Related papers: Randomly cross-linked polymer models
We study the conformational freedom of a protein made by two rigid domains connected by a flexible linker. The conformational freedom is represented as an unknown probability distribution on the space of allowed states. A new algorithm for…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
The cross-lagged panel model (CLPM) has been widely used, particularly in psychology, to infer longitudinal relations among variables. At the same time, controlling for between-person heterogeneity and capturing within-person relations as…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
We study the equilibrium properties of a model for a binary mixture of catalytically-reactive monomers adsorbed on a two-dimensional substrate decorated by randomly placed catalytic bonds. The interacting $A$ and $B$ monomer species undergo…
We describe a computational method for constructing a coarse combinatorial model of some dynamical system in which the macroscopic states are given by elementary cycling motions of the system. Our method is in particular applicable to time…
Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in probabilistic arguments concerning the emergence of…
The size of rings (also called cyclic polymers) in bidisperse blends of chemically identical rings is analyzed by computer simulations. Data of entangled ring blends and blends of interpenetrating rings are compared and it is shown that the…
We introduce a class of pairs of graphs consisting of two cliques joined by an arbitrary number of edges. The members of a pair have the property that the clique-bridging edge-set of one graph is the complement of that of the other. We…
We examine the condensed states of a simple semiflexible copolymer in which there are two monomer types that are immiscible with each other and with the solvent. Although this is similar to the well known problem of collapse for a…
By means of Langevin dynamics simulations, we investigate the gel formation of randomly functionalized polymers in solution, with the ability to form both intra- and intermolecular reversible bonds. Under highly dilute conditions, these…
Ring, or cyclic, polymers have unique properties compared to linear polymers, due to their topologically closed structure that has no beginning or end. Experimental measurements on molecular ring polymers are challenging due to their…
We study a heteropolymer model with random contact interactions introduced some time ago as a simplified model for proteins. The model consists of self-avoiding walks on the simple cubic lattice, with contact interactions between nearest…
The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical ("epigenetic") marks…
The non-equilibrium structural and dynamical properties of a flexible polymer tethered to a reflecting wall and subject to oscillatory linear flow are studied by numerical simulations. Polymer is confined in two dimensions and is modeled as…
The Langevin dynamics of a random heteropolymer and its dynamic glass transition are studied using elementary mode coupling theory. Contrary to recent reports using a similar framework, a discontinuous ergodic-nonergodic phase transition is…
The conditions of the chromosomes inside the nucleus in the Rabl configuration have been modelled as self-avoiding polymer chains under restraining conditions. To ensure that the chromosomes remain stretched out and lined up, we fixed their…
We review pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells. For that purpose, we review, first, recent theoretical and computational…
A simple, discrete, parametric model is proposed to describe conditional (correlated) deposition of particles on a surface and formation of a connecting (percolating) cluster. The surface changes spontaneously its properties (phase…
The correlations between the segments of a semidilute polymer solution are found to induce correlations in the positions of small particles added to the solution. Small means a diameter much less than the polymer's correlation length. In…