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Molecular dynamics computer simulations were used to study the protonation of bridging oxygen (Si-O-Si) sites present on the vitreous silica surface in contact with water using a dissociative water potential. In contrast to first-principles calculations based on unconstrained molecular analogs, such as H(7)Si(2)O(7)(+) molecules, the very limited flexibility of neighboring SiO(4) tetrahedra when embedded in a solid surface means that there is a relatively minor geometric response to proton adsorption, requiring sites predisposed to adsorption. Simulation results indicate that protonation of bridging oxygen occurs at predisposed sites with bridging angles in the 125 degrees-135 degrees range, well below the bulk silica mean of approximately 150 degrees, consistent with various ab initio calculations, and that a small fraction of such sites are present in all ring sizes. The energy differences between dry and protonated bridges at various angles observed in the simulations coincide completely with quantum calculations over the entire range of bridging angles encountered in the vitreous silica surface. Those sites with bridging angles near 130 degrees support adsorbed protons more stably, resulting in the proton remaining adsorbed for longer periods of time. Vitreous silica has the necessary distribution of angular strain over all ring sizes to allow protons to adsorb onto bridging oxygen at the surface, forming acidic surface groups that serve as ideal intermediate steps in proton transfer near the surface. In addition to hydronium formation and water-assisted proton transfer in the liquid, protons can rapidly move across the water-silica interface via strained bridges that are predisposed to transient proton adsorption. Thus, an excess proton at any given location on a silica surface can move by either water-assisted or strained bridge-assisted diffusion depending on the local environment. The result of this would be net migration that is faster than it would be if only one mechanism is possible. These simulation results indicate the importance of performing large size and time scale simulations of the structurally heterogeneous vitreous silica exposed to water to describe proton transport at the interface between water and the silica surface.

Molecular dynamics simulations using a dissociative water potential were applied to study transport of excess protons in water and determine the applicability of this potential to describe such behavior. While originally developed for gas-phase molecules and bulk liquid water, the potential is transferrable to nanoconfinement and interface scenarios. Applied here, it shows proton behavior consistent with ab initio calculations and empirical models specifically designed to describe proton transport. Both Eigen and Zundel complexes are observed in the simulations showing the Eigen-Zundel-Eigen-type mechanism. In addition to reproducing the short-time rattling of the excess proton between the two oxygens of Zundel complexes, a picosecond-scale lifetime was also found. These longer-lived H3O(+) ions are caused by the rapid conversion of the local solvation structure around the transferring proton from a Zundel-like form to an Eigen-like form following the transfer, effectively severing the path along which the proton can rattle. The migration of H(+) over long times (>100 ps) deviates from the conventional short-time multiexponentially decaying lifetime autocorrelation model and follows the t(-3/2) power-law behavior. The potential function employed here matches many of the features of proton transport observed in ab initio molecular dynamics simulations as well as the highly developed empirical valence bond models, yet is computationally very efficient, enabling longer time and larger systems to be studied.

Molecular dynamics simulations employing reactive potentials were used to determine the activation barriers to the dissolution of the amorphous SiO2 surface in the presence of a 2 nm overlayer of water. The potential of mean force calculations of the reactions of water molecules with 15 different starting Q4 sites (Qi is the Si site with i bridging oxygen neighbors) to eventually form the dissolved Q0 site were used to obtain the barriers. Activation barriers for each step in the dissolution process, from the Q4 to Q3 to Q2 to Q1 to Q0 were obtained. Relaxation runs between each reaction step enabled redistribution of the water above the surface in response to the new Qi site configuration. The rate-limiting step observed in the simulations was in both the Q32 reaction (a Q3 site changing to a Q2 site) and the Q21 reaction, each with an average barrier of ∼14.1 kcal mol(-1). However, the barrier for the overall reaction from the Q4 site to a Q0 site, averaged over the maximum barrier for each of the 15 samples, was 15.1 kcal mol(-1). This result is within the lower end of the experimental data, which varies from 14-24 kcal mol(-1), while ab initio calculations using small cluster models obtain values that vary from 18-39 kcal mol(-1). Constraints between the oxygen bridges from the Si site and the connecting silica structure, the presence of pre-reaction strained siloxane bonds, and the location of the reacting Si site within slight concave surface contours all affected the overall activation barriers.

A robust and accurate dissociative potential that reproduces the structural and dynamic properties of bulk and nanoconfined water, and proton transport similar to ab initio calculations in bulk water, is used for reactive molecular dynamics simulations of the proton dynamics at the silica/water interface. The simulations are used to evaluate the lifetimes of protonated sites at the interfaces of water with planar amorphous silica surfaces and cylindrical pores in amorphous silica with different densities of water confined in the pores. In addition to lifetimes, the donor/acceptor sites are evaluated and discussed in terms of local atomistic structure. The results of the lifetimes of the protonated sites, including H 3 O + , SiOH, SiOH 2 + , and Si−(OH + )−Si sites, are considered. The lifetime of the hydronium ion, H 3 O + , is considerably shorter near the interface than in bulk water, as are the lifetimes of the other protonated sites. The results indicate the beneficial effect of the amorphous silica surface in enhancing proton transport in wet silica as seen in electrochemical studies and provide the specific molecular mechanisms.

A variable charge potential is developed that is suitable for the simulations of energy conversion materials FeF2 and FeF3. Molecular dynamics simulations using this potential show that the calculated structural and elastic properties of both FeF2 and FeF3 are in good agreement with experimental data. Such a transferability of this potential rests in the fact that the difference in the bond characteristic between FeF2 and FeF3 is properly accounted for by the variable charge approach. The calculated equilibrium charges are also in excellent agreement with first-principles Bader charges. Surface energies obtained by the variable charge method are closer to the first-principles data than are fixed charge models, indicating the importance of variable charge method for the simulations of the surface. A significant decrease in atomic charges is observed only for the outermost one or two layers, which is also observed in the first-principles calculations.

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I/O performance is a critical aspect of data-intensive scientific computing. We seek to advance the state of the practice in understanding and diagnosing I/O performance issues through investigation of a comprehensive I/O performance data set that captures a full year of production storage activity at two leadership-scale computing facilities. We demonstrate techniques to identify regions of interest, perform focused investigations of both long-term trends and transient anomalies, and uncover the contributing factors that lead to performance fluctuation.We find that a year in the life of a parallel file system is comprised of distinct regions of long-term performance variation in addition to short-term performance transients. We demonstrate how systematic identification of these performance regions, combined with comprehensive analysis, allows us to isolate the factors contributing to different performance maladies at different time scales. From this, we present specific lessons learned and important considerations for HPC storage practitioners.