Related papers: Proteins analysed as virtual knots
Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…
We discuss the entropy of a circular polymer under a topological constraint. We call it the {\it topological entropy} of the polymer, in short. A ring polymer does not change its topology (knot type) under any thermal fluctuations. Through…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the presence of such topological obstacles is a debated question in…
As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…
Stochastic simulations of coarse-grained protein models are used to investigate the propensity to form knots in early stages of protein folding. The study is carried out comparatively for two homologous carbamoyltransferases, a…
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 2002, D. Hrencecin and L.H. Kauffman defined a filamentation invariant on oriented chord diagrams that may determine whether the corresponding flat virtual knot diagrams are non-trivial. A virtual knot diagram is non-classical if its…
We analyze the connections between the mathematical theory of knots and quantum physics by addressing a number of algorithmic questions related to both knots and braid groups. Knots can be distinguished by means of `knot invariants', among…
In this manuscript we introduce a method to measure entanglement of curves in 3-space that extends the notion of knot and link polynomials to open curves. We define the bracket polynomial of curves in 3-space and show that it has real…
We study the formation of knots on a macroscopic ball-chain, which is shaken on a horizontal plate at 12 times the acceleration of gravity. We find that above a certain critical length, the knotting probability is independent of chain…
It is well-known that intrinsically disordered proteins (IDP) are highly dynamic, which is related to their functionality in various biological processes. However, the characterization of the intricate structures of IDP has been a…
A virtual knot, which is one of generalizations of knots in $\mathbb{R}^{3}$ (or $S^{3}$), is, roughly speaking, an embedded circle in thickened surface $S_{g} \times I$. In this paper we will discuss about knots in 3 dimensional $S_{g}…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
This paper defines a theory of cobordism for virtual knots and studies this theory for standard and rotational virtual knots and links. Non-trivial examples of virtual slice knots are given. Determinations of the four-ball genus of positive…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
The problem of finding robust and effective methods for locating entanglement in embedded curves is relevant to both applications and theoretical investigations. Rather than focusing on an exact determination, we introduce the knot…
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…
The interplay between the topological and geometrical properties of a polymer ring can be clarified by establishing the entanglement trapped in any portion (arc) of the ring. The task requires to close the open arcs into a ring, and the…
Physical knots and links are one-dimensional submanifolds of R^3 with fixed length and thickness. We show that isotopy classes in this category can differ from those of classical knot and link theory. In particular we exhibit a Gordian…