Document is a thesis.

Because of the diversity of physical phenomena occuring in boiling, flashing, and bubble collapse, and of the length and time scales of LWR systems, it is imperative that the models have the following features: • Both vapor and liquid phases (and noncondensible phases, if present) must be treated as compressible. • Models must be mathematically and numerically well-posed. • The models methodology must be multi-scale. A fundamental derivation of the multiphase governing equation system, that should be used as a basis for advanced multiphase modeling in LWR coolant systems, is given in the Appendix using the ensemble averaging method. The remainder of this work focuses specifically on the compressible, well-posed, and multi-scale requirements of advanced simulation methods for these LWR coolant systems, because without these are the most fundamental aspects, without which widespread advancement cannot be claimed. Because of the expense of developing multiple special-purpose codes and the inherent inability to couple information from the multiple, separate length- and time-scales, efforts within CASL should be focused toward development of a multi-scale approaches to solve those multiphase flow problems relevant to LWR design and safety analysis. Efforts should be aimed at developing well-designed unified physical/mathematical and high-resolution numerical models for compressible, …

Production of H{sup -} beam for accelerators applications by charge exchange of high brightness hydrogen neutral beam in a sodium jet cell is experimentally studied in joint BNL-BINP experiment. In the experiment, a hydrogen-neutral beam with 3-6 keV energy, equivalent current up to 5 A and 200 microsecond pulse duration is used. The atomic beam is produced by charge exchange of a proton beam in a pulsed hydrogen target. Formation of the proton beam is performed in an ion source by four-electrode multiaperture ion-optical system. To achieve small beam emittance, the apertures in the ion-optical system have small enough size, and the extraction of ions is carried out from the surface of plasma emitter with a low transverse ion temperature of {approx}0.2 eV formed as a result of plasma jet expansion from the arc plasma generator. Developed for the BNL optically pumped polarized ion source, the sodium jet target with recirculation and aperture diameter of 2 cm is used in the experiment. At the first stage of the experiment H{sup -} beam with 36 mA current, 5 keV energy and {approx}0.15 cm {center_dot} mrad normalized emittance was obtained. To increase H{sup -} beam current ballistically focused hydrogen neutral beam will …

Local thermal hot-spots in microprocessors lead to worst case provisioning of global cooling resources, especially in large-scale systems. However, efficiency of cooling solutions degrade non-linearly with supply temperature, resulting in high power consumption and cost in cooling - 50 {approx} 100% of IT power. Recent advances in active cooling techniques have shown on-chip thermoelectric coolers (TECs) to be very efficient at selectively eliminating small hot-spots, where applying current to a superlattice film deposited between silicon and the heat spreader results in a Peltier effect that spreads the heat and lowers the temperature of the hot-spot significantly to improve chip reliability. In this paper, we propose that hot-spot mitigation using thermoelectric coolers can be used as a power management mechanism to allow global coolers to be provisioned for a better worst case temperature leading to substantial savings in cooling power. In order to quantify the potential power savings from using TECs in data center servers, we present a detailed power model that integrates on-chip dynamic and leakage power sources, heat diffusion through the entire chip, TEC and global cooler efficiencies, and all their mutual interactions. Our multiscale analysis shows that, for a typical data center, TECs allow global coolers to operate …

A number of the Commercial Building Partnership Projects (CBPs) will require metering, monitoring, data analysis and verification of savings after the retrofits are complete. Although monitoring and verification (M&V) agents are free to use any metering and monitoring devices that they chose, the data they collect should be reported to Pacific Northwest National Laboratory (PNNL) in a standard format. PNNL will store the data collected in its CBP database for further use by PNNL and U.S. Department of Energy. This document describes the data storage process and the deliver format of the data from the M&V agents.

