Related papers: RNA foldings and Stuck Knots
Knotted line defects in continuous fields entrain a complex arrangement of the material sur- rounding them. Recent experimental realisations in optics, fluids and nematic liquid crystals make it important to fully characterise these…
This is a report on our ongoing research on a combinatorial approach to knot recognition, using coloring of knots by certain algebraic objects called quandles. The aim of the paper is to summarize the mathematical theory of knot coloring in…
In this paper, we study a geometric/topological measure of knots and links called the nullification number. The nullification of knots/links is believed to be biologically relevant. For example, in DNA topology, one can intuitively regard…
This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…
We establish a version of Seiberg--Witten Floer $K$-theory for knots, as well as a version of Seiberg-Witten Floer $K$-theory for 3-manifolds with involution. The main theorems are 10/8-type inequalities for knots and for involutions. The…
Optical knots and links have attracted great attention because of their exotic topological characteristics. Recent investigations have shown that the information encoding based on optical knots could possess robust features against external…
Ng constructed an invariant of knots in ${\mathbb{R}}^3$, a combinatorial knot contact homology. Extending his study, we construct an invariant of surface-knots in ${\mathbb{R}}^4$ using marked graph diagrams.
Bonded knots arise naturally in topological protein modeling, where intramolecular interactions such as disulfide bridges stabilize folded configurations. These structures extend classical knot theory by incorporating embedded graphs, and…
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
In this paper we study properties of topological RNA structures, i.e.~RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological…
Recently Witten introduced a type IIB brane construction with certain boundary conditions to study knot invariants and Khovanov homology. The essential ingredients used in his work are the topologically twisted N = 4 Yang-Mills theory,…
Knot theory is the Mathematical study of knots. In this paper we have studied the Composition of two knots. Knot theory belongs to Mathematical field of Topology, where the topological concepts such as topological spaces, homeomorphisms,…
An elementary introduction to knot theory and its link to quantum field theory is presented with an intention to provide details of some basic calculations in the subject, which are not easily found in texts. Study of Chern-Simons theory…
We use mesoscopic non-equilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so…
We introduce topological invariants of knots and braid conjugacy classes, in the form of differential graded algebras, and present an explicit combinatorial formulation for these invariants. The algebras conjecturally give the relative…
Biracks are algebraic structures related to knots and links. We define a new enhancement of the birack counting invariant for oriented classical and virtual knots and links via algebraic structures called birack dynamical cocycles. The new…
Knot Floer homology is a knot invariant defined using holomorphic curves. In more recent work, taking cues from bordered Floer homology,the authors described another knot invariant, called "bordered knot Floer homology", which has an…
We consider knots equipped with a representation of their knot groups onto a dihedral group D_{2n} (where n is odd). To each such knot there corresponds a closed 3-manifold, the (irregular) dihedral branched covering space, with the…
Three new knot invariants are defined using cocycles of the generalized quandle homology theory that was proposed by Andruskiewitsch and Gra\~na. We specialize that theory to the case when there is a group action on the coefficients. First,…