Related papers: Confinement and Viscoelastic effects on Chain Clos…
Recent experiments showing scaling of the intrachromosomal contact probability, $P(s)\sim s^{-1}$ with the genomic distance $s$, are interpreted to mean a self-similar fractal-like chromosome organization. However, scaling of $P(s)$ varies…
The linear viscoelastic response of flexible polymer solutions in the dilute and semidilute unentangled regimes is investigated using Brownian dynamics simulations. The relaxation modulus and dynamic moduli are computed over a wide range of…
We use non-equilibrium atomistic molecular dynamics simulations of unentangled melts of linear and star polymers ($\mathrm{C_{25}H_{52}}$) to study the steady-state viscoelastic response under confinement within nanoscale hematite $\left (…
We study the dynamical response of a single semiflexible polymer chain based on the theory developed by Hallatschek et al. for the wormlike-chain model. The linear viscoelastic response under oscillatory forces acting at the two chain ends…
We analyse the nature of the confinement of an infinitely long (and finite) linear semiflexible homo-polymer chain confined in between two geometrical constraints (A&B) under good solvent condition in two dimensions. The constraints are…
We compare the Rubinstein-Duke model for reptation to a model where the boundary dynamics is modified by calculating the viscosity of polymer melts. The question is investigated whether the viscosity is determined by details of the dynamics…
For biologically relevant macromolecules such as intrinsically disordered proteins, internal degrees of freedom that allow for shape changes have a large influence on both the motion and function of the compound. A detailed understanding of…
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…
The longitudinal response of single semiflexible polymers to sudden changes in externally applied forces is known to be controlled by the propagation and relaxation of backbone tension. Under many experimental circumstances, realized, e.g.,…
In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This…
Based on the Wilemski-Fixman approach (J. Chem. Phys. 60, 866 (1974)) we showed that for a flexible chain in theta solvent hydrodynamic interaction treated with an pre-averaging approximation makes ring closing faster if the chain is not…
We study the effect of confinement on diffusion limited bimolecular reactions within a lattice model where a small number of reactants diffuse amongst a much larger number of inert particles. When the number of inert particles is held…
We investigated the viscoelastic response of model interphase chromosomes by tracking the three-dimensional motion of hundreds of dispersed Brownian particles of sizes ranging from the thickness of the chromatin fiber up to slightly above…
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…
We study the combined effects of nonlocal elasticity and confinement induced ordering on the dynamics of thermomolecular pressure gradient driven premelted films bound by an elastic membrane. The confinement induced ordering is modeled…
I develop a kinetic mechanism to explain chain folding in polymer crystallization which is based on the competition between the formation of stems, which is due to frequent occupations of trans states along the chains in the supercooled…
We study the influence of solid boundaries on dynamics and structure of active fluids as the height of the container, $z$, changes. Along the varying dimension, the geometry systematically increases, therefore, the confinement ($z$)…
This paper examines the effect of cooling on disentanglement forces in polymers and the implications for both single chain pullout and polymer dynamics. I derive the explicit dependence of the distribution of these forces on temperature,…
Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…
The adhesion between a polymer melt and substrate is studied in the presence of chemically attached chains on the substrate surface. Extensive molecular dynamics simulations have been carried out to study the effect of temperature, tethered…