Gyration radius of a circular polymer under a topological constraint with excluded volume

It is nontrivial whether the average size of a ring polymer should become smaller or larger under a topological constraint. Making use of some knot invariants, we evaluate numerically the mean square radius of gyration for ring polymers having a fixed knot type, where the ring polymers are given by self-avoiding polygons consisting of freely-jointed hard cylinders. We obtain plots of the gyration radius versus the number of polygonal nodes for the trivial, trefoil and figure-eight knots. We discuss possible asymptotic behaviors of the gyration radius under the topological constraint. In the asymptotic limit, the size of a ring polymer with a given knot is larger than that of no topological constraint when the polymer is thin, and the effective expansion becomes weak when the polymer is thick enough.Comment: 12pages,3figure

Force-Extension Relations for Polymers with Sliding Links

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 size. For a single loop in a phantom chain, we obtain exact expressions for the average end-to-end separation: The linear response to a small force is related to the properties of the unstressed chain, while for a large force the polymer backbone can be treated as a sequence of Pincus--de Gennes blobs, the constraint effecting only a single blob. Generalizing this picture, scaling arguments are used to include self-avoiding effects.Comment: 4 pages, 5 figures; accepted to Phys. Rev. E (Brief Report

Knots in Charged Polymers

The interplay of topological constraints and Coulomb interactions in static and dynamic properties of charged polymers is investigated by numerical simulations and scaling arguments. In the absence of screening, the long-range interaction localizes irreducible topological constraints into tight molecular knots, while composite constraints are factored and separated. Even when the forces are screened, tight knots may survive as local (or even global) equilibria, as long as the overall rigidity of the polymer is dominated by the Coulomb interactions. As entanglements involving tight knots are not easy to eliminate, their presence greatly influences the relaxation times of the system. In particular, we find that tight knots in open polymers are removed by diffusion along the chain, rather than by opening up. The knot diffusion coefficient actually decreases with its charge density, and for highly charged polymers the knot's position appears frozen.Comment: Revtex4, 9 pages, 9 eps figure

Statistical mechanics of semiflexible ribbon polymers

The statistical mechanics of a ribbon polymer made up of two semiflexible chains is studied using both analytical techniques and simulation. The system is found to have a crossover transition at some finite temperature, from a type of short range order to a fundamentally different sort of short range order. In the high temperature regime, the 2-point correlation functions of the object are identical to worm-like chains, while in the low temperature regime they are different due to a twist structure. The crossover happens when the persistence length of individual strands becomes comparable to the thickness of the ribbon. In the low temperature regime, the ribbon is observed to have a novel ``kink-rod'' structure with a mutual exclusion of twist and bend in contrast to smooth worm-like chain behaviour. This is due to its anisotropic rigidity and corresponds to an {\it infinitely} strong twist-bend coupling. The double-stranded polymer is also studied in a confined geometry. It is shown that when the polymer is restricted in a particular direction to a size less than the bare persistence length of the individual strands, it develops zigzag conformations which are indicated by an oscillatory tangent-tangent correlation function in the direction of confinement. Increasing the separation of the confining plates leads to a crossover to the free behaviour, which takes place at separations close to the bare persistence length. These results are expected to be relevant for experiments which involve complexation of two or more stiff or semiflexible polymers.Comment: 20 pages, 11 figures. PRE (in press

Micromechanics of Single Supercoiled DNA Molecules

Abstract. The theory of the mechanical response of single DNA molecules un-der stretching and twisting stresses is reviewed. Using established results for the the semiflexible polymer including the effect of torsional stress, and for the free energy of plectonemic supercoils, a theory of coexisting plectonemic and extended DNA is con-structed and shown to produce phenomena observed experimentally. Analytical results for DNA extension and torque are presented, and effects of anharmonicities in the plec-tonemic free energy are described. An application of the theory to the problem of torsional-stress-induced cruciform extrusion is also discussed. Key words. DNA, molecular biology, statistical mechanics, polymer physics. AMS(MOS) subject classifications. 82D60, 92C05, 92C40

The elusiveness of polymer knots

36.20.Ey Conformation (statistics and dynamics), 02.10.Kn Knot theory,