Equilibrium size of large ring molecules

The equilibrium properties of isolated ring molecules were investigated using an off-lattice model with no excluded volume but with dynamics that preserve the topological class. Using an efficient set of long range moves, chains of more than 2000 monomers were studied. Despite the lack of any excluded volume interaction, the radius of gyration scaled like that of a self avoiding walk, as had been previously conjectured. However this scaling was only seen for chains greater than 500 monomers.Comment: 11 pages, 3 eps figures, latex, psfi

Topological effects in the thermal properties of knotted polymer rings

The topological effects on the thermal properties of several knot configurations are investigated using Monte Carlo simulations. In order to check if the topology of the knots is preserved during the thermal fluctuations we propose a method that allows very fast calculations and can be easily applied to arbitrarily complex knots. As an application, the specific energy and heat capacity of the trefoil, the figure-eight and the $8_1$ knots are calculated at different temperatures and for different lengths. Short-range repulsive interactions between the monomers are assumed. The knots configurations are generated on a three-dimensional cubic lattice and sampled by means of the Wang-Landau algorithm and of the pivot method. The obtained results show that the topological effects play a key role for short-length polymers. Three temperature regimes of the growth rate of the internal energy of the system are distinguished.Comment: 7 pages, 12 figures, LaTeX + RevTeX. With respect to the first version, in the second version the text has been improved and all figures are now in black and whit

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

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

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

Muscle metabolic and neuromuscular determinants of fatigue during cycling in different exercise intensity domains.

This is the author accepted manuscript. The final version is available from American Physiological Society via the DOI in this record.The lactate or gas exchange threshold (GET) and the critical power (CP) are closely associated with human exercise performance. We tested the hypothesis that the limit of tolerance (Tlim) during cycle exercise performed within the exercise intensity domains demarcated by GET and CP is linked to discrete muscle metabolic and neuromuscular responses. Eleven males performed a ramp incremental exercise test, 4-5 severe-intensity (SEV; >CP) constant-work-rate (CWR) tests until Tlim, a heavy-intensity (HVY; GET) CWR test until Tlim, and a moderate-intensity (MOD; 0.05) muscle metabolic milieu (i.e., low pH and [PCr] and high [lactate]) was attained at Tlim (~2-14 min) for all SEV exercise bouts. The muscle metabolic perturbation was greater at Tlim following SEV compared to HVY, and also following SEV and HVY compared to MOD (all P0.05). Neural drive to the VL increased during SEV (4±4%; P0.05). During SEV and HVY, but not MOD, the rates of change in M-wave amplitude and neural drive were correlated with changes in muscle metabolic ([PCr], [lactate]) and blood ionic/acid-base status ([lactate], [K(+)]) (P<0.05). The results of this study indicate that the metabolic and neuromuscular determinants of fatigue development differ according to the intensity domain in which the exercise is performed

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.

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

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

Numerical study of linear and circular model DNA chains confined in a slit: metric and topological properties

Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $\mu$m range and slits widths spanning continuously the 50--1250nm range. The metric scaling predicted by de Gennes' blob model is shown to hold for both linear and circularised DNA up to the strongest levels of confinement. More notably, the topological properties of the circularised DNA molecules have two major differences compared to three-dimensional confinement. First, the overall knotting probability is non-monotonic for increasing confinement and can be largely enhanced or suppressed compared to the bulk case by simply varying the slit width. Secondly, the knot population consists of knots that are far simpler than for three-dimensional confinement. The results suggest that nano-slits could be used in nano-fluidic setups to produce DNA rings having simple topologies (including the unknot) or to separate heterogeneous ensembles of DNA rings by knot type.Comment: 12 pages, 10 figure