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We present a fast Monte-Carlo algorithm for simulating epitaxial surface growth, based on the continuous-time Monte-Carlo algorithm of Bortz, Kalos and Lebowitz. When simulating realistic growth regimes, much computational time is consumed…
We present a lattice Monte Carlo algorithm based on the one originally proposed by Maggs and Rossetto for simulating electrostatic interactions in inhomogeneous dielectric media. The original algorithm is known to produce attractive…
An extension of the synchronous parallel kinetic Monte Carlo (pkMC) algorithm developed by Martinez {\it et al} [{\it J.\ Comp.\ Phys.} {\bf 227} (2008) 3804] to discrete lattices is presented. The method solves the master equation…
Lattice simulations are an important class of problems in crystalline solids, surface science, alloys, adsorption, absorption, separation, catalysis, to name a few. We describe a fast computational method for performing lattice…
The kinetic Monte Carlo method is a standard approach for simulating physical systems whose dynamics are stochastic or that evolve in a probabilistic manner. Here we show how to calculate the system time for such simulations.
In this work, we develop an atomistic, graph-based kinetic Monte Carlo (KMC) simulation routine to predict crystal morphology. Within this routine, we encode the state of the supercell in a binary occupation vector and the topology of the…
Accurately and efficiently estimating system performance under uncertainty is paramount in power system planning and operation. Monte Carlo simulation is often used for this purpose, but convergence may be slow, especially when detailed…
A high-fidelity kinetic Monte Carlo (KMC) simulation method (T. Treeratanaphitak, M. Pritzker, N. M. Abukhdeir, Electrochim. Acta 121 (2014) 407--414) using the semi-empirical multi-body embedded-atom method (EAM) potential has been…
Kinetic Monte-Carlo simulation is applied to study the partial oxidation of methane over a nickel catalyst. Based on the Langmuir-Hinshelwood mechanism, the kinetic behavior of this reaction is analyzed and the results are compared with…
In lattice quantum field theory studies, parameters defining the lattice theory must be tuned toward criticality to access continuum physics. Commonly used Markov chain Monte Carlo (MCMC) methods suffer from critical slowing down in this…
We review the application of lattice QCD techniques, most notably the Hybrid Monte-Carlo (HMC) simulations, to first-principle study of tight-binding models of crystalline solids with strong inter-electron interactions. After providing a…
The effect of different move sets on the folding kinetics of the Monte Carlo simulations is analysed based on the conformation-network and the temperature-dependent folding kinetics. A new scheme of implementing Metropolis algorithm is…
A new Markov Chain Monte Carlo method for simulating the dynamics of molecular systems characterized by hard-core interactions is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is…
We present a cross-language C++/Python program for simulations of quantum mechanical systems with the use of Quantum Monte Carlo (QMC) methods. We describe a system for which to apply QMC, the algorithms of variational Monte Carlo and…
We simulate the sintering of particle aggregates due to surface diffusion. As a method we use Kinetic Monte-Carlo simulations in which elasticity can explicitly be taken into account. Therefore it is possible to investigate the shape…
An efficient method for the simulation of strained heteroepitaxial growth with intermixing using kinetic Monte Carlo is presented. The model used is based on a solid-on-solid bond counting formulation in which elastic effects are…
The speed, bandwidth and cost characteristics of today's PC graphics cards make them an attractive target as general purpose computational platforms. High performance can be achieved also for lattice simulations but the actual…
This is an introductory article about Markov Chain Monte Carlo (MCMC) simulation for pedestrians. Actual simulation codes are provided, and necessary practical details, which are skipped in most textbooks, are shown. The second half is…
We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on the FCC lattice which takes explicitly into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer…
While boundary plasmas in present-day tokamaks generally fall in a fluid regime, neutral species near the boundary often require kinetic models due to long mean-free-paths compared to characteristic spatial scales in the region. Monte-Carlo…