相关论文: Folding in lattice models with side chains
We study autocorrelation times of physical observables in lattice QCD as a function of the molecular dynamics trajectory length in the hybrid Monte-Carlo algorithm. In an interval of trajectory lengths where energy and reversibility…
Using Monte Carlo methods, the short-time dynamic scaling behaviour of two-dimensional critical XY systems is investigated. Our results for the XY model show that there exists universal scaling behaviour already in the short-time regime,…
Over the past few decades, oscillating flexible foils have been used to study the physics of organismal propulsion in different fluid environments. Here we extend this work to a study of flexible foils in a frictional environment. When the…
We study the finite size scaling behaviour of the specific heat of thin films in the neighbourhood of the lambda-transition. To this end we have simulated the improved two-component phi^4 model on the simple cubic lattice. We employ free…
We consider a lattice model in which a tracer particle moves in the presence of randomly distributed immobile obstacles. The crowding effect due to the obstacles interplays with the quasi-confinement imposed by wrapping the lattice onto a…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
We obtain the dynamic correlation function of two-dimensional lattice gas with nearest-neighbor repulsion in ordered c(2$\times$2) phase (antiferromagnetic ordering) under the condition of low concentration of structural defects. It is…
Ordering processes in fcc-alloys with composition A_3B (like Cu_3Au, Cu_3Pd, CoPt_3 etc.) are investigated by Monte Carlo simulation within a class of lattice models based on nearest-neighbor (NN) and second-neighbor (NNN) interactions.…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
We study dynamical properties of the one- and two-dimensional Falicov-Kimball model using lattice Monte Carlo simulations. In particular, we calculate the spreading of charge correlations in the equilibrium model and after an interaction…
We present a new Monte Carlo algorithm for studying site or bond percolation on any lattice. The algorithm allows us to calculate quantities such as the cluster size distribution or spanning probability over the entire range of site or bond…
The correlations in the motion of reptating polymers in their melt are investigated by means of kinetic Monte Carlo simulations of the three dimensional slithering snake version of the bond-fluctuation model. Surprisingly, the slithering…
We investigate the dependence of the displacements of a molecular motor embedded inside a glassy material on its folding characteristic time. We observe two different time regimes. For slow foldings (regime I) the diffusion evolves very…
In the first part of this work the classical and statistical aspects of the dynamics of an inextensible chain in three dimensions are investigated. In the second part the special case of a chain admitting only fixed angles with respect to…
We study an induced dynamics in the space of energy of single-spin-flip Monte Carlo algorithm. The method gives an efficient reweighting technique. This dynamics is shown to have relaxation times proportional to the specific heat. Thus, it…
Monte Carlo simulations have been performed to investigate the relaxation of the L10 long-range order in dimensionally reduced systems. The effect of the number of (001)-type monatomic layers and of the pair interaction energies on these…
We consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a…
An off-lattice Monte Carlo algorithm for solutions of equilibrium polymers (EP) is proposed. At low and moderate densities this is shown to reproduce faithfully the (static) properties found recently for flexible linear EP using a lattice…
Scaling of folding times in Go models of proteins and of decoy structures with the Lennard-Jones potentials in the native contacts reveal %robust power law trends when studied under optimal folding conditions. The power law exponent depends…
The behavior of a Lattice Monte Carlo algorithm (if it is designed correctly) must approach that of the continuum system that it is designed to simulate as the time step and the mesh step tend to zero. However, we show for an algorithm for…