Instrumentation was developed in 2004 and 2005 to measurethe quantum efficiency of the Lawrence Berkeley National Lab(LBNL)total-depletion CCD's, intended for astronomy and spaceapplications. This paper describes the basic instrument. Although it isconventional even to the parts list, there are important innovations. Axenon arc light source was chosen for its high blue/UV and low red/IRoutput as compared with a tungsten light. Intensity stabilization hasbeen difficult, but sinceonly flux ratios matter this is not critical.Between the light source andan Oriel MS257 monochromator are a shutterand two filter wheels. High-bandpass and low-bandpass filter pairsisolate the 150-nm wide bands appropriate to the wavelength, thusminimizing scattered light and providing order blocking. Light from theauxiliary port enters a 20-inch optical sphere, and the 4-inch outputport is at right angles to the input port. An 80 cm drift space producesnear-uniform illumination on the CCD. Next to the cold CCD inside thehorizontal dewar is a calibrated reference photodiode which is regulatedto the PD calibration temperature, 25$^\circ$ C. The ratio ofthe CCD andin-dewar reference PD signals provides the QE measurement. Additionalcross-calibration to a PD on the integrating spherepermitslower-intensity exposures.

Atomic-nuclear coupling experiments are described, with an emphasis on recent experiments aimed at demonstrating the NEET mechanism in atomic nuclei. Upper limits for x-ray induced decay of the Hf-178 31-y isomer reported by Ahmad and his colleagues are presented, and these upper limits are contrasted with the positive reports of Collins and coworkers.

We report the first detection of radio emission from any anomalous X-ray pulsar (AXP). Data from the Very Large Array (VLA) MAGPIS survey with angular resolution 6'' reveals a point-source of flux density 4.5 {+-} 0.5 mJy at 1.4 GHz at the precise location of the 5.54 s pulsar XTE J1810-197. This is greater than upper limits from all other AXPs and from quiescent states of soft gamma-ray repeaters (SGRs). The detection was made in 2004 January, 1 year after the discovery of XTE J1810-197 during its only known outburst. Additional VLA observations both before and after the outburst yield only upper limits that are comparable to or larger than the single detection, neither supporting nor ruling out a decaying radio afterglow related to the X-ray turn-on. Another hypothesis is that, unlike the other AXPs and SGRs, XTE J1810-197 may power a radio synchrotron nebula by the interaction of its particle wind with a moderately dense environment that was not evacuated by previous activity from this least luminous, in X-rays, of the known magnetars.

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There are a number of binaries, fairly wide and with one or even two evolved giant components, that do not agree very well with conventional stellar evolution: the secondaries are substantially larger (oversized) than they should be because their masses are quite low compared with the primaries. I discuss the possibility that these binaries are former triples, in which a merger has occurred fairly recently in a short-period binary sub-component. Some mergers are expected, and may follow a phase of contact evolution. I suggest that in contact there is substantial transfer of luminosity between the components due to differential rotation, of the character observed by helioseismology in the Sun's surface convection zone.

Liquid and solid radioactive wastes are formed during conversion of plutonium metal to oxide and during fabrication of weapons-grade plutonium into mixed-oxide (MOX) fuel. In Russia, these wastes are to be processed for disposition by immobilization in either borosilicate glass or cement matrices depending upon the waste stream-specific radionuclide contents. Vitrification is planned for the liquid high-level waste raffinate stream containing the bulk of the Am-241 produced from Pu-241 decay. Previous work on the Russian MOX Fuel Fabrication Facility (R-MFFF) by the Public Joint Stock Corporation (TVEL) [1] showed that this waste stream may contain significant amounts of silver derived from the electrochemical dissolution of PuO2 using a Ag(II) catalyst. The work reported here further investigated silver solubility limits, which, if exceeded in a production glass melter, allow discrete silver grains to form in the glass and also deposit over time on the bottom of a joule-heated ceramic melter. In melters with immersed electrodes, such as the Russian EP-100 for phosphate glasses or the US Duratek DP-100 type melters for borosilicate glasses that are being considered for use at the Siberian Chemical Combine (SCC) Tomsk site, the undissolved silver could cause a short circuit and an unacceptable production melter failure. …

The damage test procedure for qualifying a coating run of anti-reflection coated optics consists of scanning a pulsed 1064 nm laser over a 1 cm x 1 cm area on a test sample to illuminate approximately 2400 sites. Scans are repeated at 3 J/cm{sup 2} increments until the fluence specification for the optic is reached. In the past, initiation of 1 or more damage sites was classified as a failed coating run, requiring the production optics in the corresponding coating lot be reworked and recoated. Recent laser damage growth tests of 300 repetitive pulses performed on numerous damage sites revealed that all were stable up to 20 J/cm{sup 2}. Therefore the acceptance criteria has been modified to allow a moderate number of damage sites, as long as they are smaller than the allowed dig size and are stable (do not grow). Consequently many coating runs that previously would have been rejected are now accepted, resulting in higher yield, lower cost, and improved delivery schedule. The new test also provides assurance that initiated damage sites are stable during long term operation.

