Related papers: Proteins in a shear flow
Results are presented for the phase separation process of a binary mixture subject to an uniform shear flow quenched from a disordered to a homogeneous ordered phase. The kinetics of the process is described in the context of the…
The mechanical unfolding of proteins is investigated by extending the Wako-Saito-Munoz-Eaton model, a simplified protein model with binary degrees of freedom, which has proved successful in describing the kinetics of protein folding. Such a…
The effect of strong shear flow on highly fluctuating lamellar systems stabilized by intermembrane collisions via the Helfrich interaction is studied. Advection enters the microscopic equation of motion for a single membrane via a…
Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be…
Using molecular dynamics simulation we examine dynamics in sheared polycrystal states in a binary mixture containing 10% larger particles in two dimensions. We find large stress fluctuations arising from sliding motions of the particles at…
The rheology of cohesive granular materials, under a constant pressure condition, is studied using molecular dynamics simulations. Depending on the shear rate, pressure, and interparticle cohesiveness, the system exhibits four distinctive…
We propose a simple continuum model to interpret the shearing motion of dense, dry and cohesion-less granular media. Compressibility, dilatancy and Coulomb-like friction are the three basic ingredients. The granular stress is split into a…
Using Brownian dynamics (BD) simulations we investigate the impact of shear flow on structural and dynamical properties of a system of charged colloids confined to a narrow slit pore. Our model consists of spherical microions interacting…
Granular materials segregate by size under shear, and the ability to quantitatively predict the time required to achieve complete segregation is a key test of our understanding of the segregation process. In this paper, we apply the…
We investigate the folding behavior of protein sequences by numerically studying all sequences with maximally compact lattice model through exhaustive enumeration. We get the prion-like behavior of protein folding. Individual proteins…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…
We present an experimental investigation of shear elastic wave propagation along the surface of a dense granular suspension. Using an ultrafast ultrasound scanner, we monitor the softening of the shear wave velocity inside the optically…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
Biological membranes are host to proteins and molecules which may form domain-like structures resulting in spatially-varying material properties. Vesicles with such heterogeneous membranes can exhibit intricate shapes at equilibrium and…
We study the dynamics of asymmetric, deformable particles in oscillatory, linear shear flow. By simulating the motion of a dumbbell, a ring polymer, and a capsule we show that cross-stream migration occurs for asymmetric elastic particles…
We study the rheology of a two-fluid emulsion in semi-concentrated conditions; the solute is Newtonian while the solvent an inelastic power law fluid. The problem at hand is tackled by means of direct numerical simulations using the volume…
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…
The short-time motion of Brownian particles in an incompressible Newtonian fluid under shear, in which the fluid inertia becomes important, was investigated by direct numerical simulation of particulate flows. Three-dimensional simulations…
Recent computer simulations reveal several intriguing features in the evolution of properties of amorphous solids subjected to repeated cyclic shear deformation. These include the divergence of the number of cycles to reach steady states as…
Using non-equilibrium Brownian dynamics computer simulations, we have investigated the steady state statistics of a polymer chain under three different shear environments: i) linear shear flow in the bulk (no walls), ii) shear vorticity…