Related papers: Bubble relaxation dynamics in homopolymer DNA sequ…
Understanding the effect of glassy dynamics on the stability of bio-macromolecules and investigating the underlying relaxation processes governing degradation processes of these macromolecules are of immense importance in the context of…
We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…
Microphase separation is common in active biological systems as exemplified by the separation of RNA and DNA-rich phases in the cell nucleus driven by the transcriptional activity of polymerase enzymes acting similarly to amphiphiles in a…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
We study dynamical correlation functions in the random-field Heisenberg chain, which probes the relaxation times at different length scales. Firstly, we show that the relaxation time associated with the dynamical imbalance (examining the…
We present simulations on a binary blend of bead-spring polymer chains. The introduction of monomer size disparity yields very different relaxation times for each component of the blend. Competition between two different arrest mechanisms,…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
We address the relaxation dynamics in hydrogen-bonded super-cooled liquids near the glass transition, measured via Broad-Band Dielectric Spectroscopy (BDS). We propose a theory based on decomposing the relaxation of the macroscopic dipole…
Self-oscillations underlie many natural phenomena such as heartbeat, ocean waves, and the pulsation of variable stars. From pendulum clocks to the behavior of animal groups, self-oscillation is one of the keys to the understanding of…
The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…
Under steady shear, a foam relaxes stress through intermittent rearrangements of bubbles accompanied by sudden drops in the stored elastic energy. We use a simple model of foam that incorporates both elasticity and dissipation to study the…
In this study, we present an experimental work on bubble nucleation and growth using a model system comprised of viscoelastic polyvinyl butyral confined in a Hele-Shaw cell geometry that is decompressed at elevated temperatures. The…
Using molecular dynamics simulations we investigate the finite-size dependence of the dynamical properties of a diatomic supercooled liquid. The simplicity of the molecule permits us to access the microsecond time scale. We find that the…
We use molecular dynamics computer simulations to investigate the relaxation dynamics of a simple model for a colloidal gel at a low volume fraction. We find that due to the presence of the open spanning network this dynamics shows at low…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
Like emulsions, pastes and many other forms of soft condensed matter, aqueous foams present slow mechanical relaxations when subjected to a stress too small to induce any plastic flow. To identify the physical origin of this viscoelastic…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
Understanding the influence of activity on dense amorphous assemblies is crucial for biological processes such as wound healing, embryogenesis, or cancer progression. Here, we study the effect of self-propulsion forces of amplitude $f_0$…
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…