A5087189543- Diamond and Carbon-based Materials Research
- High-pressure geophysics and materials
- Electrostatics and Colloid Interactions
- Laser-induced spectroscopy and plasma
- Spectroscopy and Quantum Chemical Studies
- Atomic and Molecular Physics
- Protein Structure and Dynamics
- Parallel Computing and Optimization Techniques
- Theoretical and Computational Physics
- Nuclear physics research studies
- Metal and Thin Film Mechanics
- Advanced Data Storage Technologies
- Force Microscopy Techniques and Applications
- nanoparticles nucleation surface interactions
- Distributed and Parallel Computing Systems
- Electrochemical Analysis and Applications
- Dust and Plasma Wave Phenomena
- Laser-Plasma Interactions and Diagnostics
- Plasma Diagnostics and Applications
- Energetic Materials and Combustion
- Advanced Chemical Physics Studies
- Boron and Carbon Nanomaterials Research
- Molecular Junctions and Nanostructures
- Computational Drug Discovery Methods
- ECG Monitoring and Analysis
Lawrence Livermore National Laboratory
2013-2024
New Mexico Consortium
2017
Michigan State University
2017
University of California System
1996
IBM Research - Almaden
1992-1995
IBM (United States)
1993
Simon Fraser University
1987-1990
TRIUMF
1988-1989
A first order phase transition is found in liquid carbon using atomistic simulation methods and Brenner's bond potential. The line terminated by a critical point at 8801 K 10.56 GPa triple on the graphite melting 5133 1.88 GPa. change associated with density structural changes. low-density predominantly $\mathrm{sp}$ bonded little ${\mathrm{sp}}^{3}$ character. high-density mostly This nonempirical evidence of liquid-liquid between thermodynamically stable fluids.
Molecular dynamics is used to model the friction between two ordered monolayers of alkane chains six units long bound at their ends rigid substrates. Depending on interfacial interaction strength, energy dissipation occurs by a discontinuous ``plucking'' mechanism and continuous viscous mechanism. The plucking follows simple thermal activation model, while for mechanism, force enhanced rotator transition temperature films.
Significance Here we present an unprecedented multiscale simulation platform that enables modeling, hypothesis generation, and discovery across biologically relevant length time scales to predict mechanisms can be tested experimentally. We demonstrate our predictive simulation-experimental validation loop generates accurate insights into RAS-membrane biology. Evaluating over 100,000 correlated simulations, show RAS–lipid interactions are dynamic evolving, resulting in: 1) a reordering...
We report the computational advances that have enabled first micron-scale simulation of a Kelvin-Helmholtz (KH) instability using molecular dynamics (MD). The are in three key areas for massively parallel computation such as on BlueGene/L (BG/L): fault tolerance, application kernel optimization, and highly efficient I/O. In particular, we developed novel capabilities handling hardware parity errors improving speed interatomic force calculations, while achieving near optimal I/O speeds BG/L,...
Interdependence across time and length scales is common in biology, where atomic interactions can impact larger-scale phenomenon. Such dependence especially true for a well-known cancer signaling pathway, the membrane-bound RAS protein binds an effector called RAF. To capture driving forces that bring RAF (represented as two domains, RBD CRD) together on plasma membrane, simulations with ability to calculate detail while having long large length- are needed. The Multiscale Machine-Learned...
Abstract The oncogene RAS, extensively studied for decades, presents persistent gaps in understanding, hindering the development of effective therapeutic strategies due to a lack precise details on how RAS initiates MAPK signaling with RAF effector proteins at plasma membrane. Recent advances X-ray crystallography, cryo-EM, and super-resolution fluorescence microscopy offer structural spatial insights, yet molecular mechanisms involving protein-protein protein-lipid interactions RAS-mediated...
Although computer simulation has played a central role in the study of nucleation and growth since earliest molecular dynamics simulations almost 50 years ago, confusion surrounding effect finite size on such limited their applicability. Modeling solidification molten tantalum Blue Gene/L computer, we report here first atomistic that verifies independence from finite-size effects during entire process, up to onset coarsening. We show scaling theory explains observed maximal grain sizes for...
A model Hamiltonian is advanced which provides a computationally efficient means of investigating nuclear dynamics. The includes both Coulomb and isospin-dependent terms, incorporates antisymmetrization effects through momentum-dependent potential. Unlike many other classical or semiclassical models, the nuclei this simulation have well-defined ground state with nonvanishing 〈${p}^{2}$〉. It shown that binding energies per nucleon rms radii these states are close to measured values over wide...
