A5085416077- Protein Structure and Dynamics
- Enzyme Structure and Function
- Parallel Computing and Optimization Techniques
- Mass Spectrometry Techniques and Applications
- Nanopore and Nanochannel Transport Studies
- Model Reduction and Neural Networks
- Numerical methods for differential equations
- Electromagnetic Simulation and Numerical Methods
- Particle accelerators and beam dynamics
- Scientific Research and Discoveries
- Classical Antiquity Studies
- Advanced NMR Techniques and Applications
- Advanced Data Storage Technologies
- Advanced Chemical Physics Studies
- Distributed and Parallel Computing Systems
- Photosynthetic Processes and Mechanisms
- Machine Learning in Materials Science
- Lipid Membrane Structure and Behavior
- Electrostatics and Colloid Interactions
- SARS-CoV-2 and COVID-19 Research
- Single-cell and spatial transcriptomics
- Metalloenzymes and iron-sulfur proteins
- Spectroscopy and Quantum Chemical Studies
- Electromagnetic Scattering and Analysis
- Supercapacitor Materials and Fabrication
University of Birmingham
2023-2024
University of Illinois Urbana-Champaign
2010-2023
Missouri University of Science and Technology
1995
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,...
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...
Incorporating the influence of induced polarization in large-scale atomistic molecular dynamics (MD) simulations is a critical challenge progress toward computations increased accuracy. One computationally efficient treatment based on classical Drude oscillator which an auxiliary charged particle attached by spring to each nucleus. Here, we report first implementation this model program NAMD. An extended Lagrangian with dual-Langevin thermostat scheme applied Drude−nucleus pairs employed...
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...
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...
Abstract Presented in the context of classical molecular mechanics and dynamics are multilevel summation methods for fast calculation energies/forces pairwise interactions, which based on hierarchical interpolation interaction potentials multiple grids. The concepts details underlying multigrid described. For integration use different time steps interactions allows longer many this can be combined with grids space. Comparison is made to multipole method, evidence presented suggesting that...
The advent of systems biology requires the simulation ever-larger biomolecular systems, demanding a commensurate growth in computational power. This paper examines use NVIDIA Tesla C870 graphics card programmed through CUDA toolkit to accelerate calculation cutoff pair potentials, one most prevalent computations required by many different molecular modeling applications. We present algorithms calculate electrostatic potential maps for potentials. Whereas straightforward approach decomposing...
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 ubiquitous particle–mesh Ewald (PME) method, offering better scaling on parallel computers permitting more modeling flexibility, with support periodic systems as does PME but also semiperiodic nonperiodic systems. version available simulation...
Harnessing the power of graphics processing units (GPUs) to accelerate molecular dynamics (MD) simulations in context free-energy calculations has been a longstanding effort toward development versatile, high-performance MD engines. We report new GPU-based implementation NAMD perturbation (FEP), one oldest, most popular importance-sampling approaches for determination differences that underlie alchemical transformations. Compared CPU available since 2001 NAMD, our benchmarks indicate FEP...
NAMD (NAnoscale Molecular Dynamics) is a parallel molecular dynamics application that has been used to make breakthroughs in understanding the structure and of large biomolecular complexes, such as viruses like HIV various types influenza. State-of-the-art simulations often require integration billions timesteps, computing all interatomic forces for each femtosecond timestep. simulation systems long-timescale biological phenomena requires tremendous power. harnesses power thousands...
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 generates coherent thermodynamic properties trajectories for analysis. To validate highlight its capabilities, hybrid Monte Carlo/molecular dynamics (MC/MD) simulations are performed SPC/E water in isobaric-isothermal (NPT) grand canonical (GC) ensembles as well with Gibbs ensemble Carlo (GEMC). The MC/MD approach...
One of the most fruitful ways to analyze effects discretization error in numerical solution a system differential equations is examine "modified equations," which are that exactly satisfied by (approximate) discrete solution. These do not actually exist general but rather defined an asymptotic expansion powers parameter. Nonetheless, if suitably truncated, resulting modified have remarkably close In case Hamiltonian ordinary equations, also and only integrator symplectic. Evidence for...
The visualization of molecular orbitals (MOs) is important for analyzing the results quantum chemistry simulations. functions describing MOs are computed on a three-dimensional lattice, and resulting data can then be used plotting isocontours or isosurfaces as well other types analyses. Existing software packages that render perform calculations CPU require runtimes tens to hundreds seconds depending complexity system.
Oseltamivir (Tamiflu) is currently the frontline antiviral drug employed to fight flu virus in infected individuals by inhibiting neuraminidase, a protein responsible for release of newly synthesized virions. However, oseltamivir resistance has become critical problem due rapid mutation virus. Unfortunately, how mutations actually confer not well understood. In this study, we employ molecular dynamics (MD) and steered (SMD) simulations, as graphics processing unit (GPU)-accelerated...
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...
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 ob-scure our understanding transmission. demonstrate how integrated data-driven platform...
The E. coli Paraquat Inducible (Pqi) Pathway is a putative Gram-negative phospholipid transport system. pathway comprises three components: an integral inner membrane protein (PqiA), periplasmic spanning MCE family (PqiB) and outer lipoprotein (PqiC). Interactions between all complex components, including stoichiometry, remain uncharacterised; nevertheless, once assembled into their quaternary complex, the trio of Pqi proteins are anticipated to provide continuous channel membranes diderms....