Related papers: Knotting probabilities after a local strand passag…
Stochastic simulations are used to characterize the knotting distributions of random ring polymers confined in spheres of various radii. The approach is based on the use of multiple Markov chains and reweighting techniques, combined with…
We study numerically the tightness of prime flat knots in a model of self-attracting polymers with excluded volume. We find that these knots are localised in the high temperature swollen regime, but become delocalised in the low temperature…
The role of the topology and its relation with the geometry of biopolymers under different physical conditions is a nontrivial and interesting problem. Aiming at understanding this issue for a related simpler system, we use Monte Carlo…
We consider a natural model of random knotting- choose a knot diagram at random from the finite set of diagrams with n crossings. We tabulate diagrams with 10 and fewer crossings and classify the diagrams by knot type, allowing us to…
We study by Monte Carlo simulations a model of knotted polymer ring adsorbing onto an impenetrable, attractive wall. The polymer is described by a self-avoiding polygon (SAP) on the cubic lattice. We find that the adsorption transition…
We report on a computational study of the statics and dynamics of long flexible linear polymers that spontaneously knot and unknot. Specifically, the equilibrium self-entanglement properties, such as the knotting probability, knot length…
The probability of a random polygon (or a ring polymer) having a knot type $K$ should depend on the complexity of the knot $K$. Through computer simulation using knot invariants, we show that the knotting probability decreases exponentially…
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,…
We study random knots, which we define as a triple of random periodic functions (where a random function is a random trigonometric series, \[f(\theta) = \sum_{k=1}^\infty a_k \cos (k \theta) +b_k (\sin k \theta),\] with $a_k, b_k$ are…
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…
We give two different, statistically consistent definitions of the length l of a prime knot tied into a polymer ring. In the good solvent regime the polymer is modelled by a self avoiding polygon of N steps on cubic lattice and l is the…
The statistical mechanics of a long knotted collapsed polymer is determined by a free-energy with a knot-dependent subleading term, which is linked to the length of the shortest polymer that can hold such knot. The only other parameter…
Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and…
Theta-graphs are a type of spatial graph with two vertices connected by three edges. We investigate embeddings of theta-graphs in the square and simple cubic lattices, using a combination of the Wang-Landau Monte Carlo method with a variant…
We discuss the probability of random knotting for a model of self-avoiding polygons whose segments are given by cylinders of unit length with radius $r$. We show numerically that the characteristic length of random knotting is roughly…
Twisting a given knot $K$ about an unknotted circle $c$ a full $n \in \mathbb{N}$ times, we obtain a "twist family" of knots $\{ K_n \}$. Work of Kouno-Motegi-Shibuya implies that for a non-trivial twist family the crossing numbers…
Based on an estimate of the knot entropy of a worm-like chain we predict that the interplay of bending energy and confinement entropy will result in a compact metastable configuration of the knot that will diffuse, without spreading, along…
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…
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…
Recent studies classify the topology of proteins by analysing the distribution of their projections using knotoids. The approximation of this distribution depends on the number of projection directions that are sampled. Here we investigate…