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Software Presentations and Publications

2013    2012    2011    2010     2009     2008     2007     2006     2005     2004     2003     2002     2001     2000     Pre-2000

Below are lectures, talks, and other presentations by TCB development staff, in meetings and conferences locally and around the world, about TCBG software applications (e.g., VMD, NAMD, and BioCoRE). Non-faculty papers by development staff (available via the publications database) are also listed by year.

2013

• May 2013, Cape Town, South Africa, GPGPU Computing with CUDA Workshop
  Lecture: “Programming in CUDA: the Essentials” (John Stone)
  Lecture: “CUDA Applications I” (John Stone)
  Lecture: “CUDA Applications II” (John Stone)
  Lecture: “Programming for Hybrid Architectures” (John Stone)
  
  
  
• March 2013, San Jose, CA, GPU Technology Conference
  Lecture: “VMD: GPU-Accelerated Visualization and Analysis of Petascale Molecular Dynamics Simulations” (John Stone)
  Lecture: “Petascale Molecular Dynamics Simulations on Titan and Blue Waters” (James Phillips)

2012

• December 2012, Chicago, IL, University of Chicago, Flash Center SIMACWorkshop
  Lecture: “NAMD on Future Architectures” (James Phillips)
  
  
• November 2012, Salt Lake City, UT, ACM/IEEE, SC12 BOF
  Lecture: “Application Grand Challenges in the Heterogeneous Accelerator Era” (James Phillips)
  Lecture: “Charm++: Adaptive Runtime-Assisted Parallel Programming” (James Phillips)
  
  
• August 2012, Urbana, IL, University of Illinois, National Center for Supercomputing Applications, VSCSE Many-core Processors
  Lecture: “Keynote: Broadening the Use of Scalable Kernels in NAMD/VMD” (John Stone)
  
  
• July 2012, Des Plaines, IL, XSEDE Extreme Scaling Workshop
  Lecture: “Petascale Molecular Dynamics with NAMD” (James Phillips)
  
  
• June 2012, Notre Dame, IN, University of Notre Dame, Scalable Software for Scientific Computing Workshop
  Lecture: “GPU-Accelerated Analysis of Petascale Molecular Dynamics Simulations with VMD” (John Stone)
  
  
• June 2012, Urbana, IL, University of Illinois, Beckman Institute, Imaging at Illinois, The Next Generation: Computational Imaging and Visualization
  Lecture: “Visualization of petascale molecular dynamics simulations” (John Stone)
  
  
• May 2012, Edinburgh, Scotland, NAIS: State-of-the-Art Algorithms for Molecular Dynamics
  Lecture: “Future Direction with NAMD” (David Hardy)
  Lecture: “Demonstration: Using NAMD, NAIS: State-of-the-Art Algorithms for Molecular Dynamics” (David Hardy)
  Lecture: “Multilevel Summation Method in NAMD and VMD” (David Hardy)
  Lecture: “Generalized Born Implicit Solvent Algorithm in NAMD” (David Hardy)
  Lecture: “Short-Range (Non-Bonded) Interactions in NAMD” (David Hardy)
  Lecture: “NAMD Algorithms and HPC Functionality” (David Hardy)
  Lecture: “Analysis and Visualization Algorithms in VMD” (David Hardy)
  
  
• May 2012, San Jose, CA, Accelerating HPC Symposium
  Lecture: “Accelerating NAMD” (James Phillips)
  Lecture: “In-Situ Visualization and Analysis of Petascale Molecular Dynamics Simulations with VMD” (John Stone)

• May 2012, San Jose, CA, GPU Technology Conference
  Lecture: “High Performance Molecular Visualization and Analysis on GPUs” (John Stone)
  Lecture: “Petascale Molecular Dynamics Simulations on GPU-Accelerated Supercomputers” (James Phillips)
  
  
• May 2012, Urbana, IL, University of Illinois at Urbana-Champaign, Department of Computer Science, 10th Annual Workshop on Charm++ and its Applications
  Panel: “What do computational scientists need from computer scientists?” (Jim Phillips)

Papers

• Michael Krone, John E. Stone, Thomas Ertl, and Klaus Schulten. Fast visualization of Gaussian density surfaces for molecular dynamics and particle system trajectories. In EuroVis - Short Papers 2012, pp. 67-71, 2012. DOI: 10.2312/PE/EuroVisShort/EuroVisShort2012/067-071.
  
