a. Mathematical upscaling: derivation of coarse-scale equations directly from atomistic equations using Generalized Mathematical Homogenization theory (Fish, Chen, Li, 2007). b. Computational upscaling: reducing the complexity of solving an atomistic problem to a manageable size that can be adapted based on available computational resources. Our model reduction approach is based on the space-ti...

The optical properties of metallic nanoparticles with nanometre dimensions exhibit features that cannot be described by classical electrodynamics. In this quantum size regime, the near-field properties are significantly modified and depend strongly on the geometric arrangements. However, simulating realistically sized systems while retaining the atomistic description remains computationally int...

A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation l...

We report studies of the mechanical properties of tropocollagen molecules under different types of mechanical loading including tension, compression, shear, and bending. Our modeling yields predictions of the fracture strength of single tropocollagen molecules and polypeptides, and also allows for quantification of the interactions between tropocollagen molecules. Atomistic modeling predicts a ...

We develop coarse-grained force fields for poly (vinyl alcohol) and poly (acrylic acid) oligomers. In both cases, one monomer is mapped onto a coarsegrained bead. The new force fields are designed to match structural properties such as radial distribution functions of various kinds derived by atomistic simulations of these polymers. The mapping is therefore constructed in a way to take into acc...

The modeling of processes involving multiple length scales is an area of pressing concern, especially in problems such as nanoidentation and crack tip dislocation activity. In these cases, there is more than one characteristic dimension with the nanometer scale arising due to the presence of extended defects such as dislocations and a second length scale at least 2 orders of magnitude larger se...

We carry out an error analysis for the heterogeneous multi-scale method for the case when the macroscale process is that of gas dynamics or more generally nonlinear conservation laws and the microscale process is an atomistic model such as kinetic Monte Carlo methods or molecular dynamics (MD). We will consider problems of type B as defined in [4], i.e. the macroscale constitutive relations are...

We investigate solidification in tantalum and uranium systems ranging in size from 64,000 to 524,288,000 atoms on the IBM BlueGene/L computer at LLNL. Using the newly developed ddcMD code, we achieve performance rates as high as 103 TFlops, with a performance of 101.7 TFlop sustained over a 7 hour run on 131,072 cpus. We demonstrate superb strong and weak scaling. Our calculations are significa...