Water diffusion through OmpF, a porin in the outer membrane of Escherichia coli, is studied by molecular dynamics simulation. A first passage time approach allows characterizing the diffusive properties of a well-defined region of this channel. A carbon nanotube, which is considerably more homogeneous, serves as a model to validate the methodology. Here we find, in addition to the expected regular behavior, a gradient of the diffusion coefficient at the channel ends, witness of the transition from confinement in the channel to bulk behavior in the connected reservoirs. Moreover, we observe the effect of a kinetic boundary layer, which is the counterpart of the initial ballistic regime in a mean square displacement analysis. The overall diffusive behavior of water in OmpF shows remarkable similarity with that in a homogeneous channel. However, a small fraction of the water molecules appears to be trapped by the protein wall for considerable lengths of time. The distribution of trapping times exhibits a broad power law distribution ͑ ͒ϳ −2.4 , up to = 10 ns, a bound set by the length of the simulation run. We discuss the effect of this distribution on the dynamic properties of water in OmpF in terms of incomplete sampling of phase space.

We studied the influence of a liquid-vapor interface on dynamic properties like reorientation and diffusion as well as the surface tension of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF(6)]) by molecular dynamics simulations. In the interfacial region, reorientation of a short molecular axis is slightly faster than that in the central layer, while that of the longer molecular axis is retarded. The molecular reorientation is well-described by a stretched exponential decay modeled by the Kohlrausch-Williams-Watts equation. Analysis of the average translational diffusion coefficient of molecules in a central layer shows consistency with the Vogel-Fulcher-Tamann equation in a temperature range from 300 to 380 K. A first-passage time analysis of the system at 380 K yields a more refined spatial characterization of translational diffusion perpendicular to the liquid-vapor interfaces. In the central region of the slab, the diffusion coefficient of cations is only marginally higher than that of anions, but close to an interface, this difference is much higher, up to 50%. Apparent activation energies for rotational and diffusional dynamics, respectively, were estimated assuming Arrhenius behavior. They indicate that reorientation of the long molecular axis depends on the diffusion ability, whereas for the reorientation of the short axis, no such correlation is observed. The results are in general agreement with the literature, with slightly overestimated absolute values. This applies as well for the surface tension, where, however, a dependence on the treatment of the electrostatics was found. Particle-mesh Ewald (PME) or reaction field (RF) and the treatment of bonds by constraints have an influence. If no bond constraints are applied, the results are consistent for both methods for the description of the electrostatics.

Thin films on substrates are usually in a stressed state. An important, but trivial, contribution to that stress stems from the difference in thermal expansion coefficient of substrate and film. Much more interesting are the intrinsic stresses, resulting from the growth and/or microstructure of the film. Intrinsic compressive stress was explained by d'Heurle in 1970. Intrinsic tensile stress for recrystallizing metal films was treated succesfully by Doljack and Hoffman in 1972. In the present letter we explain the occurrence of tensile stress in nonrecrystallizing metal films. The explanation is based on modern grain growth models and accurate stress measurements. The key ingredient to the explanation is the proof of the existence of a stress gradient in nonrecrystallizing metal films.

No abstract