  
• David E. Tanner, James C. Phillips, and Klaus Schulten. GPU/CPU algorithm for generalized Born / solvent-accessible surface area implicit solvent calculations. Journal of Chemical Theory and Computation, 8:2521-2530, 2012. (PMC: 3464051)

2011

Papers

• John E. Stone, David J. Hardy, Barry Isralewitz, and Klaus Schulten. GPU algorithms for molecular modeling. 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.
  
  
• John E. Stone, David J. Hardy, Jan Saam, Kirby L. Vandivort, and Klaus Schulten. GPU-accelerated computation and interactive display of molecular orbitals. In Wen-mei Hwu, editor, GPU Computing Gems, chapter 1, pp. 5-18. Morgan Kaufmann Publishers, 2011.
  
  
• David J. Hardy, John E. Stone, Kirby L. Vandivort, David Gohara, Christopher Rodrigues, and Klaus Schulten. Fast molecular electrostatics algorithms on GPUs. In Wen-mei Hwu, editor, GPU Computing Gems, chapter 4, pp. 43-58. Morgan Kaufmann Publishers, 2011.
  
  
• John E. Stone, Kirby L. Vandivort, and Klaus Schulten. Immersive out-of-core visualization of large-size and long-timescale molecular dynamics trajectories. Lecture Notes in Computer Science, 6939:1-12, 2011. (PMC: 3032211)
  
  
• Wei Jiang, David Hardy, James Phillips, Alex MacKerell, Klaus Schulten, and Benoit Roux. High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. Journal of Physical Chemistry Letters, 2:87-92, 2011. (PMC: 3092300)
  
  
• David E. Tanner, Kwok-Yan Chan, James Phillips, and Klaus Schulten. Parallel generalized Born implicit solvent calculations with NAMD. Journal of Chemical Theory and Computation, 7:3635-3642, 2011. (PMC: 3222955)

2010

Lectures

• September 17, 2010, Oak Ridge, TN, Oak Ridge National Laboratory, Bio-molecular Simulations on Future Computing Architectures
  Lecture: "Simulating Biomolecules on GPUs with the Multilevel Summation Method" (David Hardy)
• August 6-8, 2010, Urbana, IL, Beckman Institute, Workshop on GPU Programming for Molecular Modeling
  Lecture: "Introductory Lecture, Participant Introductions" (John Stone)
  Lecture: "GPU Particle-Grid Algorithms: Electrostatics" (John Stone)
  Lecture: "GPU Particle-Particle Algorithms: Non-bonded Force Calculation" (David Hardy)
  Lecture: "GPU Histogramming: Radial Distribution Functions" (John Stone)
  Lecture: "CUDA Algorithms for Stochastic Simulation of Biochemical Reactions" (Andrew Magis)
  Lecture: "Single-Node Multi-GPU Algorithms: Molecular Orbitals" (John Stone)
  Lecture: "NAMD: Molecular Dynamics on GPU Clusters" (Jim Phillips)
• July 2010, Urbana, IL, University of Illinois at Urbana-Champaign, Universal Parallel Computing Research Center, 2010 Universal Parallel Computing Research Center Summer School
  Lecture: "The OpenCL Programming Model, Part 1" (John Stone)
  Lecture: "The OpenCL Programming Model, Part 2" (John Stone)
• July 2, 2010, Edinburgh, Scotland, University of Edinburgh, Multiscale Molecular Modelling
  Lecture: "Using GPUs to Compute the Multilevel Summation of Electrostatic Forces" (David Hardy)
• April 2010, Urbana, IL, Department of Computer Science, 8th Annual Workshop on Charm++ and its Applications
  Lecture: "Charm++ Hits and Misses - A NAMD Perspective" (Jim Phillips)
• March 2010, Pittsburgh, PA, The 11th LCI International Conference on High-Performance Clustered Computing
  Panel: "Pedal to the metal: Experiences programming accelerators for HPC" (Jim Phillips)
• January 2010, Tokyo, Japan, Accelerated Computing Conference (Riken/NVIDIA)
  Lecture: "Accelerating Molecular Modeling Applications" (Jim Phillips)

