Most prokaryotes of interest to DOE are poorly understood. Even when full genomic sequences are available, the function of only a small number of gene products are clear. The critical question is how to best infer the most probable network architectures in cells that are poorly characterized. The project goal is to create a computational hypothesis testing (CHT) framework that combines large-scale dynamical simulation, a database of bioinformatics-derived probable interactions, and numerical parallel architecture data-fitting routines to explore many “what if ?” hypotheses about the functions of genes and proteins within pathways and their downstream effects on molecular concentration profiles and corresponding phenotypes. From this framework we expect to infer signal transduction pathways and gene expression networks in prokaryotes. Detailed mechanistic models of E. Coli have been developed that directly incorporate DNA sequence information. The CHT framework is implemented in the NIEngine network inference software. NIEngine has been applied to recover gene regulatory networks in E. coli to assess performance. Application to Shewanel la oneidensi and other organism of interest DOE will be conducted in partnership with Jim Collin's Lab at Boston University and other academic partners. The CHT framework has also found broad application in the automated learning of …

To better understand the role of groundwater-level changes on rock-slope deformation and damage, a carbonate rock slope (30 m x 30 m x 15 m) was extensively instrumented for mesoscale hydraulic and mechanical measurements during water-level changes. The slope is naturally drained by a spring that can be artificially closed or opened by a water gate. In this study, a 2-hour slope-dewatering experiment was analyzed. Changes in fluid pressure and deformation were simultaneously monitored, both at discontinuities and in the intact rock, using short-base extensometers and pressure gauges as well as tiltmeters fixed at the slope surface. Field data were analyzed with different coupled hydromechanical (HM) codes (ROCMAS, FLAC{sup 3D}, and UDEC). Field data indicate that in the faults, a 40 kPa pressure fall occurs in 2 minutes and induces a 0.5 to 31 x 10{sup -6} m normal closure. Pressure fall is slower in the bedding-planes, lasting 120 minutes with no normal deformation. No pressure change or deformation is observed in the intact rock. The slope surface displays a complex tilt towards the interior of the slope, with magnitudes ranging from 0.6 to 15 x 10{sup -6} rad. Close agreement with model for both slope surface and internal measurements …

The U.S. Department of Energy (DOE) Office of Legacy Management conducted annual sampling at the Rulison, Colorado site, for the Long-Term Hydrologic Monitoring Program (LTHMP) on May 12, and 13, 2008. Samples were analyzed by the U.S. Environmental Protection Agency (EPA) Radiation&Indoor Environments National Laboratory in Las Vegas, Nevada. Samples were analyzed for gamma-emitting radionuclides by high-resolution gamma spectroscopy and tritium using the conventional and enriched methods

Where Martian rocks have been exposed to liquid water, chemistry versus depth profiles could elucidate both Martian climate history and potential for life. The persistence of primary minerals in weathered profiles constrains the exposure time to liquid water: on Earth, mineral persistence times range from {approx}10 ka (olivine) to {approx}250 ka (glass) to {approx}1Ma (pyroxene) to {approx}5Ma (plagioclase). Such persistence times suggest mineral persistence minima on Mars. However, Martian solutions may have been more acidic than on Earth. Relative mineral weathering rates observed for basalt in Svalbard (Norway) and Costa Rica demonstrate that laboratory pH trends can be used to estimate exposure to liquid water both qualitatively (mineral absence or presence) and quantitatively (using reactive transport models). Qualitatively, if the Martian solution pH > {approx}2, glass should persist longer than olivine; therefore, persistence of glass may be a pH-indicator. With evidence for the pH of weathering, the reactive transport code CrunchFlow can quantitatively calculate the minimum duration of exposure to liquid water consistent with a chemical profile. For the profile measured on the surface of Humphrey in Gusev Crater, the minimum exposure time is 22 ka. If correct, this estimate is consistent with short-term, episodic alteration accompanied by ongoing surface …

This report summarizes the methodology and results of a user perspectives study conducted by the Community Driven Improvement of Globus Software (CDIGS) project. The purpose of the study was to document the work-related goals and challenges facing today's scientific technology users, to record their perspectives on Globus software and the distributed-computing ecosystem, and to provide recommendations to the Globus community based on the observations. Globus is a set of open source software components intended to provide a framework for collaborative computational science activities. Rather than attempting to characterize all users or potential users of Globus software, our strategy has been to speak in detail with a small group of individuals in the scientific community whose work appears to be the kind that could benefit from Globus software, learn as much as possible about their work goals and the challenges they face, and describe what we found. The result is a set of statements about specific individuals experiences. We do not claim that these are representative of a potential user community, but we do claim to have found commonalities and differences among the interviewees that may be reflected in the user community as a whole. We present these as a series …