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VMD - Visual Molecular Dynamics.
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2

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.
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Rajeev Sharma, Michael Zeller, Vladimir I. Pavlovic, Thomas S. Huang, Zion Lo, Stephen Chu, Yunxin Zhao, James C. Phillips, and Klaus Schulten.
Speech/gesture interface to a visual-computing environment.
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4

Simon Cross, Michelle M. Kuttell, John E. Stone, and James E. Gain.
Visualization of cyclic and multi-branched molecules with VMD.
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5

John E. Stone, Axel Kohlmeyer, Kirby L. Vandivort, and Klaus Schulten.
Immersive molecular visualization and interactive modeling with commodity hardware.
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6

John E. Stone, Kirby L. Vandivort, and Klaus Schulten.
Immersive out-of-core visualization of large-size and long-timescale molecular dynamics trajectories.
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7

John E. Stone, William R. Sherman, and Klaus Schulten.
Immersive molecular visualization with omnidirectional stereoscopic ray tracing and remote rendering.
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8

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.
A visual computing environment for very large scale biomolecular modeling.
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9

John E. Stone, Justin Gullingsrud, Paul Grayson, and Klaus Schulten.
A system for interactive molecular dynamics simulation.
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10

Matthieu Chavent, Tyler Reddy, Joseph Goose, Anna Caroline E. Dahl, John E. Stone, Bruno Jobard, and Mark S.P. Sansom.
Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems.
Faraday Discuss., 169:455-475, 2014.

11

Benjamin G. Levine, John E. Stone, and Axel Kohlmeyer.
Fast analysis of molecular dynamics trajectories with graphics processing units-radial distribution function histogramming.
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12

John Stone and Mark Underwood.
Rendering of numerical flow simulations using MPI.
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13

John E. Stone.
An Efficient Library for Parallel Ray Tracing and Animation.
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14

John E. Stone, Barry Isralewitz, and Klaus Schulten.
Early experiences scaling VMD molecular visualization and analysis jobs on Blue Waters.
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I. Wald, G. Johnson, J. Amstutz, C. Brownlee, A. Knoll, J. Jeffers, J. Gunther, and P. Navratil.
OSPRay - a CPU ray tracing framework for scientific visualization.
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16

John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten.
Accelerating molecular modeling applications with graphics processors.
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17

John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, and James C. Phillips.
GPU computing.
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18

Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, and Wen-mei W. Hwu.
GPU acceleration of cutoff pair potentials for molecular modeling applications.
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David J. Hardy, John E. Stone, and Klaus Schulten.
Multilevel summation of electrostatic potentials using graphics processing units.
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20

Volodymyr Kindratenko, Jeremy Enos, Guochun Shi, Michael Showerman, Galen Arnold, John E. Stone, James Phillips, and Wen-mei Hwu.
GPU clusters for high performance computing.
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21

John E. Stone, David J. Hardy, Ivan S. Ufimtsev, and Klaus Schulten.
GPU-accelerated molecular modeling coming of age.
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22

John E. Stone, David Gohara, and Guochun Shi.
OpenCL: A parallel programming standard for heterogeneous computing systems.
Comput. in Sci. and Eng., 12:66-73, 2010.

23

Jeremy Enos, Craig Steffen, Joshi Fullop, Michael Showerman, Guochun Shi, Kenneth Esler, Volodymyr Kindratenko, John E. Stone, and James C. Phillips.
Quantifying the impact of GPUs on performance and energy efficiency in HPC clusters.
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24

John E. Stone, David J. Hardy, Barry Isralewitz, and Klaus Schulten.
GPU algorithms for molecular modeling.
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25

David J. Hardy, Zhe Wu, James C. Phillips, John E. Stone, Robert D. Skeel, and Klaus Schulten.
Multilevel summation method for electrostatic force evaluation.
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26

John E. Stone, Ryan McGreevy, Barry Isralewitz, and Klaus Schulten.
GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting.
Faraday Discuss., 169:265-283, 2014.