Papers

• John E. Stone, Axel Kohlmeyer, Kirby L. Vandivort, and Klaus Schulten. Immersive molecular visualization and interactive modeling with commodity hardware. Lecture Notes in Computer Science, 6454:382-393, 2010.
  
  
• John E. Stone, David J. Hardy, Ivan S. Ufimtsev, and Klaus Schulten. GPU-accelerated molecular modeling coming of age. Journal of Molecular Graphics and Modelling, 29:116-125, 2010. (PMC: 2934899)

2009

Lectures

• December 10, 2009, Urbana, IL, Beckman Institute for Advanced Science and Technology, GPUComputing.net Webinar
  Lecture: "An Introduction to OpenCL" (John Stone)
   
• November 15-18, 2009, Portland, OR, Supercomputing 2009 Conference
  Lecture for OpenCL BOF: "OpenCL for Molecular Modeling Applications: Early Experiences" (John Stone)
  Exhibition: "Accelerating Molecular Modeling Applications with GPU Computing" (John Stone)
  Tutorial: "High Performance Computing with CUDA Case Study: Molecular Modeling Applications" (John Stone)
  Tutorial - CUDA: "High Performance Computing with CUDA Case Study: Molecular Modeling Applications" (John Stone)
   
• October 21, 2009, Urbana, IL, University of Illinois, IACAT/CCOE GPU Brown Bag Forum
  Lecture: "An Introduction to OpenCL" (John Stone)
   
• October 20, 2009, Urbana, IL, Beckman Institute for Advanced Science and Technology, Beckman Institute Forum for Imaging and Visualization
  Lecture: "High Performance Molecular Visualization and Analysis with GPU Computing" (John Stone)
   
• October 20, 2009, San Jose, CA, NVIDIA GPU Technology Conference
  Lecture: "GPU Accelerated Visualization and Analysis in VMD and Recent NAMD Developments" (John Stone)
  Lecture: "Experience with NAMD on GPU-Accelerated Clusters" (Jim Phillips)
  BOF Panel: "The Art of Performance Tuning for the CUDA Architecture" (Jim Phillips)
   
• October 2, 2009, Lugano, Switzerland, CECAM Workshop
  Lecture: "Using GPU Computing to Accelerate Molecular Modeling Applications" (David Hardy)
   
• October 1, 2009, San Jose, CA, GPU Technology Conference
  Lecture: "GPU Accelerated Visualization and Analysis in VMD and Recent NAMD Developments" (John Stone)
   
• September 9, 2009, West Lafayette, IN, Purdue University, CS&E Seminar
  Lecture: "Multilevel Summation of Electrostatic Potentials Using GPUs" (David Hardy)
   
• September 2009, New Orleans, LA, IEEE Cluster 2009
  Tutorial Lecture: "High Performance Computing with CUDA: Biomolecular Modeling Applications of GPUs and GPU-Accelerated Clusters" (Jim Phillips)
   
• August 18, 2009, Washington, DC, Walter E. Washington Convention Center, Fall 2009 ACS National Meeting & Exposition
  Lecture: "A General Interface to Quantum Chemistry Simulations in VMD" (Jan Saam)
   
• August 10-14, 2009, Champaign, IL, iHotel and Conference Center, 'Hands-on' Workshop on Computational Biophysics
  Lecture: "VMD 1.8.7 - Key Features of Recent Release" (John Stone)
  Lecture: "NAMD 2.7 - Key Features of Upcoming Release" (Chris Harrison)
  Lecture: "Sequence analysis in VMD 1.8.7 - Key Features" (Kirby Vandivort)
  Lecture: "GPU accelerated NAMD 2.7" (Jim Phillips)
  Lecture: "Highlights of VMD Plugins" (Robert Brunner)
   
