相关论文: Proteins in a shear flow

We study two types of intrinsic uncertainties, statistical errors and system size effects, in estimating shear viscosity via equilibrium molecular dynamics simulations and compare them with the corresponding uncertainties in evaluating the…

In this work we develop a theoretical framework for the localization of flow in the steadily flowing regime of sheared disordered solids with inertial dynamics on a microscopic scale. To this aim we perform rheology studies at fixed shear…

We investigate the rheology of granular materials via molecular dynamics simulations of homogeneous, simple shear flows of soft, frictional, noncohesive spheres. In agreement with previous results for frictionless particles, we observe…

The three-dimensional dynamics of a single non-Brownian flexible fiber in shear flow is evaluated numerically, in the absence of inertia. A wide range of ratios A of bending to hydrodynamic forces and hundreds of initial configurations are…

This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…

A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…

We investigate the shear of a dense bed of refracting supermillimetric grains confined within a transparent horizontal annular cell with a rotating top. The local time correlation functions of interferometric images allow to characterize…

When polydisperse granular systems are sheared, the transverse dynamics is characterized by the interplay of size segregation and diffusion. Segregation in nonuniform and confined shearing flows is studied using annular shear cell…

We employ a multi-phase smoothed particle hydrodynamics (SPH) method to study droplet dynamics in shear flow. With an extensive range of Reynolds number, capillary number, wall confinement, and density/viscosity ratio between the droplet…

We present the spectral analysis of three-dimensional dynamics of an elastic filament in a shear flow of a viscous fluid at a low Reynolds number in the absence of Brownian motion. The elastica model is used. The fiber initially is almost…

In typical single-molecule force spectroscopy experiments the mechanical unfolding of molecular complexes or biomolecules is studied applying a force ramp to one end of the system while the other end is kept fixed in space. The…

Instabilities at interface of two stream granular flows have been reported in recent experiment [1] that breaking waves can form at the interface between two streams of identical grains flowing on an inclined plane downstream of a splitter…

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…

Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…

Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…

Intracellular protein patterns are described by (nearly) mass-conserving reaction-diffusion systems. While these patterns initially form out of a homogeneous steady state due to the well-understood Turing instability, no general theory…

Starting from the equations of Stokes flow and the mass conservation of particles as determined by shear-induced diffusion, we derive the coupled equations for the dynamics of particle concentration and film thickness for the free-surface…

Particles that are immersed in a fluid exchange momentum via the fluid, hence their Brownian motion is correlated. By means of multiparticle-collision dynamics simulations we study the interactions between two colloidal beads in a sheared…

An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…

Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…