Models incorporating interactions between surface and subsurface flow are commonly based on the conductance concept that presumes a distinct interface at the land surface, separating the surface from the subsurface domain. In these models the subsurface and surface domains are linked via an exchange flux that depends upon the magnitude and direction of the hydraulic gradient across the interface and a proportionality constant (a measure of the hydraulic connectivity). Because experimental evidence of such a distinct interface is often lacking in the field, a more general coupled modeling approach would be preferable. We present a more general approach that incorporates a two-dimensional overland flow simulator into the parallel three-dimensional variably saturated subsurface flow code ParFlow developed at LLNL. This overland flow simulator takes the form of an upper, free-surface boundary condition and is, thus, fully integrated without relying on the conductance concept. Another advantage of this approach is the efficient parallelism of ParFlow, which is exploited by the overland flow simulator. Several verification and simulation examples are presented that focus on the two main processes of runoff production: excess infiltration and saturation. The usefulness of our approach is demonstrated in an application of the model to an urban watershed. The …

A methodology has been developed based on the Kozeny-Carman equation to predict frictional pressure drops during water permeation of packed columns containing essentially noncompressible, but highly irregular particles. The resulting model accurately predicts pressure drop as a function of liquid flow rate and resin particle size for this system. A total of five particle sieve cuts across the range -20 to +70 mesh were utilized for testing using deionized water as the mobile phase. The Rosin-Rammler equation was used to fit the raw particle size data (wet sieve analysis) for the as-received resin sample and generate a continuous cumulative distribution function based on weight percent passing through the sieve. Probability distribution functions were calculated from the cumulative distribution for each particle sieve cut tested. Nine particle diameter definitions (i.e., number mean, volume mean, etc.) were then selected from the distribution function for each sample to represent the average spherically-equivalent particle diameter as input to the Kozeny-Carman equation. Nonlinear least squares optimization of the normalized pressure drop residuals were performed by parameter estimation of particle shape factor and bed porosity for all samples simultaneously using a given average particle diameter definition. Good fits to the full experimental data set were obtained …

Solid-state infrared spectroscopy, differential scanning calorimetry, and elemental analysis have been used to evaluate the reactivity of resorcinol formaldehyde resin with nitric acid and characterize the solid product. Two distinct reactions were identified within the temperature range 25-55 C. The first reaction is primarily associated with resin nitration, while the second involves bulk oxidation and degradation of the polymer network leading to dissolution and off-gassing. The threshold conditions promoting reaction have been identified. Reaction was confirmed with nitric acid concentrations as low as 3 M at 25 C applied temperature and 0.625 M at 66 C. Although a nitrated resin product can be isolated under appropriate experimental conditions, calorimetry testing indicates no significant hazard associated with handling the dry material.

A sensitivity analysis of the remote detection NMR techniqueis presented. With remote detection, information about a sample isencoded onto a mobile sensor fluid, which facilitates a spatialseparation of encoding and detection of spin magnetization. This approachcan be interpreted as a two-dimensional NMR experiment, therefore thesame general formalism can be used for a sensitivity analysis. Eventhough remote detection is a point-by-point experiment, the sensitivitydoes not scale unfavorably with the number of detected points compared totransient detection. It is proportional to the relative sensitivitybetween the remote detector and the circuit that is used for encoding.The influence of the different signal decay times is analyzed, and thedistinction between spectroscopy and imaging experiments ismade.

