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.

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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.

The surface complexation of actinides with iron oxides plays a key role in actinide transport and retardation in geosphere-biosphere systems. The development of accurate actinide transport models therefore requires a mechanistic understanding of surface complexation reactions (i.e. knowledge of chemical speciation at mineral/fluid interfaces). Iron oxides are particularly important actinide sorbents due to their pH dependent surface charges, relatively high surface areas and ubiquity in oxic and suboxic near-surface systems. In this paper we present results from field and laboratory investigations that elucidate the mechanisms involved in binding uranium and neptunium to iron oxide mineral substrates in near neutral groundwaters. The field study involved sampling and characterizing uranium-bearing groundwaters and solids from a saprolite aquifer overlying an unmined uranium deposit in the Virginia Piedmont. The groundwaters were analyzed by inductively coupled mass spectrometry and ion chromatography and the aquifer solids were analyzed by electron microprobe. The laboratory study involved a series of batch sorption tests in which U(VI) and Np(V) were reacted with goethite, hematite and magnetite in simulated groundwaters. The pH, ionic strength, aging time, and sorbent/sorbate ratios were varied in these experiments. The oxidation state and coordination environment of neptunium in solutions and sorbents from the batch tests …

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].

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Environmental Energy Inc has shown that BUTANOL REPLACES GASOLINE - 100 pct and has no pollution problems, and further proved it is possible to produce 2.5 gallons of butanol per bushel corn at a production cost of less than $1.00 per gallon. There are 25 pct more Btu-s available and an additional 17 pct more from hydrogen given off, from the same corn when making butanol instead of ethanol that is 42 pct more Btu-s more energy out than it takes to make - that is the plow to tire equation is positive for butanol. Butanol is far safer to handle than gasoline or ethanol. Butanol when substituted for gasoline gives better gas mileage and does not pollute as attested to in 10 states. Butanol should now receive the same recognition as a fuel alcohol in U.S. legislation as ethanol. There are many benefits to this technology in that Butanol replaces gasoline gallon for gallon as demonstrated in a 10,000 miles trip across the United States July-August 2005. No modifications at all were made to a 1992 Buick Park Avenue; essentially your family car can go down the road on Butanol today with no modifications, Butanol replaces gasoline. It is …

Our research program focuses on the development of a method to cool atoms and molecules of any choice as long as they have a stable gaseous phase. Our approach starts with a very cold supersonic beam of He seeded with the molecules of choice. The internal temperature can reach 1 milliKelvin or less. The high center of mass velocity of the particles forming the beam will be reduced by elastically scattering the atoms/molecules from a very cold single crystal surface (20-40K), which moves in the beam direction. This will enable the continuous control of the mean velocity over a large range, after scattering, down to a few tens of m/s or even below as the crystal surface's velocity approaches v/2 of the impacting particles. We will use the decelerated particles as a source for a white-fringe matter-wave interferometer, where one reflector is a very cold surface of interest. The interference pattern will reveal the real part (via integral intensities) and the imaginary part (via phase shifts) of the scattering cross sections. This is particularly interesting for H{sub 2} and resonance structures. This interferometer set-up follows closely Prichard's arrangement.

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 have received CDAC allotments of beam time at HPCAT that were used to carryout investigations that included angle-dispersive x-ray diffraction of beryllium at high pressures and inelastic x-ray scattering (x-ray Raman) of high pressure phases of water. These CDAC beam time allotments have permitted us to broaden and supplement the scope of our research. The beam time has also been used in experiments that had graduate student participants (Z Jenei and A Lazicki) and thus the experiments also incorporated a component of training and education. Water (H{sub 2}O) is a major constituent of terrestrial systems, and furthering our understanding of this ubiquitous system and hydrogen bonding structures impacts a broad range of systems; including geophysics, life sciences, the environment and technology development. Our inelastic x-ray scattering studies (x-ray Raman spectroscopy) of high-pressure phases of water and ice are aimed at addressing controversies regarding the high-pressure structure of water. Using the inelastic x-ray scattering system at HPCAT we have measured x-ray Raman spectra of water at 1 and 17 GPa. X-Ray Raman is a relatively new technique that provides data that is equivalent to x-ray absorption, but utilizes a hard x-ray to avoid short absorption lengths and surface effects to …

