Related papers: Slipknotting in Random Diagrams
In polymer physics it is typically assumed that excluded volume interactions are effectively screened in polymer melts. Hence, chains could be described by an effective random walk without excluded volume interactions. In this letter, we…
The flip symmetry on knot diagrams induces an involution on Khovanov homology. We prove that this involution is determined by its behavior on unlinks; in particular, it is the identity map when working over $\mathbb{F}_2$. This confirms a…
The fundamental quandle is a complete invariant for unoriented tame knots \cite{JO, Ma} and non-split links \cite{FR}. The proof involves proving a relationship between the components of the fundamental quandle and the cosets of the…
The notion of a pseudoknot is defined as an equivalence class of knot diagrams that may be missing some crossing information. We provide here a topological invariant schema for pseudoknots and their relatives, 4-valent rigid vertex spatial…
We study here global and local entanglements of open protein chains by implementing the concept of knotoids. Knotoids have been introduced in 2012 by Vladimir Turaev as a generalization of knots in 3-dimensional space. More precisely,…
Using methods of high performance computing, we have found indications that knotlike structures appear as stable finite energy solitons in a realistic 3+1 dimensional model. We have explicitly simulated the unknot and trefoil…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…
Spin networks, essentially labeled graphs, are ``good quantum numbers'' for the quantum theory of geometry. These structures encompass a diverse range of techniques which may be used in the quantum mechanics of finite dimensional systems,…
Given a (genus 2) cube-with-holes M, i.e. the complement in S^3 of a handlebody H, we relate intrinsic properties of M (like its cut number) with extrinsic features depending on the way the handlebody H is knotted in S^3. Starting from a…
In this paper, we use skein-theoretic techniques to classify all virtual knot polynomials and trivalent graph invariants with certain smallness conditions. The first half of the paper classifies all virtual knot polynomials giving…
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…
We systematically evaluate the (in-)stability of state-of-the-art node embedding algorithms due to randomness, i.e., the random variation of their outcomes given identical algorithms and graphs. We apply five node embeddings…
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…
Randomized Neural Networks explore the behavior of neural systems where the majority of connections are fixed, either in a stochastic or a deterministic fashion. Typical examples of such systems consist of multi-layered neural network…
The representation of knots by petal diagrams (Adams et al. 2012) naturally defines a sequence of distributions on the set of knots. In this article we establish some basic properties of this randomized knot model. We prove that in the…
We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable…
The Strong Lottery Ticket Hypothesis (SLTH) states that randomly-initialised neural networks likely contain subnetworks that perform well without any training. Although unstructured pruning has been extensively studied in this context, its…
We modify the definition of spherical knotoids to include a framing, in analogy to framed knots, and define a further modification that includes a secondary 'coframing' to obtain 'biframed' knotoids. We exhibit topological spaces whose…
The Slope Conjecture relates a quantum knot invariant, (the degree of the colored Jones polynomial of a knot) with a classical one (boundary slopes of incompressible surfaces in the knot complement). The degree of the colored Jones…
Cyclically ordered graphs, or cogs, sit between abstract graphs and cellularly embedded graphs. They arise naturally in topological graph theory, knot theory, and mathematical biology. We develop a formal theory of cogs and establish a…