Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs …

This report is part of a series of reports on building energy efficiency codes in countries associated with the Asian Pacific Partnership (APP) - Australia, South Korea, Japan, China, India, and the United States of America (U.S.). This reports gives an overview of the development of building energy codes in Korea, including national energy policies related to building energy codes, history of building energy codes, recent national projects and activities to promote building energy codes. The report also provides a review of current building energy codes (such as building envelope, HVAC, and lighting) for commercial buildings in Korea.

As the Seneca Nation of Indians (SNI) continues to refine and finalize its Strategic Energy Plan, it became necessary to insure that a sustainable organization structure was developed through which the energy program and its initiatives could be nurtured and managed. To that end, SNI undertook a study to thoroughly evaluate the existing organizational structures and assess the requisite changes and/or additions to that framework that would complement the mission of the Strategic Plan. The goal of this study was to analyze, work with staff and leadership and recommend the most effective plan for the development of an organizational framework within which the Seneca could more effectively exercise energy sovereignty – control and manage their natural resource assets – i.e. develop its own energy resources, meet the current and projected energy needs of their community, and “sit at the table” with other regional energy providers to deal with issues on a peer-to-peer basis.

Ionization cooling requires low-Z energy absorbers immersed in a strong magnetic field and high-gradient, large-aperture RF cavities to be able to cool a muon beam as quickly as the short muon lifetime requires. RF cavities that operate in vacuum are vulnerable to dark-current- generated breakdown, which is exacerbated by strong magnetic fields, and they require extra safety windows that degrade cooling, to separate RF regions from hydrogen energy absorbers. RF cavities pressurized with dense hydrogen gas will be developed that use the same gas volume to provide the energy absorber and the RF acceleration needed for ionization cooling. The breakdown suppression by the dense gas will allow the cavities to operate in strong magnetic fields. Measurements of the operation of such a cavity will be made as functions of external magnetic field and charged particle beam intensity and compared with models to understand the characteristics of this technology and to develop mitigating strategies if necessary.

Multilateral mechanisms for the fuel cycle are seen as a potentially important way to create an industrial infrastructure that will support a renaissance and at the same time not contribute to the risk of nuclear proliferation. In this way, international nuclear fuel cycle centers for enrichment can help to provide an assurance of supply of nuclear fuel that will reduce the likelihood that individual states will pursue this sensitive technology, which can be used to produce nuclear material directly usable nuclear weapons. Multinational participation in such mechanisms can also potentially promote transparency, build confidence, and make the implementation of IAEA safeguards more effective or more efficient. At the same time, it is important to ensure that there is no dissemination of sensitive technology. The Russian Federation has taken a lead role in this area by establishing an International Uranium Enrichment Center (IUEC) for the provision of enrichment services at its uranium enrichment plant located at the Angarsk Electrolysis Chemical Complex (AECC). This paper describes how the IUEe is organized, who its members are, and the steps that it has taken both to provide an assured supply of nuclear fuel and to ensure protection of sensitive technology. It also describes the …

We have directly observed motion of inorganic nanoparticles during fluid evaporation using a Transmission Electron Microscope. Tracking real-time diffusion of both spherical (5-15 nm) and rod-shaped (5x10 nm) gold nanocrystals in a thin-film of water-15percentglycerol reveals complex movements, such as rolling motions coupled to large-step movements and macroscopic violations of the Stokes-Einstein relation for diffusion. As drying patches form during the final stages of evaporation, particle motion is dominated by the nearby retracting liquid front.

