This summer I had the privilege of working at Lawrence Livermore National Laboratory under the Nonproliferation, Homeland and International Security Directorate in the Chemical and Biological Countermeasures Division. I worked exclusively on the Viral Identification and Characterization Initiative (VICI) project focusing on the development of multiplexed polymerase chain reaction (PCR) assays. The goal of VICI is to combine several disciplines such as molecular biology, microfluidics, and bioinformatics in order to detect viruses and identify them in order to effectively and quickly counter infectious disease, natural or engineered. The difficulty in such a countermeasure is that little is known about viral diversity due to the ever changing nature of these organisms. In response, VICI is developing a new microfluidic bioanalytical platform to detect known and unknown viruses by analyzing every virus in a sample by isolating them into picoliter sized droplets on a microchip and individually analyzing them. The sample will be injected into a channel of oil to form droplets that will contain viral nucleic acids that will be amplified using PCR. The multiplexed PCR assay will produce a series of amplicons for a particular virus genome that provides an identifying signature. A device will then detect whether or not …

Many different materials are used in the National Ignition Facility, NIF, located at Lawrence Livermore National Laboratory, LLNL. Some of these are exposed to significant doses of ionizing radiation. Two elastomers are of special interest because they are used in sealing applications with long expected lifetimes. These are LPU4, a polyurethane formulated at LLNL, and Dow Corning DC93-500, a silicone RTV elastomer. In 2004 a program to determine the impact of ionizing radiation on the stress relaxation and compression set characteristics of these two elastomers was undertaken. Since the materials are used in continuous compression and must reliably seal, the primary test utilized was a stress relaxation test. This test provides insight into the ability of a seal to remain functional in a static seal. The test determines how much residual force remains after a certain period of time under compression. The temperature and absorbed radiation dose can dramatically impact this property. In this study the only independent environmental variable studied is the effect of radiation at ambient temperatures. Two levels of radiation exposure were studied, 1 MRad, and 10 MRad. One of the independent test parameters is the compression deflection during storage and in this test the value used …

Tank Farms Operations removed an electrochemical noise probe from Tank 241-AN-107. In the field, the probe was cut into four sections, wrapped, and placed in a 55-gallon drum, This drum was delivered to the 222-S Laboratory. The 222 S Laboratory unpackaged the sections of the AN-107 electrochemical noise probe and examined the material for evidence of corrosion. Each of the four sections contained three C-ring and three bullet specimens. The specimens were examined for pitting corrosion, crevice corrosion, and stress corrosion cracking. No evidence of stress corrosion cracking was found in the stressed C-ring specimens. Minor pitting was evident on some surfaces. Crevice corrosion was the dominant type of corrosion observed.

This study predicts new hybrid lighting applications for LEDs. In hybrid lighting, LEDs provide a low-energy 'standby' light level while another, more powerful, efficient light source provides light for occupied periods. Lighting controls will allow the two light sources to work together through an appropriate control strategy, typically motion-sensing. There are no technical barriers preventing the use of low through high CRI LEDs for standby lighting in many interior and exterior applications today. The total luminous efficacy of LED systems could be raised by increasing the electrical efficiency of LED drivers to the maximum practically achievable level (94%). This would increase system luminous efficacy by 20-25%. The expected market volumes for many types of LEDs should justify the evolution of new LED drivers that use highly efficient ICs and reduce parts count by means of ASICs. Reducing their electronics parts count by offloading discrete components onto integrated circuits (IC) will allow manufacturers to reduce the cost of LED driver electronics. LED luminaire manufacturers will increasingly integrate the LED driver and thermal management directly in the LED fixture. LED luminaires of the future will likely have no need for separable lamp and ballast because the equipment life of all the LED …

This procedure provides instructions forassembling the following CH packaging payload: Drum payload assembly Standard Waste Box (SWB) assembly Ten-Drum Overpack (TDOP)

This document outlines a proposal for extending UPC'spoint-to-point memcpy library with support for explicitly non-blockingtransfers, and non-contiguous (indexed and strided) transfers. Variousportions of this proposal could stand alone as independent extensions tothe UPC library. The designs presented here are heavily influenced byanalogous functionality which exists in other parallel communicationsystems, such as MPI, ARMCI, Titanium, and network hardware API's such asQuadrics elan, Infiniband vapi, IBM LAPI and Cray X-1. Each sectioncontains proposed extensions to the libraries in the UPC LanguageSpecification (section 7) and corresponding extensions to the GASNetcommunication system API.

