Related papers: Random knotting in very long off-lattice self-avoi…
Knots are commonly found in molecular chains such as DNA and proteins, and they have been considered to be useful models for structural analysis of these molecules. One interested quantity is the minimum number of monomers necessary 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 use new algorithms, based on the finite lattice method of series expansion, to extend the enumeration of self-avoiding walks and polygons on the triangular lattice to length 40 and 60, respectively. For self-avoiding walks to length 40…
The size of a zero thickness (no excluded volume) polymer ring is shown to scale with chain length $N$ in the same way as the size of the excluded volume (self-avoiding) linear polymer, as $N^{\nu}$, where $\nu \approx 0.588$. The…
The statistical properties of random lattice knots, the topology of which is determined by the algebraic topological Jones-Kauffman invariants was studied by analytical and numerical methods. The Kauffman polynomial invariant of a random…
We construct a tractable model to describe the rate at which a knotted polymer is ejected from a spherical capsid via a small pore. Knots are too large to fit through the pore and must reptate to the end of the polymer for ejection to…
The list of knots with up to 10 crossings is commonly referred to as the Rolfsen Table. This paper presents a way to generate the Rolfsen table in a simple, clear, and reproducible manner. The methods we use are similar to those used by J.…
We study the dynamics of a knot in a semiflexible polymer confined to a narrow channel of width comparable to the polymers' persistence length. Using a combination of Brownian dynamics simulations and a coarse-grained stochastic model, we…
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…
In this paper we study how randomly generated knots occupy a volume of space using topological methods. To this end, we consider the evolution of the first homology of an immersed metric neighbourhood of a knot's embedding for growing…
We give a criterion for distinguishing a prime knot $K$ in $S^3$ from every other knot in $S^3$ using the finite quotients of $\pi_1(S^3\setminus K)$. Using recent work of Baldwin-Sivek, we apply this criterion to the hyperbolic knots…
We present new computations of tight shapes obtained using the constrained gradient descent code RIDGERUNNER for 544 composite knots with 12 and fewer crossings, expanding our dataset to 943 knots and links. We use the new data set to…
This paper visualizes a knot reduction algorithm
We present an algorithm that, with high probability, generates a random spanning tree from an edge-weighted undirected graph in $\tilde{O}(n^{4/3}m^{1/2}+n^{2})$ time (The $\tilde{O}(\cdot)$ notation hides $\operatorname{polylog}(n)$…
Let $\mbox{Len}(K)$ be the minimum length of a knot on the cubic lattice (namely the minimum length necessary to construct the knot in the cubic lattice). This paper provides upper bounds for $\mbox{Len}(K)$ of a nontrivial knot $K$ in…
We consider the problem of deciding whether a polygonal knot in 3-dimensional Euclidean space is unknotted, capable of being continuously deformed without self-intersection so that it lies in a plane. We show that this problem, {\sc…
The first algorithm for sampling the space of thick equilateral knots, as a function of thickness, will be described. This algorithm is based on previous algorithms of applying random reflections. To prove the existence of the algorithm, we…
We develop a framework for discrete p-density and compression-radius profiles of lattice knots. For lattice polygons representing a fixed knot type, we define scale-free density quantities by dividing lattice length by chord-length spread…
Self-avoiding polymers in strictly two-dimensional ($d=2$) melts are investigated by means of molecular dynamics simulation of a standard bead-spring model with chain lengths ranging up to N=2048. % The chains adopt compact configurations…
The stick number of a knot is the minimum number of segments needed to build a polygonal version of the knot. Despite its elementary definition and relevance to physical knots, the stick number is poorly understood: for most knots we only…