Stretching fields and mixing near the transition to nonperiodic two-dimensional flow.

Although time-periodic fluid flows sometimes produce mixing via Lagrangian chaos, the additional contribution to mixing caused by nonperiodicity has not been quantified experimentally. Here, we do so for a quasi-two-dimensional flow generated by electromagnetic forcing. Several distinct measures of mixing are found to vary continuously with the Reynolds number, with no evident change in magnitude or slope at the onset of nonperiodicity. Furthermore, the scaled probability distributions of the mean Lyapunov exponent have the same form in the periodic and nonperiodic flow states.

Internal granular dynamics, shear-induced crystallization, and compaction steps.

Internal imaging using index matching, and sensitive volume measurement, are used to investigate the spatial order and dynamics of a deep disordered layer of spheres sheared under a fixed load. Shearing triggers a crystallization transition accompanied by a step compaction event. The delay preceding the transition depends strongly on the layer thickness and can require a translation of about 10(5) particle diameters. The mean velocity varies with depth by more than five decades, and its profile is qualitatively altered by the transition.

Two-dimensional granular Poiseuille flow on an incline: multiple dynamical regimes.

We investigate experimentally the flow of a monolayer of spherical beads through a channel on a smooth incline that is bounded by rough sidewalls. Using high-speed video imaging and particle tracking, we measure the positions and velocities of all particles in the field of view. We find that the flows are accelerating and dilute if the channel exit is open. On the other hand, if the exit is constricted, flows can reach a state in which the local time-averaged velocity is invariant along the stream. In the latter case, we find a continuous transition from an oscillatory two-phase flow (2PF) regime with wide density variations to a uniform dense flow regime, depending on the channel width and the mean flow speed. These two regimes exhibit distinct density variation, time regularity, and transverse profiles. The rough sidewalls are found to be necessary for the 2PF regime. In the dense regions of both flows, particles exhibit temporary arches, long-range correlated velocities, inhomogenuous propagation of disturbances, and hexagonal lattice structures. On the other hand, the dilute regions of the two-phase flow are nearly collisionless. Existing models can neither fully describe the dynamics of both the dense and the dilute regions nor explain the spontaneous switching between them.

The formation and dynamics of proton wires in channel environments.

By virtue of an accurate interaction model, the equilibrium and dynamical properties of an excess proton in aqueous systems are studied, in which the water and excess proton are confined to hydrophobic cylindrical channels. Solvation structures of the excess proton and its mobility along the channel are considered as a function of the channel radius. It is found that when the aqueous proton systems are sufficiently constricted there is a substantial increase in the diffusion of the excess proton charge accompanied by a decrease in the diffusion of water molecules along the channel. Such systems present clear evidence for the possible existence of "proton wires."

Fluid particle accelerations in fully developed turbulence.

The motion of fluid particles as they are pushed along erratic trajectories by fluctuating pressure gradients is fundamental to transport and mixing in turbulence. It is essential in cloud formation and atmospheric transport, processes in stirred chemical reactors and combustion systems, and in the industrial production of nanoparticles. The concept of particle trajectories has been used successfully to describe mixing and transport in turbulence, but issues of fundamental importance remain unresolved. One such issue is the Heisenberg-Yaglom prediction of fluid particle accelerations, based on the 1941 scaling theory of Kolmogorov. Here we report acceleration measurements using a detector adapted from high-energy physics to track particles in a laboratory water flow at Reynolds numbers up to 63,000. We find that, within experimental errors, Kolmogorov scaling of the acceleration variance is attained at high Reynolds numbers. Our data indicate that the acceleration is an extremely intermittent variable--particles are observed with accelerations of up to 1,500 times the acceleration of gravity (equivalent to 40 times the root mean square acceleration). We find that the acceleration data reflect the anisotropy of the large-scale flow at all Reynolds numbers studied.

Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane.