• June 9, 2009, Philadelphia, PA, University of Pennsylvania, Center for Molecular Modeling
  Lecture: "GPU Accelerated Visualization and Analysis in VMD" (John Stone)
   
• May 20, 2009, Ontario, Canada, University of Waterloo, Second Sharcnet Symposium on GPU and Cell Computing
  Lecture: "Keynote: Accelerating Molecular Modeling Applications with GPU Computing" (John Stone)
   
• April 2, 2009, Urbana, IL, National Center for Supercomputing Applications, Path to Petascale: Adapting GEO/CHEM/ASTRO Applications for Accelerators and Accelerator Clusters
  Lecture: "Experience with NAMD on GPU-accelerated Clusters" (Jim Phillips)
  Lecture: "Experiences with Multi-GPU Acceleration in VMD" (John Stone)
   
• March 24, 2009, Salt Lake City, UT, Spring 2009 American Chemical Society Meeting
  Lecture: "Biomolecular Applications of Graphics Processors: High Performance Computation and Interactive Display of Molecular Orbitals" (Jan Saam)


• March 8, 2009, Washington, DC, Second Workshop on General-Purpose Processing on Graphics Processing Units
  Lecture: "High Performance Computation and Interactive Display of Molecular Orbitals on GPUs and Multi-core CPUs" (John Stone)
   
• January 23, 2009, Urbana, IL, National Center for Supercomputing Applications, IACAT Accelerator Workshop
  Lecture: "Adapting a Message-Driven Parallel Application to GPU-Accelerated Clusters" (Jim Phillips)
  Lecture: "New Breakthroughs in NAMD/VMD and Quantum Chemistry CUDA Development and Useful Infrastructure Code" (John Stone, Jim Phillips, Dave Hardy, Jan Saam, and Klaus Schulten)
  Lecture: "High Performance Computation and Interactive Display of Molecular Orbitals on GPUs and Multi-core CPUs" (John Stone, Jim Phillips, Dave Hardy, Jan Saam, and Klaus Schulten)

Papers

• Probing Biomolecular Machines with Graphics Processors. James C. Phillips, John E. Stone. 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, Wen-mei Hwu. In Workshop on Parallel Programming on Accelerator Clusters (PPAC), IEEE Cluster 2009. In press.
   
• Visualisation of Cyclic and Multi-Branched Molecules with VMD. Simon Cross, Michelle M. Kuttel, John E. Stone, James E. Gain. Journal of Molecular Graphics and Modelling, 2009. In press.

2008

• November 17, 2008, Austin, TX, ACM/IEEE, SC08
  Tutorial Lecture: "High Performance Computing with CUDA: Molecular Dynamics" (Jim Phillips)
  Tutorial Lecture: "Molecular Visualization and Analysis" (John Stone)
  Technical Paper Lecture: "Adapting a Message-Driven Parallel Application to GPU-Accelerated Clusters" (Jim Phillips)
  
• November 11, 2008, Urbana, IL, University of Illinois, ECE 598SP: Massively Parallel Processors
  Lecture: "GPU Computing Case Study: Molecular Modeling Applications" (John Stone)


• October 28, 2008, Cape Town, South Africa, Cape Linux Users Group
  Lecture: "GPU Computing" (John Stone)


• October 27, 2008, Cape Town, South Africa, CSIR Rosebank Campus, Centre for High Performance Computing
  Lecture: "Visualizing Biomolecular Complexes with VMD" (John Stone)
  Lecture: "An Introduction to Molecular Visualization with VMD" (John Stone)


• October 23, 2008, Cape Town, South Africa, University of Cape Town, Computer Science Department
  Lecture: "Accelerating Molecular Modeling Applications with Graphics Processors" (John Stone)


• August 26, 2008, San Jose, CA, NVISION 2008
  Lecture: "Accelerating Computational Biology by 100x Using CUDA" (John Stone)


