相关论文: Secondary Structures in Long Compact Polymers

Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…

We introduce an efficient, scalable Monte Carlo algorithm to simulate cross-linked architectures of freely-jointed and discrete worm-like chains. Bond movement is based on the discrete tractrix construction, which effects conformational…

Voids exist in proteins as packing defects and are often associated with protein functions. We study the statistical geometry of voids in two-dimensional lattice chain polymers. We define voids as topological features and develop a simple…

The effect of different Monte Carlo move sets on the the folding kinetics of lattice polymer chains is studied from the geometry of the conformation-network. The networks have the characteristics of small- world. The Monte Carlo move, rigid…

Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain proteins decreases with chain length. We find…

We show how a Monte Carlo method for generating self-avoiding walks on lattice geometries which employs a binary-tree data structure can be adapted for hard-sphere polymers with continuous degrees of freedom. Data suggests that the time per…

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…

Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is…

Ladder polymers, known for their rigid, ladder-like structures, exhibit exceptional thermal stability and mechanical strength, positioning them as candidates for advanced applications. However, accurately determining their structure from…

Bridging algorithms are global Monte Carlo moves which allow for an efficient sampling of single polymer chains. In this manuscript we discuss the adaptation of three bridging algorithms from lattice to continuum models, and give details on…

We study the static properties of a semiflexible polymer exposed to a quenched random environment by means of computer simulations. The polymer is modeled as two-dimensional Heisenberg chain. For the random environment we consider hard…

We introduce a two-dimensional lattice model for the description of knotted polymer rings. A polymer configuration is modeled by a closed polygon drawn on the square diagonal lattice, with possible crossings describing pairs of strands of…

The structure of a polystyrene matrix filled with tightly cross-linked polystyrene nanoparticles, forming an athermal nanocomposite system, is investigated by means of a Monte Carlo sampling formalism. The polymer chains are represented as…

We present a Monte Carlo method that allows efficient and unbiased sampling of Hamiltonian walks on a cubic lattice. Such walks are self-avoiding and visit each lattice site exactly once. They are often used as simple models of globular…

Due to the complex characteristics of bottle-brush polymers, it became a challenge to develop an efficient algorithm for studying such macromolecules under various solvent conditions or some constraints in the space by using computer…

We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on the FCC lattice which takes explicitly into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer…

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 use Monte Carlo simulations to study polymer melts consisting of fully flexible and moderately stiff chains in the bond fluctuation model at a volume fraction $0.5$. In order to reduce the local density fluctuations, we test a…

A novel family of dynamical Monte Carlo algorithms for lattice polymers is proposed. Our central idea is to simulate an extended ensemble in which the self-avoiding condition is systematically weakened. The degree of the self-overlap is…

We perform simulations for long hard-sphere polymer chains using a recently developed binary-tree based Monte Carlo method. Systems in two to five dimensions with free and periodic boundary conditions and up to $10^7$ repeat units are…