The goal of this project has been to develop a lossless compression algorithm for message-passing libraries that can accelerate HPC systems by reducing the communication time. Because both compression and decompression have to be performed in software in real time, the algorithm has to be extremely fast while still delivering a good compression ratio. During the first half of this project, they designed a new compression algorithm called FPC for scientific double-precision data, made the source code available on the web, and published two papers describing its operation, the first in the proceedings of the Data Compression Conference and the second in the IEEE Transactions on Computers. At comparable average compression ratios, this algorithm compresses and decompresses 10 to 100 times faster than BZIP2, DFCM, FSD, GZIP, and PLMI on the three architectures tested. With prediction tables that fit into the CPU's L1 data acache, FPC delivers a guaranteed throughput of six gigabits per second on a 1.6 GHz Itanium 2 system. The C source code and documentation of FPC are posted on-line and have already been downloaded hundreds of times. To evaluate FPC, they gathered 13 real-world scientific datasets from around the globe, including satellite data, crash-simulation data, and …

The Heavy-Ion Fusion Sciences Virtual National Laboratory is pursuing an approach to target heating experiments in the warm dense matter regime, using space-charge-dominated ion beams that are simultaneously longitudinally bunched and transversely focused. Longitudinal beam compression by large factors has been demonstrated in the Neutralized Drift Compression Experiment (NDCX) with controlled ramps and forced neutralization. Using an injected 30 mA K{sup +} ion beam with initial kinetic energy 0.3 MeV, axial compression leading to {approx}50X current amplification and simultaneous radial focusing to a few mm have led to encouraging energy deposition approaching the intensities required for eV-range target heating experiments. We discuss the status of several improvements to NDCX to reach the necessary higher beam intensities, including: beam diagnostics, greater axial compression via a longer velocity ramp; and plasma injection improvements to establish a plasma density always greater than the beam density, expected to be > 10{sup 13} cm{sup -3}.

SUBMITTED AS A DOCTORAL DISSERTATION IN COMPLETION OF REQUIREMENTS FOR THE DEGREE OF ED.D THROUGH WASHINGTON STATE UNIVERSITY. The overall purpose of this action research study was to explore the experiences of ten middle school science teachers involved in a three-year partnership program between scientists and teachers at a Department of Energy national laboratory, including the impact of the program on their professional development, and to improve the partnership program by developing a set of recommendations based on the study’s findings. This action research study relied on qualitative data including field notes recorded at the summer academies and data from two focus groups with teachers and scientists. Additionally, the participating teachers submitted written reflections in science notebooks, participated in open-ended telephone interviews that were transcribed verbatim, and wrote journal summaries to the Department of Energy at the end of the summer academy. The analysis of the data, collaboratively examined by the teachers, the scientists, and the science education specialist acting as co-researchers on the project, revealed five elements critical to the success of the professional development of science teachers. First, scientist-teacher partnerships are a unique contribution to the professional development of teachers of science that is not replicated in other …

We present a search for the decay B{sup +} {yields} {ell}{sup +} {nu}{sub {ell}} ({ell} = {tau}, {mu}, or e) in (458.9 {+-} 5.1) x 10{sup 6} {Upsilon}(4S) decays recorded with the BABAR detector at the SLAC PEP-IIB-Factory. A sample of events with one reconstructed exclusive semi-leptonic B decay (B{sup -} {yields} D{sup 0} {ell}{sup -}{bar {nu}}X) is selected, and in the recoil a search for B{sup +} {yields} {ell}{sup +}{nu}{sub {ell}} signal is performed. The {tau} is identified in the following channels: {tau}{sup +} {yields} e{sup +}{nu}{sub e}{nu}{sub {tau}}, {tau}{sup +} {yields} {mu}{sup +}{nu}{sub {mu}}{nu}{sub {tau}}, {tau}{sup +} {yields} {pi}{sup +}{nu}{sub {tau}}, and {tau}{sup +} {yields} {pi}{sup +}{pi}{sup 0}{nu}{sub {tau}}. The analysis strategy and the statistical procedure is set up for branching fraction extraction or upper limit determination. We determine from the dataset a preliminary measurement of {Beta}(B{sup +} {yields} {tau}{sup +}{nu}{sub {tau}}) = (1.8 {+-} 0.8 {+-} 0.1) x 10{sup -4}, which excludes zero at 2.4{sigma}, and f{sub B} = 230 {+-} 57 MeV. Combination with the hadronically tagged measurement yields {Beta}(B{sup +} {yields} e{sup +}{nu}{sub e}) = (1.8 {+-} 0.6) x 10{sup -4}. We also set preliminary limits on the branching fractions at {Beta}(B{sup +} {yields} e{sup …

