Related papers: Folding in lattice models with side chains
We present a high-precision Monte Carlo study of the O(3) spin theory on the lattice in four dimensions. This model exhibits interesting dynamical features, in particular in the broken-symmetry phase, where suitable boundary conditions can…
We develop a model to describe the motional (i.e., external degree of freedom) energy spectra of atoms trapped in a one-dimensional optical lattice, taking into account both axial and radial confinement relative to the lattice axis. Our…
We study the iteration of block spin transformations in the O(3) symmetric non-linear sigma-model on a two-dimensional square lattice with help of the Monte Carlo method. In contrast to the classical Monte Carlo Renormalization Group…
In contrast to what happens for ferromagnets, the lattice structure participates in a crucial way to determine existence and type of critical behaviour in antiferromagnetic systems. It is an interesting question to investigate how the…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…
We have studied the aging effect on the dynamics of unbinding of a double stranded directed polymer in a random medium. By using the Monte Carlo dynamics of a lattice model in two dimensions, for which disorder is known to be relevant, the…
A lattice approach is developed to measure the sphaleron free energy. Its feasibility is demonstrated through a Monte Carlo study of the two-dimensional O(3) sigma model.
We present a Monte Carlo algorithm that provides efficient and unbiased sampling of polymer melts consisting of two chains of equal length that jointly visit all the sites of a cubic lattice with rod geometry L x L x rL and non-periodic…
Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal…
We present the results of a study of the three-dimensional $XY$-model on a simple cubic lattice using the single cluster updating algorithm combined with improved estimators. We have measured the susceptibility and the correlation length…
The dynamical behavior of a quantum many-particle system is characterized by the lifetime of its excitations. When the system is perturbed, observables of any non-conserved quantity decay exponentially, but those of a conserved quantity…
We calculate the efficiency of a rejection-free dynamic Monte Carlo method for $d$-dimensional off-lattice homogeneous particles interacting through a repulsive power-law potential $r^{-p}$. Theoretically we find the algorithmic efficiency…
We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…
We introduce a quantum Monte Carlo method to simulate the reversible dynamics of correlated many-body systems. Our method is based on the Laplace transform of the time-evolution operator which, as opposed to most quantum Monte Carlo…
Molecular motors interacting with cytoskeletal filaments undergo peculiar random walks consisting of alternating sequences of directed movements along the filaments and diffusive motion in the surrounding solution. An ensemble of motors is…
Using Monte Carlo simulations we study a lattice model of a prey-predator system. We show that in the three-dimensional model populations of preys and predators exhibit coherent periodic oscillations but such a behaviour is absent in…
We study the splitting of regular square lattices subject to stochastic intermittent flows. Various flow patterns are produced by different groupings of the nodes, based on their random alternation between two possible states. The resulting…
We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries.…
The temporal evolution of step-edge fluctuations under electromigration conditions is analysed using a continuum Langevin model. If the electromigration driving force acts in the step up/down direction, and step-edge diffusion is the…
By carrying out Monte Carlo simulations,we study step bunching during solution growth. For simplicity, we consider a square lattice, which represents a diffusion field in a solution, and express the diffusion of atoms as the hopping of…