Related papers: Capturing knots in polymers
The work in this article is inspired by a classical problem: the statistical physical properties of a closed polymer loop that is wound around a rod. Historically the preserved topology of this system has been addressed through…
The role of the topology and its relation with the geometry of biopolymers under different physical conditions is a nontrivial and interesting problem. Aiming at understanding this issue for a related simpler system, we use Monte Carlo…
We study how confinement affects topology and conformations in polymer films of varying thickness $h$. The knotting probability exhibits a maximum at intermediate thicknesses near the bulk radius of gyration $h \approx R_\mathrm{g,bulk}$,…
The statistical mechanics of a long knotted collapsed polymer is determined by a free-energy with a knot-dependent subleading term, which is linked to the length of the shortest polymer that can hold such knot. The only other parameter…
We point out the connection between mathematical knot theory and spin glass/search problem. In particular, we present a statistical mechanical formulation of the problem of computing a knot invariant; p-colorability problem, which provides…
Using canonical Monte Carlo simulations, we introduce a new numerical procedure for comparing the entropic exponents of polymers with different constraints and/or topologies. Setting up competitions between polymer segments which can…
We present a row reduction algorithm to compute the barcode decomposition of persistence modules. This algorithm dualises the standard persistence one and clarifies the symmetry between clear and compress optimisations.
Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible…
We prove that any knot or link in any 3-manifold can be nicely decomposed (splitted) by a filling Dehn sphere. This has interesting consequences in the study of branched coverings over knots and links. We give an algorithm for computing…
These notes present two normal surface theory algorithms to detect the unknot and use the split-link algorithm to prove that the figure-eight knot is knotted.
We have examined the behaviors of a knotted linear polymer in narrow tubes using Langevin dynamics simulation to investigate the knot localization property in one-dimensional (1D) geometry. We have found that the knot is strongly localized…
We present an elementary introduction to one of the most important today knot theory approaches, which gives rise to a representation for a class of knot polynomials in terms of quantum groups. Historically, the approach was at the same…
In this paper the new model of plastic deformation is constructed. For classification of plastic statuses the theory of knot is used.
We analyze the connections between the mathematical theory of knots and quantum physics by addressing a number of algorithmic questions related to both knots and braid groups. Knots can be distinguished by means of `knot invariants', among…
The entropic pressure in the vicinity of a cubic lattice knot is examined as a model of the entropic pressure near a knotted ring polymer in a good solvent. A model for the scaling of the pressure is developed and this is tested numerically…
This paper builds a novel bridge between algebraic coding theory and mathematical knot theory, with applications in both directions. We give methods to construct error-correcting codes starting from the colorings of a knot, describing…
Given a knot or link in the form of plat closure of a braid, we describe an algorithm to obtain a braid representing the same knot or link with the standard closure, and vice-versa. We analyze the three cases of knots and links: in…
Knot theory is the Mathematical study of knots. In this paper we have studied the Composition of two knots. Knot theory belongs to Mathematical field of Topology, where the topological concepts such as topological spaces, homeomorphisms,…
The study of knots and links from a probabilistic viewpoint provides insight into the behavior of "typical" knots, and opens avenues for new constructions of knots and other topological objects with interesting properties. The knotting of…
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…