This month's issue has the following 3 articles: (1) Kathy Yelick is the new director for the National Energy Research Scientific Computing Center (NERSC); (2) Head of the Class--A cray XT4 named Franklin passes a rigorous test and becomes an official member of the NERSC supercomputing family; and (3) Model Comparisons--Fusion research group published several recent papers examining the results of two types of turbulence simulations and their impact on tokamak designs.

Time-synchronized measurements provide rich information for estimating a power-system's electromechanical modal properties via advanced signal processing. This information is becoming critical for the improved operational reliability of interconnected grids. A given mode's properties are described by its frequency, damping, and shape. Modal frequencies and damping are useful indicators of power-system stress, usually declining with increased load or reduced grid capacity. Mode shape provides critical information for operational control actions. This project investigated many advanced techniques for power system identification from measured data focusing on mode frequency and damping ratio estimation. Investigators from the three universities coordinated their effort with Pacific Northwest National Laboratory (PNNL). Significant progress was made on developing appropriate techniques for system identification with confidence intervals and testing those techniques on field measured data and through simulation. Experimental data from the western area power system was provided by PNNL and Bonneville Power Administration (BPA) for both ambient conditions and for signal injection tests. Three large-scale tests were conducted for the western area in 2005 and 2006. Measured field PMU (Phasor Measurement Unit) data was provided to the three universities. A 19-machine simulation model was enhanced for testing the system identification algorithms. Extensive simulations were run with this model …

BackgroundIncreasing energy costs and environmental concerns have motivated engineering microbes for the production of ?second generation? biofuels that have better properties than ethanol.Results& ConclusionsSaccharomyces cerevisiae was engineered with an n-butanol biosynthetic pathway, in which isozymes from a number of different organisms (S. cerevisiae, Escherichia coli, Clostridium beijerinckii, and Ralstonia eutropha) were substituted for the Clostridial enzymes and their effect on n-butanol production was compared. By choosing the appropriate isozymes, we were able to improve production of n-butanol ten-fold to 2.5 mg/L. The most productive strains harbored the C. beijerinckii 3-hydroxybutyryl-CoA dehydrogenase, which uses NADH as a co-factor, rather than the R. eutropha isozyme, which uses NADPH, and the acetoacetyl-CoA transferase from S. cerevisiae or E. coli rather than that from R. eutropha. Surprisingly, expression of the genes encoding the butyryl-CoA dehydrogenase from C. beijerinckii (bcd and etfAB) did not improve butanol production significantly as previously reported in E. coli. Using metabolite analysis, we were able to determine which steps in the n-butanol biosynthetic pathway were the most problematic and ripe for future improvement.

Research supported by this grant focuses on molecular scale understanding of central issues related to the structure and dynamics of geochemically important fluids, fluid-mineral interfaces, and confined fluids using computational modeling and experimental methods. Molecular scale knowledge about fluid structure and dynamics, how these are affected by mineral surfaces and molecular-scale (nano-) confinement, and how water molecules and dissolved species interact with surfaces is essential to understanding the fundamental chemistry of a wide range of low-temperature geochemical processes, including sorption and geochemical transport. Our principal efforts are devoted to continued development of relevant computational approaches, application of these approaches to important geochemical questions, relevant NMR and other experimental studies, and application of computational modeling methods to understanding the experimental results. The combination of computational modeling and experimental approaches is proving highly effective in addressing otherwise intractable problems. In 2006-2007 we have significantly advanced in new, highly promising research directions along with completion of on-going projects and final publication of work completed in previous years. New computational directions are focusing on modeling proton exchange reactions in aqueous solutions using ab initio molecular dynamics (AIMD), metadynamics (MTD), and empirical valence bond (EVB) approaches. Proton exchange is critical to understanding the structure, dynamics, …

Proteins of a serine/arginine-rich (SR) family are part of the spliceosome and are implicated in both constitutive and alternative splicing of pre-mRNAs. With the funding from DOE we have been studying alternative of splicing of genes encoding serine/arginine-rich (SR) proteins and the roles of SR proteins that interact with U1-70K in regulating basic and alternative splicing. Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins and its regulation by hormones and stresses: We analyzed the splicing of all 19 Arabidopsis genes in different tissues, during different seedling stages and in response to various hormonal and stress treatments. Remarkably, about 90 different transcripts are produced from 15 SR genes, thereby increasing the transcriptome complexity of SR genes by about five fold. Using the RNA isolated from polysomes we have shown that most of the splice variants are recruited for translation. Alternative splicing of some SR genes is controlled in a developmental and tissue-specific manner (Palusa et al., 2007). Interestingly, among the various hormones and abiotic stresses tested, temperature stress (cold and heat) and ultraviolet light dramatically altered alternative splicing of pre-mRNAs of several SR genes whereas hormones altered the splicing of only two SR genes (Palusa et al., 2007). Localization and dynamics …