An evaluation of the statistical significance of Rh, Ru, and Hg on DWPF Sludge Receipt and Adjustment Tank (SRAT) cycle catalytic hydrogen generation and process chemistry was conducted by the Savannah River National Laboratory (SRNL) using a full-factorial experimental design. This test design can identify significant interactions between these three species in addition to individual effects. Statistical modeling of data from the Rh-Ru-Hg matrix study has been completed. Preliminary data and conclusions were given in an earlier report. This final report concludes the work on the Rh-Ru-Hg matrix study. Modeling results are summarized below. Rhodium was found to: Promote increased total hydrogen mass; Promote an increase in the maximum hydrogen generation rate; Promote an increase in the hydrogen generation rate shortly after acid addition; Shorten the elapsed time between acid addition and the maximum hydrogen generation rate; Increase formate loss; Inhibit NO{sub 2} and total NO{sub x} off-gas species formation; and Reduce nitrite-to-nitrate conversion. Ruthenium was found to: Promote increased total hydrogen mass; Promote an increase in the maximum hydrogen generation rate; Promote an increase in the hydrogen generation rate in the second half of the SRAT cycle; Promote an increase in total CO{sub 2} generated; Increase formate loss; Promote …

The U.S. Department of Energy’s (DOE) commitment to assuring the health and safety of its workers includes the conduct of illness and injury surveillance activities that provide an early warning system to detect health problems among workers. The Illness and Injury Surveillance Program monitors illnesses and health conditions that result in an absence, occupational injuries and illnesses, and disabilities and deaths among current workers.

The objective of this study was to determine if it was feasible to collect information regarding energy use and hot water delivery from tankless gas water heaters using the sensors and controls built into the water heaters. This could then be used to determine the water heater efficiency ? the ratio of energy out (hot water delivered) to energy in (energy in the gas) in actual residential installations. The goal was to be as unobtrusive as possible, and to avoid invalidating warranties or exposing researchers to liability issues. If feasible this approach would reduce the costs of instrumentation.This paper describes the limited field and laboratory investigations to determine if using the sensors and controls built into tankless water heaters is feasible for field monitoring.It was more complicated to use the existing gas flow, water and temperature sensors than was anticipated. To get the signals from the existing sensors and controls is difficult and may involve making changes that would invalidate manufacturer warrantees. The procedures and methods for using signals from the existing gas valves, water flow meters and temperature sensors will vary by model. To be able to monitor different models and brands would require detailed information about each model …

Large-scale carbon capture and sequestration (CCS) projects involving annual injections of millions of tons of CO2 are a key infrastructural element needed to substantially reduce greenhouse gas emissions. The large rate and volume of injection will induce pressure and stress gradients within the formation that could activate existing fractures and faults, or drive new fractures through the caprock. We will present results of an ongoing investigation to identify conditions that will activate existing fractures/faults or make new fractures within the caprock using the Livermore Distinct Element Code (LDEC). LDEC is a multiphysics code, developed at LLNL, capable of simulating dynamic fracture of rock masses under a range of conditions. As part of a recent project, LDEC has been extended to consider fault activation and dynamic fracture of rock masses due to pressurization of the pore-space. We will present several demonstrations of LDEC functionality and an application of LDEC to a CO2 injection scenario. We present results from our investigations of Teapot Dome using LDEC to study the potential for fault activation during injection. Using this approach, we built finite element models of the rock masses surrounding bounding faults and explicitly simulated the compression and shear on the fault interface. A …

The 100-F-54 waste site, part of the 100-FR-2 Operable Unit, is the soil associated with the former pastures for holding domestic farm animals used in experimental toxicology studies. Evaluation of historical information resulted in identification of the experimental animal farm pastures as having potential residual soil contamination due to excrement from experimental animals. The 100-F-54 animal farm pastures confirmatory sampling results support a reclassification of this site to No Action. The current site conditions achieve the remedial action objectives and the corresponding remedial action goals established in the Remaining Sites ROD. The results of confirmatory sampling show that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River.