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory - still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could overcome these difficulties and facilitate the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV, a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus and demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique or that shared structural similarity with structures that are distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local alignments, one can infer potential structural or functional importance of specific …

As part of our past research and development work, we have created and developed the LISE++ simulation code [Tar04, Tar08]. The LISE++ package was significantly extended with the addition of a Monte Carlo option that includes an option for calculating ion trajectories using a Taylor-series expansion up to fifth order, and implementation of the MOTER Monte Carlo code [Kow87] for ray tracing of the ions into the suite of LISE++ codes. The MOTER code was rewritten from FORTRAN into C++ and transported to the MS-Windows operating system. Extensive work went into the creation of a user-friendly interface for the code. An example of the graphical user interface created for the MOTER code is shown in the left panel of Figure 1 and the results of a typical calculation for the trajectories of particles that pass through the A1900 fragment separator are shown in the right panel. The MOTER code is presently included as part of the LISE++ package for downloading without restriction by the worldwide community. The LISE++ was extensively developed and generalized to apply to any projectile fragment separator during the early phase of this grant. In addition to the inclusion of the MOTER code, other important additions to …

Graphene grown by chemical vapor deposition and supported on SiO2 and sapphire substrates was studied following controlled introduction of defects induced by 35 keV carbon ion irradiation. Changes in Raman spectra following fluences ranging from 1012 cm-2 to 1015 cm-2 indicate that the structure of graphene evolves from a highly-ordered layer, to a patchwork of disordered domains, to an essentially amorphous film. These structural changes result in a dramatic decrease in the Hall mobility by orders of magnitude while, remarkably, the Hall concentration remains almost unchanged, suggesting that the Fermi level is pinned at a hole concentration near 1x1013 cm-2. A model for scattering by resonant scatterers is in good agreement with mobility measurements up to an ion fluence of 1x1014 cm-2.

Environmental health focus with training conducted as part of the United Negro College Fund Special Programs Corporation/National Library of Medicine HBCU ACCESS Project at Winston-Salem State University, NC on November 10, 2010.

5098-SR-04-0 PROJECT-SPECIFIC TYPE A VERIFICATION FOR THE HIGH FLUX BEAM REACTOR UNDERGROUND UTILITIES REMOVAL PHASE 3 TRENCH 5, BROOKHAVEN NATIONAL LABORATORY

The International Perspectives on Mitigating Laboratory Biorisks workshop, held at the Renaissance Polat Istanbul Hotel in Istanbul, Republic of Turkey, from October 25 to 27, 2010, sought to promote discussion between experts and stakeholders from around the world on issues related to the management of biological risk in laboratories. The event was organized by Sandia National Laboratories International Biological Threat Reduction program, on behalf of the US Department of State Biosecurity Engagement Program and the US Department of Defense Cooperative Biological Engagement Program. The workshop came about as a response to US Under Secretary of State Ellen O. Tauscher's statements in Geneva on December 9, 2009, during the Annual Meeting of the States Parties to the Biological Weapons Convention (BWC). Pursuant to those remarks, the workshop was intended to provide a forum for interested countries to share information on biorisk management training, standards, and needs. Over the course of the meeting's three days, participants discussed diverse topics such as the role of risk assessment in laboratory biorisk management, strategies for mitigating risk, measurement of performance and upkeep, international standards, training and building workforce competence, and the important role of government and regulation. The meeting concluded with affirmations of the utility …

High quality ZnO:Al (AZO) thin films were prepared on glass substrates by direct current filtered cathodic arc deposition. Substrate temperature was varied from room temperature to 425oC, and samples were grown with and without the assistance of low power oxygen plasma (75W). For each growth condition, at least 3 samples were grown to give a statistical look at the effect of the growth environment on the film properties and to explore the reproducibility of the technique. Growth rate was in the 100-400 nm/min range but was apparently random and could not be easily traced to the growth conditions explored. For optimized growth conditions, 300-600 nm AZO films had resistivities of 3-6 x 10-4 ?Omega cm, carrier concentrations in the range of 2-4 x 1020 cm3, Hall mobility as high as 55 cm2/Vs, and optical transmittance greater than 90percent. These films are also highly oriented with the c-axis perpendicular to the substrate and a surface roughness of 2-4 nm.