The purpose of this report is to develop and analyze the engineered barrier system (EBS) radionuclide transport abstraction model, consistent with Level I and Level II model validation, as identified in ''Technical Work Plan for: Near-Field Environment and Transport: Engineered Barrier System: Radionuclide Transport Abstraction Model Report Integration'' (BSC 2005 [DIRS 173617]). The EBS radionuclide transport abstraction (or EBS RT Abstraction) is the conceptual model used in the total system performance assessment for the license application (TSPA-LA) to determine the rate of radionuclide releases from the EBS to the unsaturated zone (UZ). The EBS RT Abstraction conceptual model consists of two main components: a flow model and a transport model. Both models are developed mathematically from first principles in order to show explicitly what assumptions, simplifications, and approximations are incorporated into the models used in the TSPA-LA. The flow model defines the pathways for water flow in the EBS and specifies how the flow rate is computed in each pathway. Input to this model includes the seepage flux into a drift. The seepage flux is potentially split by the drip shield, with some (or all) of the flux being diverted by the drip shield and some passing through breaches in …

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In an extensive molecular dynamics (MD) study of shock compression of aluminum containing such microscopic defects as found in aged plutonium, LLNL scientists have demonstrated that ASC supercomputers live up to their promise as powerful tools to predict aging phenomena in the nuclear stockpile. Although these MD investigations are carried out on material samples containing only about 10 to 40 million atoms, and being not much bigger than a virus particle, they have shown that reliable materials properties and relationships between them can be extracted for density, temperature, pressure, and dynamic strength. This was proven by comparing their predictions with experimental data of the Hugoniot, with dynamic strength inferred from gas-gun experiments, and with the temperatures behind the shock front as calculated with hydro-codes. The effects of microscopic helium bubbles and of radiation-induced dislocation loops and voids on the equation of state were also determined and found to be small and in agreement with earlier theoretical predictions and recent diamond-anvil-cell experiments. However, these microscopic defects play an essential role in correctly predicting the dynamic strength for these nano-crystalline samples. These simulations also prove that the physics involved in shock compression experiments remains the same for macroscopic specimens used in gas-gun …

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.

Real-time pricing (RTP) has been advocated as an economically efficient means to send price signals to customers to promote demand response (DR) (Borenstein 2002, Borenstein 2005, Ruff 2002). However, limited information exists that can be used to judge how effectively RTP actually induces DR, particularly in the context of restructured electricity markets. This report describes the second phase of a study of how large, non-residential customers' adapted to default-service day-ahead hourly pricing. The customers are located in upstate New York and served under Niagara Mohawk, A National Grid Company (NMPC)'s SC-3A rate class. The SC-3A tariff is a type of RTP that provides firm, day-ahead notice of hourly varying prices indexed to New York Independent System Operator (NYISO) day-ahead market prices. The study was funded by the California Energy Commission (CEC)'s PIER program through the Demand Response Research Center (DRRC). NMPC's is the first and longest-running default-service RTP tariff implemented in the context of retail competition. The mix of NMPC's large customers exposed to day-ahead hourly prices is roughly 30% industrial, 25% commercial and 45% institutional. They have faced periods of high prices during the study period (2000-2004), thereby providing an opportunity to assess their response to volatile hourly prices. …

Discusses the impact of lubricant formulation on the performance of oxides of nitrogen (NOx) Adsorber Catalysts, including background/motivation for study, experimental design, and results.

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. …

Discusses the full useful life exhaust emission performance of a NOx (nitrogen oxides) adsorber and diesel particle filter equipped light-duty and medium-duty engine using ultra low sulfur diesel fuel.

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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.

It has been predicted that world energy demand will soon put enormous pressure on the currently available energy sources. Fusion energy is a potential solution to this problem if it can be controlled and converted into electricity in an economically feasible manner. One type of potential fusion energy plant uses heavy-ion beam drivers for inertial fusion energy. As part of the High Current Experiment (HCX), we seek to understand the injection, transport and focusing of high-current ion beams, by investigating the interactions of background gas and electrons (which can deteriorate the beam quality) with the primary K{sup +} beam. We present here a method of analyzing the electrostatic potential distribution due to the beam space charge within the grounded conducting vacuum pipe. This method enables tracking of ions arising from the ionization of background gas atoms by the incident K{sup +} beam. The beam intensity distribution is obtained from images gathered using a scintillator placed in the beam path. These data are used to calculate the expelled ion energy distribution, which is then compared to data collected from a Retarding Potential Analyzer (RPA). The comparison of the image analysis with RPA measurements is in fair agreement, given model and experimental …

The purpose of this model report is to provide documentation of the conceptual and mathematical model for atmospheric dispersion and subsequent depositions of ash on the land surfaces from a potential volcano eruptions at Yucca Mountain Nevada.