Related papers: Viscoelasticity of model interphase chromosomes
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
The dynamical properties and diffusive behavior of a collection of mutually interacting particles are numerically investigated for two types of long-range interparticle interactions: Coulomb-electrostatic and dipole-electrodynamic. It is…
We investigate crack propagation in a simple two-dimensional visco-elastic model and find a scaling regime in the relation between the propagation velocity and energy release rate or fracture energy, together with lower and upper bounds of…
We study the phase behavior of polar Active Brownian Particles moving in two-spatial dimensions and interacting through volume exclusion and velocity alignment. We combine particle-based simulations of the microscopic model with a simple…
Trajectories of endosomes inside living eukaryotic cells are highly heterogeneous in space and time and diffuse anomalously due to a combination of viscoelasticity, caging, aggregation and active transport. Some of the trajectories display…
We investigate the Brownian diffusion of particles in one spatial dimension and in the presence of finite regions within which particles can either evaporate or be reset to a given location. For open boundary conditions, we highlight the…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
We develop a mean-field model to examine the stability of a `quasi-2D suspension' of elongated particles embedded within a viscous membrane. This geometry represents several biological and synthetic settings, and we reveal mechanisms by…
Addition of particles to a viscoelastic suspension dramatically alters the properties of the mixture, particularly when it is sheared or otherwise processed. Shear-induced stretching of the polymers results in elastic stress that causes a…
We show the linear response theory of spatial-scale-dependent relaxation moduli for overdamped Brownian particle systems. We employ the Irving-Kirkwood stress tensor field as the microscopic stress tensor field. We show that the…
A Particle Tracking Velocimetry experiment has been performed in a turbulent flow at intermediate Reynolds number. We present experimentally obtained stretching rates for particle pairs in the inertial range. When compensated by a…
We investigate a diffusive motion of a system of interacting Brownian particles in quasi-one-dimensional micropores. In particular, we consider a semi-infinite 1D geometry with a partially absorbing boundary and the hard-core inter-particle…
Nonequilibrium molecular dynamics simulations are used to study the shear thinning behavior of immiscible symmetric polymer blends. The phase separated polymers are subjected to a simple shear flow imposed by moving a wall parallel to the…
We investigate the lateral dynamics in a purely viscous lipid membrane surrounded by viscoelastic media such as polymeric solutions. We first obtain the generalized frequency-dependent mobility tensor and focus on the case when the solvent…
We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-H\"uckel electrostatics and uses a two-angle zig-zag model for the geometry…
Recently, many interesting features of the hydrodynamically coupled motions of the Brownian particles in a viscous fluid have been reported which are impossible for the uncoupled motions of the similar particles. However, it is expected…
While the structure of chromatin has been studied in great detail on length scales below 30 nm, amazingly little is known about the higher-order folding motifs of chromatin in interphase. Recent experiments give evidence that the folding…
Shape changes resulting from segmental flexibility are ubiquitous in molecular and biological systems, and are expected to affect both the diffusive motion and (biological) function of dispersed objects. The recent development of colloidal…
Chromatin is a complex of DNA and specific proteins forming an intermediary level of organization of eukaryotic genomes, between double-stranded DNA and chromosome. Within a generic modeling of the chromatin assembly, we investigate the…
We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of slip-link-like proteins, mimicking the behaviour of cohesin molecules. We recently proposed that diffusive sliding is sufficient to…