The program EON2 is a distributed implementation of the adaptive kinetic Monte Carlo method for long time scale simulations of tomistic systems. The method is based on the transition state theory approach within the harmonic approximation and the key step s the identification of relevant saddle points on the potential energy rim surrounding the energy minimum corresponding to a state f the syst...

We present a variational method for the segmentation of piecewise affine flow fields. Compared to other approaches to motion segmentation, we minimize a single energy functional both with respect to the affine motion models in the separate regions and with respect to the shape of the separating contour. In the manner of region competition, the evolution of the segmenting contour is driven by a ...

The system-level dynamics of multivalent biomolecular interactions can be simulated using a rule-based kinetic Monte Carlo method in which a rejection sampling strategy is used to generate reaction events. This method becomes inefficient when simulating aggregation processes with large biomolecular complexes. Here, we present a rejectionfree method for determining the kinetics of multivalent bi...

We develop a hierarchy of approximations to the master equation for systems that exhibit translational invariance and finite-range spatial correlation. Each approximation within the hierarchy is a set of ordinary differential equations that considers spatial correlations of varying lattice distance; the assumption is that the full system will have finite spatial correlations and thus the behavi...

The idea of acoustic activation of surface diffusion is explored theoretically and in atomistic simulations. It is found that a substantial diffusion enhancement by surface acoustic waves is possible via (1) transient surface straininduced modification of the diffusion barriers, (2) adiabatic variation in the surface temperature, and (3) dynamic coupling of the acoustic waves with vibrational s...

We propose a method for efficiently coupling the finite element method with atomistic simulations, while using molecular dynamics or kinetic Monte Carlo techniques. Our method can dynamically build an optimized unstructured mesh that follows the geometry defined by atomistic data. On this mesh, different multiphysics problems can be solved to obtain distributions of physical quantities of inter...

We investigate the diffusion of particles on heterogeneous lattices with two kinds of nonequivalent sites. General analytical expressions for the chemical and jump diffusion coefficients have been derived in the case of strong inhomogeneity. We have calculated coverage dependencies of the diffusion coefficients and other necessary thermodynamic quantities for some representative values of the l...

We revisit recent derivations of kinetic equations based on Tsallis' entropy concept. The method of kinetic functions is introduced as a standard tool for extensions of classical kinetic equations in the framework of Tsallis' statistical mechanics. Our analysis of the Boltzmann equation demonstrates a remarkable relation between thermodynamics and kinetics caused by the deformation of macroscop...

Is it possible to solve Boltzmann-type kinetic equations using only a small number of particle velocities? We introduce a technique of solving kinetic equations with a (arbitrarily) large number of particle velocities using only a lattice Boltzmann method on standard, low-symmetry lattices. The renormalized kinetic equation is validated with an exact solution of the planar Couette flow at moder...