EON: software for long time simulations of atomic scale systems

EON: software for long time simulations of atomic scale systems

The EON software is designed for simulations of the state-to-state evolution of atomic scale systems over timescales greatly exceeding that of direct classical dynamics. States are defined as collections of atomic configurations from which a minimization of the potential energy gives the same inherent structure. The time evolution is assumed to be governed by rare events, where transitions betw...

A partition-based algorithm for clustering large-scale software systems

Clustering techniques are used to extract the structure of software for understanding, maintaining, and refactoring. In the literature, most of the proposed approaches for software clustering are divided into hierarchical algorithms and search-based techniques. In the former, clustering is a process of merging (splitting) similar (non-similar) clusters. These techniques suffered from the drawba...

Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations

The integration of atomic-resolution experimental and computational methods offers the potential for elucidating key aspects of protein folding that are not revealed by either approach alone. Here, we combine equilibrium NMR measurements of thermal unfolding and long molecular dynamics simulations to investigate the folding of gpW, a protein with two-state-like, fast folding dynamics and cooper...

Simulations of atomic-scale sliding friction.

Long Time Scale Simulations of Al(100) Crystal Growth

We have carried out simulations of Al(100) crystal growth using a combination of classical dynamics simulations and a new long time scale simulation method based on harmonic transition state theory. Atoms are deposited using classical dynamics over a time interval of a few picoseconds, but once the system has thermalized, the long time interval in between deposition events, a millisecond, is si...