Related papers: Temperature-dependent mechanisms for the dynamics …
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…
Studies of liquid water in its supercooled region have led to many insights into the structure and behavior of water. While bulk water freezes at its homogeneous nucleation temperature of approximately 235 K, for protein hydration water,…
First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…
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…
We use molecular dynamics computer simulations and nuclear magnetic resonance experiments to investigate the dynamics of water at interfaces of molecular roughness and low mobility. We find that, when approaching such interfaces, the…
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…
Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of…
Water hydrating phospholipid membranes determine their stability and function, as well as their interaction with other molecules. In this article we study, using all-atom molecular dynamics simulations, the rotational and translational…
We study hydrogen-bond dynamics in liquid water at low temperatures using molecular dynamics simulations. We find that bond lifetime (``fast dynamics'') has Arrhenius temperature dependence. We also calculate the bond correlation function…
We have investigated temperature trends of the microscopic structure of the SPC/E and TIP4P-Ew water models in terms of the pair distribution functions, coordination numbers, the average number of hydrogen bonds, the distribution of bonding…
We refine a protein model that reproduces fundamental aspects of protein thermodynamics. The model exhibits two transitions, hot and cold unfolding. The number of relevant parameters is reduced to three: 1) binding energy of folding…
Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of…
The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use quasi-elastic neutron…
Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent…
The dynamic properties of fluid, including density, surface tension, diffusivity and viscosity, are temperature-dependent and can significantly influence the flow dynamics of mesoscopic non-isothermal systems. To capture the correct…
Water plays a major role in bio-systems, greatly contributing to determine their structure, stability and even function. It is well know, for instance, that proteins require a minimum amount of water to be functionally active. Since 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 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,…
A joint experimental / theoretical investigation of the elastin-like octapeptide GVG(VPGVG) was carried out. In this paper a comprehensive molecular dynamics study of the temperature dependent folding and unfolding of the octapeptide is…
A structural transformation in water upon compression was recently observed at the temperature $T=277$~K in the vicinity of the pressure $p \approx 2\;000$~Atm [R.M. Khusnutdinoff, A.V. Mokshin, J. Non-Cryst. Solids \textbf{357}, 1677…