Modeling properties of chromosome territories using polymer filaments in diverse confinement geometries.

Interphase chromosomes reside within distinct nuclear regions known as chromosome territories (CTs). Recent observations from Hi-C analyses, a method mapping chromosomal interactions, have revealed varied decay in contact probabilities among different chromosomes. Our study explores the relationship between this contact decay and the particular shapes of the chromosome territories they occupy.

Polycomb proteins translate histone methylation to chromatin folding.

Epigenetic repression often involves covalent histone modifications. Yet, how the presence of a histone mark translates into changes in chromatin structure that ultimately benefits the repression is largely unclear. Polycomb group proteins comprise a family of evolutionarily conserved epigenetic repressors.

Nanoprobe diffusion in entangled polymer solutions: Linear vs. unconcatenated ring chains.

We employ large-scale molecular dynamics computer simulations to study the problem of nanoprobe diffusion in entangled solutions of linear polymers and unknotted and unconcatenated circular (ring) polymers. By tuning both the diameter of the nanoprobe and the density of the solution, we show that nanoprobes of diameter smaller than the entanglement distance (tube diameter) of the solution display the same (Rouse-like) behavior in solutions of both polymer architectures. Instead, nanoprobes with larger diameters appear to diffuse markedly faster in solutions of rings than in solutions of linear chains.

Glassiness and Heterogeneous Dynamics in Dense Solutions of Ring Polymers.

Understanding how topological constraints affect the dynamics of polymers in solution is at the basis of any polymer theory and it is particularly needed for melts of rings. These polymers fold as crumpled and space-filling objects and, yet, they display a large number of topological constraints. To understand their role, here we systematically probe the response of solutions of rings at various densities to "random pinning" perturbations.

Density effects in entangled solutions of linear and ring polymers.

In this paper, we employ molecular dynamics computer simulations to study and compare the statics and dynamics of linear and circular (ring) polymer chains in entangled solutions of different densities. While we confirm that linear chain conformations obey Gaussian statistics at all densities, rings tend to crumple becoming more and more compact as the density increases. Conversely, contact frequencies between chain monomers are shown to depend on solution density for both chain topologies.