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We study RNA foldings and investigate their topology using a combination of knot theory and embedded rigid vertex graphs. Knot theory has been helpful in modeling biomolecules, but classical knots place emphasis on a biomolecule's…

Geometric Topology · Mathematics 2022-07-28 Jose Ceniceros , Mohamed Elhamdadi , Josef Komissar , Hitakshi Lahrani

We find further evidence for the conjecture relating large N Chern-Simons theory on S^3 with topological string on the resolved conifold geometry by showing that the Wilson loop observable of a simple knot on S^3 (for any representation)…

High Energy Physics - Theory · Physics 2009-09-17 Hirosi Ooguri , Cumrun Vafa

Motivated by an amazing integrality structure conjecture for the $U(N)$ Chern-Simons quantum invariants of framed knots investigated by Mari\~no and Vafa, a new conjectural formula, named Hecke lifting conjecture, was proposed in…

Geometric Topology · Mathematics 2025-10-20 Shengmao Zhu

We claim that HOMFLY polynomials for virtual knots, defined with the help of the matrix-model recursion relations, contain more parameters, than just the usual $q$ and $A = q^N$. These parameters preserve topological invariance and do not…

High Energy Physics - Theory · Physics 2016-11-17 A. Morozov , An. Morozov , A. Popolitov

We give a geometric interpretation of Bar-Natan's universal invariant for the class of tangles in the 3-ball with four ends: we associate with such 4-ended tangles $T$ multicurves $\widetilde{\operatorname{BN}}(T)$, that is, collections of…

Geometric Topology · Mathematics 2019-12-18 Artem Kotelskiy , Liam Watson , Claudius Zibrowius

In this paper we discuss a pair of polynomial knot invariants $\Theta=(\Delta,\theta)$ which is: * Theoretically and practically fast: $\Theta$ can be computed in polynomial time. We can compute it in full on random knots with over 300…

Geometric Topology · Mathematics 2026-05-07 Dror Bar-Natan , Roland van der Veen

In this paper we work toward the HOMFLYPT skein module of $L(p, 1)$, $\mathcal{S}(L(p,1))$, via braids. Our starting point is the linear Turaev-basis, $\Lambda^{\prime}$, of the HOMFLYPT skein module of the solid torus ST, $\mathcal{S}({\rm…

Geometric Topology · Mathematics 2020-05-05 Ioannis Diamantis

We generalize Ng's two-variable algebraic/combinatorial $0$-th framed knot contact homology for framed oriented knots in $S^3$ to knots in $S^1 \times S^2$, and prove that the resulting knot invariant is the same as the framed cord algebra…

Quantum Algebra · Mathematics 2016-07-01 Shawn X. Cui , Zhenghan Wang

We extend the notion of intersection graphs for knots in the theory of finite type invariants to string links. We use our definition to develop weight systems for string links via the adjacency matrix of the intersection graph, and show…

Geometric Topology · Mathematics 2007-05-23 Blake Mellor

We define relative versions of the classical invariants of Legendrian and transverse knots in contact 3-manifolds for knots that are homologous to a fixed reference knot. We show these invariants are well-defined and give some basic…

Symplectic Geometry · Mathematics 2009-09-25 Georgi D. Gospodinov

This article is about applications of linear algebra to knot theory. For example, for odd prime p, there is a rule (given in the article) for coloring the arcs of a knot or link diagram from the residues mod p. This is a knot invariant in…

Geometric Topology · Mathematics 2018-04-10 Louis H. Kauffman , Pedro Lopes

We define a triply-graded invariant of links in a genus g handlebody, generalizing the colored HOMFLYPT (co)homology of links in the 3-ball. Our main tools are the description of these links in terms of a subgroup of the classical braid…

Quantum Algebra · Mathematics 2023-09-20 David E. V. Rose , Daniel Tubbenhauer

We study the properties of glued knots, a sub-class of real rational knots, that can be constructed by gluing ellipses. We define an invariant called the gluing degree and relate it to various classical properties of knots and classify all…

Geometric Topology · Mathematics 2021-07-28 Shane D'Mello , Vinay Gaba

Knot contact homology is an ambient isotopy invariant of knots and links in $\mathbb R^3$. The purpose of this paper is to extend this definition to an ambient isotopy invariant of tangles and prove that gluing of tangles gives a gluing…

Symplectic Geometry · Mathematics 2024-10-16 Johan Asplund

We enhance the quandle coloring quiver invariant of oriented knots and links with quandle modules. This results in a two-variable polynomial invariant with specializes to the previous quandle module polynomial invariant as well as to the…

Geometric Topology · Mathematics 2020-11-12 Karma Istanbouli , Sam Nelson

HOMFLYPT polynomials of knots in the 3-sphere in symmetric representations satisfy recursion relations. Their geometric origin is holomorphic curves at infinity on knot conormals that determine a $D$-module with characteristic variety the…

Symplectic Geometry · Mathematics 2024-07-17 Tobias Ekholm , Pietro Longhi , Lukas Nakamura

This article surveys the use of configuration space integrals in the study of the topology of knot and link spaces. The main focus is the exposition of how these integrals produce finite type invariants of classical knots and links. More…

Geometric Topology · Mathematics 2013-10-29 Ismar Volic

We construct analogs of Khovanov-Jacobsson classes and the Rasmussen invariant for links in the boundary of any smooth oriented 4-manifold. The main tools are skein lasagna modules based on equivariant and deformed versions of…

Geometric Topology · Mathematics 2026-03-06 Kim Morrison , Kevin Walker , Paul Wedrich

In this short survey article we collect the current state of the art in the nascent field of \textit{quantum enhancements}, a type of knot invariant defined by collecting values of quantum invariants of knots with colorings by various…

Geometric Topology · Mathematics 2026-02-19 Sam Nelson

We compute the invariants for a class of knots and links in arbitrary representations in $S^3/\mathbb{Z}_p$ in the large $k$ (level), large $N$ (rank) limit, keeping $N/(k+N)=\lambda$ fixed, in $U(N)$ and $Sp(N)$ Chern-Simons theories.…

High Energy Physics - Theory · Physics 2022-02-25 Kushal Chakraborty , Suvankar Dutta