A number of periodic lattices have historically been used to represent ice-1h in computer simulations. These vary in size, shape, and method of generation, and while they have served their intended purposes, their properties have rarely been documented in detail and their intercompatibility is unknown. We develop a method for generating sets of internally consistent lattices and apply it to determine eight unit cells containing from 96 to 768 water molecules in both near-cubic and slab arrangements. It can easily be applied to generate additional (larger) cells or representations of specific crystal faces. Each unit cell in this set has zero net dipole moment and minimal net quadrupole moment and is optimized using four different criteria to measure the randomness of the hydrogen bonding; if required, these criteria can easily be modified to suit the intended application and alternate sets thus generated. We find that Cota and Hoover’s much used constraint for selecting unit cells with zero dipole moment is too restrictive, not permitting a fully random hydrogen-bonding network; also, unit-cell generation methods based on potential-energy minimization are found to prefer unrepresentative, highly ordered structures.

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The temperature dependence of the internal dynamics of an isolated protein, bovine pancreatic trypsin inhibitor, is examined using normal mode analysis and molecular dynamics (MD) simulation. It is found that the protein exhibits marked anharmonic dynamics at temperatures of approximately 100-120 K, as evidenced by departure of the MD-derived average mean square displacement from that of the harmonic model. This activation of anharmonic dynamics is at lower temperatures than previously detected in proteins and is found in the absence of solvent molecules. The simulation data are also used to investigate neutron scattering properties. The effects are determined of instrumental energy resolution and of approximations commonly used to extract mean square displacement data from elastic scattering experiments. Both the presence of a distribution of mean square displacements in the protein and the use of the Gaussian approximation to the dynamic structure factor lead to quantified underestimation of the mean square displacement obtained.

The structure and dynamics of the {0001} (basal), {101̄0} (prism), {202̄1}, and {21̄1̄0} ice Ih/water interfaces have been investigated using molecular dynamics and the flexible CF1 central force model of water. The translational order profile, the average density profile, and the diffusion profile have been calculated for all four interfaces as a function of distance normal to the interface. Dynamical molecular trajectories have been used to explore the loss of translational order from within the crystal region, through the interface, and into the liquid region. The thickness of the interfaces has been determined from each order parameter and compared with results from rigid models of water and experiment. The high index faces have thinner interfacial regions than the basal and prism interfaces. All interfacial regions contain molecules that are neither ice-like nor water-like.

Proteins undergo an apparent dynamical transition on temperature variation that has been correlated with the onset of function. The transition in the mean-square displacement, AEDr 2 ae, that is observed using a spectrometer or computer simulation, depends on the relationship between the timescales of the relaxation processes activated and the timescale accessible to the instrument or simulation. Models are described of two extreme situations-an ''equilibrium'' model, in which the long-time dynamics changes with temperature and all motions are resolved by the instrument used; and a ''frequency window'' model, in which there is no change in the long-time dynamics but as the temperature increases, the relaxation frequencies move into the instrumental range. Here we demonstrate that the latter, frequency-window model can describe the temperature and timescale dependences of both the intermediate neutron scattering function and AEDr 2 ae derived from molecular dynamics simulations of a small protein in a cryosolution. The frequency-window model also describes the energy-resolution and temperature-dependences of AEDr 2 ae obtained from experimental neutron scattering on glutamate dehydrogenase in the same solvent. Although equilibrium effects should also contribute to dynamical transitions in proteins, the present results suggests that frequency-window effects can play a role in the simulations and experiments examined. Finally, misquotations of previous findings are discussed in the context of solvent activation of protein dynamics and the possible relationship of this to activity.

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