World's Best Scientists 2026 revealed!

D-Index & Metrics

Computer Science

D-Index
39
Citations
14428
World Ranking
9496
National Ranking
4023

Overview

John E. Stone is affiliated with Nvidia in the United States and has contributed extensively to the field of biochemistry, genetics, and molecular biology. Their research spans multiple subfields, including molecular biology, ecology, biomedical engineering, modeling and simulation, and biophysics.

The primary areas of study for their work encompass topics such as protein structure and dynamics, bacteriophages and microbial interactions, lipid membrane structure and behavior, COVID-19 epidemiological studies, bacterial genetics and biotechnology, nanopore and nanochannel transport studies, and SARS-CoV-2 and COVID-19 research.

Frequent coauthors collaborating with John E. Stone include David J. Hardy, J. C. Phillips, Emad Tajkhorshid, Anda Trifan, and Alexander Brace. These collaborations have contributed to a range of publications across several scientific venues.

Key publication venues where Stone's research has been featured regularly include:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • The International Journal of High Performance Computing Applications
  • Computing in Science & Engineering
  • Biophysical Journal
  • The Journal of Chemical Physics

Among recent notable papers authored or coauthored by John E. Stone are:

  • Scalable molecular dynamics on CPU and GPU architectures with NAMD (2020) in The Journal of Chemical Physics
  • AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics (2021) in The International Journal of High Performance Computing Applications
  • #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol (2022) in The International Journal of High Performance Computing Applications
  • VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations (2023) in Journal of Chemical Information and Modeling
  • AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics (2020) in bioRxiv (Cold Spring Harbor Laboratory)

Best Publications

  • Scalable molecular dynamics on CPU and GPU architectures with NAMD.

    James C. Phillips;David J. Hardy;Julio D.C. Maia;John E. Stone

  • GPU Computing

    J.D. Owens;M. Houston;D. Luebke;S. Green

  • OpenCL: A Parallel Programming Standard for Heterogeneous Computing Systems

    John E Stone;David Gohara;Guochun Shi

  • Accelerating molecular modeling applications with graphics processors

    John E. Stone;James C. Phillips;Peter L. Freddolino;David J. Hardy

  • GPU-accelerated molecular modeling coming of age

    John E. Stone;David J. Hardy;Ivan S. Ufimtsev;Klaus Schulten

  • An efficient library for parallel ray tracing and animation

    John Edward Stone

  • GPU clusters for high-performance computing

    Volodymyr V. Kindratenko;Jeremy J. Enos;Guochun Shi;Michael T. Showerman

  • Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming

    Benjamin G. Levine;John E. Stone;Axel Kohlmeyer

  • A system for interactive molecular dynamics simulation

    John E. Stone;Justin Gullingsrud;Klaus Schulten

  • An asymmetric distributed shared memory model for heterogeneous parallel systems

    Isaac Gelado;John E. Stone;Javier Cabezas;Sanjay Patel

  • NAMD goes quantum: an integrative suite for hybrid simulations.

    Marcelo C.R. Melo;Rafael C. Bernardi;Till Rudack;Till Rudack;Maximilian Scheurer;Maximilian Scheurer

  • Adapting a message-driven parallel application to GPU-accelerated clusters

    James C. Phillips;John E. Stone;Klaus Schulten

  • QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

    João V. Ribeiro;Rafael C. Bernardi;Till Rudack;John E. Stone

  • Using VMD: an introductory tutorial.

    Jen Hsin;Anton Arkhipov;Ying Yin;John E. Stone

  • Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

    Abhishek Singharoy;Ivan Teo;Ryan McGreevy;John E Stone

  • Multilevel summation of electrostatic potentials using graphics processing units

    David J. Hardy;John E. Stone;Klaus Schulten

  • GPU acceleration of cutoff pair potentials for molecular modeling applications

    Christopher I. Rodrigues;David J. Hardy;John E. Stone;Klaus Schulten

  • Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation.

    Elijah Roberts;John E. Stone;Zaida Luthey-Schulten

  • AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

    Lorenzo Casalino;Abigail C. Dommer;Zied Gaieb;Emilia P. Barros

  • Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories

    Michael Krone;John E. Stone;Thomas Ertl;Klaus Schulten

  • AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

    Lorenzo Casalino;Abigail Dommer;Zied Gaieb;Emilia P Barros

Frequent Co-Authors

Wen-mei W. Hwu
Wen-mei W. Hwu University of Illinois at Urbana-Champaign
Aleksei Aksimentiev
Aleksei Aksimentiev University of Illinois at Urbana-Champaign
Shantenu Jha
Shantenu Jha Rutgers, The State University of New Jersey
Anima Anandkumar
Anima Anandkumar Nvidia (United Kingdom)
David Luebke
David Luebke Nvidia (United States)
Ian Foster
Ian Foster University of Chicago
William N. Green
William N. Green University of Chicago
Laxmikant V. Kale
Laxmikant V. Kale University of Illinois at Urbana-Champaign
John D. Owens
John D. Owens University of California, Davis
Rick Stevens
Rick Stevens Argonne National Laboratory

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