• August 10, 2008, Urbana, IL, National Center for Supercomputing Applications, VSCSE: Accelerators for Science and Engineering Applications: GPUs and Multicore
  Lecture: "Case Study - Accelerating Molecular Dynamics Experimentation" (John Stone)

Panel: "Multidisciplinary Panel" (John Stone)

• June 17-20, 2008, Dresden, Germany, International Supercomputing Conference (ISC08)
  Tutorial Lecture: "Accelerating Molecular Modeling with Graphics Processors" (Jim Phillips)


• June 10, 2008, Urbana, IL, National Center for Supercomputing Applications, Workshop on Programming Massively Parallel Processors
  Lecture: "Accelerating Scientific Applications with GPUs" (John Stone)


• June 10, 2008, Arlington, VA, TeraGrid '08 Conference
  Lecture: "Long Time and Large Size Molecular Dynamics Simulations Made Feasible through New TeraGrid Hardware and Software" (Kirby Vandivort)


• May 1, 2008, Boulder, CO, Linux Clusters Institute Conference
  Lecture: "GPU Acceleration of Molecular Modeling Applications" (Jim Phillips, John Stone)


• March 12, 2008, Atlanta, GA, SIAM Conference on Parallel Processing for Scientific Computing
  Lecture: "Accelerating Molecular Modeling Applications with Graphics Processors" (John Stone)
  Lecture: "Accelerating NAMD with Graphics Processors" (Jim Phillips)

Papers

• 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.

2007

• November 2007, Reno, NV, ACM/IEEE, SC07
  Tutorial Lecture: "High Performance Computing with CUDA: Molecular Dynamics"
   
• November 11, 2007, Reno, NV, SC07 International Conference on High Performance Computing, Networking, Storage, and Analysis
  Tutorial: "High Performance Computing on GPUs with CUDA" (John Stone)

 
• November 9, 2007, Princeton, NJ, Princeton University, Institute for Advanced Study, AstroGPU 2007 Conference
  Lecture: "GPU Acceleration of Scientific Applications Using CUDA" (John Stone)
   
• October 15, 2007, Urbana, IL, University of Illinois, ECE 498L1: Programming Massively Parallel Processors
  Lecture: "Case Studies: Ion Placement Tool, VMD" (John Stone)

 
• October 2007, Urbana, IL, NCSA, Dell XL HPC Consortium Meeting
  Lecture: "NAMD: Scalable Biomolecular Simulations on Multicore Clusters"
   
• April 2007, Urbana, IL, Department of Computer Science, 5th Annual Workshop on Charm++ and its Applications
  Lecture: "Refactoring NAMD for Petascale Machines and Graphics Processors"


• March 14, 2007, Urbana, IL, University of Illinois, ECE 498L1: Programming Massively Parallel Processors
  Lecture: "Case Studies: Ion Placement Tool, VMD" (John Stone)

2006

• November 30-December 1, 2006, UIUC, Urbana, IL, Beckman Institute, TCBG Cluster Building Workshop
  Lecture: "Linux Clusters for High-Performance Computing: An Introduction" (Tim Skirvin, Jim Phillips)
  Lecture: "Linux Clusters: Details and Case Studies" (Jim Phillips, Tim Skirvin)
   
• August 11, 2006, Universidad Nacional Autónoma de Mexico, DGSCA
  Lecture: "Visualization of Nano-Scale Structures"

 
• April 20-21, 2006, UIUC, Urbana, IL, Beckman Institute, TCBG Cluster Building Workshop
  Lecture: "Linux Clusters for High-Performance Computing: An Introduction" (Tim Skirvin, Jim Phillips)
  Lecture: "Linux Clusters: Details and Case Studies" (Jim Phillips, Tim Skirvin)

 
• April 4, 2006, University of Texas Health Science Center at Houston
  Lecture: "Visualization of Nano-Scale Structures"

