Enabling a High Throughput Real Time Data Pipeline for a Large Radio Telescope Array with GPUs

The Murchison Widefield Array (MWA) is a next-generation radio telescope currently under construction in the remote Western Australia Outback. Raw data will be generated continuously at 5GiB/s, grouped into 8s cadences. This high throughput motivates the development of on-site, real time processing and reduction in preference to archiving, transport and off-line processing. Each batch of 8s data must be completely reduced before the next batch arrives. Maintaining real time operation will require a sustained performance of around 2.5TFLOP/s (including convolutions, FFTs, interpolations and matrix multiplications). We describe a scalable heterogeneous computing pipeline implementation, exploiting both the high computing density and FLOP-per-Watt ratio of modern GPUs. The architecture is highly parallel within and across nodes, with all major processing elements performed by GPUs. Necessary scatter-gather operations along the pipeline are loosely synchronized between the nodes hosting the GPUs. The MWA will be a frontier scientific instrument and a pathfinder for planned peta- and exascale facilities.Comment: Version accepted by Comp. Phys. Com

Knowledge-based energy functions for computational studies of proteins

This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent statistical potentials, as well as geometric statistical potentials. We also describe a geometric model for developing both linear and non-linear potential functions by optimization. Applications of knowledge-based potential functions in protein-decoy discrimination, in protein-protein interactions, and in protein design are then described. Several issues of knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe

Methane sources in gas hydrate-bearing cold-seeps : evidence from radiocarbon and stable isotopes

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Marine Chemistry 115 (2009): 102-109, doi:10.1016/j.marchem.2009.07.001.Fossil methane from the large and dynamic marine gas hydrate reservoir has the potential to influence oceanic and atmospheric carbon pools. However, natural radiocarbon (14C) measurements of gas hydrate methane have been extremely limited, and their use as a source and process indicator has not yet been systematically established. In this study, gas hydrate-bound and dissolved methane recovered from six geologically and geographically distinct high-gas-flux cold seeps was found to be 98 to 100% fossil based on its 14C content. Given this prevalence of fossil methane and the small contribution of gas hydrate (≤1%) to the present-day atmospheric methane flux, non-fossil contributions of gas hydrate methane to the atmosphere are not likely to be quantitatively significant. This conclusion is consistent with contemporary atmospheric methane budget calculations. In combination with δ13C- and δD-methane measurements, we also determine the extent to which the low, but detectable, amounts of 14C (~ 1-2 percent modern carbon, pMC) in methane from two cold seeps might reflect in situ production from near-seafloor sediment organic carbon (SOC). A 14C mass balance approach using fossil methane and 14C-enriched SOC suggests that as much as 8 to 29% of hydrate-associated methane carbon may originate from SOC contained within the upper 6 meters of sediment. These findings validate the assumption of a predominantly fossil carbon source for marine gas hydrate, but also indicate that structural gas hydrate from at least certain cold seeps contains a component of methane produced during decomposition of non-fossil organic matter in near-surface sediment.This work was supported by the Office of Naval Research and Naval Research Laboratory (NRL). Partial support was also provided by the USGS Mendenhall Postdoctoral Research Fellowship Program to JWP, and NSF Chemical Oceanography (OCE-0327423) and Integrated Carbon Cycle Research (EAR- 0403949) program support to JEB

Sex differences in the associations between L-arginine pathway metabolites, skeletal muscle mass and function, and their responses to resistance exercise, in old age

This work was supported by the Biotechnology and Biological Sciences Research Council (BB/J015911/1) and was registered at clinicaltrials.gov (ClinicalTrials. gov Identifier: NCT02843009). Supplementary email included with articlePeer reviewedPostprin