Sentences with phrase «molecular dynamics»

BCR covers such topics as molecular dynamics, genomics, proteomics, physics - based simulation, systems biology, and other research involving computational biology.

Designed and implemented molecular dynamics simulations to identify protein - DNA interaction and macro - molecular structure.

Your point that teh molecular dynamics of CO2 impact the climate are unconvincing.

Ernest: My scientific training usually prompts me to think at the molecular level; molecular dynamics rather than thermodynamics.

The simplicity I am referring to here is «emergent», roughly analogous to that of a macroscopic equation of state that emerges, in the thermodynamic limit, from exceedingly complex molecular dynamics.

Look the thermodynamics / molecular dynamics of gravitational collapse isn't really computationally all that difficult.

«Using our first - principles molecular dynamics model and molecular dynamic simulations, we were able to simulate how carbonic acid is solvated by water,» Prendergast says.

They even conducted real - time molecular dynamics simulations to study how these interactions varied over time, revealing new ways to make molecules more selective toward a specific WNK enzyme.

Its successor machines (GRAPE - DR / GRAPE -9) are still in use at the NAOJ for computer simulations and opened the way for the development of the MD - GRAPE, a specialized computer for molecular dynamics simulations to calculate intermolecular forces.

Atomistic and coarse - grained models — ranging from classical molecular dynamics to quantum mechanics and the hierarchy of models in between — have provided unprecedented levels of insight into a wide range of chemical, biological, and soft matter and solid - state phenomena.

That was unexpected, says Douglas Galvão, a professor at the University of Campinas who studies nanostructures through molecular dynamics simulations.

Using molecular dynamics simulations, the researchers calculated 24,400 independent configurations of neutral, gas - phase gold clusters containing 5 to 14 atoms at temperatures from -173 to 541 °C (100 to 814K).

Another roll of the dice gave me the opportunity to also work in cancer research, looking into underlying molecular dynamics of prostate cancer.

Uberuaga has had three outstanding scientific achievements over the past 10 years: accelerated molecular dynamics method development, amorphization resistance of complex oxides, and the discovery of a new mechanism for point defect recovery at interfaces.

His 15 - page chapter shows how these insights were obtained using dispersion - corrected density functional theory and ab initio molecular dynamics.

The theorists described the proton movement using complex calculations, including density functional theory and molecular dynamics simulations.

By combining first - principles molecular dynamics simulations with state - of - the - art electronic structure methods, the team could predict the excitation energies of the solvents and solutes, such as the ionization potentials of the solvated ions.

Recently developed, in - situ techniques for direct volume determination, acoustic wave velocity measurements, and x-ray diffraction at HPCAT, along with molecular dynamics simulations, were employed to explore the nature of the unusual and pressure - tunable, compression and elastic properties.

In a new study published in EPJ E, physicists have developed an algorithm to simulate the molecular dynamics of these patchy particles.

Required capabilities include kinetic turbulence simulations, related three - dimensional fluid simulations with gyro - Landau kinetic extensions, large - scale molecular dynamics simulations of materials, and couplings of lower - dimensional models (for fast analyses) to simulate interactions between zones and particle species.

They also used molecular dynamics simulations and cryo - SEM during the lyophilization process to shed light on the scrolling behaviour.

The theoreticians used molecular dynamics and dispersion - corrected density functional theory, powerful calculations and simulations that explained the results obtained in the experiments.

She'd been considering medical school, with an aim to design medical devices, but during the application process she found her way into a lab doing molecular dynamics.

Molecular dynamics simulations show that a preferential binding of PSS one side of the graphene oxide nanosheets gives rise to the curvature of the nanosheet during scroll formation, in part from the hydrophilic nature of the PSS layer.

Pacific Northwest National Laboratory scientists Dr. Sebastien Kerisit and Dr. Chongxuan Liu used molecular dynamics techniques and EMSL's Chinook supercomputer to calculate diffusion trajectories of uranium - containing species based on a set of equations describing the way atoms interact.

Here, I discuss a novel computational approach for the detection of allostery in protein complexes by way of molecular dynamics simulation and advanced data reduction protocols.

