Related papers: RNA foldings and Stuck Knots
We consider countable linear orders and study the quasi-order of convex embeddability and its induced equivalence relation. We obtain both combinatorial and descriptive set-theoretic results, and further extend our research to the case of…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
The theory of quandle (co)homology and cocycle knot invariants is rapidly being developed. We begin with a summary of these recent advances. One such advance is the notion of a dynamical cocycle. We show how dynamical cocycles can be used…
Computational topology is a vibrant contemporary subfield and this article integrates knot theory and mathematical visualization. Previous work on computer graphics developed a sequence of smooth knots that were shown to converge point wise…
We define ambient isotopy invariants of oriented knots and links using the counting invariants of framed links defined by finite racks. These invariants reduce to the usual quandle counting invariant when the rack in question is a quandle.…
We extend the list of known band structure topologies to include a large family of hyperbolic nodal links and knots, occurring both in conventional Hermitian systems where their stability relies on discrete symmetries, and in the…
This manuscript introduces a new framework for the study of knots by exploring the neighborhood of knot embeddings in the space of simple open and closed curves in 3-space. The latter gives rise to a knotoid spectrum, which determines the…
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of…
We define an invariant of tangles and framed tangles given a finite crossed module and a pair of functions, called a Reidemeister pair, satisfying natural properties. We give several examples of Reidemeister pairs derived from racks,…
We prove that deciding if a diagram of the unknot can be untangled using at most $k$ Riedemeister moves (where $k$ is part of the input) is NP-hard. We also prove that several natural questions regarding links in the $3$-sphere are NP-hard,…
We introduce natural language processing into the study of knot theory, as made natural by the braid word representation of knots. We study the UNKNOT problem of determining whether or not a given knot is the unknot. After describing an…
Recently there had been a great deal of activity associated with various schemes of designing both analytical and experimental methods describing knotted structures in electrodynamics and in hydrodynamics.The majority of works in…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
In this work the thermodynamic properties of short polymer knots (up to 120 segments) defined on a simple cubic lattice are studied with the help of the Wang-Landau Monte Carlo algorithm. The sampling process is performed using pivot…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
Knots are familiar entities that appear at a captivating nexus of art, technology, mathematics, and science. As topologically stable objects within field theories, they have been speculatively proposed as explanations for diverse persistent…
We discuss different invariants of knots and links that depend on a primitive root of unity. We clarify the definitions of existing invariants with the Reshetikhin-Turaev method, present the generalization of ADO invariants to…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
The interplay of topological constraints and Coulomb interactions in static and dynamic properties of charged polymers is investigated by numerical simulations and scaling arguments. In the absence of screening, the long-range interaction…