The temperature equilibration rate between electrons and protons in dense hydrogen has been calculated with molecular dynamics simulations for temperatures 10 $600\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ densities ${10}^{20}\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}3}\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}{10}^{24}\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}3}$. Careful attention devoted to convergence of the simulations, including role...
We study the problem of electron-ion temperature equilibration in plasmas. consider pure H at various densities and temperatures Ar-doped high enough so that Ar is fully ionized. Two theoretical approaches are used: classical molecular dynamics (MD) with statistical two-body potentials a generalized Lenard-Balescu (GLB) theory capable treating multicomponent weakly coupled The GLB used two modes: (1) quantum dielectric response random-phase approximation (RPA) together Coulomb interaction...
Computational models can define the functional dynamics of complex systems in exceptional detail. However, many modeling studies face seemingly incommensurate requirements: to gain meaningful insights into some phenomena requires with high resolution (microscopic) detail that must nevertheless evolve over large (macroscopic) length- and time-scales. Multiscale has become increasingly important bridge this gap. Executing multiscale on current petascale computers levels parallelism...
Estimates for the displacement of phase equilibrium lines small carbon particles containing from several hundred to tens thousands atoms are made, and an error analysis uncertainties in these estimates is derived evaluated using available experimental data. Hugoniot calculations methane, benzene, polyethylene, polybutene, based on a particle surface energy adjusted equation state, better agreement with shock pressure-volume temperature data than those obtained bulk state. The results suggest...
It has been recently suggested that elemental carbon may be a promising candidate to exhibit liquid-liquid phase transition (LLPT). We report the results of first-principles molecular dynamics simulations showing no evidence LLPT in carbon, same temperature and pressure range where such was found using empirical calculations. Our indicate continuous evolution from primarily $sp$-bonded liquid an $s{p}^{2}$-like $s{p}^{3}$-like fluid, as function pressure, above graphite melting line. The...
Molecular dynamics simulation of 216 water molecules (ST2 model) between charged flat electrodes 2.362 nm apart showed layering with a few at each surface that broke H bonds the bulk and oriented their charges towards electrode. Compared to uncharged electrodes, atomic molecular distributions were unsymmetric. When lithium an iodide ion substituted random for two molecules, contact adsorbed on anode no it The appeared weakly solvated solution side preferred engage in hydrogen bonding network...
We use classical molecular dynamics to investigate electron-ion temperature equilibration in a two-temperature SF6 plasma. choose density of 1.0 x 10;{19}SF_{6} molecules per cm;{3} and initial temperatures T_{e} = 100 eV T_{S} T_{F} 15 eV, accordance with experiments currently underway at Los Alamos National Laboratory. Our computed relaxation time lies between two oft-used variants the Landau-Spitzer formula which invoke static screening. Discrepancies are also found when comparing...
AbstractWe have developed the capability to rapidly simulate cardiac electrophysiological phenomena in a human heart discretised at resolution comparable with length of myocyte. Previous scientific investigation has generally invoked simplified geometries or coarse-resolution hearts, simulation duration limited 10s heartbeats. Using state-of-the-art high-performance computing techniques coupled one most powerful computers available (the 20 PFlop/s IBM BlueGene/Q Lawrence Livermore National...
Constant temperature molecular dynamics has been used to simulate the adsorption of hydrated halide ions X−=F−, Cl−, Br− and I−, lithium ion Li+ on flat uniformly charged surfaces. The simulations were done with either 214 water molecules two (Li+ X−) in a box 2.362 nm deep or 430 4.320 deep. boxes periodically replicated xy directions. magnitude surface charge ends was ±0.11 e/(nm)2, corresponding an electric field 2×107 V/cm. lateral dimensions simulation cell 1.862 nm×1.862 (x×y) each...
A semiclassical model developed for the computer simulation of nuclear reactions is applied to problem fragmentation in proton and heavy ion induced reactions. Simulations based on are used follow time evolution both coordinate phase space as well calculate correlations quantities such fragment positions masses. Three selected detailed study: p+Ag at 300 MeV, Ca+Ca 25 50 MeV/nucleon bombarding energy. It shown that behavior expected these from mechanical instability properties matter...