Topological constraints on spiral wave dynamics in spherical geometries with inhomogeneous excitability

We analyze the way topological constraints and inhomogeneity in the excitability influence the dynamics of spiral waves on spheres and punctured spheres of excitable media. We generalize the definition of an index such that it characterizes not only each spiral but also each hole in punctured, oriented, compact, two-dimensional differentiable manifolds and show that the sum of the indices is conserved and zero. We also show that heterogeneity and geometry are responsible for the formation of various spiral wave attractors, in particular, pairs of spirals in which one spiral acts as a source and a second as a sink -- the latter similar to an antispiral. The results provide a basis for the analysis of the propagation of waves in heterogeneous excitable media in physical and biological systems.Comment: 5 pages, 6 Figures, major revisions, accepted for publication in Phys. Rev.

The Compressibility of Minimal Lattice Knots

The (isothermic) compressibility of lattice knots can be examined as a model of the effects of topology and geometry on the compressibility of ring polymers. In this paper, the compressibility of minimal length lattice knots in the simple cubic, face centered cubic and body centered cubic lattices are determined. Our results show that the compressibility is generally not monotonic, but in some cases increases with pressure. Differences of the compressibility for different knot types show that topology is a factor determining the compressibility of a lattice knot, and differences between the three lattices show that compressibility is also a function of geometry.Comment: Submitted to J. Stat. Mec

Minimal knotted polygons in cubic lattices

An implementation of BFACF-style algorithms on knotted polygons in the simple cubic, face centered cubic and body centered cubic lattice is used to estimate the statistics and writhe of minimal length knotted polygons in each of the lattices. Data are collected and analysed on minimal length knotted polygons, their entropy, and their lattice curvature and writhe

Entropic Tightening of Vibrated Chains

We investigate experimentally the distribution of configurations of a ring with an elementary topological constraint, a ``figure-8'' twist. Using vibrated granular chains, which permit controlled preparation and direct observation of such a constraint, we show that configurations where one of the loops is tight and the second is large are strongly preferred. This agrees with recent predictions for equilibrium properties of topologically-constrained polymers. However, the dynamics of the tightening process weakly violate detailed balance, a signature of the nonequilibrium nature of this system.Comment: 4 pages, 4 figure

Knot localization in adsorbing polymer rings

We study by Monte Carlo simulations a model of knotted polymer ring adsorbing onto an impenetrable, attractive wall. The polymer is described by a self-avoiding polygon (SAP) on the cubic lattice. We find that the adsorption transition temperature, the crossover exponent $\phi$ and the metric exponent $\nu$, are the same as in the model where the topology of the ring is unrestricted. By measuring the average length of the knotted portion of the ring we are able to show that adsorbed knots are localized. This knot localization transition is triggered by the adsorption transition but is accompanied by a less sharp variation of the exponent related to the degree of localization. Indeed, for a whole interval below the adsorption transition, one can not exclude a contiuous variation with temperature of this exponent. Deep into the adsorbed phase we are able to verify that knot localization is strong and well described in terms of the flat knot model.Comment: 27 pages, 10 figures. Submitter to Phys. Rev.

Critical exponents for random knots

The size of a zero thickness (no excluded volume) polymer ring is shown to scale with chain length $N$ in the same way as the size of the excluded volume (self-avoiding) linear polymer, as $N^{\nu}$, where $\nu \approx 0.588$. The consequences of that fact are examined, including sizes of trivial and non-trivial knots.Comment: 4 pages, 0 figure

On the Dominance of Trivial Knots among SAPs on a Cubic Lattice

The knotting probability is defined by the probability with which an $N$-step self-avoiding polygon (SAP) with a fixed type of knot appears in the configuration space. We evaluate these probabilities for some knot types on a simple cubic lattice. For the trivial knot, we find that the knotting probability decays much slower for the SAP on the cubic lattice than for continuum models of the SAP as a function of $N$. In particular the characteristic length of the trivial knot that corresponds to a `half-life' of the knotting probability is estimated to be $2.5 \times 10^5$ on the cubic lattice.Comment: LaTeX2e, 21 pages, 8 figur

Abundance of unknots in various models of polymer loops

A veritable zoo of different knots is seen in the ensemble of looped polymer chains, whether created computationally or observed in vitro. At short loop lengths, the spectrum of knots is dominated by the trivial knot (unknot). The fractional abundance of this topological state in the ensemble of all conformations of the loop of $N$ segments follows a decaying exponential form, $\sim \exp (-N/N_0)$, where $N_0$ marks the crossover from a mostly unknotted (ie topologically simple) to a mostly knotted (ie topologically complex) ensemble. In the present work we use computational simulation to look closer into the variation of $N_0$ for a variety of polymer models. Among models examined, $N_0$ is smallest (about 240) for the model with all segments of the same length, it is somewhat larger (305) for Gaussian distributed segments, and can be very large (up to many thousands) when the segment length distribution has a fat power law tail.Comment: 13 pages, 6 color figure

The Computational Complexity of Knot and Link Problems

We consider the problem of deciding whether a polygonal knot in 3-dimensional Euclidean space is unknotted, capable of being continuously deformed without self-intersection so that it lies in a plane. We show that this problem, {\sc unknotting problem} is in {\bf NP}. We also consider the problem, {\sc unknotting problem} of determining whether two or more such polygons can be split, or continuously deformed without self-intersection so that they occupy both sides of a plane without intersecting it. We show that it also is in NP. Finally, we show that the problem of determining the genus of a polygonal knot (a generalization of the problem of determining whether it is unknotted) is in {\bf PSPACE}. We also give exponential worst-case running time bounds for deterministic algorithms to solve each of these problems. These algorithms are based on the use of normal surfaces and decision procedures due to W. Haken, with recent extensions by W. Jaco and J. L. Tollefson.Comment: 32 pages, 1 figur

Knotting probabilities after a local strand passage in unknotted self-avoiding polygons

We investigate the knotting probability after a local strand passage is performed in an unknotted self-avoiding polygon on the simple cubic lattice. We assume that two polygon segments have already been brought close together for the purpose of performing a strand passage, and model this using Theta-SAPs, polygons that contain the pattern Theta at a fixed location. It is proved that the number of n-edge Theta-SAPs grows exponentially (with n) at the same rate as the total number of n-edge unknotted self-avoiding polygons, and that the same holds for subsets of n-edge Theta-SAPs that yield a specific after-strand-passage knot-type. Thus the probability of a given after-strand-passage knot-type does not grow (or decay) exponentially with n, and we conjecture that instead it approaches a knot-type dependent amplitude ratio lying strictly between 0 and 1. This is supported by critical exponent estimates obtained from a new maximum likelihood method for Theta-SAPs that are generated by a composite (aka multiple) Markov Chain Monte Carlo BFACF algorithm. We also give strong numerical evidence that the after-strand-passage knotting probability depends on the local structure around the strand passage site. Considering both the local structure and the crossing-sign at the strand passage site, we observe that the more "compact" the local structure, the less likely the after-strand-passage polygon is to be knotted. This trend is consistent with results from other strand-passage models, however, we are the first to note the influence of the crossing-sign information. Two measures of "compactness" are used: the size of a smallest polygon that contains the structure and the structure's "opening" angle. The opening angle definition is consistent with one that is measurable from single molecule DNA experiments.Comment: 31 pages, 12 figures, submitted to Journal of Physics