Related papers: Correlations in nano-scale step fluctuations: comp…
Monte Carlo (MC) simulations are used to study the dynamics of polymer translocation through a nanopore in the limit where the translocation rate is sufficiently slow that the polymer maintains a state of conformational quasi-equilibrium.…
The standard kinetic Monte Carlo algorithm is an extremely efficient method to carry out serial simulations of dynamical processes such as thin-film growth. However, in some cases it is necessary to study systems over extended time and…
The probability distribution p(l) of an atom to return to a step at distance l from the detachment site, with a random walk in between, is exactly enumerated. In particular, we study the dependence of p(l) on step roughness, presence of…
Electrolyte solutions play an important role in energy storage devices, whose performance highly relies on the electrokinetic processes at sub-micron scales.\ Although fluctuations and stochastic features become more critical at small…
Energy barriers for different moves of a single Rh adatom in the vicinity of steps on Rh(111) surface are studied with molecular statics. Interatomic interactions are modeled by the semi-empirical many-body Rosato-Guillope-Legrand…
We consider several multiscale-in-time kinetic Monte Carlo models, in which some variables evolve on a fast time scale, while the others evolve on a slow time scale. In the first two models we consider, a particle evolves in a…
Fluctuations of isolated and pairs of ascending steps of monoatomic height are studied in the framework of SOS models, using mainly Monte Carlo techniques. Below the roughening transistion of the surface, the profiles of long steps show the…
In the framework of SOS models, the dynamics of isolated and pairs of surface steps of monoatomic height is studied, for step--edge diffusion and for evaporation kinetics, using Monte Carlo techniques. In particular, various interesting…
Competing phases or interactions in complex many-particle systems can result in free energy barriers that strongly suppress thermal equilibration. Here we discuss how extended ensemble Monte Carlo simulations can be used to study the…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
A rigourous Monte Carlo method for protein folding simulation on lattice model is introduced. We show that a parameter which can be seen as the rigidity of the conformations has to be introduced in order to satisfy the detailed balance…
In this paper we study from a numerical analysis perspective the Fractional Step Kinetic Monte Carlo (FS-KMC) algorithms proposed in [1] for the parallel simulation of spatially distributed particle systems on a lattice. FS-KMC are…
Thermal or finite-size scaling analyses of importance sampling Monte Carlo time series in the vicinity of phase transition points often combine different estimates for the same quantity, such as a critical exponent, with the intent to…
Molecular dynamic (MD) simulations are applied to investigate the dependency of the kinetic friction coefficient on the temperature at the nano-scale. The system is comprised of an aluminum spherical particle consisting of 32000 atoms in an…
An approximate method for studying activation over a fluctuating barrier of potential is proposed. It involves considering separately the slow and fast components of barrier fluctuations, and it applies for any value of their correlation…
We consider the six-vertex model with Domain Wall Boundary Conditions on a $N\times N$ square lattice. Our main interest is the study of the fluctuations of the extremal lattice path about the arctic curves. We address the problem through…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
We study the exchange and correlation hole of the valence shell of second row atoms using variational Monte Carlo techniques, especially correlated estimates, and norm-conserving pseudopotentials. The well-known scaling of the valence shell…
Dynamic Monte Carlo simulations are used to study coupled transport (co-transport) through sub-nanometer-diameter pores. In this classic Hodgkin-Keynes mechanism, an ion species uses the large flux of an abundant ion species to move against…
Obtaining reliable estimates of the statistical properties of complex macromolecules by computer simulation is a task that requires high computational effort as well as the development of highly efficient simulation algorithms. We present…