Related papers: RNA foldings and Stuck Knots

Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops. This shape-projection preserves the…

In this paper we study $\gamma$-structures filtered by topological genus. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A…

We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…

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.…

Deformations of knots and links in ambient space can be studied combinatorially on their diagrams via local modifications called Reidemeister moves. While it is well-known that, in order to move between equivalent diagrams with Reidemeister…

The growing significance of RNA engineering in diverse biological applications has spurred interest in developing AI methods for structure-based RNA design. While diffusion models have excelled in protein design, adapting them for RNA…

RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of…

We describe a new method for combinatorially computing the transverse invariant in knot Floer homology. Previous work of the authors and Stone used braid diagrams to combinatorially compute knot Floer homology of braid closures. However,…

Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…

We point out the connection between mathematical knot theory and spin glass/search problem. In particular, we present a statistical mechanical formulation of the problem of computing a knot invariant; p-colorability problem, which provides…

Multi-virtual knot theory was introduced in $2024$ by the first author. In this paper, we initiate the study of algebraic invariants of multi-virtual links. After determining a generating set of (oriented) multi-virtual Reidemeister moves,…

Knot contact homology studies symplectic and contact geometric properties of conormals of knots in 3-manifolds using holomorphic curve techniques. It has connections to both mathematical and physical theories. On the mathematical side, we…

mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses…

The primary objects of study in the ``knot theory of complex plane curves'' are C-links: links (or knots) cut out of a 3-sphere in the complex plane by complex plane transverse and totally tangential. Transverse C-links are naturally…

Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…

Using the duality between Wilson loop expectation values of SU(N) Chern-Simons theory on $S^3$ and topological open-string amplitudes on the local mirror of the resolved conifold, we study knots on $S^3$ and their invariants encoded in…

In the past decade, topological data analysis (TDA) has emerged as a powerful approach in data science. The main technique in TDA is persistent homology, which tracks topological invariants over the filtration of point cloud data using…

We provide a way to produce knots in $S^3$ from signed chord diagrams, and prove that every knot can be produced in this way. Using these diagrams, we generalize the fundamental theorem of finite type invariants. We also provide moves for…

Knots and links are fascinating and intricate topological objects. Their influence spans from DNA and molecular chemistry to vortices in superfluid helium, defects in liquid crystals and cosmic strings in the early universe. Here, we find…

The conventional topological description given by the fundamental group of nematic order parameter does not adequately explain the entangled defect line structures that have been observed in nematic colloids. We introduce a new topological…