A5048680880- Protein Structure and Dynamics
- Parallel Computing and Optimization Techniques
- Distributed and Parallel Computing Systems
- Advanced Data Storage Technologies
- Enzyme Structure and Function
- Computer Graphics and Visualization Techniques
- Advanced Electron Microscopy Techniques and Applications
- Bacteriophages and microbial interactions
- Advanced Fluorescence Microscopy Techniques
- Scientific Computing and Data Management
- Data Visualization and Analytics
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Photosynthetic Processes and Mechanisms
- Gene Regulatory Network Analysis
- Mass Spectrometry Techniques and Applications
- Nanopore and Nanochannel Transport Studies
- Advanced Vision and Imaging
- Photoreceptor and optogenetics research
- Bioinformatics and Genomic Networks
- Lipid Membrane Structure and Behavior
- Spectroscopy and Quantum Chemical Studies
- Evolutionary Algorithms and Applications
- Theoretical and Computational Physics
- SARS-CoV-2 and COVID-19 Research
Nvidia (United States)
2022-2024
University of Illinois Urbana-Champaign
2014-2023
University of Delaware
2022
Institute of Technology of Cambodia
2022
University of Basel
2022
Swisscom (Switzerland)
2022
CSCS - Swiss National Supercomputing Centre
2022
Sandia National Laboratories
2022
Helmholtz-Zentrum Dresden-Rossendorf
2022
Urbana University
2014-2021
NAMDis a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance petascale parallel supercomputers consisting hundreds thousands cores, as well inexpensive commodity clusters commonly found in academic environments. It is written C++ leans Charm++ optimal low-latency versatile, multipurpose code that gathers state-of-the-art algorithms to carry out apt thermodynamic ensembles,...
We provide an overview of the key architectural features recent microprocessor designs and describe programming model abstractions provided by OpenCL, a new parallel standard targeting these architectures.
The graphics processing unit (GPU) has become an integral part of today's mainstream computing systems. Over the past six years, there been a marked increase in performance and capabilities GPUs. modern GPU is not only powerful engine but also highly parallel programmable processor featuring peak arithmetic memory bandwidth that substantially outpaces its CPU counterpart. GPU's rapid both programmability capability spawned research community successfully mapped broad range computationally...
Abstract Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such are limited in size and timescale by available computing resources. State‐of‐the‐art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, tremendous resource that now be utilized for general purpose as result recent advances GPU hardware software architecture. In this article, an overview programmable GPUs is...
Abstract The proper functioning of biomolecules in living cells requires them to assume particular structures and undergo conformational changes. Both biomolecular structure motion can be studied using a wide variety techniques, but none offers the level detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling programs, namely NAMD VMD, we have created robust, user-friendly software, QwikMD, which enables novices experts alike address biomedically relevant...
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. use this investigate mechanisms infectivity SARS-CoV-2 spike protein, main viral infection machinery. Our enables more efficient investigation in variety complex environments, including within complete envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. present several novel scientific...
Large-scale GPU clusters are gaining popularity in the scientific computing community. However, their deployment and production use associated with a number of new challenges. In this paper, we present our efforts to address some challenges building running HPC environments. We touch upon such issues as balanced cluster architecture, resource sharing environment, programming models, applications for clusters.
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 an introductory tutorial. We present several step-by-step examples of some VMD's most popular features, including visualizing molecules in three dimensions with different drawing coloring methods, rendering publication-quality figures, animating analyzing the trajectory dynamics simulation,...
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 rely on programmers explicitly manage data transfers between the CPU system memory accelerator memory. This paper presents a new model computing, called Asymmetric Distributed Shared Memory (ADSM), that maintains shared logical space access objects in physical but not vice...
Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against series progressively higher resolutions, which ends original experimental resolution. Application sequential re-refinement enables to achieve radius...
Abstract Spatial stochastic simulation is a valuable technique for studying reactions in biological systems. With the availability of high‐performance computing (HPC), method poised to allow integration data from structural, single‐molecule and biochemical studies into coherent computational models cells. Here, we introduce Lattice Microbes software package simulating such cell on HPC The performs either well‐stirred or spatially resolved simulations with approximated cytoplasmic crowding...
Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their and describe topology. These introduce incompatibilities between engines, previously published software bridges the gaps many popular MD packages, such as CHARMM AMBER or GROMACS LAMMPS. While there are structure building tools available generate topologies structures in format, only recently have mechanisms been developed to convert results into...
We seek to completely revise current models of airborne transmission respiratory viruses by providing never-before-seen atomic-level views the SARS-CoV-2 virus within a aerosol. Our work dramatically extends capabilities multiscale computational microscopy address significant gaps that exist in experimental methods, which are limited their ability interrogate aerosols at atomic/molecular level and thus obscure our understanding transmission. demonstrate how integrated data-driven platform...
Modeling and simulation of small molecules such as drugs biological cofactors have been both a major focus computational chemistry for decades growing need among biophysicists who seek to investigate the interaction different types ligands with biomolecules. Of particular interest in this regard are quantum mechanical (QM) calculations that used more accurately describe molecules, which can be heterogeneous structures chemistry, either purely QM or hybrid QM/molecular mechanics (MM)...
Article A system for interactive molecular dynamics simulation Share on Authors: John E. Stone Beckman Institute, Urbana, IL ILView Profile , Justin Gullingsrud Univ. of Illinois, Urbana UrbanaView Klaus Schulten Authors Info & Claims I3D '01: Proceedings the 2001 symposium Interactive 3D graphicsMarch Pages 191–194https://doi.org/10.1145/364338.364398Online:01 March 2001Publication History 93citation1,545DownloadsMetricsTotal Citations93Total Downloads1,545Last 12 Months53Last 6 weeks6 Get...
Graphics processing units (GPUs) have become an attractive option for accelerating scientific computations as a result of advances in the performance and flexibility GPU hardware, due to availability software development tools targeting general purpose computation. However, effective use GPUs clusters presents number application system integration challenges. We describe strategies decomposition scheduling computation among CPU cores GPUs, techniques overlapping communication with kernel...
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 rely on programmers explicitly manage data transfers between the CPU system memory accelerator memory.