Related papers: Slipknotting in Random Diagrams
We study knotted polymers in equilibrium with an array of obstacles which models confinement in a gel or immersion in a melt. We find a crossover in both the geometrical and the topological behavior of the polymer. When the polymers' radius…
Many invariants of knots rely upon smoothing the knot at its crossings. To compute them, it is necessary to know how to count the number of connected components the knot diagram is broken into after the smoothing. In this paper, it is shown…
We introduce and explore the relation between knot invariants and quiver representation theory, which follows from the identification of quiver quantum mechanics in D-brane systems representing knots. We identify various structural…
The probability of a random polygon (or a ring polymer) having a knot type $K$ should depend on the complexity of the knot $K$. Through computer simulation using knot invariants, we show that the knotting probability decreases exponentially…
A plane curve is a knot diagram in which each crossing is replaced by a 4-valent vertex, and so are dual to a subset of planar quadrangulations. The aim of this paper is to introduce a new tool for sampling diagrams via sampling of plane…
The space writhe of a knot is a property of its three-dimensional embedding that contains information about its underlying topology, but the correspondence between space writhe and other topological invariants is not fully understood. We…
Random graphs are more and more used for modeling real world networks such as evolutionary networks of proteins. For this purpose we look at two different models and analyze how properties like connectedness and degree distributions are…
We report on a computational study of the statics and dynamics of long flexible linear polymers that spontaneously knot and unknot. Specifically, the equilibrium self-entanglement properties, such as the knotting probability, knot length…
This paper is a survey of knot theory and invariants of knots and links from the point of view of categories of diagrams. The topics range from foundations of knot theory to virtual knot theory and topological quantum field theory.
In this paper, we generalize the \textit{Clock Theorem} of Formal Knot Theory to knotoids in $S^2$. The clock theorem implies that clock states of a knotoid diagram form a lattice under transpositions. These states form the basis of many…
Recent studies classify the topology of proteins by analysing the distribution of their projections using knotoids. The approximation of this distribution depends on the number of projection directions that are sampled. Here we investigate…
Proteins can sometimes be knotted, and for many reasons the study of knotted proteins is rapidly becoming very important. For example, it has been proposed that a knot increases the stability of a protein. Knots may also alter enzymatic…
This survey explores knot polynomials and their categorification, culminating in the homological invariants of knots. We begin with an overview of classical knot polynomials, progressing towards the superpolynomial and its role in unifying…
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the…
A polynomial knot in $\mathbb{R}^n$ is a smooth embedding of $\mathbb{R}$ in $\mathbb{R}^n$ such that the component functions are real polynomials. In the earlier paper with Mishra, we have studied the space $\mathcal{P}$ of polynomial…
Pseudodiagrams are diagrams of knots where some information about which strand goes over/under at certain crossings may be missing. Pseudoknots are equivalence classes of pseudodiagrams, with equivalence defined by a class of…
We study the dynamics of a knot in a semiflexible polymer confined to a narrow channel of width comparable to the polymers' persistence length. Using a combination of Brownian dynamics simulations and a coarse-grained stochastic model, we…
Using a lattice model of polymers in a tube, we define one way to characterise different configurations of a given knot as either "local" or "non-local" and, for several ring polymer models, we provide both theoretical and numerical…
This manuscript introduces a new framework for the study of knots by exploring the neighborhood of knot embeddings in the space of simple open and closed curves in 3-space. The latter gives rise to a knotoid spectrum, which determines the…
We present a general method for rendering representations of multi-stranded DNA complexes from textual descriptions into 2D diagrams. The complexes can be arbitrarily pseudoknotted, and if a planar rendering is possible, the method will…