Related papers: Capturing knots in polymers
The presence of slipknots in configurations of proteins and DNA has been shown to affect their functionality, or alter it entirely. Historically, polymers are modeled as polygonal chains in space. As an alternative to space curves, we…
This is a review article on Lorenz knots.
Simulated configurations of flexible knotted rings confined inside a spherical cavity are fed into long-short term memory neural networks (LSTM NNs) designed to distinguish knot types. The results show that they perform well in knot…
In this paper we examine the relative knotting probabilities in a lattice model of ring polymers confined in a cavity. The model is of a lattice knot of size $n$ in the cubic lattice, confined to a cube of side-length $L$ and with volume…
The work addresses the analogy between trivial knotting and excluded volume in looped polymer chains of moderate length, $N<N_0$, where the effects of knotting are small. A simple expression for the swelling seen in trivially knotted loops…
We present new computations of approximately length-minimizing polygons with fixed thickness. These curves model the centerlines of "tight" knotted tubes with minimal length and fixed circular cross-section. Our curves approximately…
We discuss a semi-implicit numerical scheme that allows for minimizing the bending energy of curves within certain isotopy classes. To this end we consider a weighted sum of the bending energy and the tangent-point functional. Based on…
This is a report on our ongoing research on a combinatorial approach to knot recognition, using coloring of knots by certain algebraic objects called quandles. The aim of the paper is to summarize the mathematical theory of knot coloring in…
In this paper we constructed new model of plastic deformation. The knot theory was used to classify the plastic state.
We introduce a new combinatorial method to encode knots and links with applications to knot invariants. Clasp diagrams defined in this paper are combinatorial blueprints for building knot diagrams out of full twists on two strings rather…
Geometric modeling by constraints leads to large systems of algebraic equations. This paper studies bipartite graphs underlaid by systems of equations. It shows how these graphs make possible to polynomially decompose these systems into…
Stochastic simulations are used to characterize the knotting distributions of random ring polymers confined in spheres of various radii. The approach is based on the use of multiple Markov chains and reweighting techniques, combined with…
Polymers can be modeled as open polygonal paths and their closure generates knots. Knotted proteins detection is currently achieved via high-throughput methods based on a common framework insensitive to the handedness of knots. Here we…
In this paper the number and lengths of minimal length lattice knots confined to slabs of width $L$, is determined. Our data on minimal length verify the results by Sharein et.al. (2011) for the similar problem, expect in a single case,…
We study knotted polymers in equilibrium with an array of obstacles which models confinement in a gel or immersion in a melt. We find a crossover in both the geometrical and the topological behavior of the polymer. When the polymers' radius…
This paper details a series of experiments in searching for minimal energy configurations for knots and links using the computer program KnotPlot. The most interesting phenomena found in these experiments is the dependence of the…
We propose a splitting algorithm for solving a system of composite monotone inclusions formulated in the form of the extended set of solutions in real Hilbert spaces. The resluting algorithm is a an extension of the algorithm in [4]. The…
Algorithm of construction of all knots, links with given number of crosses on diagram of knot, link is offered. This algorithm is based on simple proposition, that there is a representation of knot (link) as closure of braid with n threads…
We present a faster direct sampling algorithm for random equilateral closed polygons in three-dimensional space. This method improves on the moment polytope sampling algorithm of Cantarella, Duplantier, Shonkwiler, and Uehara (2016) and has…
This paper explores the problem of unknotting closed braids and classical knots in mathematical knot theory. We apply evolutionary computation methods to learn sequences of moves that simplify knot diagrams, and show that this can be…