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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 that corresponds to the onset of amplified atomic fluctuations in proteins. The results indicate that the number of water molecules within a cutoff distance of each residue scales linearly with protein depth index and is not affected by the local dynamics of the backbone. Keeping track of the water molecules within the cutoff sphere, we observe an effective residence time, scaling inversely with depth index at physiological temperatures while the diffusive escape is highly reduced below the transition. A depth independent orientational memory loss is obtained for the average dipole vector of the water molecules within the sphere when the protein is functional. While below the transition temperature, the solvent is in a glassy state, acting as a solid crust around the protein, inhibiting any large scale conformational fluctuations. At the transition, most of the hydration shell unfreezes and water molecules collectively make the protein more flexible. [ABSTRACT FROM AUTHOR]

We study the rolling and sliding motion of droplets on a corrugated substrate by Molecular Dynamics simulations. Droplets are driven by an external body force (gravity) and we investigate the velocity profile and dissipation mechanisms in the steady state. The cylindrical geometry allows us to consider a large range of droplet sizes. The velocity of small droplets with a large contact angle is dominated by the friction at the substrate and the velocity of the center of mass scales like the square root of the droplet size. For large droplets or small contact angles, however, viscous dissipation of the flow inside the volume of the droplet dictates the center of mass velocity that scales linearly with the size. We derive a simple analytical description predicting the dependence of the center of mass velocity on droplet size and the slip length at the substrate. In the limit of vanishing droplet velocity we quantitatively compare our simulation results to the predictions and good agreement without adjustable parameters is found. [ABSTRACT FROM AUTHOR]

The authors propose a new method, the Helfand-moment method, to compute the shear viscosity by equilibrium molecular dynamics in periodic systems. In this method, the shear viscosity is written as an Einstein-type relation in terms of the variance of the so-called Helfand moment. This quantity is modified in order to satisfy systems with periodic boundary conditions usually considered in molecular dynamics. They calculate the shear viscosity in the Lennard-Jones fluid near the triple point thanks to this new technique. They show that the results of the Helfand-moment method are in excellent agreement with the results of the standard Green-Kubo method. [ABSTRACT FROM AUTHOR]

The thermal conductivity is calculated with the Helfand-moment method in the Lennard-Jones fluid near the triple point. The Helfand moment of thermal conductivity is here derived for molecular dynamics with periodic boundary conditions. Thermal conductivity is given by a generalized Einstein relation with this Helfand moment. The authors compute thermal conductivity by this new method and compare it with their own values obtained by the standard Green-Kubo method. The agreement is excellent. [ABSTRACT FROM AUTHOR]