Related papers: A parallel algorithm for the computation of the Jo…
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…
The deletion--contraction algorithm is perhaps the most popular method for computing a host of fundamental graph invariants such as the chromatic, flow, and reliability polynomials in graph theory, the Jones polynomial of an alternating…
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…
Knots are fascinating topological structures that have been observed in various contexts, ranging from micro-worlds to macro-systems, and are conjectured to play a fundamental role in their respective fields. In order to characterize their…
We present a parallelizable algorithm for computing the persistent homology of a filtered chain complex. Our approach differs from the commonly used reduction algorithm by first computing persistence pairs within local chunks, then…
The lectures review the state of affairs in modern branch of mathematical physics called probabilistic topology. In particular we consider the following problems: (i) We estimate the probability of a trivial knot formation on the lattice…
Using a simple recurrence relation we give a new method to compute Jones polynomials of closed braids: we find a general expansion formula and a rational generating function for Jones polynomials. The method is used to estimate degree of…
A knot is a circle piecewise-linearly embedded into the 3-sphere. The topology of a knot is intimately related to that of its exterior, which is the complement of an open regular neighborhood of the knot. Knots are typically encoded by…
Using elementary ideas from Tropical Geometry, we assign a a tropical curve to every $q$-holonomic sequence of rational functions. In particular, we assign a tropical curve to every knot which is determined by the Jones polynomial of the…
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…
The entanglement of open curves in 3-space appears in many physical systems and affects their material properties and function. A new framework in knot theory was introduced recently, that enables to characterize the complexity of…
Graph polynomials encode fundamental combinatorial invariants of graphs. Their computation is investigated using tree and path decomposition frameworks, with formal definitions of treewidth, k-trees, and pathwidth establishing the…
This paper will be an exposition of the Kauffman bracket polynomial model of the Jones polynomial, tangle methods for computing the Jones polynomial, and the use of these methods to produce non-trivial links that cannot be detected by the…
We study the problem of finding elements in the intersection of an arbitrary conic variety in $\mathbb{F}^n$ with a given linear subspace (where $\mathbb{F}$ can be the real or complex field). This problem captures a rich family of…
We present a simple phenomenological formula which approximates the hyperbolic volume of a knot using only a single evaluation of its Jones polynomial at a root of unity. The average error is just $2.86$% on the first $1.7$ million knots,…
We define a discrete-time Markov chain for abstract polymer models and show that under sufficient decay of the polymer weights, this chain mixes rapidly. We apply this Markov chain to polymer models derived from the hard-core and…
I briefly discuss a method of obtaining distinct classes of topologically equivalent knots by developing appropriate computer programs.
This monograph derives direct and concrete relations between colored Jones polynomials and the topology of incompressible spanning surfaces in knot and link complements. Under mild diagrammatic hypotheses that arise naturally in the study…
We present an algorithm for sampling tightly confined random equilateral closed polygons in three-space which has runtime linear in the number of edges. Using symplectic geometry, sampling such polygons reduces to sampling a moment…