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We study the emerging self-organization in active ring suspensions, focusing on how the rings' orientational order and geometric entanglement vary with density and spatial confinement. To quantify entanglement, we introduce the wrapping…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
The molecular dynamics simulations were used to obtain the radius of gyration of real ring polymer chains with different topological structures consisting of 360 monomers. We focus on the entropic force which is exerted by a dilute solution…
Drawing inspiration from the concept of the "primitive path" of a linear chain in melt conditions, we introduce here a numerical protocol which allows us to detect, in an unambiguous manner, the "primitive shapes" of ring polymers in…
We investigate by means of a number of different dynamical Monte Carlo simulation methods the self-assembly of equilibrium polymers in dilute, semidilute and concentrated solutions under good-solvent conditions. In our simulations, both…
By revisiting the Kirchhoff's Matrix-Tree Theorem, we give an exact formula for the number of spanning trees of a graph in terms of the quantum relative entropy between the maximally mixed state and another state specifically obtained from…
We investigate the number of permutations that occur in random labellings of trees. This is a generalisation of the number of subpermutations occurring in a random permutation. It also generalises some recent results on the number of…
We formulate code concatenation as the action of a unitary quantum circuit on an expanding tree geometry and find that for certain classes of gates, applied identically at each node, a binary tree circuit encodes a single logical qubit with…
Given a sequence composed of a limit number of characters, we try to "read" it as a "text". This involves to segment the sequence into "words". The difficulty is to distinguish good segmentation from enormous number of random ones.Aiming at…
The interplay of topological constraints and persistence length of ring polymers in their own melt is investigated by means of dynamical Monte Carlo simulations of a three dimensional lattice model. We ask if the results are consistent with…
Simulations of knotting and unknotting in polymers or other filaments rely on random processes to facilitate topological changes. Here we introduce a method of \textit{topological steering} to determine the optimal pathway by which a…
The interplay of topological constraints, excluded volume interactions, persistence length and dynamical entanglement length in solutions and melts of linear chains and ring polymers is investigated by means of kinetic Monte Carlo…
The entanglement entropy of a subsystem of a quantum system is expressed, in the replica approach, through analytic continuation with respect to n of the trace of the n-th power of the reduced density matrix. This trace can be thought of as…
We present a statistical mechanical description of randomly packed spherical particles, where the average coordination number is treated as a macroscopic thermodynamic variable. The overall packing entropy is shown to have two…
We present Monte Carlo computer simulations for melts of semiflexible randomly knotted and randomly concatenated ring polymers on the fcc lattice and in slit confinement. Through systematic variation of the slit width at fixed melt density,…
For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
Polymer chains decorated with a fraction of monomers capable of forming reversible bonds form transient polymer networks that are important in soft and biological systems. If chains are flexible and the attractive monomers are all of the…
Random heteropolymers are a minimal description of biopolymers and can provide a theoretical framework to the investigate the formation of loops in biophysical experiments. A two--state model provides a consistent and robust way to study…
In this paper we compute the leading correction to the bipartite entanglement entropy at large sub-system size, in integrable quantum field theories with diagonal scattering matrices. We find a remarkably universal result, depending only on…
We report a numerical calculation of the total number of disordered jammed configurations $\Omega$ of $N$ repulsive, three-dimensional spheres in a fixed volume $V$. To make these calculations tractable, we increase the computational…