27

Abhishek Singharoy, Ivan Teo, Ryan McGreevy, John E. Stone, Jianhua Zhao, and Klaus Schulten.
Molecular dynamics-based refinement and validation with Resolution Exchange MDFF for sub-5 Å cryo-electron microscopy maps.
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28

John E. Stone, Juan R. Perilla, C. Keith Cassidy, and Klaus Schulten.
GPU-accelerated molecular dynamics clustering analysis with OpenACC.
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29

John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wen-mei W. Hwu, and Klaus Schulten.
High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs.
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30

John E. Stone, David J. Hardy, Jan Saam, Kirby L. Vandivort, and Klaus Schulten.
GPU-accelerated computation and interactive display of molecular orbitals.
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31

John E. Stone, Michael J. Hallock, James C. Phillips, Joseph R. Peterson, Zaida Luthey-Schulten, and Klaus Schulten.
Evaluation of emerging energy-efficient heterogeneous computing platforms for biomolecular and cellular simulation workloads.
2016 IEEE International Parallel and Distributed Processing Symposium Workshop (IPDPSW), pages 89-100, 2016.

32

John E. Stone, Antti-Pekka Hynninen, James C. Phillips, and Klaus Schulten.
Early experiences porting the NAMD and VMD molecular simulation and analysis software to GPU-accelerated OpenPOWER platforms.
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33

Michael Krone, John E. Stone, Thomas Ertl, and Klaus Schulten.
Fast visualization of Gaussian density surfaces for molecular dynamics and particle system trajectories.
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34

Elijah Roberts, John E. Stone, and Zaida Luthey-Schulten.
Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation.
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35

John E. Stone, Kirby L. Vandivort, and Klaus Schulten.
GPU-accelerated molecular visualization on petascale supercomputing platforms.
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36

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.
Visualization of energy conversion processes in a light harvesting organelle at atomic detail.
In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, SC '14. IEEE Press, 2014.

37

Juan R. Perilla, Boon Chong Goh, John Stone, and Klaus Schulten.
Chemical visualization of human pathogens: the Retroviral Capsids.
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38

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.
Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing.
Parallel Computing, 55:17-27, 2016.

39

Steven G. Parker, James Bigler, Andreas Dietrich, Heiko Friedrich, Jared Hoberock, David Luebke, David McAllister, Morgan McGuire, Keith Morley, Austin Robison, and Martin Stich.
OptiX: a general purpose ray tracing engine.
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40

James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, and Klaus Schulten.
Petascale Tcl with NAMD, VMD, and Swift/T.
In SC'14 workshop on High Performance Technical Computing in Dynamic Languages, SC '14. IEEE Press, 2014.

41

Mark D. Klein and John E. Stone.
Unlocking the full potential of the Cray XK7 accelerator.
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42

John E. Stone, Peter Messmer, Robert Sisneros, and Klaus Schulten.
High performance molecular visualization: In-situ and parallel rendering with EGL.
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43

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.
Stable small quantum dots for synaptic receptor tracking on live neurons.
Angew. Chem. Int. Ed. Engl., 126:12692-12696, 2014.

44

Sergio Decherchi, Andrea Spitaleri, John Stone, and Walter Rocchia.
NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems.
Bioinformatics, page bty761, 2018.

45

Xavier Daura, Karl Gademann, Bernhard Jaun, Dieter Seebach, Wilfred F. van Gunsteren, and Alan E. Mark.
Peptide folding: When simulation meets experiment.
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46

Laurie J. Heyer, Semyon Kruglyak, and Shibu Yooseph.
Exploring expression data: identification and analysis of coexpressed genes.
Gen. Res., 9:1106-1115, 1999.

47

Alexander J Bryer, Jodi A Hadden-Perilla, John E Stone, and Juan R Perilla.
High-performance analysis of biomolecular containers to measure small-molecule transport, transbilayer lipid diffusion, and protein cavities.
Journal of chemical information and modeling, 59(10):4328-4338, 2019.

48

G. Fiorin, M. L. Klein, and J. Hénin.
Using collective variables to drive molecular dynamics simulations.
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M. Iannuzzi, A. Laio, and M. Parrinello.
Efficient exploration of reactive potential energy surfaces using car-parrinello molecular dynamics.
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E A Coutsias, C Seok, and K A Dill.
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Yuguang Mu, Phuong H. Nguyen, and Gerhard Stock.
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Alexandros Altis, Phuong H. Nguyen, Rainer Hegger, and Gerhard Stock.
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58

Reza Salari, Thomas Joseph, Ruchi Lohia, Jérôme Hénin, and Grace Brannigan.
A streamlined, general approach for computing ligand binding free energies and its application to GPCR-bound cholesterol.
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59

Eric Darve, David Rodríguez-Gómez, and Andrew Pohorille.
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75

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76

Yuqing Deng and Benoît Roux.
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79

Rong Shen, Wei Han, Giacomo Fiorin, Shahidul M Islam, Klaus Schulten, and Benoît Roux.
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