Corrosion rates using supernatant samples retrieved from near the top of the liquid layer were determined for the tanks. Corrosion rates using settled solids (saltcake) were determined. The supernatant samples were tested as received without argon sparging. The settled solid sample segments were extruded under anaerobic condition and kept under a sweep of humidified argon gas during 'the electrochemical corrosion testing. The class of steel used to construct the tank in question was used, and test coupons were allowed to equilibrate for a minimum of 18 hours before a Tafel scan was initiated. The coupons were scanned from -250 mV to +250 mV from the rest or open circuit potential. The corrosion rate is reported along with the corrosion current measurement, open circuit potential, and a chi-square statistic generated by the instrument controlling and analysis algorithm.

This tech base award has close links with the Viral Identification Characterization Initiative (VICI) ER LDRD. The tech base extends developed code to enable a capability for biodefense, biosurveillance, and clinical diagnostics. The code enables the design of signatures to detect and discover viruses, without relying on prior assumptions as to the species of virus present. This approach for primer and signature design contrasts with more traditional PCR approaches, in which a major weakness is the unlikelihood of viral discovery or detection of unanticipated species. There were three crucial areas of the project that were not research and development, so could not be funded under the ER LDRD, but were a reduction to practice of the existing VICI algorithm that were necessary for the success of overall computational project goals. These areas, funded by the 2007 Tech Base award, were: (1) improvement of the code developed under the VICI LDRD by incorporating T{sub m} and free energy predictions using Unafold; (2) porting of code developed on the kpath Sun Solaris cluster to the Yana and Zeus LC machines; and (3) application of that code to perform large numbers of simulations to determine parameter effects.

In the near future, the United States will be facing constraints on energy availability due to the heightened demand for both energy and water, especially during droughts and summers. Increasing stress on the inextricably linked resource availability of both water and energy can be mitigated with integrated planning. Exchanging data is an important component to current and future mitigation approaches within the Energy-Water Nexus. We describe the types of relationships that are formed in the United States EWN, and address the data sharing obstacles within. Approaches to removing the obstacles of data sharing are presented, based on case studies.

The International Linear Collider will give physicists a new cosmic doorway to explore energy regimes beyond the reach of today's accelerators. A proposed electron-positron collider, the ILC will complement the Large Hadron Collider, a proton-proton collider at the European Center for Nuclear Research (CERN) in Geneva, Switzerland, together unlocking some of the deepest mysteries in the universe. With LHC discoveries pointing the way, the ILC -- a true precision machine -- will provide the missing pieces of the puzzle. Consisting of two linear accelerators that face each other, the ILC will hurl some 10 billion electrons and their anti-particles, positrons, toward each other at nearly the speed of light. Superconducting accelerator cavities operating at temperatures near absolute zero give the particles more and more energy until they smash in a blazing crossfire at the centre of the machine. Stretching approximately 35 kilometres in length, the beams collide 14,000 times every second at extremely high energies -- 500 billion-electron-volts (GeV). Each spectacular collision creates an array of new particles that could answer some of the most fundamental questions of all time. The current baseline design allows for an upgrade to a 50-kilometre, 1 trillion-electron-volt (TeV) machine during the second stage of …

The 100-B-14:1 subsite encompasses the former process sewer main associated with the 105-B Reactor Building, 108-B Chemical Pumphouse and Tritium Separation Facility, 184-B Boiler House and the 100-B water treatment facilities, as well as the feeder lines associated with the 108-B facility, formerly discharging to the 116-B-7 Outfall Structure. The subsite has been remediated to achieve the remedial action objectives specified in the Remaining Sites ROD. The results of verification sampling demonstrated that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also showed that residual contaminant concentrations are protective of groundwater and the Columbia River.

In preparation for the 2006 XSD Scientific Software workshop, our committee sent a survey on June 16 to 100 users in the APS user community. This report contains the survey and the responses we received. The responses are presented in the order received.

This cleanup verification package documents completion of remedial action for the 100-F-20, Pacific Northwest Laboratory Parallel Pits waste site. This waste site consisted of two earthen trenches thought to have received both radioactive and nonradioactive material related to the 100-F Experimental Animal Farm.

