相关论文: Proteins in a shear flow
One prototypical instability in granular flows is the shear-banding instability, in which a uniform granular shear flow breaks into alternating bands of dense and dilute clusters of particles having low and high shear (shear stress or shear…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
We analyse the flow curves of a two-dimensional assembly of granular particles which are interacting via frictional contact forces. For packing fractions slightly below jamming, the fluid undergoes a large scale instability, implying a…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
The rheology of molecular brushes remains challenging to control due to the multiple length scales and relaxation processes involved and the lack of direct observation of molecular conformation during flow. We use molecular dynamics…
Using Brownian dynamics (BD) simulations we investigate a dense system of charged colloids exposed to shear flow in a confined (slit-pore) geometry. The equilibrium system at zero flow consists of three, well-pronounced layers with…
We consider dense rapid shear flow of inelastically colliding hard disks. Navier-Stokes granular hydrodynamics is applied accounting for the recent finding \cite{Luding,Khain} that shear viscosity diverges at a lower density than the rest…
Traditional models of wormlike chains in shear flows at finite temperature approximate the equation of motion via finite difference discretization (bead and rod models). We introduce here a new method based on a spectral representation in…
Cell spreading and motility on an adhesive substrate are driven by the active physical forces generated by the actin cytoskeleton. We have recently shown that coupling curved membrane complexes to protrusive forces, exerted by the actin…
The non-linear response of entangled polymers to shear flow is complicated. Its current understanding is framed mainly as a rheological description in terms of the complex viscosity. However, the full picture requires an assessment of the…
Tissue dynamics and collective cell motion are crucial biological processes. Their biological machinery is mostly known, and simulation models such as the "active vertex model" (AVM) exist and yield reasonable agreement with experimental…
Brownian dynamics of a self-propelled particle in linear shear flow is studied analytically by solving the Langevin equation and in simulation. The particle has a constant propagation speed along a fluctuating orientation and is…
We study passive scalar mixing by parallel shear flows in the presence of weak molecular diffusion. We recover the sharp uniform-in-diffusivity mixing rate for shear flows with finitely many critical points, recently proven in [1]. Our…
The mechanical stretching of single poly-proteins is an emerging tool for the study of protein (un)folding, chemical catalysis and polymer physics at the single molecule level. The observed processes i.e unfolding or reduction events, are…
The rheological behavior of polymer melts is strongly influenced by parameters such as chain length, chain stiffness, and architecture. In particular, shear thinning, characterized by a power-law decrease in shear viscosity with increasing…
In biology, cells undergo deformations under the action of flow caused by the fluid surrounding them. These flows lead to shape changes and instabilities that have been explored in detail for single component vesicles. However, cell…
We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…