Related papers: Slipknotting in Random Diagrams
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…
The knots-quivers correspondence states that various characteristics of a knot are encoded in the corresponding quiver and the moduli space of its representations. However, this correspondence is not a bijection: more than one quiver may be…
We discuss an "extrinsic" property of knots in a 3-subspace of the 3-sphere $S^3$ to characterize how the subspace is embedded in $S^3$. Specifically, we show that every knot in a subspace of the 3-sphere is transient if and only if the…
The topological framework of circuit topology has recently been introduced to complement knot theory and to help in understanding the physics of molecular folding. Naturally evolved linear molecular chains, such as proteins and nucleic…
A generalization of the Lorenz equations is proposed where the variables take values in a Lie algebra. The finite dimensionality of the representation encodes the quantum fluctuations, while the non-linear nature of the equations can…
In this paper we introduce a representation of knots and links called a cube diagram. We show that a property of a cube diagram is a link invariant if and only if the property is invariant under two types of cube diagram operations. A knot…
There are several examples of spaces of univariate functions for which we have a characterization of all sets of knots which are poised for the interpolation problem. For the standard spaces of univariate polynomials, or spline functions…
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…
A small fraction of all protein structures characterized so far are entangled. The challenge of understanding the properties of these knotted proteins, and the why and the how of their natural folding process, has been taken up in the past…
A stretched DNA molecule which is also under- or overwound, undergoes a buckling transition forming intertwined looped domains called plectonemes. Here we develop a simple theory that extends the two-phase model of stretched supercoiled…
We propose a mechanism in which two molecular knots pass through each other and swap positions along a polymer strand. Associated free energy barriers in our simulations only amount to a few $k_{B}T$, which may enable the interchange of…
Pseudodiagrams are knot or link diagrams where some of the crossing information is missing. Pseudoknots are equivalence classes of pseudodiagrams, where equivalence is generated by a natural set of Reidemeister moves. In this paper, we…
We examine computer experiments that can be performed to understand the dynamics of knots under self-repulsion. In the course of specific computer exploration we use the knot theory of rational knots and rational tangles to produce classes…
Inspired by how certain proteins "sense" knots and entanglements in DNA molecules, here we ask if there exist local geometric features that may be used as a read-out of the underlying topology of generic polymers. We perform molecular…
The Knot Entropy Conjecture states that the exponential growth rate of the number of $n$-edge lattice polygons with knot-type $K$ is the same as that for unknot polygons. Moreover, the next order growth follows a power law in $n$ with an…
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called…
An U(N)-invariant matrix model with d matrix variables is studied. It was shown that in the limit $N\to \infty $ and $d\to 0$ the model describes the knot diagrams. We realize the free partition function of the matrix model as the…
We investigate the effect of knot type on the properties of a ring polymer confined to a slit. For relatively wide slits, the more complex the knot, the more the force exerted by the polymer on the walls is decreased compared to an…
A string figure is topologically a trivial knot lying on an imaginary plane orthogonal to the fingers with some crossings. The fingers prevent cancellation of these crossings. As a mathematical model of string figure we consider a knot…
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…