Related papers: Slipknotting in Random Diagrams
This paper details a series of experiments in searching for minimal energy configurations for knots and links using the computer program KnotPlot. The most interesting phenomena found in these experiments is the dependence of the…
In contrast with knots, whose properties depend only on their extrinsic topology in $S^3$, there is a rich interplay between the intrinsic structure of a graph and the extrinsic topology of all embeddings of the graph in $S^3$ . For…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
In a polydiagonal subspace of the Euclidean space, certain components of the vectors are equal (synchrony) or opposite (anti-synchrony). Polydiagonal subspaces invariant under a matrix have many applications in graph theory and dynamical…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
The main purpose of this paper is to present a kneading theory for two-dimensional triangular maps. This is done by defining a tensor product between the polynomials and matrices corresponding to the one-dimensional basis map and fiber map.…
The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich…
One of the most elusive challenges within the area of topological data analysis is understanding the distribution of persistence diagrams. Despite much effort, this is still largely an open problem. In this paper, we present a series of…
We present computer simulations to examine probability distributions of gyration radius for the no-thickness closed polymers of N straight segments of equal length. We are particularly interested in the conditional distributions when the…
We estimate by Monte Carlo simulations the configurational entropy of $N$-steps polygons in the cubic lattice with fixed knot type. By collecting a rich statistics of configurations with very large values of $N$ we are able to analyse the…
We define the knotting probability of a knot $K$ by the probability for a random polygon (RP) or self-avoiding polygon (SAP) of $N$ segments having the knot type $K$. We show fundamental and generic properties of the knotting probability…
The classical Thistlethwaite theorem for links can be phrased as asserting that the Kauffman bracket of a link can be obtained from an evaluation of the Bollob\'as-Riordan polynomial of a ribbon graph associated to one of the link's…
The unknotting number $u$ and the genus $g$ of braid positive knots are equal, as shown by Rudolph. We prove the stronger statement that any positive braid diagram of a genus $g$ knot contains $g$ crossings, such that changing them produces…
This paper visualizes a knot reduction algorithm
We work with a generalization of knot theory, in which one diagram is reachable from another via a finite sequence of moves if a fixed condition, regarding the existence of certain morphisms in an associated category, is satisfied for every…
Given a surface with boundary and some points on its boundary, a polygon diagram is a way to connect those points as vertices of non-overlapping polygons on the surface. Such polygon diagrams represent non-crossing permutations on a surface…
Knots are deeply entangled with every branch of science. One of the biggest open challenges in knot theory is to formalise a knot invariant that can unambiguously and efficiently distinguish any two knotted curves. Additionally, the…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…
Phase diagram of the ground states of DNA in a bad solvent is studied for a semi-flexible polymer model with a generalized local elastic bending potential characterized by a nonlinearity parameter $x$ and effective self-attraction promoting…
We describe a normal surface algorithm that decides whether a knot, with known degree of the colored Jones polynomial, satisfies the Strong Slope Conjecture. We also discuss possible simplifications of our algorithm and state related open…