Related papers: Knotting statistics for polygons in lattice tubes
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…
This paper explores the problem of unknotting closed braids and classical knots in mathematical knot theory. We apply evolutionary computation methods to learn sequences of moves that simplify knot diagrams, and show that this can be…
Streamlines, vortex lines and magnetic flux tubes in turbulent fluids and plasmas display a great amount of coiling, twisting and linking, raising the question as to whether their topological complexity (continually created and destroyed by…
We study the dynamics of an exactly solvable lattice model for inhomogeneous interface growth. The interface grows deterministically with constant velocity except along a defect line where the growth process is random. We obtain exact…
In this note, I describe a formalism for treating knots as geometric spaces, and make an application to a simple statistical mechanics computation. The motivation for this study is the natural visual symmetry of the knot, and I describe how…
We use Brownian dynamics simulations and advanced topological profiling methods to characterize the out-of-equilibrium evolution of self-entanglement in linear polymers confined into nano-channels and under periodic compression. We…
Vortex stretching is a common feature of many complex flows, including turbulence. Experiments and simulations of isolated vortex knots demonstrate that this behavior can also be seen in relatively simple systems, and appears to be…
The representation of knots by petal diagrams (Adams et al. 2012) naturally defines a sequence of distributions on the set of knots. In this article we establish some basic properties of this randomized knot model. We prove that in the…
We study the dynamics of knotted vortices in a bulk excitable medium using the FitzHugh-Nagumo model. From a systematic survey of all knots of at most eight crossings we establish that the generic behaviour is of unsteady, irregular…
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 mechanics of single polymer knots is studied using Monte Carlo simulations. The polymers are considered on a cubic lattice and their conformations are randomly changed with the help of pivot transformations. After each…
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…
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,…
Whether turbulence intermittencies shall be described by a log-Poisson, a log-stable pdf or other distributions is still debated nowadays. In this paper, a bridge between polymer physics, self-avoiding walk and random vortex stretching is…
This paper investigates the extension complexity of polytopes by exploiting the correspondence between non-negative factorizations of slack matrices and randomized communication protocols. We introduce a geometric characterization of…
The presence of slipknots in configurations of proteins and DNA has been shown to affect their functionality, or alter it entirely. Historically, polymers are modeled as polygonal chains in space. As an alternative to space curves, we…
Voids exist in proteins as packing defects and are often associated with protein functions. We study the statistical geometry of voids in two-dimensional lattice chain polymers. We define voids as topological features and develop a simple…
For a positive integer $n\ge 3$, the collection of $n$-sided polygons embedded in $3$-space defines the space of geometric knots. We will consider the subspace of equilateral knots, consisting of embedded $n$-sided polygons with unit length…
A {\it stuck knot} is a knot diagram containing designated crossings, called {\it stuck crossings}, whose incident strands are required to remain locally non-separable. These rigidity constraints restrict the allowable ambient isotopies and…
We consider the expected value for the total curvature of a random closed polygon. Numerical experiments have suggested that as the number of edges becomes large, the difference between the expected total curvature of a random closed…