VMD Publications and Presentations

VMD Research Publications:

2019
• 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.

2018
• 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.
• 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 Nesse, Klaus Schulten, and Zaida Luthey-Schulten. Nature Methods, 15:351-354, 2018.

2017
• 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.

2016
• 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), pp. 188-206, 2016.
• QwikMD-integrative molecular dynamics toolkit for novices and experts. Joao V. Ribeiro, Rafael C. Bernardi, Till Rudack, John E. Stone, James C. Phillips, Peter L. Freddolino, and Klaus Schulten. Scientific Reports, 6:26536, 2016.
• Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps. Abhishek Singharoy, Ivan Teo, Ryan McGreevy, John E. Stone, Jianhua Zhao, and Klaus Schulten. eLife, 10.7554/eLife.16105, 2016.
• Immersive molecular visualization with omnidirectional stereoscopic ray tracing and remote rendering. John E. Stone, William R. Sherman, and Klaus Schulten. 2016 IEEE International Parallel and Distributed Processing Symposium Workshop (IPDPSW), pp. 1048-1057, 2016.
• 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, Joao 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. Parallel Computing, 55:17-27, 2016.
• High performance molecular visualization: In-situ and parallel rendering with EGL. John E. Stone, Peter Messmer, Robert Sisneros, and Klaus Schulten. 2016 IEEE International Parallel and Distributed Processing Symposium Workshop (IPDPSW), pp. 1014-1023, 2016.
• 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. 2016 IEEE International Parallel and Distributed Processing Symposium Workshop (IPDPSW), pp. 89-100, 2016.

2015
• 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.
• Chemical visualization of human pathogens: the Retroviral Capsids. Juan R. Perilla, Boon Chong Goh, John Stone, and Klaus Schulten. Proceedings of the 2015 ACM/IEEE Conference on Supercomputing, 2015. (4 pages).

2014
• 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. In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, SC '14. IEEE Press, 2014. (4 pages).
• 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. In SC'14 workshop on High Performance Technical Computing in Dynamic Languages, SC '14, pp. 6-17. IEEE Press, 2014.
• Unlocking the full potential of the Cray XK7 accelerator. Mark D. Klein and John E. Stone. In Cray User Group Conference. Cray, 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.
• 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.
• 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 Wilson, Sung Jun Lim, Michelle Baird, John Stone, Kwan Young Lee, Michael Davidson, Hee Jung Chung, Klaus Schulten, Andrew Smith, William Green, and Paul R. Selvin. Angewandte Chemie - International Edition in English, 126:12692-12696, 2014.

2013
• GPU-accelerated molecular visualization on petascale supercomputing platforms. John E. Stone, Kirby L. Vandivort, and Klaus Schulten. In Proceedings of the 8th International Workshop on Ultrascale Visualization, UltraVis '13, pp. 6:1-6:8, New York, NY, USA, 2013. ACM.
• Early experiences scaling VMD molecular visualization and analysis jobs on Blue Waters. John E. Stone, Barry Isralewitz, and Klaus Schulten. In Extreme Scaling Workshop (XSW), 2013, pp. 43-50, Aug. 2013.

2012
• 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, 34:245-255, 2013.
• Fast visualization of Gaussian density surfaces for molecular dynamics and particle system trajectories. Michael Krone, John E. Stone, Thomas Ertl, and Klaus Schulten. In EuroVis - Short Papers 2012, pp. 67-71, 2012.

2011
• Immersive out-of-core visualization of large-size and long-timescale molecular dynamics trajectories. John E. Stone, Kirby L. Vandivort, and Klaus Schulten. Lecture Notes in Computer Science, 6939:1-12, 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, 230:3556-3569, 2011.
• 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. Morgan Kaufmann Publishers, 2011.
• 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. Morgan Kaufmann Publishers, 2011.
• 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, chapter 16, pp. 351-371. Chapman & Hall/CRC Press, 2011.

2010
• Immersive molecular visualization and interactive modeling with commodity hardware. John E. Stone, Axel Kohlmeyer, Kirby L. Vandivort, and Klaus Schulten. Lecture Notes in Computer Science, 6454:382-393, 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. In 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, 29:116-125, 2010.
• OpenCL: A parallel programming standard for heterogeneous computing systems. John E. Stone, David Gohara, and Guochun Shi. Computing in Science and Engineering, 12:66-73, 2010.

