Related papers: Slipknotting in Random Diagrams
Knots in open strands such as ropes, fibers, and polymers, cannot typically be described in the language of knot theory, which characterizes only closed curves in space. Simulations of open knotted polymer chains, often parameterized to…
We review pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells. For that purpose, we review, first, recent theoretical and computational…
The advent of solid state nanodevices allows for interrogating the physico-chemical properties of a polyelectrolyte chain by electrophoretically driving it through a nanopore. Salient dynamical aspects of the translocation process have been…
In previous papers, the author realized the following principle for many knot theories: if a knot diagram is complicated enough then it reproduces itself, i.e., is a subdiagram of any other diagram equivalent to it. This principle is…
Unlabeled multigraphs have diverse applications across scientific fields, from transportation and social networks to polymer physics. In particular, multigraphs are essential for studying the relationship between the spatial organization…
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…
This paper focuses on the graphs in the Petersen family, the set of minor minimal intrinsically linked graphs. We prove there is a relationship between algebraic linking of an embedding and knotting in an embedding. We also present a more…
Tests of the integrality properties of a scalar operator in topological strings on a resolved conifold background or orientifold of conifold backgrounds have been performed for arborescent knots and some non-arborescent knots. The recent…
Knots in proteins have been proposed to resist proteasomal degradation. Ample evidence associates proteasomal degradation with neurodegeneration. One interesting possibility is that indeed knotted conformers stall this machinery leading to…
Knotted molecules occur naturally and are designed by scientists to gain special biological and material properties. Understanding and utilizing knotting require efficient methods to recognize and generate knotted structures, which are…
As a generalization of the classical knots, knotoids deal with the open ended knot diagrams in a surface. In recent years, many polynomial invariants for knotoids have appeared, such as the bracket polynomial, the index polynomial and the…
A knot is a circle piecewise-linearly embedded into the 3-sphere. The topology of a knot is intimately related to that of its exterior, which is the complement of an open regular neighborhood of the knot. Knots are typically encoded by…
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…
Given a tame knot K presented in the form of a knot diagram, we show that the problem of determining whether K is knotted is in the complexity class NP, assuming the generalized Riemann hypothesis (GRH). In other words, there exists a…
We offer a pedestrian level review of the wall-crossing invariants. The story begins from the scattering theory in quantum mechanics where the spectrum reshuffling can be related to permutations of S-matrices. In non-trivial situations,…
We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem…
It is shown, using sutured manifold theory, that if there are any 2-component counterexamples to the Generalized Property R Conjecture, then any knot of least genus among components of such counterexamples is not a fibered knot. The general…
We perform theoretical studies of stretching of 20 proteins with knots within a coarse grained model. The knot's ends are found to jump to well defined sequential locations that are associated with sharp turns whereas in homopolymers they…
The statistical properties of random lattice knots, the topology of which is determined by the algebraic topological Jones-Kauffman invariants was studied by analytical and numerical methods. The Kauffman polynomial invariant of a random…
We have examined the behaviors of a knotted linear polymer in narrow tubes using Langevin dynamics simulation to investigate the knot localization property in one-dimensional (1D) geometry. We have found that the knot is strongly localized…