Phagocytosis is the central process by which macrophage cellsinternalize and eliminate infectious microbes as well as apoptoticcells. During maturation, phagosomes containing engulfed particlesfuse with various endosomal compartments through theaction of regulatory molecules on the phagosomal membrane. Inthis study, we performed a proteomic analysis of the membranefraction from latex bead-containing (LBC) phagosomes isolatedfrom macrophages. The profile, which comprised 546 proteins,suggests diverse functions of the phagosome and potential connectionsto secretory processes, toll-like receptor signaling, andautophagy. Many identified proteins were not previously knownto reside in the phagosome. We characterized several proteins inLBC phagosomes that change in abundance on induction of autophagy,a process that has been previously implicated in the hostdefense against microbial pathogens. These observations suggestcrosstalk between autophagy and phagocytosis that may be relevantto the innate immune response of macrophages.

The objective of this project is to develop anovel technique for remote, non-destructive, non-radiation-based detection of materials of interest to Nonproliferation Programs. We propse the development of a detection system based on magnetic resonance principles (NAR), which would work where radiation detection is not possible. The approach would be non-intrusive, penetrating, applicable to many materials of interest for Nonproliferation, and be able to identify the nuclear samples under investigation.

Portable, single-sided NMR sensors can operate under conditions inaccessible to conventional NMR while featuring lower cost, portability, and the ability to analyze arbitrary-sized objects. Such sensors can nondestructively probe the interior of samples by collecting images and measuring relaxation and diffusion constants,and, given careful shimming schemes, even perform chemical analysis. The inherently strong magnetic-field gradients of single-sided sensors developed so far has prevented imaging of materials with high water content, such as biological tissues, over large volumes whereas designs with more homogeneous fields suffer from low field strength and typically cannot probe volumes larger than 10 cm3. We present a design with a continuously adjustable sensitive volume, enabling the effective volume to be enlarged several fold. This process allows for imaging in reasonable times of much bigger objects and opens the door to the possibility of clinical imaging with portable sensors. We demonstrate MRI in axial and saggital planes, at different depths of the sensitive volume and T1-weighted contrast in a tissue sample.

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This document presents an As Low As Reasonably Achievable Control Technology (ALARACT) demonstration for evaluating corrosion on the I-beam supporting filter housing No.9 for the 291-A-l emission unit of the Plutonium-Uranium Extraction (PUREX) Facility, located in the 200 East Area of the Hanford Site. The PUREX facility is currently in surveillance and maintenance mode. During a State of Washington, Department of Health (WDOH) 291-A-l emission unit inspection, a small amount of corrosion was observed at the base of a high-efficiency particulate air (HEPA) filter housing. A series of internal and external inspections identified the source of the corrosion material as oxidation of a small section of one of the carbon steel I-beams that provides support to the stainless steel filter housing. The inspections confirmed the corrosion is isolated to one I-beam support location and does not represent any compromise of the structural support or filter housing integrity. Further testing and inspections of the support beam corrosion and its cause were conducted but did not determine the cause. No definitive evidence was found to support any degradation of the housing. Although no degradation of the housing was found, a conservative approach will be implemented. The following actions will be taken: (1) …

Development of advanced hydrogen separation membranes in support of hydrogen production processes such as coal gasification and as front end gas purifiers for fuel cell based system is paramount to the successful implementation of a national hydrogen economy. Current generation metallic hydrogen separation membranes are based on Pd-alloys. Although the technology has proven successful, at issue is the high cost of palladium. Evaluation of non-noble metal based dense metallic separation membranes is currently receiving national and international attention. The focus of the reported work was to develop a scaled reactor with a VNi-Ti alloy membrane to replace a production Pd-alloy tube-type purification/diffuser system.

It is recognized that hydrogen separation membranes are a key component of the emerging hydrogen economy. A potentially exciting material for membrane separations are bulk metallic glass materials due to their low cost, high elastic toughness and resistance to hydrogen 'embrittlement' as compared to crystalline Pd-based membrane systems. However, at elevated temperatures and extended operation times structural changes including partial crystallinity may appear in these amorphous metallic systems. A systematic evaluation of the impact of partial crystallinity/devitrification on the diffusion and solubility behavior in multi-component Metallic Glass materials would provide great insight into the potential of these materials for hydrogen applications. This study will report on the development of time and temperature crystallization mapping and their use for interpretation of 'in-situ' hydrogen permeation at elevated temperatures.

