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

Comment on "Theory and computer simulation for the equation of state of additive hard-disk fluid mixtures"

A flaw in the comparison between two different theoretical equations of state for a binary mixture of additive hard disks and Monte Carlo results, as recently reported in C. Barrio and J. R. Solana, Phys. Rev. E 63, 011201 (2001), is pointed out. It is found that both proposals, which require the equation of state of the single component system as input, lead to comparable accuracy but the one advocated by us [A. Santos, S. B. Yuste, and M. L\'{o}pez de Haro, Mol. Phys. 96, 1 (1999)] is simpler and complies with the exact limit in which the small disks are point particles.Comment: 4 pages, including 1 figur

The critical fugacity for surface adsorption of self-avoiding walks on the honeycomb lattice is 1+21+\sqrt{2}

In 2010, Duminil-Copin and Smirnov proved a long-standing conjecture of Nienhuis, made in 1982, that the growth constant of self-avoiding walks on the hexagonal (a.k.a. honeycomb) lattice is $\mu=\sqrt{2+\sqrt{2}}.$ A key identity used in that proof was later generalised by Smirnov so as to apply to a general O(n) loop model with $n\in [-2,2]$ (the case $n=0$ corresponding to SAWs). We modify this model by restricting to a half-plane and introducing a surface fugacity $y$ associated with boundary sites (also called surface sites), and obtain a generalisation of Smirnov's identity. The critical value of the surface fugacity was conjectured by Batchelor and Yung in 1995 to be $y_{\rm c}=1+2/\sqrt{2-n}.$ This value plays a crucial role in our generalized identity, just as the value of growth constant did in Smirnov's identity. For the case $n=0$, corresponding to \saws\ interacting with a surface, we prove the conjectured value of the critical surface fugacity. A crucial part of the proof involves demonstrating that the generating function of self-avoiding bridges of height $T$, taken at its critical point $1/\mu$, tends to 0 as $T$ increases, as predicted from SLE theory.Comment: Major revision, references updated, 25 pages, 13 figure

Exact sampling of self-avoiding paths via discrete Schramm-Loewner evolution

We present an algorithm, based on the iteration of conformal maps, that produces independent samples of self-avoiding paths in the plane. It is a discrete process approximating radial Schramm-Loewner evolution growing to infinity. We focus on the problem of reproducing the parametrization corresponding to that of lattice models, namely self-avoiding walks on the lattice, and we propose a strategy that gives rise to discrete paths where consecutive points lie an approximately constant distance apart from each other. This new method allows us to tackle two non-trivial features of self-avoiding walks that critically depend on the parametrization: the asphericity of a portion of chain and the correction-to-scaling exponent.Comment: 18 pages, 4 figures. Some sections rewritten (including title and abstract), numerical results added, references added. Accepted for publication in J. Stat. Phy

Geometrical complexity of conformations of ring polymers under topological constraints

One measure of geometrical complexity of a spatial curve is the number of crossings in a planar projection of the curve. For $N$-noded ring polymers with a fixed knot type, we evaluate numerically the average of the crossing number over some directions. We find that the average crossing number under the topological constraint are less than that of no topological constraint for large $N$. The decrease of the geometrical complexity is significant when the thickness of polymers is small. The simulation with or without a topological constraint also shows that the average crossing number and the average size of ring polymers are independent measures of conformational complexity.Comment: 8 pages, 4figure

A review of Monte Carlo simulations of polymers with PERM

In this review, we describe applications of the pruned-enriched Rosenbluth method (PERM), a sequential Monte Carlo algorithm with resampling, to various problems in polymer physics. PERM produces samples according to any given prescribed weight distribution, by growing configurations step by step with controlled bias, and correcting "bad" configurations by "population control". The latter is implemented, in contrast to other population based algorithms like e.g. genetic algorithms, by depth-first recursion which avoids storing all members of the population at the same time in computer memory. The problems we discuss all concern single polymers (with one exception), but under various conditions: Homopolymers in good solvents and at the $\Theta$ point, semi-stiff polymers, polymers in confining geometries, stretched polymers undergoing a forced globule-linear transition, star polymers, bottle brushes, lattice animals as a model for randomly branched polymers, DNA melting, and finally -- as the only system at low temperatures, lattice heteropolymers as simple models for protein folding. PERM is for some of these problems the method of choice, but it can also fail. We discuss how to recognize when a result is reliable, and we discuss also some types of bias that can be crucial in guiding the growth into the right directions.Comment: 29 pages, 26 figures, to be published in J. Stat. Phys. (2011

Field theory and random walks

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Thicknesses of Knots

In this paper we define a set of radii called thickness for simple closed curves denoted by K, which are assumed to be differentiable. These radii capture a balanced view between the geometric and the topological properties of these curves. One can think of these radii as representing the thickness of a rope in space and of K as the core of the rope. Great care is taken to define our radii in order to gain freedom from small pieces with large curvature in the curve. Intuitively, this means that we tend to allow the surface of the ropes that represent the knots to deform into a non smooth surface. But as long as the radius of the rope is less than the thickness so defined, the surface of the rope will remain a two manifold and the rope (as a solid torus) can be deformed onto K via strong deformation retract. In this paper we explore basic properties of these thicknesses and discuss the relationship among them. Keywords: Knots, Thickness of Knots, Energy of Knots. 1. INTRODUCTION In this..

Exchange Symmetries in Motzkin Path and Bargraph Models of Copolymer Adsorption

In a previous work [26], by considering paths that are partially weighted, the generating function of Dyck paths was shown to possess a type of symmetry, called an exchange relation, derived from the exchange of a portion of the path between weighted and unweighted halves. This relation is particularly useful in solving for the generating functions of certain models of vertex-coloured Dyck paths; this is a directed model of copolymer adsorption, and in a particular case it is possible to find an asymptotic expression for the adsorption critical point of the model as a function of the colouring. In this paper we examine Motzkin path and partially directed walk models of the same adsorbing directed copolymer problem. These problems are an interesting generalisation of previous results since the colouring can be of either the edges, or the vertices, of the paths. We are able to find..