We present a detailed study of a new, optimized coarse-grained (CG) model of polystyrene (PS) and compare it with a recently published one (Harmandaris et al., Macromolecules 2006, 39, 6708). By implementing a different mapping scheme, the new model, augmented with softer nonbonded interactions, better reproduces the local chain conformations and melt packing observed in atomistic simulations o...

We present an atomistic tight-binding approach to calculating the electronic structure of semiconductor nanostructures. We start by deriving the strain distribution in the structure using the valence force field model. The strain field is incorporated into the tight-binding electronic structure calculation carried out in the frame of the effective bond orbital model and the fully atomistic sp3d...

Epitaxy is the growth of a thin film by attachment to an existing substrate in which the crystalline properties of the film are determined by those of the substrate. In heteroepitaxy, the substrate and film are of different materials, and the resulting mismatch between lattice constants can introduce stress into the system. We have developed an island dynamics model for epitaxial growth that is...

The energy barrier for the cross slip of screw dislocations in face-centered cubic (FCC) nickel as a function of multiple stress components is predicted by both continuum line tension and discrete atomistic models. Contrary to Escaig's claim that the Schmid stress component has a negligible effect on the energy barrier, we find that the line tension model, when solved numerically, predicts comp...

We present an adaptive mesh and algorithmic refinement (AMAR) scheme for modeling multi-scale hydrodynamics. The AMAR approach extends standard conservative adaptive mesh refinement (AMR) algorithms by providing a robust flux-based method for coupling an atomistic fluid representation to a continuum model. The atomistic model is applied locally in regions where the continuum description is inva...

We propose that sharp stability estimates are essential for evaluating the predictive capability of atomistic-to-continuum coupling methods up to the limit load for atomistic instabilities such as fracture, dislocation movement, or crack tip propagation. Using rigorous analysis, asymptotic methods, and numerical experiments, we obtain such sharp stability estimates for the basic conservative qu...

A numerical method that combines molecular dynamics simulation and finite element analysis to simulate the mechanical behaviors of materials and structures at nano-scale is proposed. In this combined method, the initial atomistic model is transformed to continuum model, and an approximate solution is first obtained with the finite element method for the system under the specified boundary condi...

Many biologically interesting phenomena occur on a time scale that is too long to be studied by atomistic simulations. These phenomena include the dynamics of large proteins and self-assembly of biological materials. Coarse-grained (CG) molecular modeling allows computer simulations to be run on length and time scales that are 2-3 orders of magnitude larger compared to atomistic simulations, pr...