The K East (KE) Basin facilities are located near the north end of the Hanford Site's 100 K area. The facilities were built in 1950 as part of the KE Reactor complex and constructed within 400 meters of the Columbia River, which is the largest river in the Pacific Northwest and by volume the fourth largest river in the United States. The basin, located adjacent to the reactor, was used for the underwater storage of irradiated nuclear fuel discharged from the reactor. The basin was covered by a superstructure comprising steel columns and beams, concrete, and cement asbestos board (CAB) siding. The project's mission was to complete demolition of the structure over the K East basin within six months of tumover from facility deactivation activities. The demolition project team implemented open-air demolition techniques to demolish the facility to slab-on-grade. Several innovative techniques were used to control contamination and maintain contamination control within the confines of the demolition exclusion zone. The techniques, which focused on a defense-in-depth approach, included spraying fixatives on interior and exterior surfaces before demolition began; applying fixatives; misting using a fine spray of water during demolition; and demolishing the facility systematically. Another innovation that aided demolition was …

Fast intermittent transport has been observed in the scrape-off layer (SOL) of major tokamaks including Alcator C-Mod, DIII-D, and NSTX. This kind of transport is not diffusive but rather convective. It strongly increases plasma flux to the chamber walls and enhances the recycling of neutral particles in the main chamber. We discuss anomalous cross-field convection (ACFC) model for impurity and main plasma ions and its relation to intermittent transport events, i.e. plasma density blobs and holes in the SOL. Along with plasma diffusivity coefficients, our transport model introduces time-independent anomalous cross-field convective velocity. In the discharge modelling, diffusivity coefficients and ACFC velocity profiles are adjusted to match a set of representative experimental data. We use this model in the edge plasma physics code UEDGE to simulate the multi-fluid two-dimensional transport for these three tokamaks. We present simulation results suggesting the dominance of anomalous convection in the far SOL transport. These results are consistent with the hypothesis that the chamber wall is an important source of impurities and that different impurity charge states have different directions of anomalous convective velocity.

This ICN corrects a typing error that was identified for one of the wells listed in Tables 4.1 and 4.2 on page 4.3 of the original document.

We present the longitudinal coherence measurement of the transient inversion collisional x-ray laser for the first time. The Ni-like Pd x-ray laser at 14.68 nm is generated by the LLNL COMET laser facility and is operating in the gain-saturated regime. Interference fringes are produced using a Michelson interferometer setup in which a thin multilayer-coated membrane is used as a beam splitter. The longitudinal coherence length for the picosecond duration 4d{sup 1}S{sub 0} {yields} 4p{sup 1}P{sub 1} lasing transition is determined to be {approx}400 {micro}m (1/e HW) by adjusting the length of one interferometer arm and measuring the resultant variation in fringe visibility. This is four times improved coherence than previous measurements on quasi-steady state schemes largely as a result of the narrower line profile in the lower temperature plasma. The inferred gain-narrowed linewidth of {approx}0.29 pm is also substantially narrower than previous measurements on quasi-steady state x-ray laser schemes. This study shows that the coherence of the x-ray laser beam can be improved by changing the laser pumping conditions. The x-ray laser is operating at 4 - 5 times the transform-limited pulse.

Redd counts are routinely used to document the spawning distribution of fall Chinook salmon (Oncorhynchus tshawytscha) in the Snake River basin upriver of Lower Granite Dam. The first reported redd counts were from aerial searches conducted intermittently between 1959 and 1978 (Irving and Bjornn 1981, Witty 1988; Groves and Chandler 1996)(Appendix 1). In 1986, the Washington Department of Fish and Wildlife began an annual monitoring program that, in addition to the Snake River, included aerial searches of the Grande Ronde River the first year (Seidel and Bugert 1987), and the Imnaha River in subsequent years (Seidel et al. 1988; Bugert et al. 1989-1991; Mendel et al. 1992). The U. S. Fish and Wildlife Service and Idaho Power Company began contributing to this effort in 1991 by increasing the number of aerial searches conducted each year and adding underwater searches in areas of the Snake River that were too deep to be searched from the air (Connor et al. 1993; Garcia et al. 1994a, 1994b, 1996-2007; Groves 1993; Groves and Chandler 1996). The Nez Perce Tribe added aerial searches in the Clearwater River basin beginning in 1988 (Arnsberg et. al 1992), and the Salmon River beginning in 1992. Currently searches are …

Compilation of Advanced Light Source newsletter, ALSNews, for 2009, Volumes 294-304.

