenda

"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, Blogs, and Whitepapers:

"HPC Visualization on NVIDIA Tesla GPUs"
John Stone
NVIDIA Parallel ForAll Developer Blog, March 12, 2015

"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 Clustering Analysis of Molecular Dynamics Trajectories Using QCP and PAM (2015),
    Devin King and Julie Xia
  • 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

Press Articles and Interviews:

Consulting Activities:

I served 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, 2013-2016.
  • "Antenna Placement Optimization on Large, Airborne, Naval Platforms", SBIR N101-022, funded by NAVAIR, U.S. Navy, 2010-2013.

I served 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 PAR-07-160, 1R44GM088867, funded by the National Institutes of Health, 2010-2014.

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:

Winner of the ACM Gordon Bell Special Prize for High Performance Computing-Based COVID-19 Research for the paper entitled: "AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics"

Winner of the SC'19 Visualization and Data Analytics Showcase for the movie and accompanying paper entitled: "An Accessible Visual Narrative for the Primary Energy Source of Life from the Fulldome Show Birth of Planet Earth"

IBM Champion for Power, 2017, 2018, 2019 IBM Champion web badge

Finalist, 2016 GPU Center of Excellence Achievement Award: "Interactive Molecular Ray Tracing on GPU-Accelerated PCs, Remote Clouds and Supercomputers, and VR HMDs"

Our 2016 article Molecular dynamics-based refinement and validation for sub-5Å cryo-electron microscopy maps has received an F1000Prime recommendation Access the recommendation on F1000Prime

Finalist, 2015 NVIDIA Global Impact Award "Enabling Computational Virology with GPU Computing"

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.

Member in good standing of ACM, Siggraph, and IEEE.

I hold an FCC Amateur Extra Class radio license KC9VGG, and a GMRS radio license. ARRL life member, and AMSAT-NA member. AMSAT OSCAR Satellite Communications Achievement Award #594, Limited Edition 50th Anniversary, March 6, 2019. ARRL WAS awards for Digital (JT65) #1900, and Mixed #60792, communication modes. WPX Digital award #983. ARISS SSTV award, Febaruary 2019.

Member of the Champaign-Urbana Astronomical Society (CUAS). I have previously served 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

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.

Member of the Kappa Kappa Psi national honorary band fraternity while a graduate student at University of Missouri-Rolla.

Founding member of the University of Missouri-Rolla Solar Car Team while an undergraduate student.

Member of the six man ISRA junior rifle team that won the 1990 National Trophy Team match at the National Trophy Rifle Matches at Camp Perry, Ohio.