Glenn K. Lockwood

Bridging oxygen as a site for proton adsorption on the vitreous silica surface

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.

Lifetimes of excess protons in water using a dissociative water potential

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.

SR-IOV: Performance Benefits for Virtualized Interconnects

The demand for virtualization within high-performance computing is rapidly growing as new communities, driven by both new application stacks and new computing modalities, continue to grow and expand. While virtualization has traditionally come with significant penalties in I/O performance that have precluded its use in mainstream large-scale computing environments, new standards such as Single Root I/O Virtualization (SR-IOV) are emerging that promise to diminish the performance gap and make high-performance virtualization possible. To this end, we have evaluated SR-IOV in the context of both virtualized InfiniBand and virtualized 10 gigabit Ethernet (GbE) using micro-benchmarks and real-world applications. We compare the performance of these interconnects on non-virtualized environments, Amazons SR-IOV-enabled C3 instances, and our own SR-IOV-enabled InfiniBand cluster and show that SR-IOV significantly reduces the performance losses caused by virtualization. InfiniBand demonstrates less than 2% loss of bandwidth and less than 10% increase in latency when virtualized with SR-IOV. Ethernet also benefits, although less dramatically, when SR-IOV is enabled on Amazons cloud.

Storage utilization in the long tail of science

The increasing expansion of computations in non-traditional domain sciences has resulted in an increasing demand for research cyberinfrastructure that is suitable for small- and mid-scale job sizes. The computational aspects of these emerging communities are coming into focus and being addressed through the deployment of several new XSEDE resources that feature easy on-ramps, customizable software environments through virtualization, and interconnects optimized for jobs that only use hundreds or thousands of cores; however, the data storage requirements for these emerging communities remains much less well characterized. To this end, we examined the distribution of file sizes on two of the Lustre file systems within the Data Oasis storage system at the San Diego Supercomputer Center (SDSC). We found that there is a very strong preference for small files among SDSCs users, with 90% of all files being less than 2 MB in size. Furthermore, 50% of all file system capacity is consumed by files under 2 GB in size, and these distributions are consistent on both scratch and projects storage file systems. Because parallel file systems like Lustre and GPFS are optimized for parallel IO to large, widestripe files, these findings suggest that parallel file systems may not be the most suitable storage solutions when designing cyberinfrastructure to meet the needs of emerging communities.

Efficient 3D Movement-Based Kernel Density Estimator and Application to Wildlife Ecology

We describe an efficient implementation of a 3D movement-based kernel density estimator for determining animal space use from discrete GPS measurements. This new method provides more accurate results, particularly for species that make large excursions in the vertical dimension. The downside of this approach is that it is much more computationally expensive than simpler, lower-dimensional models. Through a combination of code restructuring, parallelization and performance optimization, we were able to reduce the time to solution by up to a factor of 1000x, thereby greatly improving the applicability of the method.

Correction: Reactive simulations of the activation barrier to dissolution of amorphous silica in water

Correction for ‘Reactive simulations of the activation barrier to dissolution of amorphous silica in water’ by Michael Kagan et al., Phys. Chem. Chem. Phys., 2014, 16, 9294–9301.