相关论文: Proteins in a shear flow
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along…
Buckling plays a critical role in the transport and dynamics of elastic microfilaments in Stokesian fluids. However, previous work has only considered filaments with homogeneous structural properties. Filament backbone stiffness can be…
Inhomogeneous flows and shear banding are of interest for a range of applications but have been eluding a comprehensive theoretical understanding, mostly due to the lack of a framework comparable to equilibrium statistical mechanics. Here…
Granular materials react to shear stresses differently than do ordinary fluids. Rather than deforming uniformly, materials such as dry sand or cohesionless powders develop shear bands: narrow zones containing large relative particle motion…
Nonequilibrium molecular dynamics simulations are used to study the shear thinning behavior of immiscible symmetric polymer blends. The phase separated polymers are subjected to a simple shear flow imposed by moving a wall parallel to the…
The shear rheology of dense colloidal and granular suspensions is strongly nonlinear, as these materials exhibit shear-thinning and shear-thickening, depending on multiple physical parameters. We numerically study the rheology of a simple…
We use numerical simulations to study the flow of athermal, frictionless, soft-core two dimensional spherocylinders driven by a uniform steady-state simple shear applied at a fixed volume and a fixed finite strain rate $\dot\gamma$. Energy…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…
Dynamics of flexible non-Brownian fibers in shear flow at low-Reynolds-number are analyzed numerically for a wide range of the ratios A of the fiber bending force to the viscous drag force. Initially, the fibers are aligned with the flow,…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
The phase separation of a two-dimensional active binary mixture is studied under the action of an applied shear through numerical simulations. It is highlighted how the strength of the external flow modifies the initial shape of growing…
Force-clamp spectroscopy reveals the unfolding and disulfide bond rupture times of single protein molecules as a function of the stretching force, point mutations and solvent conditions. The statistics of these times reveal whether the…
In contrast to normal fluids, a granular fluid under shear supports a steady state with uniform temperature and density since the collisional cooling can compensate locally for viscous heating. It is shown that the hydrodynamic description…
When a block made of an elastomer is subjected to large shear, its surface remains flat. When a block of biological soft tissue is subjected to large shear, it is likely that its surface in the plane of shear will buckle (apparition of…
We report a numerical study addressing the dynamics of compound vesicles confined in a channel under shear flow. The system comprises a smaller vesicle embedded within a larger one and can be used to mimic, for example, leukocytes or…
We study numerically phase separation in a binary fluid subject to an applied shear flow in two dimensions, with full hydrodynamics. To do so, we introduce a mixed finite-differencing/spectral simulation technique, with a transformation to…
Understanding the process of protein unfolding plays a crucial role in various applications such as design of folding-based protein engines. Using the well-established kinetostatic compliance (KCM)-based method for modeling of protein…
Nonequilibrium dynamics of biomembranes with active inclusions is considered. The inclusions represent protein molecules which perform cyclic internal conformational motions driven by the energy brought with ATP ligands. As protein…