Related papers: Conformational properties of compact polymers
We study the conformational behavior of a polymer adsorbed at an attractive nanostring and construct the complete structural phase diagram in dependence of the binding strength and effective thickness of the string. For this purpose, Monte…
Discrepancies play an important role in the study of uniformity properties of point sets. Their probability distributions are a help in the analysis of the efficiency of the Quasi Monte Carlo method of numerical integration, which uses…
Inspired by recent advances in the chromosome capture techniques, a method is proposed to study the structural organization of systems of polymers rings with topological constraints.To this purpose, the system is divided into compartments…
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…
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…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
We review pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells. For that purpose, we review, first, recent theoretical and computational…
Experiments using nanofluidic devices have proven effective in characterizing the physical properties of polymers confined to small cavities. Two recent studies using such methods examined the organization and dynamics of two DNA molecules…
Multiblock copolymer chains in implicit nonselective solvents are studied by Monte Carlo method which employs a parallel tempering algorithm. Chains consisting of 120 $A$ and 120 $B$ monomers, arranged in three distinct microarchitectures:…
The effective quasistatic conductivity of composite polymeric electrolytes is studied in terms of a hard-core--penetrable-layer model. Used to incorporate the interface phenomena (such as amorphization of the polymer matrix around filler…
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…
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…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
Monte Carlo methods are widely used to estimate observables in many-body quantum systems. However, conventional sampling schemes often require a large number of samples to achieve sufficient accuracy. In this work we propose the…
We review recent simulation studies of interfaces between immiscible homopolymer phases. Special emphasis is given to the presentation of efficient simulation techniques and powerful methods of data analysis, such as the analysis of…
Unconcatenated, unknotted polymer rings in the melt are subject to strong interactions with neighboring chains due to the presence of topological constraints. We study this by computer simulation using the bond-fluctuation algorithm for…
By means of contact-density chain-growth simulations, we investigate a simple lattice model of a flexible polymer interacting with an attractive substrate. The contact density is a function of the numbers of monomer-substrate and…
A range of percolation models of cluster systems of composites is discussed. In the models the parameters of the clusters of a substance and inner boundaries were obtained by the Monte Carlo method, and the possibility of affecting the…
The liquid crystalline model biomembrane system consisting of a stack of interacting membranes is studied by the newly developed Fourier Monte Carlo simulation technique. In comparison to perturbation theory, substantial quantitative…
Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the variation in the conformational free energy with respect to the end-to-end distance of the…