Related papers: RNAlike polymer model: exact calculation on the Be…
We solve a model of self-avoiding walks with up to two monomers per site on the Bethe lattice. This model, inspired on the Domb-Joyce model, was recently proposed to describe the collapse transition observed in interacting polymers [J.…
We present a Bethe approximation to study lattice models of linear polymers. The approach is variational in nature and based on the cluster variation method (CVM). We focus on a model with $(i)$ a nearest neighbor attractive energy…
There have been separate studies of the polymer collapse transition, where the collapse was induced by two different types of attraction. In each case, the configurations of the polymer were given by the same subset of random walks being…
We study the statistics of thermodynamic quantities in two related systems with quenched disorder: A (1+1)-dimensional planar lattice of elastic lines in a random potential and the 2-dimensional random bond dimer model. The first system is…
A lattice model is presented for the simulation of dynamics in polymeric systems. Each polymer is represented as a chain of monomers, residing on a sequence of nearest-neighbor sites of a face-centered-cubic lattice. The polymers are self-…
RNA molecules form a sequence-specific self-pairing pattern at low temperatures. We analyze this problem using a random pairing energy model as well as a random sequence model that includes a base stacking energy in favor of helix…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
In probability theory, reinforced walks are random walks on a lattice (or more generally a graph) that preferentially revisit neighboring `locations' (sites or bonds) that have been visited before. In this paper, we consider walks with…
Trails (bond-avoiding walks) provide an alternative lattice model of polymers to self-avoiding walks, and adding self-interaction at multiply visited sites gives a model of polymer collapse. Recently, a two-dimensional model (triangular…
We present results from extensive Monte Carlo simulations of polymer models where each lattice site can be visited by up to $K$ monomers and no restriction is imposed on the number of bonds on each lattice edge. These \textit{multiple…
We study the localisation of lattice polymer models near a permeable interface in two dimensions. Localisation can arise due to an interaction between the polymer and the interface, and can be altered by a preference for the bulk solvent on…
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…
We study simple lattice systems to demonstrate the influence of interpenetrating bond networks on phase behavior. We promote interpenetration by using a Hamiltonian with a weakly repulsive interaction with nearest neighbors and an…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
In the multiple monomers per site (MMS) model, polymeric chains are represented by walks on a lattice which may visit each site up to K times. We have solved the unrestricted version of this model, where immediate reversals of the walks are…
This report deals with phase transition in Bond Fluctuation Model (BFM) of a linear homo polymer on a two dimensional square lattice. Each monomer occupies a unit cell of four lattice sites. The condition that a lattice site can at best be…
A lattice model for active matter is studied numerically, showing that it displays wettings transitions between three distinctive phases when in contact with an impenetrable wall. The particles in the model move persistently, tumbling with…
In this paper we develop a Bethe approximation, based on the cluster variation method, which is apt to study lattice models of branched polymers. We show that the method is extremely accurate in cases where exact results are known as, for…
The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…