Related papers: Off-lattice Monte Carlo Simulation of Supramolecul…
We introduce a `virtual-move' Monte Carlo (VMMC) algorithm for systems of pairwise-interacting particles. This algorithm facilitates the simulation of particles possessing attractions of short range and arbitrary strength and geometry, an…
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…
The endpoint distribution and dynamics of semiflexible fibers is studied by numerical simulation. A brief overview is given over the analytical theory of flexible and semiflexible polymers. In particular, a closed expression is given for…
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…
The effect of different move sets on the folding kinetics of the Monte Carlo simulations is analysed based on the conformation-network and the temperature-dependent folding kinetics. A new scheme of implementing Metropolis algorithm is…
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 introduce a powerful Monte Carlo (MC) algorithm for the atomistic simulation of bulk models of oligo- and poly-thiophenes by redesigning MC moves originally developed for considerably simpler polymer structures and architectures, such as…
Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation…
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…
We present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by…
We present a hybrid Brownian dynamics / Monte Carlo algorithm for simulating solutions of highly entangled semiflexible polymers or filaments. The algorithm combines a Brownian dynamics time-stepping approach with an efficient scheme for…
We present Monte Carlo computer simulations for melts of semiflexible randomly knotted and randomly concatenated ring polymers on the fcc lattice and in slit confinement. Through systematic variation of the slit width at fixed melt density,…
We introduce a Monte-Carlo algorithm for the simulation of charged particles moving in the continuum. Electrostatic interactions are not instantaneous as in conventional approaches, but are mediated by a constrained, diffusing electric…
Polymer models describing the statistics of biomolecules under confinement have applications to a wide range of single molecule experimental techniques and give insight into biologically relevant processes {\em{in vivo}}. In this paper, we…
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…
A rigourous Monte Carlo method for protein folding simulation on lattice model is introduced. We show that a parameter which can be seen as the rigidity of the conformations has to be introduced in order to satisfy the detailed balance…
We perform equilibrium computer simulations of a two-dimensional pinned flexible polymer exposed to a quenched disorder potential consisting of hard disks. We are especially interested in the high-density regime of the disorder, where…
We present a Markov-chain Monte Carlo algorithm of "worm"type that correctly simulates the O(n) loop model on any (finite and connected) bipartite cubic graph, for any real n>0, and any edge weight, including the fully-packed limit of…
We show that the mechanical properties of a worm-like-chain (WLC) polymer, of contour length $L$ and persistence length $\l$ such that $t=L/\l\sim{\cal O}(1)$, depend both on the ensemble and the constraint on end-orientations. In the…
We present data of Monte Carlo simulations for monodisperse linear polymer chains in dense melts with degrees of polymerization between N=16 and N=512. The aim of this study is to investigate the crossover from Rouse-like dynamics for short…