Related papers: Equilibrium shapes of flat knots
We study equilibrium shapes and shape transformations of a confined semiflexible chain inside a soft lipid tubule using simulations and continuum theories. The deformed tubular shapes and chain conformations depend on the relative magnitude…
We partially determine grid homology (combinatorial knot Floer homology) of diagonal knots, which are conjectured to be equivalent to positive braid knots, by exploiting nice grid diagrams. Its next-to-top term detects the number of prime…
We use computer simulations to compare the dynamical behaviour of torus and even-twist knots in polymers under tension. The knots diffuse through a mechanism similar to reptation. Their friction coefficients grow linearly with average knot…
In this paper we provide a combinatorial tool to help study some topological properties of modular knots. We construct templates for the infinitely many Anosov flows on the trefoil complement, which are lifts of the geodesic flow on the…
Simulations in which a globular ring polymer with delocalized knots is separated in two interacting loops by a slipping link, or in two non-interacting globuli by a wall with a hole, show how the minimal crossing number of the knots…
In this paper we examine the relative knotting probabilities in a lattice model of ring polymers confined in a cavity. The model is of a lattice knot of size $n$ in the cubic lattice, confined to a cube of side-length $L$ and with volume…
The classical knot groups are the fundamental groups of the complements of smooth or piecewise-linear (PL) locally-flat knots. For PL knots that are not locally-flat, there is a pair of interesting groups to study: the fundamental group of…
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…
Let T denote the group of smooth concordance classes of topologically sice knots. We show that the first quotient in the bipolar filtration of T (i.e. 0-bipolar knots modulo 1-bipolar knots) has infinite rank, even modulo Alexander…
We give criteria for oriented links to be periodic of prime order using the quantum $\mathrm{SL}(N)$-invariant. The criteria are based upon an observation on the linking number between a periodic knot and its axis of the rotation.
For a polygonal knot K, it is shown that a tube of radius R(K), the polygonal thickness radius, is an embedded torus. Given a thick configuration K, perturbations of size r<R(K) define satellite structures, or local knotting. We explore…
The space of n-sided polygons embedded in three-space consists of a smooth manifold in which points correspond to piecewise linear or ``geometric'' knots, while paths correspond to isotopies which preserve the geometric structure of these…
We investigate experimentally the distribution of configurations of a ring with an elementary topological constraint, a ``figure-8'' twist. Using vibrated granular chains, which permit controlled preparation and direct observation of such a…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
We investigate the conformations of a semiflexible polymer confined to a square box. Results of Monte Carlo simulations show the existence of a shape transition when the persistence length of the polymer becomes comparable to the dimensions…
We present two models for the space of knots which have endpoints at fixed boundary points in a manifold with boundary, one model defined as an inverse limit of spaces of maps between configuration spaces and another which is cosimplicial.…
A ring polymer in a confining space may exhibit at least two phases, namely an expanded (or solvent-rich phase) if its concentration is small, or a collapsed (or polymer-rich phase) when it is concentrated and compressed. These phases are…
Nonequilibrium active polymers provide a minimal framework to investigate biopolymers such as DNA and chromatin under the action of molecular motors. Here we study active ring polymers with controlled topology and show that knot type…
For $p$ prime and $\ell = \frac{p-1}{2}$, we show that the shapes of pure prime degree number fields lie on one of two $\ell$-dimensional subspaces of the space of shapes, and which of the two subspaces is dictated by whether or not $p$…
We present a novel phenomenological theory describing how topological constraints in prime-knot ring polymers induce collective (cooperative) modes of motion. In low-complexity knots, chain segments can move quasi-independently. However, as…