2009
• Probing biomolecular machines with graphics processors. James C. Phillips and John E. Stone. Communications of the ACM, 52:34-41, 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. In Cluster Computing and Workshops, 2009. CLUSTER '09. IEEE International Conference on, pp. 1-8, 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. In Proceedings of the IEEE International Parallel & Distributed Processing Symposium, pp. 1-8, 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.
• 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, New York, NY, USA, 2009. ACM.
• Multilevel summation of electrostatic potentials using graphics processing units. David J. Hardy, John E. Stone, and Klaus Schulten. Journal of Parallel Computing, 35:164-177, 2009.

2008 and earlier
• 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.
• 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.
• Continuous fluorescence microphotolysis and correlation spectroscopy using 4Pi microscopy. Anton Arkhipov, Jana Hüve, Martin Kahms, Reiner Peters, and Klaus Schulten. Biophysical Journal, 93:4006-4017, 2007.
• 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.
• A system for interactive molecular dynamics simulation. John E. Stone, Justin Gullingsrud, Paul Grayson, and Klaus Schulten. In John F. Hughes and Carlo H. Séquin, editors, 2001 ACM Symposium on Interactive 3D Graphics, pp. 191-194, New York, 2001. ACM SIGGRAPH.
• Speech/gesture interface to a visual-computing environment. Rajeev Sharma, Michael Zeller, Vladimir I. Pavlovic, Thomas S. Huang, Zion Lo, Stephen Chu, Yunxin Zhao, James C. Phillips, and Klaus Schulten. IEEE Computer Graphics and Applications, 20:29-37, 2000.
• A visual computing environment for very large scale biomolecular modeling. Michael Zeller, James C. Phillips, Andrew Dalke, William Humphrey, Klaus Schulten, Rajeev Sharma, T. S. Huang, V. I. Pavlovic, Y. Zhao, Z. Lo, and S. Chu. In Proceedings of the 1997 IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP), pp. 3-12. IEEE Computer Society Press, 1997.
• Speech/gesture interface to a visual computing environment for molecular biologists. R. Sharma, T. S. Huang, V. I. Pavlovic, K. Schulten, A. Dalke, J. Phillips, M. Zeller, W. Humphrey, Y. Zhao, Z. Lo, and S. Chu. In Proceedings of 13th ICPR 96, volume 3, pp. 964-968, 1996.
• VMD - Visual Molecular Dynamics. William Humphrey, Andrew Dalke, and Klaus Schulten. Journal of Molecular Graphics, 14:33-38, 1996.

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VMD presentations:

2019
• Scalable Molecular Visualization with VMD, Argonne Exascale Training Program, Q Center, St. Charles, IL (08/05/2019)
• Birth of Planet Earth, Siggraph Computer Animation Festival, Los Angeles, CA (07/28/2019 to 8/3/2019)
• Interactive GPU Ray Tracing for Molecular Visualization, NVIDIA Exhibition, Siggraph, Los Angeles, CA (07/29/2019)
• Omnidirectional Stereoscopic Projections for VR, BoF on Immersive Visualisation for Science, Research, and Art, Siggraph, Los Angeles, CA (07/29/2019)
• Immersive Visualization and Interactive HPC Analytics for Analysis of Molecular and Cellular Simulations, Immersive Visualization Workshop, Siggraph, Los Angeles, CA (07/28/2019)
• 2019 PRACE HPC Summer School on Biomolecular Simulation, KTH, Stockholm, Sweden (06/10/2019 to 6/14/2019)
• Bringing State-of-the-Art GPU Accelerated Molecular Modeling Tools to the Research Community, GPU Technology Conference, San Jose, CA (03/20/2019)
• Interactive High Fidelity Biomolecular and Cellular Visualization with RTX Ray Tracing APIs, GPU Technology Conference, San Jose, CA (03/20/2019)
• Molecular Visualization and Simulation in VR, Indiana University, IN (3/6/2019)
• Adapting Scientific Software and Designing Algorithms for Next Generation GPU Computing Platforms, SIAM Conference on Computational Science and Engineering, Spokane, WA (02/27/2019)
• Challenges for Analysis and Visualization of Atomic-Detail Simulations of Minimal Cells, SIAM Conference on Computational Science and Engineering, Spokane, WA (02/26/2019)
2018
• Optimizing NAMD and VMD for the IBM Power9 Platform, IBM Power User's Group, Supercomputing 2018, Dallas, TX (11/15/2018)
• NVIDIA HPC and University Computing Panel, Supercomputing 2018, Dallas, TX (11/14/2018)
• Using AWS EC2 GPU Instances for Computational Microscopy and Biomolecular Simulation, Amazon AWS Theater, Supercomputing 2018, Dallas, TX (11/14/2018)
• Interactivity in HPC BoF, Supercomputing 2018, Dallas, TX (11/13/2018)
• Putting High-Octane GPU-Accelerated Molecular Modeling Tools in the Hands of Scientists, NVIDIA Theater, Supercomputing 2018, Dallas, TX (11/13/2018)
• GPU-Accelerated OptiX Ray Tracing for Scientific Visualization, NVIDIA Theater, Siggraph 2018, Vancouver BC, Canada (8/15/2018)
• VMD: Immersive Molecular Visualization with High-Fidelity Ray Tracing, Immersive Visualization for Science and Research, Siggraph 2018, Vancouver BC, Canada (8/13/2018)
• Argonne Training Program on Exascale Computing, Q Center, St. Charles, IL (8/9/2018)
• Preparing and Analyzing Large Molecular Simulations with VMD, Modeling Supra-molecular Structures with LAMMPS, Temple University, Philadelphia, PA (7/9 to 7/13, 2018)
• Interactive HPC Requirements, Challenges, and Solutions for Cutting Edge Molecular Simulation Science Campaigns, First Workshop on Interactive High-Performance Computing, ISC 2018, Frankfurt, Germany (6/28/2018)
• Visualizing the Atomic Detail Dynamics of Biomolecular Complexes in Our Compute-Rich but I/O-Constrained Future, Visualization in HPC Focus Session, ISC 2018, Frankfurt, Germany (6/25/2018)
• Keynote: Visualization Challenges and Opportunities Posed by Petascale Molecular Dynamics Simulations, Workshop on Molecular Graphics and Visual Analysis of Molecular Data, EuroVis 2018, Brno, Czech Republic (6/4/2018)
• Advances in Biomolecular Simulation with NAMD and VMD, Pawsey Supercomputing Centre, Perth, Australia (4/19/2018)
• Pawsey GPU Hackathon, Pawsey Supercomputing Centre, Perth, Australia (4/16 to 4/20, 2018)
• VMD: Biomolecular Visualization from Atoms to Cells Using Ray Tracing, Rasterization, and VR, GPU Technology Conference, San Jose, CA (3/29/2018)
• Using Accelerator Directives to Adapt Science Applications for State-of-the-Art HPC Architectures, GPU Technology Conference, San Jose, CA (3/27/2018)
• Accelerating Molecular Modeling on Desktop and Pre-Exascale Supercomputers, GPU Technology Conference, San Jose, CA (3/26/2018)
• Optimizing HPC Simulation and Visualization Code Using NVIDIA Nsight Systems, GPU Technology Conference, San Jose, CA (3/29/2018)
2017
• VMD: GPU-Accelerated Analysis of Biomolecular and Cellular Simulations, Cray Analytics Symposium (remote webinar presentation), Radisson Blu MOA, Bloomington, MN (05/26/2017)
• GPUs Unleashed: Analysis of Petascale Molecular Dynamics Simulations with VMD, GPU Technology Conference, San Jose, CA (05/10/2017)
