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The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of knots in their backbones using topological invariants. However, this approach requires to close the…
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
Classifying the topology of closed curves is a central problem in low dimensional topology with applications beyond mathematics spanning protein folding, polymer physics and even magnetohydrodynamics. The central problem is how to determine…
In multivariate spline regression, the number and locations of knots influence the performance and interpretability significantly. However, due to non-differentiability and varying dimensions, there is no desirable frequentist method to…
Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that…
Knotted molecules occur naturally and are designed by scientists to gain special biological and material properties. Understanding and utilizing knotting require efficient methods to recognize and generate knotted structures, which are…
I briefly discuss a method of obtaining distinct classes of topologically equivalent knots by developing appropriate computer programs.
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…
Knots are deeply entangled with every branch of science. One of the biggest open challenges in knot theory is to formalise a knot invariant that can unambiguously and efficiently distinguish any two knotted curves. Additionally, the…
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 a previous paper (q-alg/9501022) we suggested some algorithms that could be useful in solving the problem of knot classification. Here we continue this discussion by answering questions raised in that paper and by commenting on practical…
In this paper we discuss the applications of knotoids to modelling knots in open curves and produce new knotoid invariants. We show how invariants of knotoids generally give rise to well-behaved measures of how much an open curve is…
Given two closed curves in a surface, we propose an algorithm to detect whether they are of the same type or not.
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…
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…
This manuscript introduces a new framework for the study of knots by exploring the neighborhood of knot embeddings in the space of simple open and closed curves in 3-space. The latter gives rise to a knotoid spectrum, which determines the…
We present a systematic classification of uncolored bonded knots with singularity number at most seven. Bonded knots provide a topological model for closed protein chains with intramolecular bridges, such as disulfide bonds. Following the…
By a fixed continuous map from a $3$-space to itself, a knot in the $3$-space may be mapped to another knot in the $3$-space. We analyze possible knot types of them. Then we map a knot repeatedly by a fixed continuous map and analyze…
We study a certain type of braid closure which resembles the plat closure but has certain advantages; for example, it maps pure braids to knots. The main results of this note are a Markov-type theorem and a description of how Vassiliev…
A knot is an an embedding of a circle into three-dimensional space. We say that a knot is unknotted if there is an ambient isotopy of the embedding to a standard circle. By representing knots via planar diagrams, we discuss the problem of…