Related papers: Rotational friction on small globular proteins: Co…
We theoretically explore the effect of a transverse electric field on the frictional response of a bi-layer of packed zwitterionic molecules. The dipole-moment reorientation promoted by the electric field can lead to either stick-slip or…
To analyze hydration effects on macromolecular diffusion, the friction coefficients of macromolecules were examined using molecular dynamics simulations with an all-atom model. In the present study, a method was introduced to decompose the…
The static friction between crystalline surfaces separated by a molecularly thin layer of adsorbed molecules is calculated using molecular dynamics simulations. These molecules naturally lead to a finite static friction that is consistent…
In this study, the additional heat capacity which appear during the water dissociation of the proteins that are one of the soft materials, have been considered by the statistical mechanical methods. For this purpose, taking the electric…
We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…
Tangential interactions between particles play a central role in suspension rheology. We show theoretically that these interactions, often attributed to contact friction, are a direct consequence of fluid flows between rough particles in…
We incorporate hydrodynamic interactions in a structure-based model of ubiquitin and demonstrate that the hydrodynamic coupling may reduce the peak force when stretching the protein at constant speed, especially at larger speeds.…
We report on the frictional behaviour of thin poly(dimethylacrylamide) (PDMA) hydrogels films grafted on glass substrates in sliding contact with a glass spherical probe. Friction experiments are carried out at various velocities and…
The goal of this PhD thesis was to characterize the properties of friction in nanotubes and from a more general point of view the understanding of the microscopic origin of friction. Indeed, the relative simplicity of the system allows us…
We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has…
We examine the interactions between actively rotating proteins moving in a membrane. Experimental evidence suggests that such rotor proteins, like the ATP synthases of the inner mitochondrial membrane, can arrange themselves into lattices.…
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…
Friction experiments were conducted on hydrogel thin films sliding against a rigid sphere in a low velocity regime where molecular adsorption at the sliding interface sets the friction force, through a dissipative…
In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This…
A computationally-efficient method for evaluating friction in molecular rotary bearings is presented. This method estimates drag from fluctuations in molecular dynamics simulations via the fluctuation-dissipation theorem. This is effective…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
Hydrodynamic interactions in a suspension of spherical particles confined between two parallel planar walls are studied under creeping-flow conditions. The many-particle friction matrix in this system is evaluated using our novel numerical…
A hydrophilic liquid, such as water, forms hydrogen bonds with a hydrophilic substrate. The strength and locality of the hydrogen bonding interactions prohibit slip of the liquid over the substrate. The question then arises how the contact…
We report on the frictional properties of thin ($\approx \mu m$) poly(dimethylacrylamide) hydrogel films within contacts with spherical silica probes. In order to focus on the contribution to friction of interfacial dissipation, a dedicated…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…