 
• March 16-17, 2006, UIUC, Urbana, IL, Beckman Institute, TCBG Cluster Building Workshop
  Lecture: "Linux Clusters for High-Performance Computing: An Introduction" (Tim Skirvin)
  Lecture: "Linux Clusters: Details and Case Studies" (Jim Phillips, Tim Skirvin)

2005

• November 12-18, 2005, Seattle, WA, SC|05 International Conference for High Performance Computing, Networking, Storage and Analysis
  Presentation: "Exploring Biomolecular Machines with Supercomputers" (Jim Phillips, Jordi Cohen)
   

• November 10-11, 2005, UIUC, Urbana, IL, Beckman Institute, TCBG Cluster Workshop
  Lecture: "Linux Clusters for High-Performance Computing: An Introduction" (Tim Skirvin)
  Lecture: "Linux Clusters: Details and Case Studies" (Jim Phillips, Tim Skirvin)
   

• November 3, 2005, UIUC, Urbana, IL, National Center for Supercomputing Applications, Social Networks and Cyberinfrastructure Conference
  Lecture: "BioCoRE Overview" (Kirby Vandivort)
   

• October 25, 2005, Urbana, IL, UIUC CITES Computer Consultant Support Program Conference
  Lecture: "Linux Clustering for Scientific Computing" (ppt) (Jim Phillips, Tim Skirvin)
   

• September 22-23, 2005, UIUC, Urbana, IL, Beckman Institute, TCBG Cluster Workshop
  Lecture: "Linux Clusters for High-Performance Computing: An Introduction" (Tim Skirvin)
  Lecture: "Linux Clusters: Details and Case Studies" (Jim Phillips, Tim Skirvin)
   

• September 12, 2005, San Francisco, CA, UCSD, San Diego Supercomputer Center, Visualization of Large Biomolecular Complexes Workshop
  Lecture: "VMD: Algorithms and Methods for Large Scale Biomolecular Visualization" (John Stone)
   

• February 25, 2005, Purdue University, West Lafayette, IN, Envision Center
  Lecture: "Dancing Proteins: 3-D Visualization of Protein Structure and Dynamics on Next-Generation Graphics Hardware" (John Stone)
   

• February 22, 2005, University of Missouri at Rolla, Rolla, MO, Department of Computer Science CS Colloquium
  Lecture: "Dancing Proteins: 3-D Visualization of Protein Structure and Dynamics on Next-Generation Graphics Hardware" (John Stone)
   

• February 15, 2005, UIUC, Urbana, IL, Beckman Institute - Imaging Technology Group Forum
  Lecture: "Dancing Proteins: 3-D Visualization of Protein Structure and Dynamics on Next-Generation Graphics Hardware" (John Stone)

2004

• December 8-9, 2004, Nance, France, INRIA/CNRS ARC Docking Project
  Presentation: "VMD Biomolecular Visualization and Analysis" (John Stone)
   
• November 8-11, 2004, Pittsburgh, PA, IEEE/ACM SC2004 Conference
  Presentation: "Exploring Biomolecular Machines with Supercomputers" (James Phillips)
   
• October 3-5, 2004, Arlington, VA, NSF Cyberenabled Chemistry Workshop
  Presentation: "BioCoRE" (Kirby Vandivort)
   
• March 23, 2004, Bologna, Italy, ScicomP 9 Conference
  Lecture: "Molecular Dynamics Applications: NAMD" (Angelo Rossi (IBM) and Joachim Hein (University of Edinburgh))

2003

• November 17-20, 2003, Phoenix, AZ, IEEE/ACM SC2003 Conference
  Presentation: "NAMD, VMD, and BioCoRE, NIH NCRR Booth" (James Phillips and Robert Brunner)
  Presentation: "BioCoRE: A Collaborative Work Environment for Biomedical Research, Research Management and Training" (Robert Brunner)
  Presentation: "VMD: Visual Molecular Dynamics" (Sun personnel)
  Presentation: "NAMD and VMD: Live Molecular Dynamics Simulation on a InfiniBand Opteron Cluster" (InfiniCon Systems personnel)
   
