Related papers: Slipknotting in Random Diagrams
Simulations of knotting and unknotting in polymers or other filaments rely on random processes to facilitate topological changes. Here we introduce a method of \textit{topological steering} to determine the optimal pathway by which a…
We consider a natural model of random knotting- choose a knot diagram at random from the finite set of diagrams with n crossings. We tabulate diagrams with 10 and fewer crossings and classify the diagrams by knot type, allowing us to…
We study random knotting by considering knot and link diagrams as decorated, (rooted) topological maps on spheres and pulling them uniformly from among sets of a given number of vertices $n$, as first established in recent work with…
Knots are commonly represented and manipulated via diagrams, which are decorated planar graphs. When such a knot diagram has low treewidth, parameterized graph algorithms can be leveraged to ensure the fast computation of many invariants…
Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that…
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…
In the classical knot theory there is a well-known notion of descending diagram. From an arbitrary diagram one can easily obtain, by some crossing changes, a descending diagram which is a diagram of the unknot or unlink. In this paper the…
We introduce and study knotoids. Knotoids are represented by diagrams in a surface which differ from the usual knot diagrams in that the underlying curve is a segment rather than a circle. Knotoid diagrams are considered up to Reidemeister…
We consider the probability of knotting in equilateral random polygons in Euclidean 3-dimensional space, which model, for instance, random polymers. Results from an extensive Monte Carlo dataset of random polygons indicate a universal…
The lectures review the state of affairs in modern branch of mathematical physics called probabilistic topology. In particular we consider the following problems: (i) We estimate the probability of a trivial knot formation on the lattice…
In this paper, we study random embeddings of polymer networks distributed according to any potential energy which can be expressed in terms of distances between pairs of monomers. This includes freely jointed chains, steric effects,…
A knot is an an embedding of a circle into three-dimensional space. We say that a knot is unknotted if there is an ambient isotopy of the embedding to a standard circle. By representing knots via planar diagrams, we discuss the problem of…
Many experiments have been done to determine the relative strength of different knots, and these show that the break in a knotted rope almost invariably occurs at a point just outside the `entrance' to the knot. The influence of knots on…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
We explore free knot diagrams, which are projections of knots into the plane which don't record over/under data at crossings. We consider the combinatorial question of which free knot diagrams give which knots and with what probability.…
Knotted proteins, when forced through the pores, can get stuck if the knots in their backbone tighten under force. Alternatively, the knot can slide off the chain, making translocation possible. We construct a simple energy landscape model…
Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of the existence of alternative…
A number of recently discovered protein structures incorporate a rather unexpected structural feature: a knot in the polypeptide backbone. These knots are extremely rare, but their occurrence is likely connected to protein function in as…
In this article we discuss applications of neural networks to recognising knots and, in particular, to the unknotting problem. One of motivations for this study is to understand how neural networks work on the example of a problem for which…