相关论文: Secondary Structures in Long Compact Polymers

We perform a Monte Carlo study of $N$-step self-avoiding walks, attached to the corner of an impenetrable wedge in two dimensions ($d=2$), or the tip of an impenetrable cone in $d=3$, of sizes ranging up to $N=10^6$ steps. We find that the…

A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…

We study structural phase transition of polymer-grafted colloidal particles by Monte Carlo simulations on hard spherical particles. The interaction potential, which has a weak repulsive step outside the hard core, was validated with use of…

We study the conformations of a self-avoiding polymer confined to a channel by computing the cross-sectional distributions of the positions of its monomers. By means of Monte-Carlo simulations for a self-avoiding, freely-jointed chain we…

Polymers confined to a narrow channel are subject to strong entropic forces that tend to drive the molecules apart. In this study, we use Monte Carlo computer simulations to study the segregation behavior of two flexible hard-sphere…

The component-by-component construction is the standard method of finding good lattice rules or polynomial lattice rules for numerical integration. Several authors have reported that in numerical experiments the generating vector sometimes…

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…

We propose new polymer models for Monte Carlo simulation and apply them to a polymer chain confined in a relatively thin box which has both curved and flat sides, and show that either an ideal or an excluded-volume chain spends more time in…

We discuss a Monte Carlo Markov Chain (MCMC) procedure for the random sampling of some one-dimensional lattice paths with constraints, for various constraints. We show that an approach inspired by optimal transport allows us to bound…

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…

Collapse of the polymer chain upon the sharp decrease of solvent quality is studied. During collapse, any pair of polymer units appearing in a sufficiently close vicinity in space has the possibility with a certain probability to form an…

The parallel computational complexity of the quadratic map is studied. A parallel algorithm is described that generates typical pseudotrajectories of length t in a time that scales as log t and increases slowly in the accuracy demanded of…

Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…

Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique…

A mean field rate theory description of the homo- and co-polymerization of $f$-functional molecules is developed, which contains the formation of short cyclic structures inside the network. The predictions of this model are compared with…

We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…

A coarse-grained simulation model eliminates microscopic degrees of freedom and represents a polymer by a simplified structure. A priori, two classes of coarse-grained models may be distinguished: those which are designed for a specific…

Motivated by the way Japanese tatami mats are placed on the floor, we consider domino tilings with a constraint and estimate the number of such tilings of plane regions. We map the system onto a monomer-dimer model with a novel local…

Using data from contact maps of the DNA-polymer of $E. Coli$ (at kilobase pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain.…

We report results of extensive Dynamical Monte Carlo investigations on self-assembled Equilibrium Polymers (EP) without loops in good solvent. (This is thought to provide a good model of giant surfactant micelles.) Using a novel algorithm…