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The ground state of randomly charged polyampholytes is conjectured to have a structure similar to a necklace, made of weakly charged parts of the chain, compacting into globules, connected by highly charged stretched `strings'. We suggest a…
We consider the passage of long polymers of length N through a hole in a membrane. If the process is slow, it is in principle possible to focus on the dynamics of the number of monomers s on one side of the membrane, assuming that the two…
A comparative simulation study of polymer brushes formed by grafting at a planar surface either flexible linear polymers (chain length $N_L$) or (non-catenated) ring polymers (chain length $N_R=2 N_L$) is presented. Two distinct off-lattice…
We explore the effect of random permanent cross-links on a system of directed polymers confined between two planes with their end-points free to slide on them. We treat the cross-links as quenched disorder and we use a semimicroscopic…
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…
We explore free knot diagrams, which are projections of knots into the plane which don't record over/under data at crossings. We consider the combinatorial question of which free knot diagrams give which knots and with what probability.…
We study asymptotic properties of diffusion and other transport processes (including self-avoiding walks and electrical conduction) on large randomly branched polymers using renormalized dynamical field theory. We focus on the swollen phase…
We compare Monte Carlo simulations of knotted and unknotted polymers whose ends are connected to two parallel walls. The force $f$ exerted on the polymer is measured as a function of the separation $R$ between the walls. For unknotted…
Search patterns of randomly oriented steps of different lengths have been observed on all scales of the biological world, ranging from the microscopic to the ecological, including in protein motors, bacteria, T-cells, honeybees, marine…
We perform large scale three-dimensional molecular dynamics simulations of unlinked and unknotted ring polymers diffusing through a background gel, here a three-dimensional cubic lattice. Taking advantage of this architecture, we propose a…
We consider the expected value for the total curvature of a random closed polygon. Numerical experiments have suggested that as the number of edges becomes large, the difference between the expected total curvature of a random closed…
We employ computer simulations and thermodynamic integration to analyse the effects of bending rigidity and slit confinement on the free energy cost of tying knots, $\Delta F_{\rm knotting}$, on polymer chains under tension. A…
The problem of continuum percolation in dispersions of rods is reformulated in terms of weighted random geometric graphs. Nodes (or sites or vertices) in the graph represent spatial locations occupied by the centers of the rods. The…
Let a simple random walk run inside a torus of dimension three or higher for a number of steps which is a constant proportion of the volume. We examine geometric properties of the range, the random subgraph induced by the set of vertices…
We give a lower bound for the non-collision probability up to a long time T in a system of n independent random walks with fixed obstacles on the two-dimensional lattice. By `collision' we mean collision between the random walks as well as…
Topological constraints can affect both equilibrium and dynamic properties of polymer systems, and can play a role in the organization of chromosomes. Despite many theoretical studies, the effects of topological constraints on the…
The motivation for this work was to construct a nontrivial knot with trivial Jones polynomial. Although that open problem has not yielded, the methods are useful for other problems in the theory of knot polynomials. The subject of the…
Let K be a tame knot with irreducible exterior M(K) in a closed, connected, orientable 3--manifold Sigma such that pi_1(Sigma) is cyclic. If infinity is not a strict boundary slope, then the diameter of the set of strict boundary slopes of…
If a semiflexible polymer confined to a narrow channel bends around by 180 degrees, the polymer is said to exhibit a hairpin. The equilibrium extension statistics of the confined polymer are well understood when hairpins are vanishingly…
Simple closed curves in the plane can be mapped to nontrivial knots under the action of origami foldings that allow the paper to self-intersect. We show all tame knot types may be produced in this manner, motivating the development of a new…