Molecular dynamics calculations were carried out on models of two synthetic leucine-serine ion channels: a tetrameric bundle with sequence (LSLLLSL)(3)NH(2) and a hexameric bundle with sequence (LSSLLSL)(3)NH(2). Each protein bundle is inserted in a palmitoyloleoylphosphatidylcholine bilayer membrane and solvated by simple point charge water molecules inside the pore and at both mouths. Both systems appear to be stable in the absence of an electric field during the 4 ns of molecular dynamics simulation. The water motion in the narrow pore of the four-helix bundle is highly restricted and may provide suitable conditions for proton transfer via a water wire mechanism. In the wider hexameric pore, the water diffuses much more slowly than in bulk but is still mobile. This, along with the dimensions of the pore, supports the observation that this peptide is selective for monovalent cations. Reasonable agreement of predicted conductances with experimentally determined values lends support to the validity of the simulations.

Molecular dynamics simulations of human carbonic anhydrase II: insight into experimental results and the role of solvation.

In this paper, the carbonic anhydrase II (CA II) enzyme active site is modeled using ab initio calculations and molecular dynamics simulations to examine a number of important issues for the enzyme function. It is found that the Zn2+ ion is dominantly tetrahedrally coordinated, which agrees with X-ray crystallographic studies. However, a transient five-fold coordination with an extra water molecule is also found. Studies of His64 conformations upon a change in the protonation states of the Zn-bound water and the His64 residue also confirm the results of an X-ray study which suggest that the His64 conformation is quite flexible. However, the degree of water solvation is found to affect this behavior. Water bridge formation between the Zn-bound water and the His64 residue was found to involve a free energy barrier of 2-3 kcal/mol and an average lifetime of several picoseconds, which supports the concept of a proton transfer mechanism through such a bridge. Mutations of various residues around the active site provide further insight into the corresponding experimental results and, in fact, suggest an important role for the solvent water molecules in the CA II catalytic mechanism.

Classical molecular dynamics simulation of the photoinduced electron transfer dynamics of plastocyanin.

Classical molecular dynamics simulations are used to investigate the nuclear motions associated with photoinduced electron transfer in plastocyanin. The blue copper protein is modeled using a molecular mechanics potential; potential parameters for the copper-protein interactions are determined using an x-ray crystallographic structure and absorption and resonance Raman spectra. Molecular dynamics simulations yield a variety of information about the ground (oxidized) and optically excited (charge-transfer) states: 1) The probability distribution of the potential difference between the states, which is used to determine the coordinate and energy displacements, places the states well within the Marcus inverted region. 2) The two-time autocorrelation function of the difference potential in the ground state and the average of the difference potential after instantaneous excitation to the excited state are very similar (confirming linear response in this system); their decay indicates that vibrational relaxation occurs in about 1 ps in both states. 3) The spectral densities of various internal coordinates begin to identify the vibrations that affect the optical transition; the spectral density of the difference potential correlation function should also prove useful in quantum simulations of the back electron transfer. 4) Correlation functions of the protein atomic motions with the difference potential show that the nuclear motions are correlated over a distance of more than 20 A, especially along proposed electron transport paths.

Structure and dynamics of hydronium in the ion channel gramicidin A.

The effects of the hydronium ion, H(3)0+, on the structure of the ion channel gramicidin A and the hydrogen-bonded network of waters within the channel were studied to help elucidate a possible mechanism for proton transport through the channel. Several classical molecular dynamics studies were carried out with the hydronium in either the center of a gramicidin monomer or in the dimer junction. Structural reorganization of the channel backbone was observed for different hydronium positions, which were most apparent when the hydronium was within the monomer. In both cases the average O-O distance between the hydronium ion and its nearest neighbor water molecule was found to be approximately 2.55 A, indicating a rather strong hydrogen bond. Importantly, a subsequent break in the hydrogen-bonded network between the nearest neighbor and the next-nearest neighbor(approximately 2.7 -3.0 A) was repeatedly observed. Moreover, the carbonyl groups of gramicidin A were found to interact with the charge on the hydronium ion, helping in its stabilization. These facts may have significant implications for the proton hopping mechanism. The presence of the hydronium ion in the channel also inhibits to some degree the reorientational motions of the channel water molecules.