• Cutting Edge OptiX Ray Tracing Techniques for Visualization of Biomolecular and Cellular Simulations in VMD, GPU Technology Conference, San Jose, CA (05/09/2017)
• Turbocharging VMD Molecular Visualizations with State-of-the-Art Rendering and VR Technologies, GPU Technology Conference, San Jose, CA (05/09/2017)
• Visualizing Biomolecules in VMD, Hands-on Workshop on Computational Biophysics, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois, Urbana, IL (4/18/2017).
• VMD: Preparation and Analysis of Molecular and Cellular Simulations, HPC for Life Sciences PRACE Spring School 2017, Stockholm Sweden (4/10/2017).
2016
• Harnessing GPUs to Probe Biomolecular Machines at Atomic Detail, NVIDIA GPU Technology Theater, Supercomputing 2016, Supercomputing 2016, Salt Lake City, UT (11/16/2016).
• Visualization and Analysis of Biomolecular Complexes on Upcoming KNL-based HPC Systems: TACC Stampede-2 and ANL Aurora, Intel HPC Developers Conference, Supercomputing 2016, Salt Lake City, UT (11/13/2016).
• Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering, High Performance Data Analysis and Visualization Workshop, Chicago (5/23/2016).
• High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL, High Performance Data Analysis and Visualization Workshop, Chicago (5/23/2016)
• Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads, 25th International Heterogeneity in Computing Workshop, Chicago (5/23/2016)
• VMD+OptiX: Streaming Interactive Ray Tracing from Remote GPU Clusters to Your VR Headset, GPU Technology Conference, San Jose, CA (4/06/2016)
• VMD: Interactive Molecular Ray Tracing with NVIDIA OptiX, GPU Technology Conference, San Jose, CA (4/06/2016)
• VMD: Petascale Molecular Visualization and Analysis with Remote Video Streaming, GPU Technology Conference, San Jose, CA (4/05/2016)
• VMD: enabling preparation, visualization, and analysis of petascale and pre-exascale molecular dynamics simulations, Armadillo B453 R1001, Lawrence Livermore National Laboratory, Livermore, CA (1/5/2016)
2015
• VMD+OptiX: Bringing Interactive Molecular Ray Tracing from Remote GPU Clusters to your VR Headset, NVIDIA Theater, Supercomputing 2015, Austin, TX (11/18/2015)
• Chemical Visualization of Human Pathogens : The Retroviral Capsids, Visualization and Data Analytics Showcase, Supercomputing 2015, Austin, TX (11/18/2015)
• Frontiers of Molecular Visualization: Interactive Ray Tracing, Panoramic Displays, VR HMDs, and Remote Visualization, VisTech Workshop, Supercomputing 2015, Austin, TX (11/15/2015)
• Visualizing Biomolecular Complexes on x86 and KNL Platforms: Integrating VMD and OSPRay, Intel HPC Developer Conference, Austin TX (11/14/2015)
• VMD: Interactive Publication-Quality Molecular Ray Tracing with OptiX, NVIDIA Best of GTC Theater, Siggraph 2015, Los Angeles, CA (8/12/2015)
• VMD: Immersive Molecular Visualization and Interactive Ray Tracing for Domes, Panoramic Theaters, and Head Mounted Displays, BOF: Immersive Visualization for Science and Research, Siggraph 2015, Los Angeles, CA (8/10/2015)
• Workshop on Accelerated High-Performance Computing in Computational Sciences (SMR 2760), Abdus Salam International Centre for Theoretical Physics, Miramare - Trieste, Italy (05/27/2015)
• Panel: Data Relevancy, Locality, Diversity & More, NCSA Private Sector Program Annual Meeting, (05/06/2015)
• GPGPU 2015 Advanced Methods for Computing with CUDA, University of Cape Town, South Africa (4/20/2015)
• Proteins and Mesoscale Data: Visualization of Molecular Dynamics, Visualizing Biological Data (VIZBI) 2015 Conference, Broad Institute of MIT and Harvard, Cambridge, MA (03/26/2015)
• Publication-Quality Ray Tracing of Molecular Graphics with OptiX, GPU Technology Conference (03/19/2015)
• Guest Presentation: Integrating OptiX in VMD (in David McAllister's Innovations in OptiX presentation), GPU Technology Conference (03/18/2015)
• VMD: Visualization and Analysis of Biomolecular Complexes with GPU Computing, GPU Technology Conference (03/18/2015)
2014
• Visualization of Energy Conversion Processes in a Light Harvesting Organelle at Atomic Detail, Visualization and Data Analytics Showcase, Supercomputing 2014, New Orleans, LA (11/19/2014)
• GPU-Accelerated Analysis of Large Biomolecular Complexes, NVIDIA Booth, Supercomputing 2014, New Orleans, LA (11/18/2014)
• 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)