• July 12, 2003, La Jolla, CA, Joint Amber CHARMM Developer's Symposium
  Lecture: "University of Illinois Software Integration Opportunities" (James Phillips)
   
• June 2, 2003, Melbourne, Australia, Terascale Performance Analysis Workshop, International Conference on Computational Science 2003
  Lecture: "Scaling Molecular Dynamics to 3000 Processors with Projections: A Performance Analysis Case Study"  (Laxmikant V. Kale, Sameer Kumar, Gengbin Zheng, Chee Wai Lee)

2002

• November 18-22, 2002, Baltimore, MD, IEEE/ACM SC2002 Exhibition
  Lecture: "NAMD and VMD: Live Molecular Dynamics Simulation and Visualization on NCSA Itanium Linux Cluster and Tiled Display Wall" (Jim Phillips)
  Lecture: "NAMD and VMD: Interactive Molecular Dynamics Simulation" (Sun personnel)
  Paper: "NAMD: Biomolecular Simulation on Thousands of Processors - Gordon Bell Award Finalist NAMD Paper"
   
• October 22, 2002, Champaign, IL, NCSA Access Grid Seminar Series
  Lecture: "BioCoRE: A Biological Collaborative Research Environment" (Robert Brunner, Kirby Vandivort)
   
• September 16-18, 2002, Ballston, VA, Data and Collaboratories in the Biomedical Community Workshop
  Lecture:  "BioCoRE: A Collaboratory for Structural Biology" (Gila Budescu)
   
• August 5, 2002, Edmonton, Canada, 10th International Conference on Intelligent Systems for Molecular Biology
  Lecture: "BioCoRE: A Biological Collaborative Research Environment" (Kirby Vandivort)
   
• July 23-25, 2002, Siggraph 2002 Exhibition
  Lecture: "Biomolecular Visualization"
   
• May 20, 2002, Pittsburgh, PA,  Scaling to New Heights Workshop at the Pittsburgh Supercomputing Center
  Lecture:  "NAMD: Biomolecular Simulations on Thousands of Processors"
   
• May 2002, Alliance All Hands Meeting
  Poster: "BioCoRE: A Biological Collaborative Research Environment" (Robert Brunner, Kirby Vandivort)
   
• April 17-19, 2002, NCSA, NAMD Workshop
  Lecture: "Introduction to Molecular Dynamics Simulations" (Klaus Schulten)
  Lecture: "What Can We Learn from MD Simulations?" (Klaus Schulten)
  Lecture: "Case Study: Unfolding the Muscle Protein Titin" (Mu Gao)
  Lecture: "Case Study: Aquaporin Membrane Channels" (Emad Tajkhorshid)
  Lecture: "Case Study: ATP Synthase Stalk Rotation" (Barry Isralewitz)
  Lecture: "Overview of Applicable Hardware and Software" (Jim Phillips)
  Lecture: "Configuring and Running NAMD Simulations" (Jim Phillips)
  Lecture: "Building Molecular Structures for NAMD" (Justin Gullingsrud)
  Lecture: "Assembling Molecular Systems for NAMD" (Justin Gullingsrud)
  Lecture: "Integrating the Equations of Motion" (Jim Phillips)
  Lecture: "Accelerating Processes via Steered MD" (Klaus Schulten)
  Lecture: "Analysis of MD Trajectories" (Justin Gullingsrud)
  Lecture: "Efficient Evaluation of Forces" (Jim Phillips)
  Lecture: "NAMD Serial and Parallel Performance" (Jim Phillips)
   
• March 8-9, 2002, Champaign-Urbana, IL, University of Illinois at Champaign-Urbana, Beckman Institute for Advanced Science and Technology Open House
  Lecture: "An Interactive Tour of the Living Cell"
   
• February 2002, Biophysical Society Meeting
  Poster: "BioCoRE: A Biological Collaborative Research Environment" (Kirby Vandivort, Robert Brunner, Gila Budescu, Barry Isralewitz, Laxmikant V. Kale, Klaus J. Schulten)

