Related papers: Under-knotted and Over-knotted Polymers: Unrestric…
Given a tame knot K presented in the form of a knot diagram, we show that the problem of determining whether K is knotted is in the complexity class NP, assuming the generalized Riemann hypothesis (GRH). In other words, there exists a…
The segment distribution around the center of gravity is derived for unperturbed ring polymers. We show that, although a small difference is observed, the exact distribution can be well approximated by the Gaussian probability distribution…
In this paper we study how randomly generated knots occupy a volume of space using topological methods. To this end, we consider the evolution of the first homology of an immersed metric neighbourhood of a knot's embedding for growing…
We consider a continuous time simple random walk on a subset of the square lattice with wired boundary conditions: the walk transitions at unit edge rate on the graph obtained from the lattice closure of the subset by contracting the…
We study the probability distribution, $P_N(T)$, of the coincidence time $T$, i.e. the total local time of all pairwise coincidences of $N$ independent Brownian walkers. We consider in details two geometries: Brownian motions all starting…
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 report on a computational study of the statics and dynamics of long flexible linear polymers that spontaneously knot and unknot. Specifically, the equilibrium self-entanglement properties, such as the knotting probability, knot length…
It is known that any open necklace with beads of $t$ types in which the number of beads of each type is divisible by $k$, can be partitioned by at most $(k-1)t$ cuts into intervals that can be distributed into $k$ collections, each…
Motivated by the recent experimental observations of the DNA loop extrusion by protein motors, in this paper we investigate the statistical properties of the growing polymer loops within the ideal chain model. The loop conformation is…
This paper is based on the study of random lozenge tilings of non-convex polygonal regions with interacting non-convexities (cuts) and the corresponding asymptotic kernel as in [3] and [4] (discrete tacnode kernel). Here this kernel is used…
Monte Carlo dynamics of the lattice 48 monomers toy protein is interpreted as a random walk in an abstract (discrete) space of conformations. To test the geometry of this space, we examine the return probability $P(T)$, which is the…
We present new computations of approximately length-minimizing polygons with fixed thickness. These curves model the centerlines of "tight" knotted tubes with minimal length and fixed circular cross-section. Our curves approximately…
While stretching of a polymer along a flat surface is hardly different from the classical Pincus problem of pulling chain ends in free space, the role of curved geometry in conformational statistics of the stretched chain is an exciting…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase…
We study several related models of self-avoiding polygons in a tubular subgraph of the simple cubic lattice, with a particular interest in the asymptotics of the knotting statistics. Polygons in a tube can be characterised by a finite…
We have evaluated by numerical simulation the average size $R_K$ of random polygons of fixed knot topology $K = \emptyset, 3_1, 3_1\sharp4_1$, and we have confirmed the scaling law $R^2_K \sim N^{2\nu_K}$ for the number $N$ of polygonal…
Every smooth closed curve can be represented by a suitable Fourier sum. We show that the ensemble of curves generated by randomly chosen Fourier coefficients with amplitudes inversely proportional to spatial frequency (with a smooth…
We propose a novel combinatorial algorithm for efficient generation of Hamiltonian walks and cycles on a cubic lattice, modeling the conformations of lattice toy proteins. Through extensive tests on small lattices (allowing complete…
We estimate by Monte Carlo simulations the configurational entropy of $N$-steps polygons in the cubic lattice with fixed knot type. By collecting a rich statistics of configurations with very large values of $N$ we are able to analyse the…
In this paper, we study random embeddings of polymer networks distributed according to any potential energy which can be expressed in terms of distances between pairs of monomers. This includes freely jointed chains, steric effects,…