John E. Stone

NVIDIA | Nvidia · Developer Technology

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 replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics, we investigate changes in chrom...

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 interaction of different types of ligands with biomolecules. Of particular interest in this regard are quantum mechanic...

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 capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental m...

This paper assesses and reports the experience of eleven application teams working to build, validate, and benchmark several HPC applications on a novel GPU-accerated Arm testbed. The testbed consists of the latest, at time of writing, Arm Devkits from NVIDIA with server-class Arm CPUs and NVIDIA A100 GPUs. The applications and mini-apps are writte...

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 pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g. cryo-electron microscopy...

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 trajectories for analysis. To validate the workflow and highlight its capabilities, hybrid Monte Carlo/molecular dynamics...

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 applications have historically embedded custom-written renderers to enable them to provide the necessary combination of fe...

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 optimized for analysis, particularly 3-D spatial analysis. These efforts also leverage hardware-accelerated ray tracing...

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 capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental m...

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 urgently seek out all available biomolecular structure information, appropriate molecular modeling and simulation...

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 pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy...

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 pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy...

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 protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynami...

Conversion of sunlight into chemical energy, namely photosynthesis, is the primary energy source of life on Earth. A visualization depicting this process, based on multiscale computational models from electronic to cell scales, is presented in the form of an excerpt from the fulldome show Birth of Planet Earth. This accessible visual narrative show...

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 protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynami...

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. Here, the Frontera supercomputer is leveraged for large-scale modeling and analysis of authentic viral envelope...

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 hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments....

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 infected cell. By employing molecular dynamics simulations to characterize the dynamical and chemical-physical prop...

This visualization of the quantum-mechanical process of photosynthesis involved combining structural models from atomic, protein, organelle, and cell scales. We descend into a prehistoric hot spring, revealing primitive bacteria which use an early form of photosynthesis to turn sunlight into chemical energy in structures called chromatophores. This...

We report a 100-million atom-scale model of an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium, that reveals the cascade of energy conversion steps culminating in the generation of ATP from sunlight. Molecular dynamics simulations of this vesicle elucidate how the integral membrane complexes influence local cur...

We report a 100-million atom-scale model of an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium, that reveals the cascade of energy conversion steps culminating in the generation of ATP from sunlight. Molecular dynamics simulations of this vesicle elucidate how the integral membrane complexes influence local cur...

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 infection. Molecular dynamics simulations provide a mechanism to study biomolecular containers and the influence they...

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 infection. Molecular dynamics simulations provide a mechanism to study biomolecular containers and the influence they...

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 panoramic and stereoscopic projections without sacrificing image quality. This camera implementation supports antia...

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 engines that can directly generate publication-quality images for scientific manuscripts while also providing high...

NAMD 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 types of influenza. State-of-the-art biomolecular simulations often require integration of billions of timesteps, computing all interatomic force...

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 robustness and accuracy of the approach. Among the other features, NanoShaper provides volume, surface area, including tha...

This article highlights the Oak Ridge Leadership Compute Facilitys GPU Hackathon, presenting the training format used, trends observed, and reasons for teams successes and failures. It also summarizes participant outcomes and takeaways while demonstrating how educators could adopt this hackathon format for use in their respective institutions.

Hybrid methods that combine quantum mechanics (QM) and molecular mechanics (MM) can be applied to studies of reaction mechanisms in locations ranging from active sites of small enzymes to multiple sites in large bioenergetic complexes. By combining the widely used molecular dynamics and visualization programs NAMD and VMD with the quantum chemistry...

This chapter explores the use of OpenACC directives to accelerate the calculation of a so-called dissimilarity matrix, the most costly computation required for clustering analysis of molecular dynamics simulations. By the end of this chapter, the reader will have an understanding of: Key algorithmic analysis steps that help guide decision making in...

