Related papers: Capturing knots in polymers
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…
We construct a new type of geometric knot theory, plumbers' knots, and solve the problems of distinguishing and enumerating such knots at a fixed level of complexity. (v2) Minor edits, added theorem 3.18. (v3) Substantial revisions,…
We compare Monte Carlo simulations of knotted and unknotted polymers whose ends are connected to two parallel walls. The force $f$ exerted on the polymer is measured as a function of the separation $R$ between the walls. For unknotted…
The interplay of geometrical and topological entanglement in semiflexible knotted polymer rings confined inside a spherical cavity is investigated using advanced numerical methods. By using stringent and robust algorithms for locating…
I briefly discuss a method of obtaining distinct classes of topologically equivalent knots by developing appropriate computer programs.
This paper is an introduction to the subject of virtual knot theory, combined with a discussion of some specific new theorems about virtual knots. The new results are as follows: We prove, using a 3-dimensional topology approach that if a…
The mechanical properties of polymer knots under stretching in a bad or good solvent are investigated by applying a given force $F$ to a point of the knot while keeping another point fixed. The Monte Carlo sampling of the polymer…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase…
Knots in wood are critical to both aesthetics and structural integrity, making their detection and pairing essential in timber processing. However, traditional manual annotation was labor-intensive and inefficient, necessitating automation.…
For all natural numbers $N$ and prime numbers $p$, we find a knot $K$ whose skein polynomial $P_K(a,z)$ evaluated at $z=N$ has trivial reduction modulo $p$. An interesting consequence of our construction is that all polynomials $P_K(a,N)$…
A classical knot is described by a one-stroke trajectory with entanglements of a string. The replica method appears as a powerful tool in statistical mechanics for a polymer or self-avoiding walk. We consider this replica N to 0 limit in…
We consider the probability of knotting in equilateral random polygons in Euclidean 3-dimensional space, which model, for instance, random polymers. Results from an extensive Monte Carlo dataset of random polygons indicate a universal…
We present experimental results on knotting in off-lattice self-avoiding polygons in the bead-chain model. Using Clisby's tree data structure and the scale-free pivot algorithm, for each $k$ between $10$ and $27$ we generated $2^{43-k}$…
An analysis of extensive simulations of interacting self-avoiding polygons on cubic lattice shows that the frequencies of different knots realized in a random, collapsed polymer ring decrease as a negative power of the ranking order, and…
Tensor network contraction is central to problems ranging from many-body physics to computer science. We describe how to approximate tensor network contraction through bond compression on arbitrary graphs. In particular, we introduce a…
An implementation of BFACF-style algorithms on knotted polygons in the simple cubic, face centered cubic and body centered cubic lattice is used to estimate the statistics and writhe of minimal length knotted polygons in each of the…
Inspired by how certain proteins "sense" knots and entanglements in DNA molecules, here we ask if there exist local geometric features that may be used as a read-out of the underlying topology of generic polymers. We perform molecular…
Knitting, an ancient fiber art, creates a structured fabric consisting of loops or stitches. Publishing hand knitting patterns involves lengthy testing periods and numerous knitters. Modeling knitting patterns with graphs can help expedite…
This project explores the mathematical study of knots and links in topology, focusing on differentiating between the two-component Unlink and the Hopf Link using a computational tool named LINKAGE. LINKAGE employs the linking number,…
The Knot Entropy Conjecture states that the exponential growth rate of the number of $n$-edge lattice polygons with knot-type $K$ is the same as that for unknot polygons. Moreover, the next order growth follows a power law in $n$ with an…