Error Analysis of Coarse-grained Kinetic Monte Carlo Method

System Level Numerical Analysis of a Monte Carlo Simulation of the E. Coli Chemotaxis

Over the past few years it has been demonstrated that “coarse timesteppers” establish a link between traditional numerical analysis and microscopic/ stochastic simulation. The underlying assumption of the associated “lift-run-restrict-estimate” procedure is that macroscopic models exist and close in terms of a few governing moments of microscopically evolving distributions, but they are unavail...

Coarse-Grained Kinetic Monte Carlo Simulation of Copper Electrodeposition with Additives

A (2+1)D kinetic Monte Carlo (KMC) code was developed for coarse-grained as well as atomic-scale simulations that require detailed consideration of complex surface-reaction mechanisms associated with electrodeposition of copper in the presence of additives. The physical system chosen for simulation is similar to that used by the microelectronics industry to fabricate on-chip interconnects, wher...

Kinetic Monte Carlo Simulation of Statistical Mechanical Models and Coarse-Grained Mesoscale Descriptions of Catalytic Reactionâ•fiDiffusion Processes: 1D Nanoporous and 2D Surface Systems

Kinetic Monte Carlo method applied to nucleic acid hairpin folding.

Kinetic Monte Carlo on coarse-grained systems, such as nucleic acid secondary structure, is advantageous for being able to access behavior at long time scales, even minutes or hours. Transition rates between coarse-grained states depend upon intermediate barriers, which are not directly simulated. We propose an Arrhenius rate model and an intermediate energy model that incorporates the effects ...

Coarse-grained stochastic processes and Monte Carlo simulations in lattice systems

In this paper we present a new class of coarse-grained stochastic processes and Monte Carlo simulations, derived directly from microscopic lattice systems and describing mesoscopic length scales. As our primary example, we mainly focus on a microscopic spin-flip model for the adsorption and desorption of molecules between a surface adjacent to a gas phase, although a similar analysis carries ov...