Joseph C. Fogarty

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Molecular Simulation (MS) is a powerful tool for studying physical/chemical features of large systems and has seen applications in many scientific and engineering domains. During the simulation process, the experiments generate a very large number of atoms and intend to observe their spatial and temporal relationships for scientific analysis. The sheer data(More)
Molecular dynamics modeling has provided a powerful tool for simulating and understanding diverse systems – ranging from materials processes to biophysical phenomena. Parallel formulations of these methods have been shown to be among the most scalable scientific computing applications. Many instances of this class of methods rely on a static bond structure(More)
We report our study of a silica-water interface using reactive molecular dynamics. This first-of-its-kind simulation achieves length and time scales required to investigate the detailed chemistry of the system. Our molecular dynamics approach is based on the ReaxFF force field of van Duin et al. [J. Phys. Chem. A 107, 3803 (2003)]. The specific ReaxFF(More)
We present a new atom density profile (ADP) model and a statistical approach for extracting structural characteristics of lipid bilayers from X-ray and neutron scattering data. Models for five lipids with varying head and tail chemical composition in the fluid phase, 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC),(More)
We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder-Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site.(More)
Many scientific fields generate, and require manipulation of big data. Known scientific data analysis systems, as well as traditional DBMSs, follow a pull-based architectural design, where the executed queries mandate the data needed. This design, while suitable for traditional transaction-based workloads where number of queries retrieve small parts of data(More)
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