相关论文: Folding in lattice models with side chains

The dynamics of elongated inertial particles in an extensional flow is studied numerically by performing simulations of freely jointed bead-rod chains. The coil-stretch transition and the tumbling instability are characterized as a function…

We propose two lattice models in one dimension, with stochastically hopping particles which aggregate on contact. The hops are guided by "velocity rates" which themselves evolve according to the rules of ballistic aggregation as in a sticky…

The many-body Monte Carlo method is used to evaluate the frequency dependent conductivity and the average mobility of a system of hopping charges, electronic or ionic on a one-dimensional chain or channel of finite length. Two cases are…

We present a Monte Carlo study of the one-component $\phi^4$ model on the cubic lattice in three dimensions. Leading order scaling corrections are studied using the finite size scaling method. We compute the corrections to scaling exponent…

A recently introduced model describing the folding of the triangular lattice is generalized allowing for defects in the lattice and written as an Ising model with nearest-neighbor and plaquette interactions on the honeycomb lattice. Its…

A folded chain, with one end fixed at the ceiling and the other end released from the same elevation, is commonly modeled as an energy-conserving system in one-dimension. However, the analytical paradigms in previous literature is…

Using an elaborate set of simulational tools and statistically optimized methods of data analysis we investigate the scaling behavior of the correlation lengths of three-dimensional classical O($n$) spin models. Considering…

We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…

The driven lattice gas (DLG) evolving at low temperature helps understanding the kinetics of pattern formation in unstable mixtures under anisotropic conditions. We here develop a simple theoretical description of kinetics in Monte Carlo…

We present Monte Carlo simulations in a modification of the north-or-east-or-front model recently investigated by Berthier and Garrahan [J. Phys. Chem. B 109, 3578 (2005)]. In this coarse-grained model for relaxation in supercooled liquids,…

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…

We show how to generalize the Lattice Switch Monte Carlo method to calculate the phase diagram of a binary system. A global coordinate transformation is combined with a modification of particle diameters, enabling the multi-component system…

We study the dynamics of a single chain polymer confined to a two dimensional cell. We introduce a kinetically constrained lattice gas model that preserves the connectivity of the chain, and we use this kinetically constrained model to…

The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not…

By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are…

A simple lattice model is used to study compaction in granular media. As in real experiments, we consider a series of taps separated by large enough waiting times. The relaxation of the density exhibits the characteristic inverse…

The aqueous solvent profoundly influences protein folding, yet its effects are relatively poorly understood. In this study, we investigate the impact of solvation on the folding of lattice proteins by using Monte Carlo simulations. The…

Monte Carlo simulations and dynamical mean-field approximations are performed to study the phase transition in a driven lattice gas with nearest-neighbor exclusion on a square lattice. A slight extension of the microscopic dynamics with…

In this study we present a Microcanonical Monte Carlo investigation of one dimensional self-gravitating toy models. We study the effect of hard-core potentials and compare to those results obtained with softening parameters and also the…

Experimental studies on the irreversible growth of field-induced chains of dipolar particles suggest an asymptotic power-law behavior of several relevant quantities. We introduce a Monte Carlo model of chain growth that explicitly…