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The flow of motor proteins on a filamental track is modelled within the the framework of lattice driven diffusive systems. Motors, considered as hopping particles, perform a highly biased asymmetric exclusion process when bound to the…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…
The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been…
Using different segmental dynamics and relaxation, characteristics of the interface growth is examined in an electrophoretic deposition of polymer chains on a three (2+1) dimensional discrete lattice with a Monte Carlo simulation.…
We examine the phase transition of polymer adsorption as well as the underlying kinetics of polymer binding from dilute solutions on a structureless solid surface. The emphasis is put on the properties of regular multiblock copolymers,…
We develop Monte Carlo simulations for uniformly charged polymers and machine learning algorithm to interpret the intra-polymer structure factor of the charged polymer system, which can be obtained from small-angle scattering experiments.…
We study the effect of physical aging on the mechanical properties of a model polymer glass using molecular dynamics simulations. The creep compliance is determined simultaneously with the structural relaxation under a constant uniaxial…
We consider the lateral diffusion of a protein interacting with the curvature of the membrane. The interaction energy is minimized if the particle is at a membrane position with a certain curvature that agrees with the spontaneous curvature…
We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic…
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 report a numerical study of the diffusiophoresis of short polymers using non-equilibrium molecular dynamics simulations. More precisely, we consider polymer chains in a fluid containing a solute which has a concentration gradient, and…
The bulk dynamics of dense granular materials arise through a combination of particle-scale and mesoscale effects. Theoretical and numerical studies have shown that collective effects are created by particle-scale anisotropic structures…
In granular media, the presence of even small amounts of interparticle cohesion manifests as an increase in the bulk strength and stiffness, effects that are typically associated with an increase in the average number of constraints per…
The assembly of nanometer-sized building blocks into complex morphologies is not only of fundamental interest but also plays a key role in material science and nanotechnology. We show that the shape of self-assembled superstructures formed…
Curvature-inducing proteins containing a Bin/Amphiphysin/Rvs domain often have intrinsically disordered domains. Recent experiments have shown that these disordered chains enhance curvature sensing and generation. Here, we report on the…
We consider a linear polymer chain in a disordered environment modeled by percolation clusters on a square lattice. The disordered environment is meant to roughly represent molecular crowding as seen in cells. The model may be viewed as the…
We measure the response of open-cell polyurethane foams filled with a dense suspension of fumed silica particles in polyethylene glycol at compression speeds spanning several orders of magnitude. The gradual compressive stress increase of…
The paper addresses the underlying source of two forms of induced anisotropy in granular materials: contact orientation anisotropy and contact force anisotropy. A rational, mathematical structure is reviewed for the manner in which fabric…
Drawing an analogy to the paradigm of quasi-elastic neutron scattering, we present a general approach for quantitatively investigating the spatiotemporal dependence of structural anisotropy relaxation in deformed polymers by using…
This paper investigates the effect of moisture content upon the degradation behaviour of composite materials. A coupled phase field framework considering moisture diffusion, hygroscopic expansion, and fracture behaviour is developed. This…