The installed performance of cooking exhaust fans was evaluated through residential field experiments conducted on a sample of 15 devices varying in design and other characteristics. The sample included two rear downdraft systems, two under-cabinet microwave over range (MOR) units, three different installations of an under-cabinet model with grease screens across the bottom and no capture hood, two devices with grease screens covering the bottom of a large capture hood (one under-cabinet, one wall-mount chimney), four under-cabinet open hoods, and two open hoods with chimney mounts over islands. Performance assessment included measurement of airflow and sound levels across fan settings and experiments to quantify the contemporaneous capture efficiency for the exhaust generated by natural gas cooking burners.Capture efficiency is defined as the fraction of generated pollutants that are removed through the exhaust and thus not available for inhalation of household occupants. Capture efficiency (CE) was assessed for various configurations of burner use (e.g., single front, single back, combination of one front and one back, oven) and fan speed setting. Measured airflow rates were substantially lower than the levels noted in product literature for many of the units. This shortfall was observed for several units costing in excess of $1000. Capture …

Prokaryotic life on earth is manifested by its diversity and omnipresence. These microbes serve as natural sources of a large variety of compounds with the potential to serve the ever growing, medicinal, chemical and transportation needs of the human population. However, commercially viable production of these compounds can be realized only through significant improvement of the native production capacity of natural isolates. The most favorable way to achieve this goal is through the genetic manipulation of metabolic pathways that direct the production of these molecules. While random mutagenesis and screening have dominated the industrial production of such compounds in the past our increased understanding of microbial physiology over the last five decades has shifted this trend towards rational approaches for metabolic design. Major drivers of this trend include recombinant DNA technology, high throughput characterization of macromolecular cellular components, quantitative modeling for metabolic engine ring, targeted combinatorial engineering and synthetic biology. In this chapter we track the evolution of microbial engineering technologies from the black box era of random mutagenesis to the science and engineering-driven era of metabolic design.

High performance computing has experienced tremendous gains in system performance over the past 20 years. Unfortunately other system capabilities, such as file I/O, have not grown commensurately. In this activity, we present the results of our tests of two leading file systems (GPFS and Lustre) on the same physical hardware. This hardware is the standard commodity storage solution in use at LLNL and, while much smaller in size, is intended to enable us to learn about differences between the two systems in terms of performance, ease of use and resilience. This work represents the first hardware consistent study of the two leading file systems that the authors are aware of.

Abstract: Depressional wetlands may be restored passively by disrupting prior drainage to recover original hydrology and relying on natural revegetation. Restored hydrology selects for wetland vegetation; however, depression geomorphology constrains the achievable hydroperiod, and plant communities are influenced by hydroperiod and available species pools. Such constraints can complicate assessments of restoration success. Sixteen drained depressions in South Carolina, USA, were restored experimentally by forest clearing and ditch plugging for potential crediting to a mitigation bank. Depressions were assigned to alternate revegetation methods representing desired targets of herbaceous and wet-forest communities. After five years, restoration progress and revegetation methods were evaluated. Restored hydroperiods differed among wetlands, but all sites developed diverse vegetation of native wetland species. Vegetation traits were influenced by hydroperiod and the effects of early drought, rather than by revegetation method. For mitigation banking, individual wetlands were assessed for improvement from pre-restoration condition and similarity to assigned reference type. Most wetlands met goals to increase hydroperiod, herb-species dominance, and wetland-plant composition. Fewer wetlands achieved equivalence to reference types because some vegetation targets were incompatible with depression hydroperiods and improbable without intensive management. The results illustrated a paradox in judging success when vegetation goals may be unsuited to system constraints.

