Related papers: Slipknotting in Random Diagrams
In this paper we introduce and study the theory of pseudo links in the genus $g$ handlebody, $H_g$. Pseudo links are links with some missing crossing information that naturally generalize the notion of knot diagrams. The motivation for…
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…
We consider a matrix model with d matrices NxN and show that in the limit of large N and d=0 the model describes the knot diagrams. The same limit in matrix string theory is also discussed. We speculate that a prototypical M(atrix) without…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
Common experience tells us that a knot significantly weakens the polymer strand in which it is tied, which in turn leads to more facile chain rupture under tensile loading. Using first-principles molecular dynamics calculations we describe…
The paper investigates the computational problem of predicting RNA secondary structures. The general belief is that allowing pseudoknots makes the problem hard. Existing polynomial-time algorithms are heuristic algorithms with no…
We study the interplay between entropy and topological constraints for a polymer chain in which sliding rings (slip-links) enforce pair contacts between monomers. These slip-links divide a closed ring polymer into a number of sub-loops…
Statistical analysis of a graph often starts with embedding, the process of representing its nodes as points in space. How to choose the embedding dimension is a nuanced decision in practice, but in theory a notion of true dimension is…
In this study of the Reidemeister moves within the classical knot theory, we focus on hard diagrams of knots and links, categorizing them as either rigid or shaky based on their adaptability to certain moves. We establish that every link…
This report presents a unified treatment of the density of states for the knots and folds of polymer chains. The physical realization of such systems ranges from DNA molecules to the microscopic configurations of space-time.
We take a close look at a classical magic trick performed with a string, where a trivial knot is seemingly isotoped into a trefoil, and generalize it to a family of magic tricks for transforming the unknot into other knots. We encode such a…
In this paper, we study knot diagrams for which the underlying graph has treewidth two. We give a linear time algorithm for the following problem: given a knot diagram of treewidth two, does it represent the unknot? We also show that for a…
We present a generic coarse-grained model to describe molecular motors acting on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules. The polymer is modeled as a connected chain of beads; motors are…
The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection…
This paper examines the relationship between the knotting of an embedded surface in $\R^3$ and the knotting of its fold curves, formed by the singular set of projection to a plane. The first result shows that every surface, no matter how…
The homset invariant of a knot or link L with respect to an algebraic knot coloring structure X can be identified with a set of colorings of a diagram of L by elements of X via an identification of diagrammatic generators with algebraic…
We introduce a notion of intrinsic linking and knotting for virtual spatial graphs. Our theory gives two filtrations of the set of all graphs, allowing us to measure, in a sense, how intrinsically linked or knotted a graph is; we show that…
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…
Recent progress in string theory has led to a reformulation of quantum-group polynomial invariants for knots and links into new polynomial invariants whose coefficients can be understood in topological terms. We describe in detail how to…
Given a class of objects, a pattern theorem is a powerful result describing their structure. We show that alternating knots exhibit a pattern theorem, and use this result to prove a long-standing conjecture that alternating knots grow rare.…