相关论文: A Random Loop Model for Long Polymers
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…
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…
We use Monte Carlo simulations to study polymer melts consisting of fully flexible and moderately stiff chains in the bond fluctuation model at a volume fraction $0.5$. In order to reduce the local density fluctuations, we test a…
We study the dynamics of the passage of a polymer through a membrane pore (translocation), focusing on the scaling properties with the number of monomers $N$. The natural coordinate for translocation is the number of monomers on one side of…
We have studied numerically the random interchange model and related loop models on the three-dimensional cubic lattice. We have determined the transition time for the occurrence of long loops. The joint distribution of the lengths of long…
Involved in mitotic condensation, interaction of transcriptional regulatory elements or isolation of structural domains, understanding loop formation is becoming a paradigm in the deciphering of chromatin architecture and its functional…
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 consider a model of a polymer in $\mathbb{Z}^{d+1}$, constrained to join 0 and a hyperplane at distance $N$. The polymer is subject to a quenched nonnegative random environment. Alternatively, the model describes crossing random walks in…
The universal behaviour of two-dimensional loop models can change dramatically when loops are allowed to cross. We study models with crossings both analytically and with extensive Monte Carlo simulations. Our main focus (the 'completely…
We solve a hydrodynamic model of active chromatin dynamics, within a confined geometry simulating the cell nucleus. Using both analytical and numerical methods, we describe the behavior of the chromatin polymer driven by the activity of…
The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is…
The nematic ordering in semiflexible polymers with contour length $L$ exceeding their persistence length $\ell_p$ is described by a confinement of the polymers in a cylinder of radius $r_{eff}$ much larger than the radius $r_\rho$, expected…
Concentration of measure is a phenomenon in which a random variable that depends in a smooth way on a large number of independent random variables is essentially constant. The random variable will "concentrate" around its median or…
In this paper, we study random embeddings of polymer networks distributed according to any potential energy which can be expressed in terms of distances between pairs of monomers. This includes freely jointed chains, steric effects,…
Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal…
The effect of confinement in the segmental relaxation of polymers is considered. On the basis of a thermodynamic model we discuss the emerging relevance of the fast degrees of freedom in stimulating the much slower segmental relaxation, as…
Simulated annealing is an effective and general means of optimization. It is in fact inspired by metallurgy, where the temperature of a material determines its behavior in thermodynamics. Likewise, in simulated annealing, the actions that…
We introduce a 2-dimensional lattice model of granular matter. We use a combination of proof and simulation to demonstrate an order/disorder phase transition in the model, to which we associate the granular phenomenon of random close…
The chromosome is a key player of cell physiology, and its dynamics provides valuable information about its physical organization. In both prokaryotes and eukaryotes, the short-time motion of chromosomal loci has been described as a Rouse…
We study various statistical properties of the double-dimer model, a generalization of the dimer model, on rectangular domains of the square lattice. We take advantage of the Grassmannian representation of the dimer model, first to…