Related papers: A Random Loop Model for Long Polymers
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…
Drawing an analogy to the paradigm of quasi-elastic neutron scattering, we present a general approach for quantitatively investigating the spatiotemporal dependence of structural anisotropy relaxation in deformed polymers by using…
The cellular cytoplasm is organized into compartments. Phase separation is a simple manner to create membrane-less compartments in order to confine and localize particles like proteins. In many cases these particles are bound to fluctuating…
Concatenation and equilibrium swelling of Olympic gels, which are composed of entangled cyclic polymers, is studied by Monte Carlo Simulations. The average number of concatenated molecules per cyclic polymers, $f_n$, is found to depend on…
In this paper, the looping kinetics of a long polymer chain in solution has been investigated by using two state model, where one state represents open chain polymer molecule and the other represents closed chain polymer molecule. The…
These notes are devoted to the statistical mechanics of directed polymers interacting with one-dimensional spatial defects. We are interested in particular in the situation where frozen disorder is present. These polymer models undergo a…
We have developed a theory of polymer entanglement using an extended Cahn-Hilliard functional, with two extra terms. One is a nonlocal attractive term, operating over mesoscales, which is interpreted as giving rise to entanglement, and the…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
We describe random loop models and their relations to a family of quantum spin systems on finite graphs. The family includes spin 1/2 Heisenberg models with possibly anisotropic spin interactions and certain spin 1 models with…
We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of slip-link-like proteins, mimicking the behaviour of cohesin molecules. We recently proposed that diffusive sliding is sufficient to…
We study the dynamics of a polymer when it is quenched from a $\theta$ solvent into a good or bad solvent by means of a Langevin equation. The variation of the radius of gyration is studied as a function of time. For the first stage of…
A wide variety of complex networks (social, biological, information etc.) exhibit local clustering with substantial variation in the clustering coefficient (the probability of neighbors being connected). Existing models of large graphs…
This chapter deals with various aspects related to the adsorption of long chain-like macromolecules (polymers) onto solid surfaces. Physical aspects of the adsorption mechanism are elaborated mainly at thermodynamical equilibrium. The basic…
This paper considers the Monte Carlo dynamics of random dimer coverings of the square lattice, which can be mapped to a rough interface model. Two kinds of slow modes are identified, associated respectively with long-wavelength fluctuations…
Self-assembled linear structures like giant cylindrical micelles or discotic molecules in solution stacked in flexible columns are systems reminiscent of polydisperse polymer solutions.These supramolecular polymers have an equilibrium…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
We consider polymers in which M randomly selected pairs of monomers are restricted to be in contact. Analytical arguments and numerical simulations show that an ideal (Gaussian) chain of N monomers remains expanded as long as M<<N; its mean…
We report extensive simulations of the relaxation dynamics of a self-avoiding polymer confined inside a cylindrical pore. In particular, we concentrate on examining how confinement influences the scaling behavior of the global relaxation…
We introduce a sequential model for the deposition and aggregation of particles in the submonolayer regime. Once a particle has been randomly deposited on the substrate, it sticks to the closest atom or island within a distance \ell,…
We address the physics of nematic liquid crystalline elastomers randomly crosslinked in the isotropic state. To do this, we construct a phenomenological effective replica Hamiltonian in terms of two order-parameter fields: one for the…