Related papers: More than one dynamic crossover in protein hydrati…
In the present study, water is considered as a dynamic network between molecules at distances not exceeding 3.2 angstroms. The instantaneous configurations obtained by using the molecular dynamics method have been sequentially analyzed, the…
A large number of water models exists for molecular simulations. They differ in the ability to reproduce specific features of real water instead of others, like the correct temperature for the density maximum or the diffusion coefficient.…
In equilibrium and supercooled liquids, polymorphism is manifested by thermodynamic regions defined in the phase diagram, which are predominantly of different short- and medium-range order (local structure). It is found that on the phase…
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…
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…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…
The static and dynamical properties of heavy water have been studied at ambient conditions with extensive Car-Parrinello molecular-dynamics simulations in the canonical ensemble, with temperatures ranging between 325 K and 400 K.…
We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by softening of the vibrational force constant by electrostatic and van der Waals forces…
Water is a key ingredient for life and plays a central role as solvent in many biochemical reactions. However, the intrinsically quantum nature of the hydrogen nucleus, revealing itself in a large variety of physical manifestations,…
An approach has been proposed to characterize the competitive association of D2O and to study the heterogeneity of hydration water adsorbed by the protein, immunoglobulin G, using methodology for determining of non-freezing water in mixed…
New X-ray and neutron diffraction experiments have been performed on ethanol-water mixtures as a function of decreasing temperature, so that such diffraction data are now available over the entire composition range. Extensive molecular…
I have investigated the structural and dynamic properties of water by performing a series of molecular dynamic simulations in the range of temperatures from 213 K to 360 K, using the Simple Point Charge-Extended (SPC/E) model. I performed…
Supercooled water exhibits remarkably slow dynamics similar to the behavior observed for various glass-forming liquids. The local order of tetrahedral structures due to hydrogen-bonds (H-bonds) increases with decreasing temperature. Thus,…
We present neutron scattering measurements on the dynamics of hemoglobin (Hb) in human red blood cells in vivo. Global and internal Hb dynamics were measured in the ps to ns time- and {\AA} length-scale using quasielastic neutron…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
We present molecular dynamics simulations of the SPC/E model of water to probe the dynamic properties at temperatures from 350 K down to 190 K and pressures from 2.5GPa (25kbar) down to -300MPa (-3kbar). We compare our results with those…
The ability of water to dissolve biomolecules is crucial for our life. It has been shown that protein has a profound effect on the behavior of water in its hydration shell, which in turn affects the structure and function of the protein.…
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 study a coarse-grained model for a water monolayer that cannot crystallize due to the presence of confining interfaces, such as protein powders or inorganic surfaces. Using both Monte Carlo simulations and mean field calculations, we…