skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: Knot polynomials of open and closed curves
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 coefficients and is a continuous function of the curve coordinates. This is used to define the Jones polynomial in a way that it is applicable to both open and closed curves in 3-space. For open curves, the Jones polynomial has real coefficients and it is a continuous function of the curve coordinates and as the endpoints of the curve tend to coincide, the Jones polynomial of the open curve tends to that of the resulting knot. For closed curves, it is a topological invariant, as the classical Jones polynomial. We show how these measures attain a simpler expression for polygonal curves and provide a finite form for their computation in the case of polygonal curves of 3 and 4 edges.  more » « less
Award ID(s):
1913180
PAR ID:
10279657
Author(s) / Creator(s):
;
Date Published:
Journal Name:
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences
Volume:
476
Issue:
2240
ISSN:
1364-5021
Page Range / eLocation ID:
20200124
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. In this article, we define Vassiliev measures of complexity for open curves in 3-space. These are related to the coefficients of the enhanced Jones polynomial of open curves in 3-space. These Vassiliev measures are continuous functions of the curve coordinates; as the ends of the curve tend to coincide, they converge to the corresponding Vassiliev invariants of the resulting knot. We focus on the second Vassiliev measure from the enhanced Jones polynomial for closed and open curves in 3-space. For closed curves, this second Vassiliev measure can be computed by a Gauss code diagram and it has an integral formulation, the double alternating self-linking integral. The double alternating self-linking integral is a topological invariant of closed curves and a continuous function of the curve coordinates for open curves in 3-space. For polygonal curves, the double alternating self-linking integral obtains a simpler expression in terms of geometric probabilities. 
    more » « less
  2. Measuring the entanglement complexity of collections of open curves in 3-space has been an intractable, yet pressing mathematical problem, relevant to a plethora of physical systems, such as in polymers and biopolymers. In this manuscript, we give a novel definition of the Jones polynomial that generalizes the classic Jones polynomial to collections of open curves in 3-space. More precisely, first we provide a novel definition of the Jones polynomial of linkoids (open link diagrams) and show that this is a well-defined single variable polynomial that is a topological invariant, which, for link-type linkoids, coincides with that of the corresponding link. Using the framework introduced in (Panagiotou E, Kauffman L. 2020 Proc. R. Soc. A 476 , 20200124. (( doi:10.1098/rspa.2020.0124 )), this enables us to define the Jones polynomial of collections of open and closed curves in 3-space. For collections of open curves in 3-space, the Jones polynomial has real coefficients and it is a continuous function of the curves’ coordinates. As the endpoints of the curves tend to coincide, the Jones polynomial tends to that of the resultant link. We demonstrate with numerical examples that the novel Jones polynomial enables us to characterize the topological/geometrical complexity of collections of open curves in 3-space for the first time. 
    more » « less
  3. Abstract Biopolymers, like chromatin, are often confined in small volumes. Confinement has a great effect on polymer conformations, including polymer entanglement. Polymer chains and other filamentous structures can be represented by polygonal curves in three-space. In this manuscript, we examine the topological complexity of polygonal chains in three-space and in confinement as a function of their length. We model polygonal chains by equilateral random walks in three-space and by uniform random walks (URWs) in confinement. For the topological characterization, we use the second Vassiliev measure. This is an integer topological invariant for polygons and a continuous functions over the real numbers, as a function of the chain coordinates for open polygonal chains. For URWs in confined space, we prove that the average value of the Vassiliev measure in the space of configurations increases as O ( n 2 ) with the length of the walks or polygons. We verify this result numerically and our numerical results also show that the mean value of the second Vassiliev measure of equilateral random walks in three-space increases as O ( n ). These results reveal the rate at which knotting of open curves and not simply entanglement are affected by confinement. 
    more » « less
  4. In this paper we define and investigate the Fréchet edit distance problem. Here, given two polygonal curves $$\pi$$ and $$\sigma$$ and a threshhold value $$\delta$$ , we seek the minimum number of edits to $$\sigma$$ such that the Fréchet distance between the edited curve and $$\pi$$ is at most $$\delta$$. For the edit operations we consider three cases, namely, deletion of vertices, insertion of vertices, or both. For this basic problem we consider a number of variants. Specifically, we provide polynomial time algorithms for both discrete and continuous Fréchet edit distance variants, as well as hardness results for weak Fréchet edit distance variants. 
    more » « less
  5. Abstract 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 DNA, typically perform a closure operation and calculate the Alexander polynomial to assign a knot topology. This is limited in scenarios where the topology is less well-defined, for example when the chain is in the process of untying or is strongly confined. Here, we use a discretized version of the Second Vassiliev Invariant for open chains to analyze Langevin Dynamics simulations of untying and strongly confined polymer chains. We demonstrate that the Vassiliev parameter can accurately and efficiently characterize the knotted state of polymers, providing additional information not captured by a single-closure Alexander calculation. We discuss its relative strengths and weaknesses compared to standard techniques, and argue that it is a useful and powerful tool for analyzing polymer knot simulations. 
    more » « less