Related papers: Confinement-induced glassy dynamics in a model for…
Motivated by recent experiments probing shape, size and dynamics of bacterial chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell. Such…
Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
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…
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 study the effect of confinement on glassy liquids using Random First Order Transition theory as framework. We show that the characteristic length-scale above which confinement effects become negligible is related to the point-to-set…
We report molecular dynamics simulations of the segregation of two overlapping chains in cylindrical confinement. We find that the entropic repulsion between the chains can be sufficiently strong to cause segregation on a time scale that is…
Motivated by chromosomes enclosed in nucleus and the recently discovered active topological glass, we study a spherically confined melt of long nonconcatenated active polymer rings. Without activity, the rings exhibit the same average…
Motivated by recent nanofluidics experiments, we use Brownian dynamics and Monte Carlo simulations to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity. The polymers are modeled as…
Using molecular dynamics simulation, we investigate the effect of confinement on a system that comprises several stiff segmented polymer chains where each chain has similar segments, but length and stiffness of the segments vary among the…
Driven suspensions, where energy is input at a particle scale, are a framework for understanding general principles of out-of-equilibrium organization. A large number of simple interacting units can give rise to non-trivial structure and…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
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 by Molecular Dynamics simulation a dense one-component system of particles confined on a spherical substrate. We more specifically investigate the evolution of the structural and dynamical properties of the system when changing the…
4-n-octyl-4-cyanobiphenyl (8CB) has been recently shown to display an unusual sequence of phases when confined into porous silicon (PSi). The gradual increase of oriented short-range smectic (SRS) correlations in place of a phase transition…
In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the…
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…
Disks moving in a narrow channel have many features in common with the glassy behavior of hard spheres in three dimensions. In this paper we study the caging behavior of the disks which sets in at characteristic packing fraction $\phi_d$.…
We compute for an archetypical glass-forming system the excess of particle mobility distributions over the corresponding distribution of dynamic propensity, a quantity that measures the tendency of the particles to be mobile and reflects…