John E. Stone

University of Illinois Urbana-Champaign — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

41h-index13.2kcitations112works0.02yr avg
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Research Topics

Protein Structure and Dynamics(35), Parallel Computing and Optimization Techniques(23), Distributed and Parallel Computing Systems(21), Advanced Data Storage Technologies(14), Enzyme Structure and Function(12)

Publications112 total

BPS2025 - Enhancing molecular visualization, dynamics, and structural analysis tools for biomolecular studies
Biophysical Journal·2025
Dynamics of chromosome organization in a minimal bacterial cell
Biophysical Journal·2024
Dynamics of chromosome organization in a minimal bacterial cell
Frontiers in Cell and Developmental Biology·2023· 17 citedOpen Access
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations
Journal of Chemical Information and Modeling·2023· 78 citedOpen Access
Application Experiences on a GPU-Accelerated Arm-based HPC Testbed
2023· 8 citedOpen Access
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol
The International Journal of High Performance Computing Applications·2022· 87 citedOpen Access
Application Experiences on a GPU-Accelerated Arm-based HPC Testbed
arXiv (Cornell University)·2022· 2 citedOpen Access
Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action
The International Journal of High Performance Computing Applications·2022· 5 citedOpen Access
py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD
Journal of Chemical Theory and Computation·2022· 25 citedOpen Access
Analytic Rendering and Hardware-Accelerated Simulation for Scientific Applications
Computing in Science & Engineering·2022Open Access
ANARI: A 3-D Rendering API Standard
Computing in Science & Engineering·2022· 7 citedOpen Access
#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol
2021· 28 citedOpen Access
Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus
2021· 4 citedOpen Access
Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action
2021· 6 citedOpen Access
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics
The International Journal of High Performance Computing Applications·2021· 173 citedOpen Access
Stochastic Spatial Simulation of Genetic Information Processes in the Minimal Cell
Biophysical Journal·2021Open Access
Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales
Parallel Computing·2020· 16 citedOpen Access
AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics
2020· 46 citedOpen Access
Scalable Analysis of Authentic Viral Envelopes on FRONTERA
Computing in Science & Engineering·2020· 14 citedOpen Access
Scalable molecular dynamics on CPU and GPU architectures with NAMD
The Journal of Chemical Physics·2020· 3.1k citedOpen Access
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Frequent Co-authors

Klaus Schulten(22), J. C. Phillips(20), David J. Hardy(15), Zaida Luthey‐Schulten(7), Wen‐mei Hwu(6), João V. Ribeiro(5), Emad Tajkhorshid(5), Rafael C. Bernardi(4), Abhishek Singharoy(4), Lorenzo Casalino(4), Abigail C. Dommer(4), Terra Sztain(4), Surl-Hee Ahn(4), Anda Trifan(4), Alexander Brace(4), Anthony T. Bogetti(4), Heng Ma(4), Hyungro Lee(4), Matteo Turilli(4), Syma Khalid(4)