To function as gene regulatory elements in response to environmental signals, riboswitches must adopt specific secondary structures on appropriate time scales. We employ kinetic Monte Carlo simulation to model the time-dependent folding during transcription of TPP riboswitch expression platforms. According to our simulations, riboswitch transcriptional terminators, which must adopt a specific h...

While kinetic Monte Carlo simulations can provide long-time simulations of the dynamics of physical and chemical systems, it is not yet possible in general to identify the inverse Monte Carlo attempt frequency with a physical timescale. Here we demonstrate such an identification by comparing simulations with experimental data. Using a dynamic lattice-gas model for the electrosorption of Br on A...

Static calculation and preliminary kinetic Monte Carlo simulation studies are undertaken for the nucleation and growth on a model system which follows a Frank-van der Merwe mechanism. In the present case, we consider the deposition of Ag on Au(100) and Au(111) surfaces. The interactions were calculated using the embedded atom model. The process of formation and growth of 2D Ag structures on Au(...

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In this paper we present a general derivation of kinetic models for traffic flows including different kind of interaction rules. We show that most kinetic models previously derived can be cast in the actual formulation. The development of Monte Carlo methods for direct simulation of the kinetic models is considered as an initial step towards realistic and efficient computations of traffic pheno...

a r t i c l e i n f o a b s t r a c t We introduce a massively parallelized test-particle based kinetic Monte Carlo code that is capable of modeling the phase space evolution of an arbitrarily sized system that is free to move in and out of the continuum limit. Our code combines advantages of the DSMC and the Point of Closest Approach techniques for solving the collision integral. With that, it...