A dynamic coupling model for hybrid atomistic-continuum computations

A dynamic coupling model is developed for a hybrid atomistic-continuum computation in micro- and nano-fluidics. In the hybrid atomistic-continuum computation, a molecular dynamics (MD) simulation is utilized in one region where the continuum assumption breaks down and the Navier-Stokes (NS) equations are used in another region where the continuum assumption holds. In the overlapping part of these two regions, a constrained particle dynamics is needed to couple the MD simulation and the NS equations. The currently existing coupling models for the constrained particle dynamics have a coupling parameter, which has to be empirically determined. In the present work, a novel dynamic coupling model is introduced where the coupling parameter can be calculated as the computation progresses rather than inputing a priori. The dynamic coupling model is based on the momentum constraint and exhibits a correct relaxation rate. The results from the hybrid simulation on the Couette flow and the Stokes flow are in good agreement with the data from the full MD simulation and the solutions of the NS equations, respectively. (c) 2007 Elsevier Ltd. All rights reserved.

Atomistic investigation of the effects of temperature and surface roughness on diffusion bonding between Cu and Al

Molecular dynamics (MD) simulations are carried out to analyze the diffusion bonding at Cu/Al interfaces. The results indicate that the thickness of the interfacial layer is temperature-dependent, with higher temperatures yielding larger thicknesses. At temperatures below 750 K, the interface thickness is found to increase in a stepwise manner as a function of time. At temperatures above 750 K, the thickness increases rapidly and smoothly. When surface roughness is present, the bonding process consists of three stages. In the first stage, surfaces deform under stress, resulting in increased contact areas. The second stage involves significant plastic deformation at the interface as temperature increases, resulting in the disappearance of interstices and full contact of the surface pair. The last stage entails the diffusion of atoms under constant temperature. The bonded specimens show tensile strengths reaching 88% of the ideal Cu/Al contact strength. (c) 2007 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: Molecular dynamics simulation

Molecular dynamics (MD) simulations are performed to study the interaction of His-tagged peptide with three different metal surfaces in explicit water. The equilibrium properties are analyzed by using pair correlation functions (PCF) to give an insight into the behavior of the peptide adsorption to metal surfaces in water solvent. The intermolecular interactions between peptide residues and the metal surfaces are evaluated. By pulling the peptide away from the peptide in the presence of solvent water, peeling forces are obtained and reveal the binding strength of peptide adsorption on nickel, copper and gold. From the analysis of the dynamics properties of the peptide interaction with the metal surfaces, it is shown that the affinity of peptide to Ni surface is the strongest, while on Cu and An the affinity is a little weaker. In MD simulations including metals, the His-tagged region interacts with the substrate to an extent greater than the other regions. The work presented here reveals various interactions between His-tagged peptide and Ni/Cu/Au surfaces. The interesting affinities and dynamical properties of the peptide are also derived. The results give predictions for the structure of His-tagged peptide adsorbing on three different metal surfaces and show the different affinities between them, which assist the understanding of how peptides behave on metal surfaces and of how designers select amino sequences in molecule devices design. (c) 2007 Elsevier Ltd. All rights reserved.