We address the problem of classification in a partially labeled network (a.k.a. within-network classification), with an emphasis on tasks in which we have very few labeled instances to start with. Recent work has demonstrated the utility of collective classification (i.e., simultaneous inferences over class labels of related instances) in this general problem setting. However, the performance of collective classification algorithms can be adversely affected by the sparseness of labels in real-world networks. We show that on several real-world data sets, collective classification appears to offer little advantage in general and hurts performance in the worst cases. In this paper, we explore a complimentary approach to within-network classification that takes advantage of network structure. Our approach is motivated by the observation that real-world networks often provide a great deal more structural information than attribute information (e.g., class labels). Through experiments on supervised and semi-supervised classifiers of network data, we demonstrate that a small number of structural features can lead to consistent and sometimes dramatic improvements in classification performance. We also examine the relative utility of individual structural features and show that, in many cases, it is a combination of both local and global network structure that is most informative.

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Air pollution arising from the emission of nitrogen oxides as a result of combustion taking place in boilers, furnaces and engines, has increasingly been recognized as a problem. New methods to remove NO{sub x} emissions significantly and economically must be developed. The current technology for post-combustion removal of NO is the selective catalytic reduction (SCR) of NO by ammonia or possibly by a hydrocarbon such as methane. The catalytic decomposition of NO to give N{sub 2} will be preferable to the SCR process because it will eliminate the costs and operating problems associated with the use of an external reducing species. The most promising decomposition catalysts are transition metal (especially copper)-exchanged zeolites, perovskites, and noble metals supported on metal oxides such as alumina, silica, and ceria. The main shortcoming of the noble metal reducible oxide (NMRO) catalysts is that they are prone to deactivation by oxygen. It has been reported that catalysts containing tin oxide show oxygen adsorption behavior that may involve hydroxyl groups attached to the tin oxide. This is different than that observed with other noble metal-metal oxide combinations, which have the oxygen adsorbing on the noble metal and subsequently spilling over to the metal oxide. This observation …

This report provides information on groundwater monitoring at the K Basins during October, November, and December 2006. Conditions remained very similar to those reported in the previous quarterly report, with no evidence in monitoring results to suggest groundwater impact from current loss of basin water to the ground. The K Basins monitoring network will be modified in the coming months as a consequence of new wells having been installed near KW Basin as part of a pump-and-treat system for chromium contamination, and new wells installed between the KE Basin and the river to augment long-term monitoring in that area.

Accidental or terrorist releases of hazardous materials into the atmosphere can impact large populations and cause significant loss of life or property damage. Plume predictions have been shown to be extremely valuable in guiding an effective and timely response. The two greatest sources of uncertainty in the prediction of the consequences of hazardous atmospheric releases result from poorly characterized source terms and lack of knowledge about the state of the atmosphere as reflected in the available meteorological data. In this report, we discuss the development of a new event reconstruction methodology that provides probabilistic source term estimates from field measurement data for both accidental and clandestine releases. Accurate plume dispersion prediction requires the following questions to be answered: What was released? When was it released? How much material was released? Where was it released? We have developed a dynamic data-driven event reconstruction capability which couples data and predictive models through Bayesian inference to obtain a solution to this inverse problem. The solution consists of a probability distribution of unknown source term parameters. For consequence assessment, we then use this probability distribution to construct a ''''composite'' forward plume prediction which accounts for the uncertainties in the source term. Since in most …

The Department of Energy has a goal of decontaminating an estimated 180,000 metric tons of metal wastes in various surplus facilities. Uranium (U) and other radioactive actinides and lanthanides are embedded within the mixed oxide structures of the passivity layers of corroded iron and steel. These toxic metals can be dissolved out of the surface layers by a naturally occurring bacterial siderophore called Desferrioxamine B (DFB). DFB is a trihydroxamate ligand with one amine (pK1 =10.89) and three hydroxamate groups (pK2 =9.70, pK3 =9.03, and pK4 =8.30), which chelates with metals through hydroxamate coordination. Complexation of DFB with U can be utilized in decontamination strategy of the passivity layers. Therefore, we have been studying reactions of uranyl U(VI) with zerovalent iron (Fe0) followed by dissolution by DFB. The objectives were to determine the structure and speciation of solution and solid phases of U and to assess the effectiveness of DFB in U dissolution.

Report on the progress achieved in 04-ERD-058. The primary goal of the project was to investigate new methods to provide a comprehensive understanding of how reactions between light nuclei proceed in hot, dense environments, such as stellar interiors. The project sought to develop an entirely new theoretical framework to describe the dynamics of nuclear collisions based on the fundamental nuclear interactions. Based on the new theoretical framework, new computational tools were developed to address specific questions in nuclear structure and reactions. A full study of the true nature of the three-nucleon interaction was undertaken within the formalism of effective field theory. We undertook a preliminary theoretical study of the quantum corrections to electron screening in thermal plasmas to resolve a discrepancy exhibited in previous theoretical approaches.

