相关论文: Proteins in a shear flow
Non-spherical particles transported by an anisotropic turbulent flow preferentially align with the mean shear and intermittently tumble when the local strain fluctuates. Such an intricate behaviour is here studied for inertialess,…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex or the actin cytoskeleton is strongly determined by their spatial structure. Moreover it is becoming increasingly clear that the reversible nature of…
X-ray photon correlation spectroscopy was used to measure the diffusive dynamics of colloidal particles in a shear flow. The results presented here show how the intensity autocorrelation functions measure both the diffusive dynamics of the…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
We numerically study the dynamic behavior under a symmetric shear flow of selected examples of concentrated phase emulsions with multi-core morphology confined within a microfluidic channel. A variety of new nonequilibrium steady states is…
The shear viscosity in the dilute regime of a model for confined granular matter is studied by simulations and kinetic theory. The model consists on projecting into two dimensions the motion of vibrofluidized granular matter in shallow…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
Kinetics of folding of a protein held in a force-clamp are compared to an unconstrained folding. The comparison is made within a simple topology-based dynamical model of ubiquitin. We demonstrate that the experimentally observed variations…
Monodisperse suspensions of Brownian colloidal spheres crystallize at high densities, and ordering under shear has been observed at densities below the crystallization threshold. We perform large-scale simulations of a model suspension…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
Strongly confined colloidal dispersions under shear can exhibit a variety of dynamical phenomena, including depinning transitions and complex structural changes. Here, we investigate the behaviour of such systems under pure oscillatory…
The dynamics of phase separation for a binary fluid subjected to a uniform shear are solved exactly for a model in which the order parameter is generalized to an n-component vector and the large-n limit taken. Characteristic length scales…
We investigate the behavior of colloidal suspensions with different volume fractions confined between parallel walls under a range of steady shears. We model the particles using molecular dynamics (MD) with full hydrodynamic interactions…
We investigate the stationary flow of a colloidal gel under an inhomogeneous external shear force using adaptive Brownian dynamics simulations. The interparticle forces are derived from the Stillinger-Weber potential, where the three-body…
Shear-flow-induced structure formation in surfactant-water mixtures is investigated numerically using a meshless-membrane model in combination with a particle-based hydrodynamics simulation approach for the solvent. At low shear rates,…
We study the instability of a dusty simple shear flow where the dust particles are distributed non-uniformly. A simple shear flow is modally stable to infinitesimal perturbations. Also, a band of particles remains unaffected in the absence…
We study the thermodynamic and kinetic consequences of the competition between single-protein folding and protein-protein aggregation using a phenomenological model, in which the proteins can be in the unfolded (U), misfolded (M) or folded…
Motivated by the reported peculiar dynamics of a red blood cell in shear flow, we develop an analytical theory for the motion of a nearly--spherical fluid particle enclosed by a visco--elastic incompressible interface in linear flows. The…
Single molecule force spectroscopy reveals unfolding of domains in titin upon stretching. We provide a theoretical framework for these experiments by computing the phase diagrams for force-induced unfolding of single domain proteins using…