相关论文: Proteins in a shear flow
The results of Brownian dynamics simulations of a single DNA molecule in shear flow are presented taking into account the effect of internal viscosity. The dissipative mechanism of internal viscosity is proved necessary in the research of…
The properties of semiflexible polymers tethered by one end to an impenetrable wall and exposed to oscillatory shear flow are investigated by mesoscale simulations. A polymer, confined in two dimensions, is described by a linear bead-spring…
The morphological dynamics, instabilities and transitions of elastic filaments in viscous flows underlie a wealth of biophysical processes from flagellar propulsion to intracellular streaming, and are also key to deciphering the rheological…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…
We use molecular dynamics simulations to study the behavior of a compressible Lennard-Jones fluid in simple shear flow in a two-dimensional nanochannel. The system is equilibrated in the fluid phase close to the triple point at which gas,…
We perform molecular dynamics simulations to characterize the occurrence of inhomogeneous shear flows in soft jammed materials. We use rough walls to impose a simple shear flow and study the athermal motion of jammed assemblies of soft…
Based on Brownian dynamics simulations, we investigate the thermodynamic signatures of non-equilibrium steady states in a confined colloidal suspensions under shear flow. Specifically, we consider a thin film consisting of charged particles…
The alignment, ordering and rotation of elongated granular particles was studied in shear flow. The time evolution of the orientation of a large number of particles was monitored in laboratory experiments by particle tracking using optical…
Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in…
We study the mechanical unfolding of a simple model protein. The Langevin dynamics results are analyzed using Markov-model methods which allow to describe completely the configurational space of the system. Using transition path theory we…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
According to the 'old view', proteins fold along well-defined sequential pathways, whereas the 'new view' sees protein folding as a highly parallel stochastic process on funnel-shaped energy landscapes. We have analyzed parallel and…
The nonequilibrium dynamical behaviour that arises when two ordered two-dimensional monolayers of particles are sheared over each other is studied in Brownian dynamics simulations. A curious sequence of nonequilibrium states is observed as…
Mechanical unfolding and refolding of ubiquitin are studied by Monte Carlo simulations of a Go model with binary variables. The exponential dependence of the time constants on the force is verified, and folding and unfolding lengths are…
We investigate shear-induced crystallization in a very dense flow of mono-disperse inelastic hard spheres. We consider a steady plane Couette flow under constant pressure and neglect gravity. We assume that the granular density is greater…
The motion of a deformable active particle in linear shear flow is explored theoretically. Based on symmetry considerations, in two spatial dimensions, we propose coupled nonlinear dynamical equations for the particle position, velocity,…
The nonequilibrium structural and dynamical properties of semiflexible active polar polymers subject to linear flow are studied by numerical simulations. Filaments are confined in two dimensions and immersed in a fluid described by the…
Discontinuous shear-thickening in dense suspensions naturally emerges from the activation of frictional forces by shear flow in non-Brownian systems close to jamming. Yet, this physical picture is incomplete as most experiments study soft…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…