相关论文: Folding in lattice models with side chains

It has been revealed by mean-field theories and computer simulations that the nature of the collapse transition of a polymer is influenced by its bending stiffness $\epsilon_{\rm b}$. In two dimensions, a recent analytical work demonstrated…

A kinetic Monte Carlo approach is applied to studying shape instability of nanowires that results in their breaking up into chains of nanoparticles. Our approach can be used to explore dynamical features of the process that correspond to…

Phase diagram of a spin-ice type Kondo lattice model, potentially relevant to metallic pyrochlore oxides, is obtained by the Monte Carlo simulation implementing the polynomial expansion technique up to the system size with 2048 sites. We…

We study the dynamical critical behavior of multigrid Monte Carlo for the two dimensional Sine Gordon model on lattices up to 128 x 128. Using piecewise constant interpolation, we perform a W-cycle (gamma=2). We examine whether one can…

A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate…

Growth of hard--rod monolayers via deposition is studied in a lattice model using rods with discrete orientations and in a continuum model with hard spherocylinders. The lattice model is treated with kinetic Monte Carlo simulations and…

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…

A Monte Carlo study of the late time growth of $L1_2$ ordered domains on a fcc $A_3B$ binary alloy is presented. The energy of the alloy has been modeled by a nearest neighbor interaction Ising hamiltonian. The system exhibits a fourfold…

We describe a class of growth algorithms for finding low energy states of heteropolymers. These polymers form toy models for proteins, and the hope is that similar methods will ultimately be useful for finding native states of real proteins…

We present a Monte Carlo method for the direct evaluation of the difference between the free energies of two crystal structures. The method is built on a lattice-switch transformation that maps a configuration of one structure onto a…

Monte Carlo simulations of proteins are hindered by the system's high density which often makes local moves ineffective. Here we devise and test a set of long range moves that work well even when all sites of a lattice simulation are…

A simple one-dimensional lattice model is suggested to describe the experimentally observed plateau in force-stretching diagrams for some macromolecules. This chain model involves the nearest-neighbor interaction of a Morse-like potential…

In a recent Letter, Gutin, Abkevich, and Shakhnovich (GAS) reported on a series of dynamical Monte Carlo simulations on lattice models of proteins. Based on these highly simplified models, they found that four different potential energies…

We propose a new Monte Carlo scheme to study the late-time dynamics of a 2-dim hard sphere fluid, modeled by a tethered network of hard spheres. Fluidity is simulated by breaking and reattaching the flexible tethers. We study the diffusion…

A continuous time Monte Carlo lattice gas dynamics is developed to model driven steady states of vortices in two dimensional superconducting networks. Dramatic differences are found when compared to a simpler Metropolis dynamics. Subtle…

Molecular dynamics simulations in simplified models allow one to study the scaling properties of folding times for many proteins together under a controlled setting. We consider three variants of the Go models with different contact…

We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach,…

We study uniform 3-star polymers with one branch tethered to an attractive surface and another branch pulled by a force away from the surface. Each branch of the 3-star lattice is modelled as a self-avoiding walk on the simple cubic lattice…

The hydrodynamic effects on the late stage kinetics in spinodal decomposition of multicomponent fluids are examined using a lattice Boltzmann scheme with stochastic fluctuations in the fluid and at the interface. In two dimensions, the…

We present a lattice-gas (generalised Ising) model for liquid droplets on solid surfaces. The time evolution in the model involves two processes: (i) Single-particle moves which are determined by a kinetic Monte Carlo algorithm. These…