This chapter uses the electrostatic potential calculation in the VMD application to illustrate the practical use of loop transformations, thread granularity coarsening, and redundancy elimination techniques in a real application. It further shows some important details, interleaved data mapping and data structure padding, in achieving memory coales...

The OLCF GPU Hackathons are a one-week code- development/learning event to better enable attendees to utilize GPUs. It only took three years to grow from a “Let’s give this a try”-event to a repeatedly copied format with several spin- offs that inspired HPC centers around the world. Sticking to a few fundamental principles—work on your own code, le...

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 for representing data accurately while making it not only approachable, but beautiful and compelling to experts...

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 simulations of whole cells has arisen, allowing the simulation of complex biochemical networks over cell cycle times...

Initial and refined structures. DOI: http://dx.doi.org/10.7554/eLife.16105.029

Supplementary tables. (A) TRPV1 MDFF Results. (B) Structure quality indicators for TRPV1 structures. (C) MDFF for the TRPV1 TM region. (D) Structure quality indicators for γ-secretase. (E) Measures of fit for MDFF refinements of β-galactosidase prepared initially at 1000 K. (F) Structural quality indicators for MDFF-refined β-galactosidase prepared...

All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, si...

The proper functioning of biomolecules in living cells requires them to assume particular structures and to undergo conformational changes. Both biomolecular structure and motion can be studied using a wide variety of techniques, but none offers the level of detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling prog...

Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as...

Many of the continuing scientific advances achieved through computational biology are predicated on the availability of ongoing increases in computational power required for detailed simulation and analysis of cellular processes on biologically-relevant timescales. A critical challenge facing the development of future exascale supercomputer systems...

Large scale molecular dynamics simulations produce terabytes of data that is impractical to transfer to remote facilities. It is therefore necessary to perform visualization tasks in-situ as the data are generated, or by running interactive remote visualization sessions and batch analyses co-located with direct access to high performance storage sy...

Immersive molecular visualization provides the viewer with intuitive perception of complex structures and spatial relationships that are of critical interest to structural biologists. The recent availability of commodity head mounted displays (HMDs) provides a compelling opportunity for widespread adoption of immersive visualization by molecular sc...

The cellular process responsible for providing energy for most life on Earth, namely, photosynthetic light-harvesting, requires the cooperation of hundreds of proteins across an organelle, involving length and time scales spanning several orders of magnitude over quantum and classical regimes. Simulation and visualization of this fundamental energy...

The multilevel summation method (MSM) offers an efficient algorithm utilizing convolution for evaluating long-range forces arising in molecular dynamics simulations. Shifting the balance of computation and communication, MSM provides key advantages over the ubiquitous particle-mesh Ewald (PME) method, offering better scaling on parallel computers a...

We developed a coating method to produce functionalized small quantum dots (sQDs), about 9 nm in diameter, that were stable for over a month. We made sQDs in four emission wavelengths, from 527 to 655 nm and with different functional groups. AMPA receptors on live neurons were labeled with sQDs and postsynaptic density proteins were visualized with...

The Cray XK7 includes NVIDIA GPUs for acceleration of computing workloads, but the standard XK7 system software inhibits the GPUs from accelerating OpenGL and related graphics-specific functions. We have changed the operating mode of the XK7 GPU firmware, developed a custom X11 stack, and worked with Cray to acquire an alternate driver package from...

Simulation of in vivo cellular processes with the reaction-diffusion master equation (RDME) is a computationally expensive task. Our previous software enabled simulation of inhomogeneous biochemical systems for small bacteria over long time scales using the MPD-RDME method on a single GPU. Simulations of larger eukaryotic systems exceed the on-boar...

Interactions between lipids and membrane proteins play a key role in determining the nanoscale dynamic and structural properties of biological membranes. Molecular dynamics (MD) simulations provide a valuable tool for studying membrane models, complementing experimental approaches. It is now possible to simulate large membrane systems, such as simp...

Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray crystallography with molecular dynamics simulations for the determination of all-atom structures of large biomolecular complexes. Evaluating the quality-of-fit obtained from hybrid fitting is computationally demanding, particularly in the context of a multiplicity...

Nuclear pore complexes (NPCs) form gateways for material transfer across the nuclear envelope of eukaryotic cells. Disordered proteins, rich in phenylalanine-glycine repeat motifs (FG-nups), form the central transport channel. Understanding how nups are arranged in the interior of the NPC may explain how NPC functions as a selectivity filter for tr...

Super resolution imaging and high-precision single particle tracking are promising techniques to study biomolecular trafficking and localization as well as intracellular structures. The tremendous amount of data acquired from the experiments pose a great visualization and analysis challenge. VMD, a software for visualizing and analyzing trajectorie...

Heterogeneous parallel computing applications often process large data sets that require multiple GPUs to jointly meet their needs for physical memory capacity and compute throughput. However, the lack of high-level abstractions in previous heterogeneous parallel programming models force programmers to resort to multiple code versions, complex data...

All chemical reactions are inherently random discrete events; while large numbers of reacting species in well-stirred vessels my appear to be governed by deterministic expressions, the biochemistry at the heart of the living cell-which may involve only a single copy of a gene or only a handfull of proteins-can exhibit significant fluctuations from...

Petascale supercomputers create new opportunities for the study of the structure and function of large biomolecular complexes such as viruses and photosynthetic organelles, permitting all-atom molecular dynamics simulations of tens to hundreds of millions of atoms. Together with simulation and analysis, visualization provides researchers with a pow...

Pataskala molecular dynamics simulations provide a powerful tool for probing the dynamics of cellular processes at atomic and nanosecond resolution not achievable by experimental methods alone. Extraction of details about the dynamics of bimolecular from terabytes of simulation output requires powerful user-extensible molecular analysis and visuali...

Spatial stochastic simulation is a valuable technique for studying reactions in biological systems. With the availability of high-performance computing (HPC), the method is poised to allow integration of data from structural, single-molecule and biochemical studies into coherent computational models of cells. Here, we introduce the Lattice Microbes...

Traditional design guidelines for broadband antenn as do not always produce satisfactory performance for the desired frequency range of inte rest. In addition, the accurate prediction of the f ree- space antenna performance is not sufficient to dete rmine if the antenna will meet a larger system requirement because the performance of the antenna ca...

We present an efficient algorithm for computation of surface representations enabling interactive visualization of large dynamic particle data sets. Our method is based on a GPU-accelerated data-parallel algorithm for computing a volumetric density map from Gaussian weighted particles. The algorithm extracts an isovalue surface from the computed de...

Atomistic molecular dynamics (MD) simulations of biomolecules provide insight into their physical mechanisms and potential as drug targets. Unfortunately, such simulations are extremely demanding in terms of computation, storage, and visualization. Immersive visualization environments permit fast, intuitive exploration of the pharmacological potent...

Savant is a asymptotic ray-tracing CEM tool used to predict the performance of antennas installed on electrically l arge platforms, including far-field antenna patterns, near-field distributions, and ant enna-to-antenna coupling. Savant is based on the shooting and bouncing rays (SBR) formulation. While asymptotic solvers like Savant have significa...

The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming sch...

This chapter presents GPU kernels for calculating electrostatic potential maps, which are of practical importance to modeling biomolecules. Calculations on a structured grid containing a large amount of fine-grained data parallelism make this problem especially well suited to GPU computing and a worthwhile case study. The chapter discusses the effe...

This chapter presents several graphics processing unit (GPU) algorithms for evaluating molecular orbitals on three-dimensional lattices, as is commonly used for molecular visualization. The GPU kernels described here form the basis for the high-performance molecular orbital display algorithms in VMD, a popular molecular visualization and analysis t...

