Related papers: Entropic competition between knots and slip-links
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,…
In this paper we discuss two different existing algorithms for computing topological entropy and we perform one of them in order to compute the isentropes for cubic polynomials.
An analysis of extensive simulations of interacting self-avoiding polygons on cubic lattice shows that the frequencies of different knots realized in a random, collapsed polymer ring decrease as a negative power of the ranking order, and…
The work addresses the analogy between trivial knotting and excluded volume in looped polymer chains of moderate length, $N<N_0$, where the effects of knotting are small. A simple expression for the swelling seen in trivially knotted loops…
Monte-Carlo simulations are routinely used for estimating the scaling exponents of complex systems. However, due to finite-size effects, determining the exponent values is often difficult and not reliable. Here we present a novel technique…
We present a computer simulation study of the compact self-avoiding loops as regards their length and topological state. We use a Hamiltonian closed path on the cubic-shaped segment of a 3D cubic lattice as a model of a compact polymer. The…
We present a method to generate realistic, three-dimensional networks of crosslinked semiflexible polymers. The free energy of these networks is obtained from the force-extension characteristics of the individual polymers and their…
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…
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…
A new Monte Carlo method for computing thermodynamical properties of very large polyelectrolytes is presented. It is based on a renormalization group relating the original polymer to a smaller system, where in addition to the naively…
The interplay between the topological and geometrical properties of a polymer ring can be clarified by establishing the entanglement trapped in any portion (arc) of the ring. The task requires to close the open arcs into a ring, and the…
Using known entropic and information inequalities new inequalities for some classical polynomials are obtained. Examples of Jacobi and Legendre polynomials are considered.
We describe and analyze some Monte Carlo methods for manifolds in Euclidean space defined by equality and inequality constraints. First, we give an MCMC sampler for probability distributions defined by un-normalized densities on such…
A variational approach is used to calculate free energy and conformational properties in polyelectrolytes. The true bond and Coulomb potentials are approximated by a trial isotropic harmonic energy containing monomer-monomer force constants…
Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain of hard spheres. We measure the free energy of the system, F, as a function of the distance…
Single two dimensional polymers confined to a strip are studied by Monte Carlo simulations. They are described by N-step self-avoiding random walks on a square lattice between two parallel hard walls with distance 1 << D << N^\nu (\nu = 3/4…
We investigate the problem of polymer translocation through a nanopore in the absence of an external driving force. To this end, we use the two-dimensional (2D) fluctuating bond model with single-segment Monte Carlo moves. To overcome the…
Sequential Monte Carlo algorithms, or particle filters, are widely used for approximating intractable integrals, particularly those arising in Bayesian inference and state-space models. We introduce a new variance reduction technique, the…
A variational approach, based on a discrete representation of the chain, is used to calculate free energy and conformational properties in polyelectrolytes. The true bond and Coulomb potentials are approximated by a trial isotropic harmonic…
We investigate solid-solid and solid-liquid transitions of elastic flexible off-lattice polymers with Lennard-Jones monomer-monomer interaction and anharmonic springs by means of sophisticated variants of multicanonical Monte Carlo methods.…