Related papers: Randomly cross-linked polymer models
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D…
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 conformational statistics of ring polymers in melts or dense solutions is strongly affected by their quenched microscopic topological state. The effect is particularly strong for non-concatenated unknotted rings, which are known to…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop…
The rapid collapse of a polymer, due to external forces or changes in solvent, yields a long-lived `crumpled globule.' The conjectured fractal structure shaped by hierarchical collapse dynamics has proved difficult to establish, even with…
In this study, a versatile methodology for initiating polymerization from monomers in highly cross-linked materials is investigated. As polymerization progresses, force-field parameters undergo continuous modification due to the formation…
We investigate the phase transition properties of the polymer-Potts model, a chain composed of monomers with magnetic degrees of freedom, with the motivation to study the conformation and mark switching dynamics of chromatin. By the…
Conformation-dependent design of polymer sequences can be considered as a tool to control macromolecular self-assembly. We consider the monomer unit sequences created via the modification of polymers in a homogeneous melt in accordance with…
We explore the effect of random permanent cross-links on a system of directed polymers confined between two planes with their end-points free to slide on them. We treat the cross-links as quenched disorder and we use a semimicroscopic…
The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a…
We propose a polymer model for the dynamics of chromatin replication in three dimensional space. Our simulations indicate that both immobile and tracking replisomes may self-assemble during the process, reconciling previous apparently…
We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are…
The statistical mechanics of a linear non-interacting polymer chain with a large number of monomers is considered with fixed angular momentum. The radius of gyration for a linear polymer is derived exactly by functional integration. This…
In this thesis the formation and properties of a polymer gel on and at a surface are investigated. The gel under investigation is defined as a three-dimensional network of "phantom" macromolecules that form permanent links with one another…
We define the local periodic linking number, LK, between two oriented closed or open chains in a system with three-dimensional periodic boundary conditions. The properties of LK indicate that it is an appropriate measure of entanglement…
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…
Randomly branching polymers with {\em annealed} connectivity are model systems for ring polymers and chromosomes. In this context, the branched structure represents transient folding induced by topological constraints. Here we present…