Papers – Page 969 – TechConnect Briefs

Kinetic Monte Carol Simulations of Protein Folding and Unfolding

Makarov D.E., Metiu H., U.C. Santa Barbara, US

We report here kinetic Monte Carlo (KMC) studies of two problems: (1) Unfolding of the protein titin under mechanical tension and (2) The formation of native contacts in the process of folding of small, single [...]

Monte Carlo Modeling of Thin Film Deposition: Factors that influence 3D islands

Gilmer G., Dalla Torre J., Baumann F.H., Lawrence Livermore National Laboratory, US

In this paper we discuss the use of atomistic Monte Carlo simulations to predict fim microstructure evolution. We discuss physical vapor deposition, and are primarily concerned with films that are formed by the nucleation and [...]

Effects of Steering in Metal Epitaxial Growth

Amar J., Yu J., University of Toledo, US

Recent experiments on metal epitaxial growth indicate that a high-angle of incidence the long-range attraction of the surface to incoming atoms can lead to steering effects near step-edges which significantly modify the growth and contribute [...]

Investigation of the Order Continuum of Quenched Silicon using Accelerated Molecular Dynamics Techniques

Choudhary D., Clancy P., Cornell University, US

The thermodynamic, electronic and structural properties of silicon phases are inextricably linked to the underlying order in the material. While the crystalline and amorphous phases are well characterized, the existence of a glassy silicon phase [...]

Multiscale Simulation of the Thermal Desorption of Large Molecules from Solid Surfaces

Fichthorn K., Miron R.A., Kulkarni A., Pennsylvania State University, US

We use molecular-dynamics simulations and importance sampling to obtain transition-state theory rate constants for thermal desorption of an n-alkane series from Pt(111). These simulations indicate that the binding of a large molecule to a solid [...]

Growth of Copper on Ag(100) at Experimental Deposition Rates Using TAD

Sprague J., Montalenti F., Voter A.F., Naval Research Laboratory, US

The initial stages of growth of (001) Cu films on (001) Ag substrates have been investigated using the temperature accelerated dynamics (TAD) method. The acceleration provided by this method made it possible to simulate the [...]

Accelerated Dynamics Simulations of Nanotubes

Uberuaga B., Stuart S.J., Voter A.F., Los Alamos National Laboratory, US

We report on the application of accelerated dynamics techniques to the study of carbon nanotubes. We have used the parallel replica method and temperature accelerated dynamics simulations are currently in progress. In the parallel replica [...]

Multiscale Detection of Temporal Features in Molecular Dynamics Simulations:Applications to Acceleration Methods

Richie D., Kim J., Wilkins J.W., High Performance Technologies, Inc., US

Extending the time scales accessible through direct molecular dynamics simulations is an area of active research. New acceleration techniques promise to achieve experimentally relevant time scales. A common ingredient in many of these acceleration schemes [...]

Simulations of Dopant Clustering in Silicon: Dimer calculations using DFT forces

Henkelman G., Uberuaga B., Dunham S., University of Washington, US

We have carried out computer simulations to study the formation and break-up of boron clusters in crystalline silicon. Density functional theory was used to evaluate the interatomic interactions and dimer method used to nd the [...]

Accelerating Molecular Dynamics Simulations

Germann T.C., Voter A.F., Los Alamos National Laboratory, US

In contrast with the converging length scales of atomistic simulations and experimental nanoscience, large time scale discrepancies still remain, due to the time-scale limitations of molecular dynamics. We briefly review two recently developed methods, derived [...]