Related papers: Randomly cross-linked polymer models
The population-averaged contact maps generated by the chromosome conformation capture technique provide important information about the average frequency of contact between pairs of chromatin loci as a function of the genetic distance…
We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R_c$,…
We suggest a new random model for links based on meander diagrams and graphs. We then prove that trivial links appear with vanishing probability in this model, no link $L$ is obtained with probability 1, and there is a lower bound for the…
It is widely believed that the folding of the chromosome in the nucleus has a major effect on genetic expression. For example co-regulated genes in several species have been shown to colocalize in space despite being far away on the DNA…
We consider a microscopic model of a polymer blend that is prone to phase separation. Permanent crosslinks are introduced between randomly chosen pairs of monomers, drawn from the Deam-Edwards distribution. Thereby, not only density but…
Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…
We study the probability that two directed polymers in the same random potential do not intersect. We use the replica method to map the problem onto the attractive Lieb-Liniger model with generalized statistics between particles. We obtain…
By means of a minimal physical model, we investigate the interplay of two phase transitions at play in chromatin organization: (1) liquid-liquid phase separation (LLPS) within the fluid solvating chromatin, resulting in the formation of…
Creating amorphous solid states by randomly bonding an ensemble of dense liquid monomers is a common procedure which is applied to create a variety of materials such as epoxy resins, colloidal gels, and vitrimers. The properties of the…
Motivated by the problem of domain formation in chromosomes, we studied a co--polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus…
We study the phase transitions of a random copolymer chain with quenched disorder. We apply a replica variational approach based on a Gaussian trial Hamiltonian in terms of the correlation functions of monomer Fourier coordinates. This…
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…
We define a lattice model for the interaction of a polymer with water. We solve the model in a suitable approximation. In the case of a non-polar homopolymer, for reasonable values of the parameters, the polymer is found in a non-compact…
We introduce the simplest model to describe parametric interactions in a quadratically nonlinear optical medium with the fundamental harmonic containing two components with (slightly) different carrier frequencies [which is a direct analog…
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…
A mean field rate theory description of the homo- and co-polymerization of $f$-functional molecules is developed, which contains the formation of short cyclic structures inside the network. The predictions of this model are compared with…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
Abstract polymer models are systems of weighted objects, called polymers, equipped with an incompatibility relation. An important quantity associated with such models is the partition function, which is the weighted sum over all sets of…
We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic the behaviour of cohesin-like molecules, which, along with…
We study a blend of two kinds of homopolymers with tendency for segragation. Cross-links between the chains of different kinds do not allow macrophase separation. Instead microphase structure appears. Starting from a microscopic model we…