Related papers: RNA foldings and Stuck Knots
We propose a new deterministic methodology to predict RNA sequence and protein folding. Is stem enough for structure prediction? The main idea is to consider all possible stem formation in the given sequence. With the stem loop energy and…
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…
Finite-order invariants of knots in arbitrary 3-manifolds (including non-orientable ones) are constructed and studied by methods of the topology of discriminant sets. Obstructions to the integrability of admissible weight systems to…
In this paper we study how randomly generated knots occupy a volume of space using topological methods. To this end, we consider the evolution of the first homology of an immersed metric neighbourhood of a knot's embedding for growing…
Molecular structures of RNA molecules reconstructed from X-ray crystallography frequently contain errors. Motivated by this problem we examine clustering on a torus since RNA shapes can be described by dihedral angles. A previously…
Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and…
To each rail knotoid we associate two unoriented knots along with their oriented counterparts, thus deriving invariants for rail knotoids based on these associations. We then translate them to invariants of rail isotopy for rail arcs.
We model the typical behavior of knots and links using grid diagrams. Links are ubiquitous in the sciences, and their "normal" or "typical" behavior is of significant importance in understanding situations such as the topological state of…
Knots and knotted fields enrich physical phenomena ranging from DNA and molecular chemistry to the vortices of fluid flows and textures of ordered media. Liquid crystals provide an ideal setting for exploring such topological phenomena…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
To study embeddings of tangles in knots, we use quandle cocycle invariants. Computations are carried out for the tables of knots and tangles, to investigate which tangles may or may not embed in knots in the tables.
The present paper is a review of the current state of Graph-Link Theory (graph-links are also closely related to homotopy classes of looped interlacement graphs), dealing with a generalisation of knots obtained by translating the…
This project explores the mathematical study of knots and links in topology, focusing on differentiating between the two-component Unlink and the Hopf Link using a computational tool named LINKAGE. LINKAGE employs the linking number,…
We construct a new order 1 invariant for knot diagrams. We use it to determine the minimal number of Reidemeister moves needed to pass between certain pairs of knot diagrams.
This paper has two-fold goal: it provides gentle introduction to Knot Theory starting from 3-coloring, the concept introduced by R. Fox to allow undergraduate students to see that the trefoil knot is non-trivial, and ending with statistical…
Biomolecular graph analysis has recently gained much attention in the emerging field of geometric deep learning. Here we focus on organizing biomolecular graphs in ways that expose meaningful relations and variations between them. We…
This paper builds a novel bridge between algebraic coding theory and mathematical knot theory, with applications in both directions. We give methods to construct error-correcting codes starting from the colorings of a knot, describing…
Construction of representations of braid group generators from $N$-state vertex models provide an elegant route to study knot and link invariants. Using such a braid group representation, an algebraic formula for the link invariants was put…
This paper studies rotational virtual knot theory and its relationship with quantum link invariants. Every quantum link invariant for classical knots and links extends to an invariant of rotational virtual knots and links. The paper sets up…
We use planar 4-valent graphs and a graphical calculus involving such graphs to construct an invariant for balanced-oriented, knotted 4-valent graphs. Our invariant is an extension of the $sl(n)$ polynomial for classical knots and links. We…