Magnetic susceptibility measurements and X-ray data confirm that tert-butyl substituted manganocenes [(Me{sub 3}C){sub n}C{sub 5}H{sub 5-n}]{sub 2}Mn (n= 1, 2) follow the trend previously observed with the methylated manganocenes, i.e., electron donating groups attached to the Cp ring stabilize the low-spin (LS) electronic ground state relative to Cp{sub 2}Mn and exhibit higher spin-crossover (SCO) temperatures. However, introducing three CMe3 groups on each ring gives a temperature invariant high-spin (HS) state manganocene. The origin of the high-spin state in [1,2,4-(Me{sub 3}C){sub 3}C{sub 5}H{sub 2}]{sub 2}Mn is due to the significant bulk of the [1,2,4-(Me{sub 3}C){sub 3}C{sub 5}H{sub 2}]{sup -} ligand, which is sufficient to generate severe inter-ring steric strain that prevents the realization of the low-spin state. Interestingly, the spin transition in [1,3-(Me{sub 3}C){sub 2}C{sub 5}H{sub 3}]{sub 2}Mn is accompanied by a phase transition resulting in a significant irreversible hysteresis ({Delta}T{sub c} = 16 K). This structural transition was also observed by extended X-ray absorption fine-structure (EXAFS) measurements. Magnetic susceptibility studies and X-ray diffraction data on SiMe{sub 3} substituted manganocenes [(Me{sub 3}Si){sub n}C{sub 5}H{sub 5-n}]{sub 2}Mn (n= 1, 2, 3) show high-spin configuration in these cases. Although tetra- and hexasubstituted manganocenes are high-spin at all accessible temperatures, the disubstituted manganocenes exhibit …

A verification test suite has been assessed with primary focus on low reynolds number flow of liquid metals. This is representative of the interface between the armature and rail in gun applications. The computational multiphysics framework, ALE3D, is used. The main objective of the current study is to provide guidance and gain confidence in the results obtained with ALE3D. A verification test suite based on 2-D cases is proposed and includes the lid-driven cavity and the Couette flow are investigated. The hydro and thermal fields are assumed to be steady and laminar in nature. Results are compared with analytical solutions and previously published data. Mesh resolution studies are performed along with various models for the equation of state.

We propose a new Monte Carlo method to study extended X-ray sources with the European Photon Imaging Camera (EPIC) aboard XMM Newton. The Smoothed Particle Inference (SPI) technique, described in a companion paper, is applied here to the EPIC data for the clusters of galaxies Abell 1689, Centaurus and RXJ 0658-55 (the ''bullet cluster''). We aim to show the advantages of this method of simultaneous spectral-spatial modeling over traditional X-ray spectral analysis. In Abell 1689 we confirm our earlier findings about structure in temperature distribution and produce a high resolution temperature map. We also confirm our findings about velocity structure within the gas. In the bullet cluster, RXJ 0658-55, we produce the highest resolution temperature map ever to be published of this cluster allowing us to trace what looks like the motion of the bullet in the cluster. We even detect a south to north temperature gradient within the bullet itself. In the Centaurus cluster we detect, by dividing up the luminosity of the cluster in bands of gas temperatures, a striking feature to the north-east of the cluster core. We hypothesize that this feature is caused by a subcluster left over from a substantial merger that slightly displaced the …

The objective of this work is to investigate the thick diffusion limit of various spatial discretizations of the one-dimensional, steady-state, monoenergetic, discrete ordinates neutron transport equation. This work specifically addresses the two lowest order nodal methods, AHOT-N0 and AHOT-N1, as well as reconsiders the asymptotic limit of the Diamond Difference method. The asymptotic analyses of the AHOT-N0 and AHOT-N1 nodal methods show that AHOT-N0 does not possess the thick diffusion limit for cell edge or cell average fluxes except under very limiting conditions, which is to be expected considering the AHOT-N0 method limits to the Step method in the thick diffusion limit. The AHOT-N1 method, which uses a linear in-cell representation of the flux, was shown to possess the thick diffusion limit for both cell average and cell edge fluxes. The thick diffusion limit of the DD method, including the boundary conditions, was derived entirely in terms of cell average scalar fluxes. It was shown that, for vacuum boundaries, only when {sigma}{sub t}, h, and Q are constant and {sigma}{sub a} = 0 is the asymptotic limit of the DD method close to the finite-differenced diffusion equation in the system interior, and that the boundary conditions between the systems will …

