We have carried out long time scale simulations where the \dimer method" [G. Henkelman and H. J onsson, J. Chem. Phys. 111, 7010 (1999)] is used to nd the mechanism and estimate the rate of transitions within harmonic transition state theory and time is evolved by using the kinetic Monte Carlo method. Unlike traditional applications of kinetic Monte Carlo, the atoms are not assigned to lattice ...

We investigate the formation of misfit dislocations in strained heteroepitaxial crystal growth and their influence on the structure of the growing layers. We use Kinetic Monte Carlo simulations for an off-lattice model in 1+1 dimensions with Lennard-Jones interactions. Two different types of the formation of dislocations are found, depending on the sign and the magnitude of the misfit. Misfit d...

We explore aspects of the community structures generated by a simple predator-prey model of biological coevolution, using large-scale kinetic Monte Carlo simulations. The model accounts for interspecies and intraspecies competition for resources, as well as adaptive foraging behavior. It produces a metastable low-diversity phase and a stable high-diversity phase. The structures and joint indegr...

An extension of the synchronous parallel kinetic Monte Carlo (pkMC) algorithm developed by Martinez et al [J. Comp. Phys. 227 (2008) 3804] to discrete lattices is presented. The method solves the master equation synchronously by recourse to null events that keep all processors time clocks current in a global sense. Boundary conflicts are rigorously solved by adopting a chessboard decomposition ...

In this article kinetic Monte Carlo simulations for molecular beam epitaxy (MBE) and pulsed laser depositon (PLD) are compared. It will be shown that an optimal pattern conservation during MBE is achieved for a specific ratio of diffusion to deposition rate. Further on pulsed laser deposition is presented as an alternative way to control layer by layer growth. First results concerning the islan...

Based on kinetic Monte Carlo simulations, we show that modulated wires and island gratings can be formed at vicinal surfaces. The modulation (grating) wavelength along the steps can be tailored by external conditions (coverage and temperature) and intrinsic surface properties (diffusion, terrace width) via a scaling law. Above 220 K a thermodynamic saturation value for the wavelength occurs, wh...

Relating the kinetic behavior of catalytic reactions with adsorbate overlayer structure is a long-standing challenge in catalysis. Even for simple systems such as CO oxidation on Pd(111), recent studies have observed rich behavior. In particular, titration experiments by Kondoh and coworkers on this system (J. Chem. Phys. 2006, 124, 224712), demonstrated firstorder reaction kinetics with respec...

We study the dynamics of island nucleation in the presence of adsorbates using kinetic Monte Carlo simulations of a two-species growth model. Adatoms (A-atoms) and impurities (B-atoms) are codeposited, diffuse and aggregate subject to attractive AAand AB-interactions. Activated exchange of adatoms with impurities is identified as the key process to maintain decoration of island edges by impurit...

We propose that the formation of zigzag structures on Si(1 1 0) during anisotropic etching is mainly a result of the formation of inhomogeneous regions in the etchant due to diffusion phenomena. In the same way as the presence of these etchant inhomogeneities results in step bunches on miscut (1 1 1) surfaces, it results in zigzags on the (1 1 0) surface. To support this proposal, we present an...

We present a method of performing kinetic Monte Carlo simulations that does not require an a priori list of diffusion processes and their associated energetics and reaction rates. Rather, at any time during the simulation, energetics for all possible singleor multiatom processes, within a specific interaction range, are either computed accurately using a saddle-point search procedure, or retrie...