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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.
Speech/gesture interface to a visual computing environment for molecular biologists.
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3

Rajeev Sharma, Michael Zeller, Vladimir I. Pavlovic, Thomas S. Huang, Zion Lo, Stephen Chu, Yunxin Zhao, James C. Phillips, and Klaus Schulten.
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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.
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6

John E. Stone, Kirby L. Vandivort, and Klaus Schulten.
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7

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.
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8

John E. Stone, Justin Gullingsrud, Paul Grayson, and Klaus Schulten.
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9

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.

10

Benjamin G. Levine, John E. Stone, and Axel Kohlmeyer.
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11

John Stone and Mark Underwood.
Rendering of numerical flow simulations using MPI.
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12

John E. Stone.
An Efficient Library for Parallel Ray Tracing and Animation.
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13

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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14

John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, and James C. Phillips.
GPU computing.
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15

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.
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17

Volodymyr Kindratenko, Jeremy Enos, Guochun Shi, Michael Showerman, Galen Arnold, John E. Stone, James Phillips, and Wen-mei Hwu.
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18

John E. Stone, David J. Hardy, Ivan S. Ufimtsev, and Klaus Schulten.
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19

John E. Stone, David Gohara, and Guochun Shi.
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20

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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21

John E. Stone, David J. Hardy, Barry Isralewitz, and Klaus Schulten.
GPU algorithms for molecular modeling.
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22

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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23

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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24

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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25

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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26

John E. Stone, Barry Isralewitz, and Klaus Schulten.
Early experiences scaling VMD molecular visualization and analysis jobs on Blue Waters.
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27

John E. Stone, Kirby L. Vandivort, and Klaus Schulten.
GPU-accelerated molecular visualization on petascale supercomputing platforms.
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28

John E. Stone, Ryan McGreevy, Barry Isralewitz, and Klaus Schulten.
GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting.
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29

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.
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30

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.
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31

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.
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32

G. Fiorin, M. L. Klein, and J. Hénin.
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35

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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50

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51

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52

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53

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