Related papers: RNA foldings and Stuck Knots
We extend the quandle cocycle invariant to the context of stuck links. More precisely, we define an invariant of stuck links by assigning Boltzmann weights at both classical and stuck crossings. As an application, we define a…
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…
Folded linear molecular chains are ubiquitous in biology. Folding is mediated by intra-chain interactions that "glue" two or more regions of a chain. The resulting fold topology is widely believed to be a determinant of biomolecular…
Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that…
We present a systematic classification of uncolored bonded knots with singularity number at most seven. Bonded knots provide a topological model for closed protein chains with intramolecular bridges, such as disulfide bonds. Following the…
A {\it stuck knot} is a knot diagram containing designated crossings, called {\it stuck crossings}, whose incident strands are required to remain locally non-separable. These rigidity constraints restrict the allowable ambient isotopies and…
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…
The art of tying knots is exploited in nature and occurs in multiple applications ranging from being an essential part of scouting programs to engineering molecular knots. Biomolecular knots, such as knotted proteins, bear various cellular…
Classical knot theory deals with {\em diagrams} and {\em invariants}. By means of horizontal {\em trisecants}, we construct a new theory of classical braids with invariants valued in {\em pictures}. These pictures are closely related to…
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
The combinatorial approach to knot theory treats knots as diagrams modulo Reidemeister moves. Many constructions of knot invariants (e.g., index polynomials, quandle colorings, etc.) use elements of diagrams such as arcs and crossings by…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
The study of knots and links from a probabilistic viewpoint provides insight into the behavior of "typical" knots, and opens avenues for new constructions of knots and other topological objects with interesting properties. The knotting of…
RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of…
In Classical Knot Theory and in the new Theory of Quantum Invariants substantial effort was directed toward the search for unknotting moves on links. We solve, in this note, several classical problems concerning unknotting moves. Our…
Knots and links in 3-manifolds are studied by applying intersection invariants to singular concordances. The resulting link invariants generalize the Arf invariant, the mod 2 Sato-Levine invariants, and Milnor's triple linking numbers.…
We propose a new topological characterization of RNA secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc-representation of RNA secondary structures, we consider a model that couples both…
The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of knots in their backbones using topological invariants. However, this approach requires to close the…
Knot theory provides a powerful tool for the understanding of topological matters in biology, chemistry, and physics. Here knot theory is introduced to describe topological phases in the quantum spin system. Exactly solvable models with…
The aim of this paper is to define certain algebraic structures coming from generalized Reidemeister moves of singular knot theory. We give examples, show that the set of colorings by these algebraic structures is an invariant of singular…