• Using GPUs to Supercharge Visualization and Analysis of Molecular Dynamics Simulations with VMD, NVIDIA GTC Express (02/25/2014)
2013
• 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)
• Interactive ab initio molecular dynamics, 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)
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 (5/17/20120
• High Performance Molecular Visualization and Analysis on GPUs, GPU Technology Conference, San Jose, CA (5/16/2012)
2011
• Immersive Out-of-Core Visualization of Large-Size and Long-Timescale Molecular Dynamics Trajectories, ISVC 2011, Las Vegas, NV (9/26/2011)
2010
• 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)
• GPU and the Computational Microscope, GPU Technology Conference (09/22/2010)
• High Performance Molecular Simulation, Visualization, and Analysis on GPUs, GPU Technology Conference (09/22/2010)
• Simulating Biomolecules on GPUs with the Multilevel Summation Method, Oak Ridge National Laboratory (09/17/2010)
• 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 American Chemical Society, Boston, MA (08/22/2010)
• OpenCL: Molecular Modeling on Heterogeneous Computing Systems, Fall National Meeting of the American Chemical Society, Boston, MA (08/22/2010)
• Quantifying the Impact of GPUs on Performance and Energy Efficiency in HPC Clusters, The Work in Progress in Green Computing(WIPGC), Chicago, IL (08/17/2010)
• Using GPUs to compute the multilevel summation of electrostatic forces, Multiscale Molecular Modeling Conference, Edinburgh, Scotland (07/02/2010)
• Molecular Visualization and Analysis on GPUs, Symposium on Application of GPUs in Chemistry and Materials Science, University of Pittsburgh (06/29/2010)
2009
• Accelerating Molecular Modeling Applications with GPU Computing, Exhibition, Supercomputing 2009, Portland, OR (11/18/2009)
• OpenCL for Molecular Modeling Applications: Early Experiences, OpenCL BOF, Supercomputing 2009, Portland, OR (11/18/2009)
• 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)
• GPU Accelerated Visualization and Analysis in VMD, Center for Molecular Modeling, University of Pennsylvania, (6/9/2009)
• Keynote: Accelerating Molecular Modeling Applications with GPU Computing, Second Sharcnet Symposium on GPU and Cell Computing, University of Waterloo (5/20/2009)
• Experiences with Multi-GPU Acceleration in VMD, Path to Petascale: Adapting GEO/CHEM/ASTRO Applications for Accelerators and Accelerator Clusters, NCSA (4/2/2009)
• High Performance Computation and Interactive Display of Molecular Orbitals on GPUs and Multi-core CPUs, Second Workshop on General-Purpose Processing on Graphics Processing Units, Washington D.C. (3/8/2009)
• High Performance Computation and Interactive Display of Molecular Orbitals on GPUs and Multi-core CPUs, IACAT Accelerator Workshop, NCSA (1/23/2009)
2008
• GPU Computing, Cape Linux Users Group, South Africa (10/28/2008)
• 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 2008 (8/26/2008)
• GPU Acceleration of Cutoff Pair Potentials for Molecular Modeling Applications, ACM Computing Frontiers 2008 (5/7/2008)
• GPU Acceleration of Molecular Modeling Applications Linux Clusters Institute, NCSA (5/1/2008)
• Accelerating Molecular Modeling Applications with Graphics Processors SIAM Conference on Parallel Processing for Scientific Computing (3/12/2008)
2001-2007
• Tutorial: High Performance Computing on GPUs with CUDA (Supercomputing 2007)
• GPU Acceleration of Scientific Applications Using CUDA
  • AstroGPU 2007, Institute for Advanced Study, Princeton University (11/09/2007)
• ECE 498AL1: Programming Massively Parallel Processors
  • Case Studies: Ion Placement Tool, VMD (10/15/2007)
  • CUDA Student Project Pages
• ECE 498AL: Programming Massively Parallel Processors
  • Case Studies: Ion Placement Tool, VMD (3/14/2007)
• Visualization of Nano-Scale Structures
  • Universidad Nacional Autónoma de Mexico, DGSCA, 8/11/2006
  • University of Texas Health Science Center at Houston, 4/20/2006
• 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
  • INRIA/CNRS ARC Docking Project, Nancy France, 12/8/2004
• VMD: Biomolecular Visualization and Analysis
  • The Scripps Research Institute (while at Siggraph 2003)
• Biomolecular Visualization with the CAVE and VMD
  • 2001 CAVE Programming Workshop, Swedish Royal Institute of Technology
• A System for Interactive Molecular Dynamics
  • Presented at ACM Siggraph I3D 2001, matches paper below.