相关论文: Folding in lattice models with side chains
Lattice gauge theories are considered with a partial axial gauge fixing along one direction only. This leaves a residual gauge symmetry that is still local in three directions but now global in one. It is found that this $N^{d-1}$ fold…
The dynamical behaviours of a kinetically constrained spin model (Fredrickson-Andersen model) on a Bethe lattice are investigated by a perturbation analysis that provides exact final states above the nonergodic transition point. It is…
Time-dependent density functional theory, proposed recently in the context of atomic diffusion and non-equilibrium processes in solids, is tested against Monte Carlo simulation. In order to assess the basic approximation of that theory, the…
Single-chain elasticity is of fundamental importance in polymer physics, as it underlies many of the unique properties of polymer systems. Recently, there has been interest in characterizing the elastic properties of catenanes, molecular…
The triangular lattice model with nearest-neighbor attraction and third-neighbor repulsion, introduced in [J. Pekalski, A. Ciach and N. G. Almarza, arXiv:1401.0801 [cond-mat.soft]] is studied by Monte Carlo simulation. Introduction of…
Two-dimensional $CP^{N-1}$ models are investigated by Monte Carlo methods on the lattice, for values of $N$ ranging from 2 to 21. Scaling and rotation invariance are studied by comparing different definitions of correlation length $\xi$.…
The dynamics of two 12-monomer heteropolymers on the square lattice is studied exactly within the master equation approach. The time evolution of the occupancy of the native state is determined. At low temperatures, the median folding time…
Structural and kinetic aspects of 2-D irreversible metal deposition under potentiostatic conditions are analyzed by means of dynamic Monte Carlo simulations employing embedded atom potentials for a model system. Three limiting models, all…
Spin transport and spin dynamics after femtosecond laser pulse irradiation of iron (Fe) are studied using a kinetic Monte Carlo model. This model simulates spin dependent dynamics by taking into account two interaction processes during…
The site-reduction of U(1) lattice gauge theory along the spatial directions is used to model the monopole dynamics. The reduced theory is that of the angle-valued coordinates on the discrete worldline. Below the critical coupling…
Spin resistivity $R$ has been shown to result mainly from the scattering of itinerant spins with magnetic impurities and lattice spins. $R$ is proportional to the spin-spin correlation so that its behavior is very complicated near and at…
In this paper, a three-dimensional lattice model based on the Monte Carlo approach is presented. This model is developed to investigate the kinetics of morphology change during phase separation in nonstoichiometric Si oxide (SiOx, x < 2)…
We report developments of the kinetic Monte Carlo (KMC) method with improved accuracy and increased versatility for the description of atomic diffusivity on metal surfaces. The on-lattice constraint built into our recently proposed…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
We numerically investigate the long-time behavior of the density-density auto-correlation function in driven lattice gases with particle exclusion and periodic boundary conditions in one, two, and three dimensions using precise Monte Carlo…
Macroscopic properties of heterogeneous media are frequently modelled by regular lattice models, which are based on a relatively small basic cluster of lattice sites. Here, we extend one of such models to any cluster's size kxk. We also…
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…
The folding transition of single, long semiflexible polymers was studied with special emphasis on the chain length effect using Monte Carlo simulations. While a relatively short chain (10-25 Kuhn segments) undergoes a large discrete…
We study the static properties of a semiflexible polymer exposed to a quenched random environment by means of computer simulations. The polymer is modeled as two-dimensional Heisenberg chain. For the random environment we consider hard…
We present a method to generate realistic, three-dimensional networks of crosslinked semiflexible polymers. The free energy of these networks is obtained from the force-extension characteristics of the individual polymers and their…