相关论文: Secondary Structures in Long Compact Polymers

Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length $N \sim {\cal O}(10^4)$. Based on the standard simple…

Proposed here is a dynamic Monte-Carlo algorithm that is efficient in simulating dense systems of long flexible chain molecules. It expands on the configurational-bias Monte-Carlo method through the simultaneous generation of a large set of…

Monte Carlo simulations show that long-range interactions play a major role in determining the folding rates of 48-mer three-dimensional lattice polymers modelled by the Go potential. For three target structures with different native…

Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures…

We present a new Monte Carlo scheme for the efficient simulation of multi-polymer systems. The method permits chains to be inserted into the system using a biased growth technique. The growth proceeds via the use of a retractable feeler,…

A lattice model is presented for the simulation of dynamics in polymeric systems. Each polymer is represented as a chain of monomers, residing on a sequence of nearest-neighbor sites of a face-centered-cubic lattice. The polymers are self-…

The pivot algorithm is the most efficient known method for sampling polymer configurations for self-avoiding walks and related models. Here we introduce two recent improvements to an efficient binary tree implementation of the pivot…

Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…

The statistics of meander and related problems are studied as particular realizations of compact polymer chain foldings. This paper presents a general discussion of these topics, with a particular emphasis on three points: (i) the use of a…

The self-avoid random walk algorithm has been extensively used in the study of polymers. In this work we study the basic properties of the trajectories generated with this algorithm when two interactions are added to it: contact and folding…

We map the conformation space of a simple lattice polymer chain to a network, where (i) the vertices of the network have a one-to-one correspondence to the conformations of the chain, and (ii) a link between two vertices indicates the…

The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…

Many problems in materials science and biology involve particles interacting with strong, short-ranged bonds, that can break and form on experimental timescales. Treating such bonds as constraints can significantly speed up sampling their…

Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native's structure geometry, the model exhibits two broad classes of folding mechanisms for two-state folders. Folding to native structures…

We study the correlations of classical hardcore dimer models doped with monomers by Monte Carlo simulation. We introduce an efficient cluster algorithm, which is applicable in any dimension, for different lattices and arbitrary doping. We…

Topologically constrained genome-like polymers often double-fold into tree-like configurations, which can be modelled on the level of folded (ring) polymers or on the level of the underlying random trees. For both descriptions, we have…

Extensive Monte Carlo results are presented for a lattice model of a bottle-brush polymer under good solvent or Theta solvent conditions. Varying the side chain length, backbone length, and the grafting density for a rigid straight…

The interplay of topological constraints and persistence length of ring polymers in their own melt is investigated by means of dynamical Monte Carlo simulations of a three dimensional lattice model. We ask if the results are consistent with…

We study the efficiency of the incomplete enumeration algorithm for linear and branched polymers. There is a qualitative difference in the efficiency in these two cases. The average time to generate an independent sample of $n$ sites for…

Random sequential adsorption of binary mixtures of extended objects on a two-dimensional triangular lattice is studied numerically by means of Monte Carlo simulations. The depositing objects are formed by self-avoiding random walks on the…