The ability to reliably predict flow and transport in fractured porous rock is an essential condition for performance evaluation of geologic (underground) nuclear waste repositories. In this report, a suite of programs (TRIPOLY code) for calculating and analyzing flow and transport in two-dimensional fracture-matrix systems is used to model single-well injection-withdrawal (SWIW) tracer tests. The SWIW test, a tracer test using one well, is proposed as a useful means of collecting data for site characterization, as well as estimating parameters relevant to tracer diffusion and sorption. After some specific code adaptations, we numerically generated a complex fracture-matrix system for computation of steady-state flow and tracer advection and dispersion in the fracture network, along with solute exchange processes between the fractures and the porous matrix. We then conducted simulations for a hypothetical but workable SWIW test design and completed parameter sensitivity studies on three physical parameters of the rock matrix - namely porosity, diffusion coefficient, and retardation coefficient - in order to investigate their impact on the fracture-matrix solute exchange process. Hydraulic fracturing, or hydrofracking, is also modeled in this study, in two different ways: (1) by increasing the hydraulic aperture for flow in existing fractures and (2) by adding a …

This report is the final summation of Sandia's Grand Challenge LDRD project No.119351, 'Network Discovery, Characterization and Prediction' (the 'NGC') which ran from FY08 to FY10. The aim of the NGC, in a nutshell, was to research, develop, and evaluate relevant analysis capabilities that address adversarial networks. Unlike some Grand Challenge efforts, that ambition created cultural subgoals, as well as technical and programmatic ones, as the insistence on 'relevancy' required that the Sandia informatics research communities and the analyst user communities come to appreciate each others needs and capabilities in a very deep and concrete way. The NGC generated a number of technical, programmatic, and cultural advances, detailed in this report. There were new algorithmic insights and research that resulted in fifty-three refereed publications and presentations; this report concludes with an abstract-annotated bibliography pointing to them all. The NGC generated three substantial prototypes that not only achieved their intended goals of testing our algorithmic integration, but which also served as vehicles for customer education and program development. The NGC, as intended, has catalyzed future work in this domain; by the end it had already brought in, in new funding, as much funding as had been invested in it. Finally, the …

The 100-HR-3 Groundwater Operable Unit (OU) second Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA) 5-year review (DOEIRL-2006-20, The Second CERCLA Five-Year Review Report for the Hanford Site) set a milestone to conduct an investigation of deep hexavalent chromium contamination in the sediments of the Ringold upper mud (RUM) unit, which underlies the unconfined aquifer in the 100-H Area. The 5-year review noted that groundwater samples from one deep well extending below the aquitard (i.e., RUM) exceeded both the groundwater standard of 48 parts per billion (ppb) (Ecology Publication 94-06, Model Toxics Control Act Cleanup Statute and Regulation) and the federal drinking water standard of 100 {mu}g/L for hexavalent chromium. The extent of hexavalent chromium contamination in this zone is not well understood. Action 12-1 from the 5-year review is to perform additional characterization of the aquifer below the initial aquitard. Field characterization and aquifer testing were performed in the Hanford Site's 100-H Area to address this milestone. The aquifer tests were conducted to gather data to answer several fundamental questions regarding the presence of the hexavalent chromium in the deep sediments of the RUM and to determine the extent and magnitude of deeper contamination. The pumping tests …

Bremstrahlung Isochromat Spectroscopy (BIS). The XES spectra were collected using a Specs electron gun for the excitation and the XES 350 grating monochromator and channel plate system from Scienta as the photon detection. Spectra were collected in 'normal mode,' where the electron gun kinetic energy (KE) and the energy position of the center of the channel plate were both fixed and the energy distribution in the photon (hv) spectrum was derived from the intensities distributed across the channel plate detector in the energy dispersal direction. The polycrystalline Ce sample was oxidized by exposure to air at ambient pressures. After introduction to the ultra-high vacuum system, the oxidized sample was bombarded with Ar, to clean the topmost surface region and stabilize the surface and near surface regions. Although CeO{sub 2} would be the thermodynamically preferred composition in an oxygen rich environment, the combination of a vacuum environment and ion etching may have driven the near surface region into a Ce{sub 2}O{sub 3} stoichiometry. XES data collection occurred with the sample at or near room temperature. The base pressure of the system was 3 x 10{sup -10} torr, but the pressure changed depending the energy and current of the electron gun. For …

