John E. Stone
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Dynamics of chromosome organization in a minimal bacterial cell Open
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. By creating a computational framework to model systems of replicatin…
View article: VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations Open
Modeling and simulation of small molecules such as drugs and biological cofactors have been both a major focus of computational chemistry for decades and a growing need among computational biophysicists who seek to investigate the interact…
View article: Application Experiences on a GPU-Accelerated Arm-based HPC Testbed
Application Experiences on a GPU-Accelerated Arm-based HPC Testbed Open
This paper assesses and reports the experience of ten teams working to port, validate, and benchmark several High Performance Computing applications on a novel GPU-accelerated Arm testbed system. The testbed consists of eight NVIDIA Arm HP…
View article: #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol Open
We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilit…
View article: Application Experiences on a GPU-Accelerated Arm-based HPC Testbed
Application Experiences on a GPU-Accelerated Arm-based HPC Testbed Open
This paper assesses and reports the experience of ten teams working to port,validate, and benchmark several High Performance Computing applications on a novel GPU-accelerated Arm testbed system. The testbed consists of eight NVIDIA Arm HPC…
View article: 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
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 Open
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with…
py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD Open
py-MCMD, an open-source Python software, provides a robust workflow layer that manages communication of relevant system information between the simulation engines NAMD and GOMC and generates coherent thermodynamic properties and trajectori…
ANARI: A 3-D Rendering API Standard Open
ANARI is a new 3-D rendering API, an emerging Khronos standard that enables visualization applications to leverage the state-of-the-art rendering techniques across diverse hardware platforms and rendering engines. Visualization application…
Analytic Rendering and Hardware-Accelerated Simulation for Scientific Applications Open
Advances in entertainment-targeted rendering technology have been leveraged for scientific analysis. Recent progress in both hardware and software capabilities have spurred development in analytic rendering: rendering capabilities optimize…
View article: #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol
#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol Open
We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilit…
Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus Open
Over the past 18 months, the need to perform atomic detail molecular dynamics simulations of the SARS-CoV-2 virion, its spike protein, and other structures related to the viral infection cycle has led biomedical researchers worldwide to ur…
View article: Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action
Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action Open
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with…
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics Open
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike…
AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics Open
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike…
Scalable Analysis of Authentic Viral Envelopes on FRONTERA Open
Enveloped viruses, such as SARS-CoV-2, infect cells via fusion of their envelope with the host membrane. By employing molecular simulations to characterize viral envelopes, researchers can gain insights into key determinants of infection. …
View article: Scalable molecular dynamics on CPU and GPU architectures with NAMD
Scalable molecular dynamics on CPU and GPU architectures with NAMD Open
NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundre…
Scalable Analysis of Authentic Viral Envelopes on FRONTERA Open
Enveloped viruses infect host cells via fusion of their viral envelope with the plasma membrane. Upon cell entry, viruses gain access to all the macromolecular machinery necessary to replicate, assemble, and bud their progeny from the infe…
High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities Open
Compartmentalization is a central theme in biology. Cells are composed of numerous membrane-enclosed structures, evolved to facilitate specific biochemical processes; viruses act as containers of genetic material, optimized to drive infect…
High-performance analysis of biomolecular containers to measure small-molecule transport, transbilayer lipid diffusion, and protein cavities Open
Compartmentalization is a central theme in biology. Cells are composed of numerous membrane-enclosed structures, evolved to facilitate specific biochemical processes; viruses act as containers of genetic material, optimized to drive infect…
A Planetarium Dome Master Camera Open
This chapter presents a camera implementation for high-quality interactive ray tracing of planetarium dome master images using an azimuthal equidistant projection. Ray tracing is aptly suited for implementing a wide variety of special pano…
Interactive Ray Tracing Techniques for High-Fidelity Scientific Visualization Open
This chapter describes rendering techniques and implementation considerations when using ray tracing for interactive scientific and technical visualization. Ray tracing offers a convenient framework for building high-fidelity rendering eng…
Scalable molecular dynamics with NAMD on the Summit system Open
NAMD (NAnoscale Molecular Dynamics) is a parallel molecular dynamics application that has been used to make breakthroughs in understanding the structure and dynamics of large biomolecular complexes, such as viruses like HIV and various typ…
NanoShaper–VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems Open
Summary NanoShaper is a program specifically aiming the construction and analysis of the molecular surface of nanoscopic systems. It uses ray-casting for parallelism and it performs analytical computations whenever possible to maximize rob…
Communicating science through visualization in an age of alternative facts Open
Cinematic scientific visualization demystifies complex scientific concepts for general audiences, which helps them defend themselves against misinformation in popular media. Researchers from the University of Illinois will show techniques …
Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations Open
Cryo-electron tomography (cryo-ET) has rapidly emerged as a powerful tool to investigate the internal, three-dimensional spatial organization of the cell. In parallel, the GPU-based technology to perform spatially resolved stochastic simul…