Characteristic length of random knotting for cylindrical self-avoiding polygons

We discuss the probability of random knotting for a model of self-avoiding polygons whose segments are given by cylinders of unit length with radius $r$. We show numerically that the characteristic length of random knotting is roughly approximated by an exponential function of the chain thickness $r$.Comment: 5 pages, 4 figure

Topological entropy of a stiff ring polymer and its connection to DNA knots

We discuss the entropy of a circular polymer under a topological constraint. We call it the {\it topological entropy} of the polymer, in short. A ring polymer does not change its topology (knot type) under any thermal fluctuations. Through numerical simulations using some knot invariants, we show that the topological entropy of a stiff ring polymer with a fixed knot is described by a scaling formula as a function of the thickness and length of the circular chain. The result is consistent with the viewpoint that for stiff polymers such as DNAs, the length and diameter of the chains should play a central role in their statistical and dynamical properties. Furthermore, we show that the new formula extends a known theoretical formula for DNA knots.Comment: 14pages,11figure

Subclass Discriminant Analysis of Morphological and Textural Features for HEp-2 Staining Pattern Classification

Classifying HEp-2 fluorescence patterns in Indirect Immunofluorescence (IIF) HEp-2 cell imaging is important for the differential diagnosis of autoimmune diseases. The current technique, based on human visual inspection, is time-consuming, subjective and dependent on the operator's experience. Automating this process may be a solution to these limitations, making IIF faster and more reliable. This work proposes a classification approach based on Subclass Discriminant Analysis (SDA), a dimensionality reduction technique that provides an effective representation of the cells in the feature space, suitably coping with the high within-class variance typical of HEp-2 cell patterns. In order to generate an adequate characterization of the fluorescence patterns, we investigate the individual and combined contributions of several image attributes, showing that the integration of morphological, global and local textural features is the most suited for this purpose. The proposed approach provides an accuracy of the staining pattern classification of about 90%

Detecting all regular polygons in a point set

In this paper, we analyze the time complexity of finding regular polygons in a set of n points. We combine two different approaches to find regular polygons, depending on their number of edges. Our result depends on the parameter alpha, which has been used to bound the maximum number of isosceles triangles that can be formed by n points. This bound has been expressed as O(n^{2+2alpha+epsilon}), and the current best value for alpha is ~0.068. Our algorithm finds polygons with O(n^alpha) edges by sweeping a line through the set of points, while larger polygons are found by random sampling. We can find all regular polygons with high probability in O(n^{2+alpha+epsilon}) expected time for every positive epsilon. This compares well to the O(n^{2+2alpha+epsilon}) deterministic algorithm of Brass.Comment: 11 pages, 4 figure

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