These models are called classic molecular dynamics simulations with a polarizable force field.

Many of these can be obtained directly from experiments or ab initio molecular dynamics simulations in collaboration with HydroGen partners.

Molecular dynamics (MD) simulation is a powerful computational tool in structural biology, widely used for understanding conformational changes in proteins, and folding of peptides.

One possible solution, which our team has recently demonstrated for III - V photoelectrodes, is to model speciation of interfacial reaction products by coupling ambient - pressure X-ray photoelectron spectroscopy (XPS) experiments to direct simulations of XPS based on model interfaces from ab initio molecular dynamics.

My aim is to collect quantitative data about cellular processes in real time through observation and perturbation of molecular dynamics on the nanoscale in living cells.

Using large - scale molecular dynamics simulations on NaCl solutions at the National Energy Research Scientific Computing Center, the team determined the fluctuations in the charges, electric potentials and fields.

A comparison of results obtained with both methods shows that a simple two - dimensional linear - elasticity model is able to reproduce quantitatively the low - frequency part of the band structure obtained from computationally much more demanding molecular dynamics simulations of a three - dimensional atomistic model.

Within classical simulations, two main set of methodologies are used: molecular dynamics (MD) and Monte Carlo (MC).

Beyond Carpenter and Ingolfsson, the team that produced the Biophysical Journal cover story included computer scientists Harsh Bhatia and Peer - Timo Bremer and computational chemist Felice Lightstone, all of LLNL; and Siewert - Jan Marrink, a professor of molecular dynamics at the University of Groningen in The Netherlands.

For this, we discuss how we couple useful transport properties from molecular dynamics and ab initio calculations.

Supported by National Institutes of Health grants, researchers at Oak Ridge National Laboratory (ORNL), the University of Tennessee (UT), and the UT — ORNL Joint Institute for Computational Sciences (JICS) discovered a molecular «switch» in a receptor that controls cell behavior using detailed molecular dynamics simulations on a computer called Anton built by D. E. Shaw Research in New York City.

«We're not biologists, and we're not astronomers, but we had the right tools,» Paulette Clancy, a chemical molecular dynamics expert, who led the study, said, according to a statement released by Cornell University, adding: «Perhaps it helped, because we didn't come in with any preconceptions about what should be in a membrane and what shouldn't.

They used molecular dynamics simulations to compare radiation damage accumulation in two ceramics and determined three requirements for the ideal radiation - tolerant ceramic:

The simulations were density - functional theory - based molecular dynamics simulations run on a powerful computing system known as NWIce at EMSL.

Atomic force - multi-optical imaging integrated microscope for monitoring molecular dynamics in live cells.

In situ atomic force microscopy studies and molecular dynamics simulations were supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Biomolecular Materials Program at PNNL.

Indeed, the data collection already includes microED, lattice light - sheet microscopy and molecular dynamics datasets.

To better understand the nanomembranes, the team simulated how single peptoid molecules interacted with each other using molecular dynamics software.

In the paper, titled «Molecular Mechanisms of Hydrogen - Loaded β - Hydroquinone Clathrate,» the authors employed molecular dynamics simulation techniques and analyses to show how to load four hydrogen atoms inside a β - hydroquinone clathrate.

Molecular dynamics simulations of the solvation water around biomolecules shows a retardation of the H - bond dynamics for hydrophilic as well as hydrophobic protein surface areas.

Through first - principle molecular dynamics simulations and accurate energy computations, Yakobson and his colleagues determined that salt reduces the temperature at which some elements interact in a chemical vapor deposition (CVD) furnace.

an open source library for free energy calculations in molecular systems that works with some of the most popular molecular dynamics engines.

Toward the rational design of RO membranes, we performed contrast - variation neutron scattering measurements and atomistic molecular dynamics (MD) simulations on polyamide / water systems with various water contents and deuteration ratios.

Molecular dynamics and density functional theory will be employed to catalog the binding energy of adsorption of a host of organic compounds as identified by Project 1.1, onto mineral grains.