The goals of the S.H. Strauss laboratory portion of 'Genome-enabled discovery of carbon sequestration genes in poplar' are (1) to explore the functions of candidate genes using Populus transformation by inserting genes provided by Oakridge National Laboratory (ORNL) and the University of Florida (UF) into poplar; (2) to expand the poplar transformation toolkit by developing transformation methods for important genotypes; and (3) to allow induced expression, and efficient gene suppression, in roots and other tissues. As part of the transformation improvement effort, OSU developed transformation protocols for Populus trichocarpa 'Nisqually-1' clone and an early flowering P. alba clone, 6K10. Complete descriptions of the transformation systems were published (Ma et. al. 2004, Meilan et. al 2004). Twenty-one 'Nisqually-1' and 622 6K10 transgenic plants were generated. To identify root predominant promoters, a set of three promoters were tested for their tissue-specific expression patterns in poplar and in Arabidopsis as a model system. A novel gene, ET304, was identified by analyzing a collection of poplar enhancer trap lines generated at OSU (Filichkin et. al 2006a, 2006b). Other promoters include the pGgMT1 root-predominant promoter from Casuarina glauca and the pAtPIN2 promoter from Arabidopsis root specific PIN2 gene. OSU tested two induction systems, alcohol- and …

This environmental impact report (EIR) has been prepared pursuant to the applicable provisions of the California Environmental Quality Act (CEQA) and its implementing guidelines (CEQA Guidelines), and the Amended University of California Procedures for Implementation of the California Environmental Quality Act (UC CEQA Procedures). The University of California (UC or the University) is the lead agency for this EIR, which examines the overall effects of implementation of the proposed 2006 Long Range Development Plan (LRDP; also referred to herein as the 'project' for purposes of CEQA) for Lawrence Berkeley National Laboratory (LBNL; also referred to as 'Berkeley Lab,' 'the Laboratory,' or 'the Lab' in this document). An LRDP is a land use plan that guides overall development of a site. The Lab serves as a special research campus operated by the University employees, but it is owned and financed by the federal government and as such it is distinct from the UC-owned Berkeley Campus. As a campus operated by the University of California, the Laboratory is required to prepare an EIR for an LRDP when one is prepared or updated pursuant to Public Resources Code Section 21080.09. The adoption of an LRDP does not constitute a commitment to, or final …

The ARM sites and the ARM Mobile Facility (AMF) were constructed to make measurements of the atmosphere and radiation system in order to quantify deficiencies in the simulation of clouds within models and to make improvements in those models. While the measurement infrastructure of ARM is well-developed and a model parameterization testbed capability has been established, additional effort is needed to develop statistical techniques which permit the comparison of simulation output from atmospheric models with actual measurements. Our project establishes a new methodology for objectively comparing ARM measurements to the outputs of leading global climate models and reanalysis data. The quantitative basis for this comparison is provided by a statistical procedure which establishes an exhaustive set of mutually-exclusive, recurring states of the atmosphere from sets of multivariate atmospheric and cloud conditions, and then classifies multivariate measurements or simulation outputs into those states. Whether measurements and models classify the atmosphere into the same states at specific locations through time provides an unequivocal comparison result. Times and locations in both geographic and state space of model-measurement agreement and disagreement will suggest directions for the collection of additional measurements at existing sites, provide insight into the global representativeness of the current ARM sites …

The geology and tectonics of the Caucasus region (Armenia, Azerbaijan, and Georgia) are highly variable. Consequently, generating a structural model and characterizing seismic wave propagation in the region require data from local seismic networks. As of eight years ago, there was only one broadband digital station operating in the region – an IRIS station at Garni, Armenia – and few analog stations. The Caucasus Seismic Information Network (CauSIN) project is part of a nulti-national effort to build a knowledge base of seismicity and tectonics in the region. During this project, three major tasks were completed: 1) collection of seismic data, both in event catalogus and phase arrival time picks; 2) development of a 3-D P-wave velocity model of the region obtained through crustal tomography; 3) advances in geological and tectonic models of the region. The first two tasks are interrelated. A large suite of historical and recent seismic data were collected for the Caucasus. These data were mainly analog prior to 2000, and more recently, in Georgia and Azerbaijan, the data are digital. Based on the most reliable data from regional networks, a crustal model was developed using 3-D tomographic inversion. The results of the inversion are presented, and the …