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Modern single molecule fluorescence microscopy offers new, highly quantitative ways of studying the systems biology of cells while keeping the cells healthy and alive in their natural environment. In this context, a quantum optical technique, photon antibunching, has found a small niche in the continuously growing applications of single molecule techniques to small molecular complexes. Here, we review some of the most recent applications of photon antibunching in biophotonics, and we provide a guide for how to conduct photon antibunching experiments at the single molecule level by applying techniques borrowed from time-correlated single photon counting. We provide a number of new examples for applications of photon antibunching to the study of multichromophoric molecules and small molecular complexes.

In a novel approach in observational high-energy gamma-ray astronomy, observations carried out by imaging atmospheric Cherenkov telescopes provide necessary templates to pinpoint the nature of intriguing, yet unidentified EGRET gamma-ray sources. Using GeV-photons detected by CGRO EGRET and taking advantage of high spatial resolution images from H.E.S.S. observations, we were able to shed new light on the EGRET observed gamma-ray emission in the Kookaburra complex, whose previous coverage in the literature is some-what contradictory. 3EGJ1420-6038 very likely accounts for two GeV gamma-ray sources (E>1 GeV), both in positional coincidence with the recently reported pulsar wind nebulae (PWN) by HESS in the Kookaburra/Rabbit complex. PWN associations at VHE energies, supported by accumulating evidence from observations in the radio and X-ray band, are indicative for the PSR/plerionic origin of spatially coincident, but still unidentified Galactic gamma-ray sources from EGRET. This not only supports the already suggested connection between variable, but unidentified low-latitude gamma-ray sources with pulsar wind nebulae (3EGJ1420-6038 has been suggested as PWN candidate previously), it also documents the ability of resolving apparently confused EGRET sources by connecting the GeV emission as measured from a large-aperture space-based gamma-ray instrument with narrow field-of-view but superior spatial resolution observations by ground-based atmospheric Cherenkov …

This project consisted primarily of conducting energy efficiency, productivity improvement, and waste reduction assessments of small- and medium-sized industrial facilities. These assessments were carried out by groups of engineering students, mostly from Mechanical & Aerospace Engineering and Industrial Engineering, led by faculty members at Arizona State University. The assessed industries were generally energy-intensive manufacturers located throughout Arizona, as well as some facilities in the Las Vegas, Nevada area. During the first four years of the project period, on average our recommended annual savings per plant were $224,717, of which $71,135 were energy savings. Of these recommended savings, on average $49,659 were implemented, of which $31,679 were implemented annual energy savings. These implemented savings greatly exceeded our budgeted cost to DOE, which was approximately $8,000/assessment. In addition, a number of undergraduate and graduate students were employed and trained at the IAC, and have gone on to graduate studies and engineering careers.

The UM Industrial Assessment Center assisted 119 primary metals, automotive parts, metal casting, chemicals, forest products, agricultural, and glass manufacturers in Michigan, Ohio and Indiana to become more productive and profitable by identifying and recommending specific measures to improve energy efficiency, reduce waste and increase productivity. This directly benefits the environment by saving a total of 309,194 MMBtu of energy resulting in reduction of 0.004 metric tons of carbon emissions. The $4,618,740 implemented cost savings generated also saves jobs that are evaporating from the manufacturing industries in the US. Most importantly, the UM Industrial Assessment Center provided extremely valuable energy education to forty one UM graduate and undergraduate students. The practical experience complements their classroom education. This also has a large multiplier effect because the students take the knowledge and training with them.