Related papers: Conserved Linking in Single- and Double-Stranded P…
In this paper, we construct an effective model for the dynamics of an excluded-volume chain under confinement, by extending the formalism of Rouse modes. We make specific predictions about the behavior of the modes for a single polymer…
Topological entanglements in polymers are mimicked by sliding rings (slip-links) which enforce pair contacts between monomers. We study the force-extension curve for linear polymers in which slip-links create additional loops of variable…
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…
A square-lattice hard-core dimer model with links extending beyond nearest-neighbors is studied using a directed-loop Monte Carlo method. An arbitrarily small fraction of next-nearest-neighbor dimers is found to cause deconfinement, whereas…
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…
We give two different, statistically consistent definitions of the length l of a prime knot tied into a polymer ring. In the good solvent regime the polymer is modelled by a self avoiding polygon of N steps on cubic lattice and l is the…
We study bond percolation of $N$ non-interacting Gaussian polymers of $\ell$ segments on a 2D square lattice of size $L$ with reflecting boundaries. Through simulations, we find the fraction of configurations displaying {\em no} connected…
We investigate by means of a number of different dynamical Monte Carlo simulation methods the self-assembly of equilibrium polymers in dilute, semidilute and concentrated solutions under good-solvent conditions. In our simulations, both…
The linking number (topological entanglement) and the writhe (geometrical entanglement) of a model of circular double stranded DNA undergoing a thermal denaturation transition are investigated by Monte Carlo simulations. By allowing the…
The bond fluctuation method is used to simulate both non-concatenated entangled and interpenetrating melts of ring polymers. We find that the swelling of interpenetrating rings upon dilution follows the same laws as for linear chains.…
The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…
We study by Monte Carlo simulations and scaling analysis two models of pairs of confined and dense ring polymers in two dimensions. The pair of ring polymers are modelled by squared lattice polygons confined within a square cavity and they…
This paper reviews recent Monte Carlo simulation studies of the glassy behavior in thin polymer films. The simulations employ a version of the bond-fluctuation lattice model, in which the glass transition is driven by the competition…
We discuss the appropriate techniques for modelling the geometry of open ended elastic polymer molecules. The molecule is assumed to have fixed endpoints on a boundary surface. In particular we discuss the concept of the winding number, a…
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…
Ring polymers remain a major challenge to our current understanding of polymer dynamics. Experimental results are difficult to interpret because of the uncertainty in the purity and dispersity of the sample. Using both equilibrium and…
Two-dimensional semiflexible polymer rings are studied both by imaging circular DNA adsorbed on a mica surface and by Monte Carlo simulations of phantom polymers as well as of polymers with finite thickness. Comparison of size and shape of…
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 develop off-lattice simulations of semiflexible polymer chains subjected to applied mechanical forces using Markov Chain Monte Carlo. Our approach models the polymer as a chain of fixed-length bonds, with configurations updated through…