Related papers: Capturing knots in polymers
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
We present a computer simulation of entangled polymer solutions at equilibrium. The chains repel each other via a soft Gaussian potential, appropriate for semi-dilute solutions at the scale of a correlation blob. The key innovation to…
We examine the structure and dimensionality of the Jones polynomial using manifold learning techniques. Our data set consists of more than 10 million knots up to 17 crossings and two other special families up to 2001 crossings. We introduce…
In this exploration paper, we design algorithms for deforming and contracting a simply connected discrete closed manifold to a discrete sphere. Such a contraction is a kind of shrinking or reducing process. In our algorithms, we need to…
We develop a reinforcement learning pipeline for simplifying knot diagrams. A trained agent learns move proposals and a value heuristic for navigating Reidemeister moves. The pipeline applies to arbitrary knots and links; we test it on…
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…
In this paper, we approach the challenging problem of motion planning for knot tying. We propose a hierarchical approach in which the top layer produces a topological plan and the bottom layer translates this plan into continuous robot…
We use numerical simulations to study tangentially active flexible ring polymers with different knot topologies. Simple, unknotted active rings display a transition from an extended phase to a collapsed one upon increasing the degree of…
We study the minimum ribbonlength for immersed planar ribbon knots and links. Our approach is to embed the space of such knots and links into a larger more tractable space of disk diagrams. When length minimisers in disk diagram space are…
We probe the character of knotting in open, confined polymers, assigning knot types to open curves by identifying their projections as virtual knots. In this sense, virtual knots are transitional, lying in between classical knot types,…
In this paper we study some aspects of knots and links in lens spaces. Namely, if we consider lens spaces as quotient of the unit ball $B^{3}$ with suitable identification of boundary points, then we can project the links on the equatorial…
The main purpose of this paper is to report on the state of the art of computing integer hulls and their facets as well as counting lattice points in convex polytopes. Using the polymake system we explore various algorithms and…
The motivation of this work is to define cohomology classes in the space of knots that are both easy to find and to evaluate, by reducing the problem to simple linear algebra. We achieve this goal by defining a combinatorial graded cochain…
In this article we discuss applications of neural networks to recognising knots and, in particular, to the unknotting problem. One of motivations for this study is to understand how neural networks work on the example of a problem for which…
THIS PAPER IS NOW DEFUNCT: Check out "Graph Embeddings via Tensor Products and Approximately Orthonormal Codes", where it has been combined into one paper.
We introduce a notion of intrinsic linking and knotting for virtual spatial graphs. Our theory gives two filtrations of the set of all graphs, allowing us to measure, in a sense, how intrinsically linked or knotted a graph is; we show that…
We employ computer simulations and thermodynamic integration to analyse the effects of bending rigidity and slit confinement on the free energy cost of tying knots, $\Delta F_{\rm knotting}$, on polymer chains under tension. A…
Helices are the quintessential geometric motif of the microscale, from alpha-helices in proteins to double helices in DNA. Assembly of the helical geometry of biopolymers is a foundational step in a hierarchy of structure that eventually…
We give a number theoretic proof of the integrality of certain BPS invariants of knots. The formulas for these numbers are sums involving binomial coefficients and the M\"obius function. We also prove a conjecture about further divisibility…
Supervised machine learning (ML) methods are emerging as valid alternatives to standard mathematical methods for identifying knots in long, collapsed polymers. Here, we introduce a hybrid supervised/unsupervised ML approach for knot…