In the United States, markets for renewable generation--especially wind power--have grown substantially in recent years. This growth is typically attributed to technology improvements and resulting cost reductions, the availability of federal tax incentives, and aggressive state policy efforts. But another less widely recognized driver of new renewable generation is poised to play a major role in the coming years: utility integrated resource planning (IRP). Common in the late-1980s to mid-1990s, but relegated to lesser importance as many states took steps to restructure their electricity markets in the late-1990s, IRP has re-emerged in recent years as an important tool for utilities and regulators, particularly in regions such as the western United States, where retail competition has failed to take root. As practiced in the United States, IRP is a formal process by which utilities analyze the costs, benefits, and risks of all resources available to them--both supply- and demand-side--with the ultimate goal of identifying a portfolio of resources that meets their future needs at lowest cost and/or risk. Though the content of any specific utility IRP is unique, all are built on a common basic framework: (1) development of peak demand and load forecasts; (2) assessment of how these forecasts compare …

Phase transformations in 2xxx series aluminium alloys (Al-Cu-Mg) are investigated with an off-lattice atomistic kinetic Monte Carlo simulation incorporating the effects of strain around misfitting atoms and vacancies. Vacancy diffusion is modeled by comparing the energies of trial states, where the system is partially relaxed for each trial state. Only a limited precision is required for the energy of each trial state, determined by the value of k{sub B}T. Since the change in the relaxation displacement field caused by a vacancy hop decays as 1/r{sup 3}, it is sufficient to determine the next move by relaxing only those atoms in a sphere of finite radius centered on the moving vacancy. However, once the next move has been selected, the entire system is relaxed. Simulations of the early stages of phase separation in Al-Cu with elastic relaxation show an enhanced rate of clustering compared to those performed on the same system with a rigid lattice. However on a flexible lattice vacancy trapping by Mg atoms in the ternary Al-Cu-Mg system makes clustering slower than the corresponding rigid lattice calculation.

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Energy loss due to wakefields within a long undulator, if not compensated by an appropriate tapering of the magnetic field strength, can degrade the FEL process by detuning the resonant FEL frequency. The wakefields arise from the vacuum chamber wall resistivity, its surface roughness, and abrupt changes in its aperture. For LCLS parameters, the resistive-wall component is the most critical and depends upon the chamber material (e.g., Cu) and its radius. Of recent interest[1] is the so-called ''AC'' component of the resistive-wall wake which can lead to strong variations on very short timescales (e.g., {approx} 20 0fs). To study the expected performance of the LCLS in the presence of these wakefields, we have made an extensive series of start-to-end SASE simulations with tracking codes PARMELA and ELEGANT, and time-dependent FEL simulation codes GENESIS1.3 and GINGER. We discuss the impact of the wakefield losses upon output energy, spectral bandwidth, and temporal envelope of the output FEL pulse, as well as the benefits of a partial compensation of the time-dependent wake losses obtained with a slight z-dependent taper in the undulator field. We compare the taper results to those predicted analytically[2].

Protein oxidation is linked to cellular stress, aging, and disease. Protein oxidations that result in reactive species are of particular interest, since these reactive oxidation products may react with other proteins or biomolecules in an unmediated and irreversible fashion, providing a potential marker for a variety of disease mechanisms. We have developed a novel system to identify and quantitate, relative to other states, the sites of oxidation on a given protein. A specially designed Oxidation-dependent carbonyl-specific Element-Coded Affinity Mass Tag (O-ECAT), AOD, ((S)-2-(4-(2-aminooxy)-acetamido)-benzyl)-1, 4, 7, 10-tetraazacyclododecane-N, N', N'', N'''-tetraacetic acid, is used to covalently tag the residues of a protein oxidized to aldehyde or keto end products. After proteolysis, the resulting AOD-tagged peptides are affinity purified, and analyzed by nanoLC-FTICR-MS, which provides high specificity in extracting co-eluting AOD mass pairs with a unique mass difference and affords relative quantitation based on isotopic ratios. Using this methodology, we have mapped the surface oxidation sites on a model protein, recombinant human serum albumin (rHSA) in its native form (as purchased) and after FeEDTA oxidation. A variety of modified amino acid residues including lysine, arginine, proline, histidine, threonine, aspartic and glutamic acids, were found to be oxidized to aldehyde and keto end products. …

The FERMI at ELETTRA project at Sincotrone Trieste involves two FEL's, each based upon the principle of seeded harmonic generation and using the existing ELETTRA injection linac at 1.2 GeV beam energy. Scheduled to be completed in 2008, FEL-1 will operate in 40-100 nm wavelength range and will involve one stage of harmonic up-conversion. The second undulator line, FEL-2, will begin operation two years later in the 10-40 nm wavelength range and use two harmonic stages operating as a cascade. The FEL design assumes continuous wavelength tunability over the full wavelength range, and polarization tunability of the output radiation including vertical or horizontal linear as well as helical polarization. The design considers focusing properties and segmentation of realizable undulators and available input seed lasers. We review the studies that have led to our current design. We present results of simulations using GENESIS and GINGER simulation codes including studies of various shot-to-shot fluctuations and undulator errors. Findings for the expected output radiation in terms of the power, transverse and longitudinal coherence are reported.