Continuing advances in development of multi-core CPUs, GPUs, and low-cost six-degree-of-freedom virtual reality input devices have created an unprecedented opportunity for broader use of interactive molecular modeling and immersive visualization of large molecular complexes. We describe the design and implementation of VMD, a popular molecular visu...

Graphics processing units (GPUs) have traditionally been used in molecular modeling solely for visualization of molecular structures and animation of trajectories resulting from molecular dynamics simulations. Modern GPUs have evolved into fully programmable, massively parallel co-processors that can now be exploited to accelerate many scientific c...

We present an inexpensive hardware system for monitoring power usage of individual CPU hosts and externally attached GPUs in HPC clusters and the software stack for integrating the power usage data streamed in real-time by the power monitoring hardware with the cluster management software tools. We introduce a measure for quantifying the overall im...

We provide an overview of the key architectural features of recent microprocessor designs and describe the programming model and abstractions provided by OpenCL, a new parallel programming standard targeting these architectures.

Heterogeneous computing combines general purpose CPUs with accelerators to efficiently execute both sequential control-intensive and data-parallel phases of applications. Existing programming models for heterogeneous computing rely on programmers to explicitly manage data transfers between the CPU system memory and accelerator memory. This paper pr...

Computer simulation has become an integral part of the study of the structure and function of biological molecules. For years, parallel computers have been used to conduct these computationally demanding simulations and to analyze their results. These simulations function as a "computational microscope," allowing the scientist to observe details of...

We report the addition of two visualisation algorithms, termed PaperChain and Twister, to the freely available Visual Molecular Dynamics (VMD) package. These algorithms produce visualisations of complex cyclic molecules and multi-branched polysaccharides and are a generalization and optimization of those we previously developed in a standalone pack...

Abstract To address the problem of performing long time simula- tions of biochemical pathways under in vivo cellular condi- tions, we have developed a lattice-based, reaction-diffusion model that uses the graphics processing unit (GPU) as a computational,co-processor. The method,has been specifi- cally designed from the beginning to take advantage,...

The visualization of molecular orbitals (MOs) is important for analyzing the results of quantum chemistry simulations. The functions describing the MOs are computed on a three- dimensional lattice, and the resulting data can then be used for plotting isocontours or isosurfaces for visualization as well as for other types of analyses. Existing softw...

Physical and engineering practicalities involved in microprocessor design have resulted in flat performance growth for traditional single-core microprocessors. The urgent need for continuing increases in the performance of scientific applications requires the use of many-core processors and accelerators such as graphics processing units (GPUs). Thi...

Large-scale GPU clusters are gaining popularity in the scientific computing community. However, their deployment and production use are associated with a number of new challenges. In this paper, we present our efforts to address some of the challenges with building and running GPU clusters in HPC environments. We touch upon such issues as balanced...

VMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. This unit will serve as an introductory VMD tutorial. We will present several step-by-step examples of some of VMD's most popular features, including visualizing molecules...

Graphics processing units (GPUs) have become an attractive option for accelerating scientific computations as a result of advances in the performance and flexibility of GPU hardware, and due to the availability of GPU software development tools targeting general purpose and scientific computation. However, effective use of GPUs in clusters presents...

The advent of systems biology requires the simulation of ever- larger biomolecular systems, demanding a commensurate growth in computational power. This paper examines the use of the NVIDIA Tesla C870 graphics card programmed through the CUDA toolkit to accelerate the calculation of cutoff pair potentials, one of the most prevalent computations req...

The graphics processing unit (GPU) has become an integral part of today's mainstream computing systems. Over the past six years, there has been a marked increase in the performance and capabilities of GPUs. The modern GPU is not only a powerful graphics engine but also a highly parallel programmable processor featuring peak arithmetic and memory ba...

Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. State-of-the-art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremendous computationa...

Workstation clusters have become an increasingly popular alternative to traditional parallel supercomputers for many workloads requiring high performance computing. The use of parallel computing for scientific simulations has increased tremendously in the last ten years, and parallel implementations of scientific simulation codes are now in widespr...