Related papers: Configurational entropy of randomly double-folding…
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 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…
Chromosomes are crumpled polymer chains further folded into a sequence of stochastic loops via loop extrusion. While extrusion has been verified experimentally, the particular means by which the extruding complexes bind DNA polymer remains…
Taking into account the nonequivalence of fixed-force and fixed-length ensembles in the weak-force regime, equations of state are derived that describe the equilibrium extension or compression of an ideal Gaussian polymer chain in response…
Ring polymers are prevalent in natural and engineered systems, including circular bacterial DNA, crown ethers for cation chelation, and mechanical nanoswitches. The morphology and dynamics of ring polymers are governed by the chemistry and…
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…
One of the most challenging problems in polymer physics is providing a theoretical description for the behaviour of rings in dense solutions and melts. Although it is nowadays well established that the overall size of a ring in these…
A relaxed version of Gummelt's covering rules for the aperiodic decagon is considered, which produces certain random-tiling-type structures. These structures are precisely characterized, along with their relationships to various other…
Current theories on the conformation and dynamics of unknotted and non-concatenated ring polymers in melt conditions describe each ring as a tree-like double-folded object. While evidence from simulations supports this picture on a single…
While Flory theories provide an extremely useful framework for understanding the behavior of interacting, randomly branching polymers, the approach is inherently limited. Here we use a combination of scaling arguments and computer…
In this work a new strategy is proposed in order to build analytic and microscopic models of fluctuating polymer rings subjected to topological constraints. The topological invariants used to fix these constraints belong to a wide class of…
We study the unfolding of a single polymer chain due to an external force. We use a simplified model which allows to perform all calculations in closed form without assuming a Boltzmann-Gibbs form for the equilibrium distribution.…
In this paper we examine planted binary plane trees. First, we provide an exact formula for the number of planted binary trees with given Horton-Strahler orders. Then, using the notion of entropy, we examine the structural complexity of…
The entanglement properties of a class of topological stabilizer states, the so called \emph{topological color codes} defined on a two-dimensional lattice or \emph{2-colex}, are calculated. The topological entropy is used to measure the…
We propose a principled method for autoencoding with random forests. Our strategy builds on foundational results from nonparametric statistics and spectral graph theory to learn a low-dimensional embedding of the model that optimally…
We investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness A kT and twist stiffness C kT. In such a model, thermal bend fluctuations couple geometrically to…
The size of rings (also called cyclic polymers) in bidisperse blends of chemically identical rings is analyzed by computer simulations. Data of entangled ring blends and blends of interpenetrating rings are compared and it is shown that the…
Using canonical Monte Carlo simulations, we introduce a new numerical procedure for comparing the entropic exponents of polymers with different constraints and/or topologies. Setting up competitions between polymer segments which can…
By extending the breadth first search algorithm to any d-type critical or subcritical irreducible branching forest, we show that such forests may be encoded through d independent, integer valued, d-dimensional random walks. An application…
In this paper we explore how non trivial boundary conditions could influence the entanglement entropy in a topological order in 2+1 dimensions. Specifically we consider the special class of topological orders describable by the quantum…