We present here the PhIGs database, a phylogenomic resource for sequenced genomes. Although many methods exist for clustering gene families, very few attempt to create truly orthologous clusters sharing descent from a single ancestral gene across a range of evolutionary depths. Although these non-phylogenetic gene family clusters have been used broadly for gene annotation, errors are known to be introduced by the artifactual association of slowly evolving paralogs and lack of annotation for those more rapidly evolving. A full phylogenetic framework is necessary for accurate inference of function and for many studies that address pattern and mechanism of the evolution of the genome. The automated generation of evolutionary gene clusters, creation of gene trees, determination of orthology and paralogy relationships, and the correlation of this information with gene annotations, expression information, and genomic context is an important resource to the scientific community.

Multimillion atom non-equilibrium molecular dynamics simulations for shock compressed iron are analyzed using Fourier methods to determine the long scale ordering of the crystal. By analyzing the location of the maxima in k-space we can determine the crystal structure and compression due to the shock. This report presents results from a 19.6 GPa simulated shock in single crystal iron and compare them to recent experimental results of shock compressed iron where the crystal structure was determined using in-situ wide angle x-ray diffraction.

M{sub 2}Mn{sub 3}O{sub 8} (M=Ca{sup 2+}, Cu{sup 2+}) compounds were synthesized and characterized in lithium cells. The M{sup 2+} cations, which reside in the van der Waal's gaps between adjacent sheets of Mn{sub 3}O{sub 8}{sup 4-}, may be replaced chemically (by ion-exchange) or electrochemically with Li. More than 7 Li{sup +}/Cu{sub 2}Mn{sub 3}O{sub 8} may be inserted electrochemically, with concomitant reduction of Cu{sup 2+} to Cu metal, but less Li can be inserted into Ca{sub 2}Mn{sub 3}O{sub 8}. In the case of Cu{sup 2+}, this process is partially reversible when the cell is charged above 3.5 V vs. Li, but intercalation of Cu{sup +} rather than Cu{sup 2+} and Li{sup +}/Cu{sup +} exchange occurs during the subsequent discharge. If the cell potential is kept below 3.4 V, the Li in excess of 4Li{sup +}/Cu{sub 2}Mn{sub 3}O{sub 8} can be cycled reversibly. The unusual mobility of +2 cations in a layered structure has important implications both for the design of cathodes for Li batteries and for new systems that could be based on M{sup 2+} intercalation compounds.

We review the technical challenges associated with the production and use of various coal chars in a direct carbon conversion fuel cell. Existing chemical and physical deashing processes remove material below levels impacting performance at minimal cost. At equilibrium, sulfur entrained is rejected from the melt as COS in the offgas.

The {gamma}-ray energy spectra due to positron annihilation with the 3p core-level of Cu, the 4p core-level of Ag, and 5p core level of Au were obtained separately from the total annihilation spectrum by measuring the energies of {gamma}-rays time coincident with Auger electrons emitted as a result of filling the core-hole left by annihilation. The results of these measurements are compared to the total annihilation spectra and with LDA based theoretical calculations. A comparison of area normalized momentum distributions with the individual cores extracted from the Doppler measurements shows good qualitative agreement, however, in all three spectra, the calculated values of the momentum density appears to fall below the measured values as the momentum increases. The discrepancies between theory and experiment are well outside the statistical uncertainties of the experiment and become more pronounced with increasing Z going down the column from Cu to Ag to Au. The comparison with the experimental results clearly indicates that the calculations are not predicting the correct ratio of high momentum to low momentum spectral weight and suggest the need to improve the treatment of many body electron-positron correlation effects in annihilation as they pertain to core levels.

We propose an efficient variational method for Z{sub 2} lattice gauge theory based on the matrix product ansatz. The method is applied to ladder and square lattices. The Gauss law needs to be imposed on quantum states to guarantee gauge invariance when one studies gauge theory in hamiltonian formalism. On the ladder lattice, we identify gauge invariant low-lying states by evaluating expectation values of the Gauss law operator after numerical diagonalization of the gauge hamiltonian. On the square lattice, the second order phase transition is well reproduced.

We study the free energies of heavy quarks calculated from Polyakov loop correlation functions in full 2-flavour QCD using the p4-improved staggered fermion action. A small but finite baryon number density is included via Taylor expansion of the fermion determinant in the baryo-chemical potential {mu}. For temperatures above T{sub c} we extract Debye screening masses from the large distance behavior of the free energies and compare their {mu}-dependence to perturbative results.