2001

• November 12-15, 2001, SC2001 Exhibition
  Lecture: "NAMD and VMD: Interactive Molecular Dynamics Simulation" (Jim Phillips)
  Lecture: "NAMD: Scalable Molecular Dynamics" (Jim Phillips)
  Lecture: "NAMD and VMD: Live Molecular Dynamics Simulation and Visualization on NCSA Itanium Linux Cluster and Tiled Display Wall" (Michelle Gower, NCSA)
  Lecture: "Theoretical Biophysics (TBG), NCSA and Intel McKinley Demo"
  Lecture: "BioCoRE Submits, Runs, and Visualizes your Simulations From Afar" (Kirby Vandivort)
   
• August 15-18, 2001, Pittsburgh, PA, Mellon Institute Building, Pittsburgh Supercomputing Center (PSC), PSC NAMD Workshop 2001
  Lecture: "Hands-On: Viewing Molecules with VMD" (Justing Gullingsrud)
  Lecture: "Introduction to MD Simulations" (Klaus Schulten)
  Lecture: "Semi empirical Force Fields and Their Limitations" (Ioan Kosztin)
  Lecture: "Configuring and Running NAMD Simulations" (Jim Phillips)
  Lecture: "Hands-On: Simulation of BPTI at Different Temperatures" (Klaus Schulten)
  Lecture: "What Can We Learn from MD Simulations?" (Klaus Schulten)
  Lecture: "Case Study: Protein-Membrane Simulation" (Klaus Schulten)
  Lecture: "Analysis of MD results using Statistical Mechanics Methods" (Ioan Kosztin)
  Lecture: "Hands-On: Analysis of BPTI Equilibrium Properties" (Ioan Kosztin)
  Lecture: "Integrating the Equations of Motion" (Jim Phillips)
  Lecture: "Building Molecular Structures for NAMD" (Jim Phillips)
  Lecture: "Assembling Molecular Systems for NAMD" (Justin Gullingsrud)
  Lecture: "Hands-On: Assembly of Gramicidin in a Membrane" (Justin Gullingsrud)
  Lecture: "Efficient Evaluation of Forces" (Jim Phillips)
  Lecture: "Analysis of MD Trajectories" (Ioan Kosztin)
  Lecture: "Case Study: Signaling Proteins" (Ioan Kosztin)
  Lecture: "Hands-On: Equilibration of Gramicidin in a Membrane" (Justin Gullingsrud)
  Lecture: "NAMD Serial and Parallel Performance" (Jim Phillips)
  Lecture: "Case Study: Steered MD Simulation" (Justin Gullingsrud)
   
• August 14-16, 2001, Siggraph 2001 Exhibition
  Lecture: "VMD - Visual Molecular Dynamics"
   
• July 13, 2001
  Lecture: "NAMD Linux Cluster Tutorial" (Jim Phillips, Tim Skirvin, John Stone)
   
• June 26, 2001, NCSA Linux Revolution Conference
  Lecture: "NAMD Linux Cluster Tutorial" (Jim Phillips, Tim Skirvin, John Stone)
   
• June 19, 2001
  Lecture: "NAMD Linux Cluster Tutorial" (Jim Phillips, Tim Skirvin, John Stone)

2000

• October 27-29, 2000, Pittsburgh, PA, NCRR Biomedical Collaboratories Workshop Pittsburgh Supercomputer Center.
   
• April 27, 2000, UIUC Beckman Institute, Urbana, IL, Beckman Institute for Advanced Science and Technology ITG Forum
  Lecture:  "BioCoRE: A Collaboratory for Structural Biology, Imaging Technology Group Forum"
   
• April 2000, University of Missouri-Rolla, VMD - High Performance Molecular Visualization
   
• April 2000, University of Notre Dame, VMD - High Performance Molecular Visualization

• November 1998, University of Missouri-Rolla, VMD - A Molecular Visualization System
   
• November 11, 1999, Champaign-Urbana, IL, University of Illinois at Champaign-Urbana, Beckman Institute for Advanced Science and Technology ITG Forum
  Lecture: "Linux Clusters" (Jim Phillips, John Stone)