The Savannah River Site (SRS) is a 310-square-mile United States Department of Energy nuclear facility located along the Savannah River (SRS) near Aiken, South Carolina. Nuclear weapons material production began in the early 1950s, utilizing five production reactors. In the early 1990s all SRS production reactor operations were terminated. The first reactor closure end state declaration was recently institutionalized in a Comprehensive Environmental Response and Compensation and Liability Act (CERCLA) Early Action Record of Decision. The decision for the final closure of the 318,000 square foot 105-P Reactor was determined to be in situ decommissioning (ISD). ISD is an acceptable and cost effective alternative to off-site disposal for the reactor building, which will allow for consolidation of remedial action wastes generated from other cleanup activities within the P Area. ISD is considered protective by the regulators, U. S. Environmental Protection Agency (US EPA) and the South Carolina Department of Health and Environmental Control (SCDHEC), public and stakeholders as waste materials are stabilized/immobilized, and radioactivity is allowed to naturally decay, thus preventing future exposure to the environment. Stakeholder buy-in was critical in the upfront planning in order to achieve this monumental final decision. Numerous public meetings and workshops were held in …

Possible environmental effects of marine and hydrokinetic (MHK) energy development are not well understood, and yet regulatory agencies are required to make decisions in spite of substantial uncertainty about environmental impacts and their long-term effects. An understanding of risk associated with likely interactions between MHK installations and aquatic receptors, including animals, habitats, and ecosystems, can help reduce the level of uncertainty and focus regulatory actions and scientific studies on interactions of most concern. As a first step in developing the Pacific Northwest National Laboratory (PNNL) Environmental Risk Evaluation System (ERES), PNNL scientists conducted a preliminary risk screening analysis on three initial MHK cases - a tidal project in Puget Sound using Open Hydro turbines, a wave project off the coast of Oregon using Ocean Power Technologies point attenuator buoys, and a riverine current project in the Mississippi River using Free Flow turbines. Through an iterative process, the screening analysis revealed that top-tier stressors in all three cases were the effects of the dynamic physical presence of the device (e.g., strike), accidents, and effects of the static physical presence of the device (e.g., habitat alteration). Receptor interactions with these stressors at the four highest tiers of risk were dominated by marine …

As part of a small follow-on study, the burn rate of the ammonium perchlorate (AP) based material TAL-1503 was studied at a relatively mild pressure. The goal of this final experiment was to burn TAL-1503 at the lowest pressures possible using the LLNL High Pressure Strand Burner (LLNL-HPSB). The following is a description of the experiment and the results with a brief discussion of data and a comparison to the higher pressure data. This is not meant to be a stand-alone report and readers should refer to the main report for experimental details and discussion. High pressure deflagration rate measurements of a unique AP/HTPB based material (TAL-1503) were performed using the LLNL high pressure strand burner apparatus. The material burns in a well behaved, laminar fashion between 20 and 300 MPa with a burn law of B = (0.6 {+-} 0.1) x P{sup (1.05{+-}0.02)} that was calculated based on the best data available from the experiments. In the pressure range of 2 and 10 MPa the material burned laminarly with a burn law of B = (2.0 {+-} 0.2) x P{sup (0.66{+-}0.05)}. In these results, B is the burn rate in mm/s and P is the pressure in units of …

The CDF experiment at the Tevatron p{bar p} collider established that extensive and detailed exploration of the b-quark dynamics is possible in hadron collisions, with results competitive and supplementary to those from e{sup +}e{sup -} colliders. This provides an unique, rich, and highly rewarding program that is currently reaching full maturity. I report a few recent world-leading results on rare decays, CP-violation in B{sub s}{sup 0} mixing, and b {yields} s penguin decays.