Related papers: Knotting statistics for polygons in lattice tubes
Knots are commonly found in molecular chains such as DNA and proteins, and they have been considered to be useful models for structural analysis of these molecules. One interested quantity is the minimum number of monomers necessary to…
The theory of tunnel number 1 knots detailed in our previous paper, The tree of knot tunnels, provides a non-negative integer invariant called the depth of the tunnel. We give various results related to the depth invariant. Noting that it…
Twisting a given knot $K$ about an unknotted circle $c$ a full $n \in \mathbb{N}$ times, we obtain a "twist family" of knots $\{ K_n \}$. Work of Kouno-Motegi-Shibuya implies that for a non-trivial twist family the crossing numbers…
We define the notion of a knot type having Legendrian large cables and show that having this property implies that the knot type is not uniformly thick. Moreover, there are solid tori in this knot type that do not thicken to a solid torus…
We consider the large-$N$ asymptotics of a system of discrete orthogonal polynomials on an infinite regular lattice of mesh $\frac{1}{N}$, with weight $e^{-NV(x)}$, where $V(x)$ is a real analytic function with sufficient growth at…
We present an update on the study of topological structure of QCD. Issues addressed include a comparison between the plaquette and the geometric methods of calculating the topological density. We show that the improved gauge action based on…
Two geometric spaces are in the same topological class if they are related by certain geometric deformations. We propose machine learning methods that automate learning of topological invariance and apply it in the context of knot theory,…
A polynomial is presented that models a topological knot in a unique manner. It distinguishes all types of knots including the orientation and has a group theory interpretation. The topologies may be labeled via a number, which upon a base…
Scaling arguments are used to analyze the size of topologically constrained closed ring polymer with excluded volume. It is found that there exists a finite range of polymer thickness (excluded volume) in which self-avoidance is unimportant…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
Under certain topological assumptions, we show that two monotone Lagrangian submanifolds embedded in the standard symplectic vector space with the same monotonicity constant cannot link one another and that, individually, their smooth knot…
A construction of polytopes is given based on integers. These geometries are constructed through a mapping to pure numbers and have multiple applications, including statistical mechanics and computer science. The number form is useful in…
Recent measurements of the force versus extension curves in stretched single stranded DNA, under conditions where the hydrogen bonding between complementary bases is inhibited, provide a new handle for the study of self-avoiding effects in…
We study solutions of three-term recurrence relations whose $N$-step transfer matrices belong to the uniform Stolz class. In particular, we derive the first order of their uniform asymptotics. For orthonormal polynomials we show more.…
We develop a theoretical description of the topological disentanglement occurring when torus knots reach the ends of a semi-flexible polymer under tension. These include decays into simpler knots and total unknotting. The minimal number of…
We present a general construction of divergence-free knotted vector fields from complex scalar fields, whose closed field lines encode many kinds of knots and links, including torus knots, their cables, the figure-8 knot and its…
We study numerically the tightness of prime flat knots in a model of self-attracting polymers with excluded volume. We find that these knots are localised in the high temperature swollen regime, but become delocalised in the low temperature…
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…
Diffusion properties of a self-avoiding polymer embedded in regularly distributed obstacles with spacing a=20 and confined in two dimensions is studied numerically using the extended bond fluctuation method which we have developed recently.…
We elaborate one- and two-dimensional (1D and 2D) models of media with self-repulsive cubic nonlinearity, whose local strength is subject to spatial modulation that admits the existence of flat-top solitons of various types, including…