相关论文: Proteins in a shear flow

We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…

Results are presented for the phase separation process of a binary mixture subject to an uniform shear flow quenched from a disordered to a homogeneous ordered phase. The kinetics of the process is described in the context of the…

The dynamics of two Brownian particles trapped by two neighboring harmonic potentials in a linear shear flow is investigated. The positional correlation functions in this system are calculated analytically and analyzed as a function of the…

We use a custom shear cell coupled to an optical microscope to investigate at the particle level the yielding transition in concentrated emulsions subjected to an oscillatory shear deformation. By performing experiments lasting thousands of…

The slow flow of amorphous solids exhibits striking heterogeneities: swift localised particle rearrangements take place in the midst of a more or less homogeneously deforming medium. Recently, experimental as well as numerical work has…

Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…

The dynamic of complex ordering systems with active rotational degrees of freedom exemplified by protein self-assembly is explored using a machine learning workflow that combines deep learning-based semantic segmentation and rotationally…

We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…

We investigate numerically the influence of an homogeneous shear flow on the spinodal decomposition of a binary mixture by solving the Cahn-Hilliard equation in a two-dimensional geometry. Several aspects of this much studied problem are…

The behavior of shear-oscillated amorphous materials is studied using a coarse-grained model. Samples are prepared at different degrees of annealing and then subject to athermal and quasistatic oscillatory deformations at various fixed…

Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…

Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…

Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…

A number of dense particle suspensions experience a dramatic increase in viscosity with the shear stress, up to a solid-like response. This shear-thickening process is understood as a transition under flow of the nature of the contacts,…

Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…

Separated flows past complex geometries are modelled by discrete vortex techniques. The flows are assumed to be rotational and inviscid, and a new technique is described to determine the streamfunctions for linear shear profiles. The…

The long time dynamics of large particles trapped in two inhomogeneous turbulent shear flows is studied experimentally. Both flows present a common feature, a shear region that separates two colliding circulations, but with different…

We study numerically the crystallization process in a supersaturated suspension of repulsive colloidal particles driven by simple shear flow. The effect of the shear flow on crystallization is two-fold: while it suppresses the initial…

We model protein folding as a physical stochastic process as follows. The unfolded protein chain is treated as a random coil described by SAW (self-avoiding walk). Folding is induced by hydrophobic forces and other interactions, such as…

The shearing instability of a dilute granular mixture composed of smooth inelastic hard spheres or disks is investigated. By using the Navier-Stokes hydrodynamic equations, it is shown that the scaled transversal velocity mode exhibits a…