Lattice Knots in a Slab

In this paper the number and lengths of minimal length lattice knots confined to slabs of width $L$, is determined. Our data on minimal length verify the results by Sharein et.al. (2011) for the similar problem, expect in a single case, where an improvement is found. From our data we construct two models of grafted knotted ring polymers squeezed between hard walls, or by an external force. In each model, we determine the entropic forces arising when the lattice polygon is squeezed by externally applied forces. The profile of forces and compressibility of several knot types are presented and compared, and in addition, the total work done on the lattice knots when it is squeezed to a minimal state is determined

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

Partially directed paths in a wedge

The enumeration of lattice paths in wedges poses unique mathematical challenges. These models are not translationally invariant, and the absence of this symmetry complicates both the derivation of a functional recurrence for the generating function, and solving for it. In this paper we consider a model of partially directed walks from the origin in the square lattice confined to both a symmetric wedge defined by $Y = \pm pX$, and an asymmetric wedge defined by the lines $Y= pX$ and Y=0, where $p > 0$ is an integer. We prove that the growth constant for all these models is equal to $1+\sqrt{2}$, independent of the angle of the wedge. We derive functional recursions for both models, and obtain explicit expressions for the generating functions when $p=1$. From these we find asymptotic formulas for the number of partially directed paths of length $n$ in a wedge when $p=1$. The functional recurrences are solved by a variation of the kernel method, which we call the ``iterated kernel method''. This method appears to be similar to the obstinate kernel method used by Bousquet-Melou. This method requires us to consider iterated compositions of the roots of the kernel. These compositions turn out to be surprisingly tractable, and we are able to find simple explicit expressions for them. However, in spite of this, the generating functions turn out to be similar in form to Jacobi $\theta$-functions, and have natural boundaries on the unit circle.Comment: 26 pages, 5 figures. Submitted to JCT

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

Punctured polygons and polyominoes on the square lattice

We use the finite lattice method to count the number of punctured staircase and self-avoiding polygons with up to three holes on the square lattice. New or radically extended series have been derived for both the perimeter and area generating functions. We show that the critical point is unchanged by a finite number of punctures, and that the critical exponent increases by a fixed amount for each puncture. The increase is 1.5 per puncture when enumerating by perimeter and 1.0 when enumerating by area. A refined estimate of the connective constant for polygons by area is given. A similar set of results is obtained for finitely punctured polyominoes. The exponent increase is proved to be 1.0 per puncture for polyominoes.Comment: 36 pages, 11 figure

Confinement of knotted polymers in a slit

We investigate the effect of knot type on the properties of a ring polymer confined to a slit. For relatively wide slits, the more complex the knot, the more the force exerted by the polymer on the walls is decreased compared to an unknotted polymer of the same length. For more narrow slits the opposite is true. The crossover between these two regimes is, to first order, at smaller slit width for more complex knots. However, knot topology can affect these trends in subtle ways. Besides the force exerted by the polymers, we also study other quantities such as the monomer-density distribution across the slit and the anisotropic radius of gyration.Comment: 9 pages, 6 figures, submitted for publicatio

Fasting plasma glucose and risk factor assessment: Comparing sensitivity and specificity in identifying gestational diabetes in urban black African women

Background. Identifying women with gestational diabetes mellitus (GDM) allows interventions to improve perinatal outcomes. A fasting plasma glucose (FPG) level ≥5.1 mmol/L is 100% specific for a diagnosis of GDM. The International Association of Diabetes and Pregnancy Study Groups acknowledges that FPG <4.5 mmol/L is associated with a low probability of GDM.Objectives. The validity of selective screening based on the presence of risk factors was compared with the universal application of FPG ≥4.5 mmol/L to identify women with GDM. FPG ≥4.5 mmol/L or the presence of one or more risk factors was assumed to indicate an intermediate to high risk of GDM and therefore the need for an oral glucose tolerance test (OGTT).Methods. Consecutive black South African (SA) women were recruited to a 2-hour 75 g OGTT at 24 - 28 weeks’ gestation in an urban community health clinic. Of 969 women recruited, 666 underwent an OGTT, and of these 589 were eligible for analysis. The glucose oxidase laboratory method was used to measure plasma glucose concentrations. The World Health Organization GDM diagnostic criteria were applied. All participants underwent a risk factor assessment. The χ2 test was used to determine associations between risk factors and a positive diagnosis of GDM. The sensitivity and specificity of a positive diagnosis of GDM were calculated for FPG ≥4.5 mmol/L, FPG ≥5.1 mmol/L, and the presence of one or more risk factors.Results. The prevalence of overt diabetes mellitus and GDM was 0.5% and 7.0%, respectively. Risk factor-based selective screening indicated that 204/589 (34.6%) of participants needed an OGTT, but 18/41 (43.9%) of positive GDM diagnoses were missed. Universal screening using the FPG threshold of ≥4.5 mmol/L indicated that 152/589 (25.8%) of participants needed an OGTT, and 1/41 (2.4%) of positive diagnoses were missed. An FPG of ≥5.1 mmol/L identified 36/41 (87.8%) of GDM-positive participants. The sensitivity and specificity of the presence of one or more risk factors were 56% and 67%, respectively. The sensitivity and specificity of FPG ≥4.5 mmol/L were 98% and 80%, respectively.Conclusions. Universal screening using FPG ≥4.5 mmol/L had greater sensitivity and specificity in identifying GDM-affected women and required fewer women to undergo a resource-intensive diagnostic OGTT than risk factor-based selective screening. A universal screening strategy using FPG ≥4.5 mmol/L may be more efficient and cost-effective than risk factor-based selective screening for GDM in black SA women.

Collapsing lattice animals and lattice trees in two dimensions

We present high statistics simulations of weighted lattice bond animals and lattice trees on the square lattice, with fugacities for each non-bonded contact and for each bond between two neighbouring monomers. The simulations are performed using a newly developed sequential sampling method with resampling, very similar to the pruned-enriched Rosenbluth method (PERM) used for linear chain polymers. We determine with high precision the line of second order transitions from an extended to a collapsed phase in the resulting 2-dimensional phase diagram. This line includes critical bond percolation as a multicritical point, and we verify that this point divides the line into two different universality classes. One of them corresponds to the collapse driven by contacts and includes the collapse of (weakly embeddable) trees, but the other is {\it not yet} bond driven and does not contain the Derrida-Herrmann model as special point. Instead it ends at a multicritical point $P^*$ where a transition line between two collapsed phases (one bond-driven and the other contact-driven) sparks off. The Derrida-Herrmann model is representative for the bond driven collapse, which then forms the fourth universality class on the transition line (collapsing trees, critical percolation, intermediate regime, and Derrida-Herrmann). We obtain very precise estimates for all critical exponents for collapsing trees. It is already harder to estimate the critical exponents for the intermediate regime. Finally, it is very difficult to obtain with our method good estimates of the critical parameters of the Derrida-Herrmann universality class. As regards the bond-driven to contact-driven transition in the collapsed phase, we have some evidence for its existence and rough location, but no precise estimates of critical exponents.Comment: 11 pages, 16 figures, 1 tabl

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.