Bulletin of the American Physical Society
78th Annual Meeting of the Southeastern Section of the APS
Volume 56, Number 9
Wednesday–Saturday, October 19–22, 2011; Roanoke, Virginia
Session CD: Advances in Computing |
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Chair: Leo Piilonen, Virginia Polytechnic Institute and State University Room: Crystal Ballroom DE |
Thursday, October 20, 2011 10:45AM - 11:15AM |
CD.00001: Open Science Grid: Linking Universities and Laboratories In National Cyberinfrastructure Invited Speaker: Open Science Grid is a consortium of researchers from universities and national laboratories that operates a national computing infrastructure serving large-scale scientific and engineering research. While OSG's scale has been primarily driven by the demands of the LHC experiments, it currently serves particle and nuclear physics, gravitational wave searches, digital astronomy, genomic science, weather forecasting, molecular modeling, structural biology and nanoscience. The OSG distributed computing facility links campus and regional computing resources and is a major component of the Worldwide LHC Computing Grid (WLCG) that handles the massive computing and storage needs of experiments at the Large Hadron Collider. This collaborative work has provided a wealth of results, including powerful new software tools and services; a uniform packaging scheme (the Virtual Data Toolkit) that simplifies software deployment across many sites in the US and Europe; integration of complex tools and services in large science applications; multiple education and outreach projects; and new approaches to integrating advanced network infrastructure in scientific computing applications. More importantly, OSG has provided unique collaborative opportunities between researchers in a variety of research disciplines. [Preview Abstract] |
Thursday, October 20, 2011 11:15AM - 11:45AM |
CD.00002: Evolving from TeraGrid to XSEDE Invited Speaker: Since 2001, the TeraGrid has developed into a world-class integrated, national-scale computational science infrastructure with funding from the NSF's Office of Cyberinfrastructure (OCI). Recently, the TeraGrid project came to an end and has been supplanted by the NSF's eXtreme Digital program, opening a new chapter in cyberinfrastructure by creating the most advanced, powerful, and robust collection of integrated advanced digital resources and services in the world. This talk will introduce the new project, XSEDE: the eXtreme Science and Engineering Discovery Environment, which began July 1, 2011. [Preview Abstract] |
Thursday, October 20, 2011 11:45AM - 12:15PM |
CD.00003: Quantum transport and nanoplasmonics with carbon nanorings - using HPC in computational nanoscience Invited Speaker: Central theme of this talk is the theoretical study of toroidal carbon nanostructures as a new form of metamaterial. The interference of ring-generated electromagnetic radiation in a regular array of nanorings driven by an incoming polarized wave front may lead to fascinating new optoelectronics applications. The tight-binding method is used to model charge transport in a carbon nanotorus: All transport observables can be derived from the Green's function of the device region in a non-equilibrium Green's function algorithm. We have calculated density-of-states D(E) and transmissivities T(E) between two metallic leads under a small voltage bias. Electron-phonon coupling is included for low-energy phonon modes of armchair and zigzag nanorings with atomic displacements determined by a collaborator's finite-element based code. A numerically fast and stable algorithm has been developed via parallel linear algebra matrix routines (PETSc) with MPI parallelism to reach significant speed-up. Production runs are planned on the NSF XSEDE network. This project was supported in parts by a 2010 NSF TeraGrid Fellowship and the Sunshine State Education and Research Computing Alliance (SSERCA). Two summer students were supported as 2010 and 2011 NCSI/Shodor Petascale Computing undergraduate interns.\\[4pt] In collaboration with Leon W. Durivage, Adam Byrd, and Mario Encinosa. [Preview Abstract] |
Thursday, October 20, 2011 12:15PM - 12:45PM |
CD.00004: Discrete Molecular Dynamics Simulation of Biomolecules Invited Speaker: Discrete molecular dynamics (DMD) simulation of hard spheres was the first implementation of molecular dynamics (MD) in history. DMD simulations are computationally more efficient than continuous MD simulations due to simplified interaction potentials. However, also due to these simplified potentials, DMD has often been associated with coarse-grained modeling, and hence continuous MD has become the dominant approach used to study the internal dynamics of biomolecules. With the recent advances in DMD methodology, including the development of high-resolution models for biomolecules and approaches to increase DMD efficiency, DMD simulations are emerging as an important tool in the field of molecular modeling, including the study of protein folding, protein misfolding and aggregation, and protein engineering. Recently, DMD methodology has been ~applied to modeling RNA folding and protein-ligand recognition. With these improvements to DMD methodology and the continuous increase in available computational power, we expect a growing role of DMD simulations in our understanding of biology. [Preview Abstract] |
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