A request for studying the spectral performance of in-vacuum undulators (IVUs) for the APS storage ring was recently put forward. In-vacuum undulators are prevalent at other synchrotron radiation facilities such as the ESRF and the Spring-8. However, they never made it into the arsenal of undulators at the APS because the brilliance tuning curves were sufficiently wide due to the fact that the undulator minimum gap could be set as low as 10.5 mm. For sector 3, which in the past used a narrow-gap vacuum chamber, the minimum undulator pole gap was allowed to be set as low as 8.5 mm, providing contiguous tuning curves between the first and third harmonic radiation for a 2.7-cm-period device. (Subsequently, the narrow-gap vacuum chamber was removed and replaced with a standard vacuum chamber, which allows a minimum gap of 10.5 mm.) For sector 4, which currently holds the only narrow-gap vacuum chamber at the APS, the minimum gap is 9.5 mm. In this sector, a permanent magnet hybrid undulator with SmCo magnets is used instead of NdFeB magnets because of their higher radiation resistance and their better protection against radiation-induced demagnetization of the magnets. In the realm of looking to the future, new …

The January-July runoff volume above the Dalles Dam in 2007 was 89% of the average runoff volume for the 1971-2000 historical record. The April-July runoff volume at Lower Granite Dam was 68% of the 1971-2000 historical record. Over the 79 year historical record from 1929 through 2007, the 2007 January-July runoff volume at the Dalles was the 50th lowest year out of the 79th year record. The January through July runoff volume at Lower Granite was the 65th lowest runoff year out of 79 on record. This year can be characterized by steadily decreasing snowpack which was below average in the Columbia Basin by the end of April. The combination of runoff volume, decreasing snowpack and reservoir operations resulted in spring migration flows at McNary Dam averaging 239 Kcfs, slightly above the Biological Opinion flow objective of 237 Kcfs. However the spring period migration flows in the Snake River averaged 61 Kcfs at Lower Granite Dam, substantially below the Biological Opinion flow objective of 85 Kcfs. Summer migration period Biological Opinion flow objectives averaged 163 Kcfs at McNary Dam, substantially below the summer flow objective of 200 Kcfs. Summer migration period flows in the Snake River at Lower Granite Dam …

The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With a view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.

A method is developed to monitor the rate of loss of air from aphrons at elevated pressures. This technique is used to study the effects of pressure, fluid composition and rates of pressurization and depressurization on the kinetics of air loss from aphrons in APHRON ICS{trademark} drilling fluids.

We report a two-step growth method to obtain uniformly coalesced epitaxial lateral overgrown a-plane GaN by metal-organic chemical vapor deposition (MOCVD). By obtaining a large wing height to width aspect ratio in the first step followed by enhanced lateral growth in the second step via controlling the growth temperature, we reduced the tilt angle between the advancing Ga-polar and N-polar wings for improved properties. Transmission electron microscopy (TEM) showed that the threading dislocation density in the wing area was 1.0 x 10{sup 8}cm{sup -2}, more than two orders of magnitude lower than that in the window area (4.2 x 10{sup 10} cm{sup -2}). However, a high density of basal stacking faults, 1.2 x 10{sup 4} cm{sup -1}, was still observed in the wing area. Near field scanning optical microscopy (NSOM) at room temperature revealed that the luminescence was mainly from the wing regions with very little contribution from the windows and meeting fronts. These observations suggest that due to significant reduction of threading dislocations radiative recombination is enhanced in the wings.

Density increases in caustic-side solvent extraction (CSSX) solvent have been observed in separate experimental programs performed by different groups of researchers. Such changes indicate a change in chemical composition. Increased density adversely affects separation of solvent from denser aqueous solutions present in the CSSX process. Identification and control of factors affecting solvent density are essential for design and operation of the centrifugal contactors. The goals of this research were to identify the factors affecting solvent density (composition) and to develop correlations between easily measured solvent properties (density and viscosity) and the chemical composition of the solvent, which will permit real-time determination and adjustment of the solvent composition. In evaporation experiments, virgin solvent was subjected to evaporation under quiescent conditions at 25, 35, and 45 C with continuously flowing dry air passing over the surface of the solvent. Density and viscosity were measured periodically, and chemical analysis was performed on the solvent samples. Chemical interaction tests were completed to determine if any chemical reaction takes place over extended contact time that changes the composition and/or physical properties. Solvent and simulant, solvent and strip solution, and solvent and wash solution were contacted continuously in agitated flasks. They were periodically sampled and the …