The material in this report summarizes the Diversa technical effort in development of a biocatalyst for the biodesulfurization of Petro Star diesel as well as an economic report of standalone and combined desulfurization options, prepared by Pelorus and Anvil, to support and inform the development of a commercially viable process. We will discuss goals of the projected as originally stated and their modification as guided by parallel efforts to evaluate commercialization economics and process parameters. We describe efforts to identify novel genes and hosts for the generation of an optimal biocatalyst, analysis of diesel fuels (untreated, chemically oxidized and hydrotreated) for organosulfur compound composition and directed evolution of enzymes central to the biodesulfurization pathway to optimize properties important for their use in a biocatalyst. Finally we will summarize the challenges and issues that are central to successful development of a viable biodesulfurization process.

Forty-three subjects worked in a private office with switchable electrochromic windows, manually-operated Venetian blinds, and dimmable fluorescent lights. The electrochromic window had a visible transmittance range of approximately 3-60%. Analysis of subject responses and physical data collected during the work sessions showed that the electrochromic windows reduced the incidence of glare compared to working under a fixed transmittance (60%) condition. Subjects used the Venetian blinds less often and preferred the variable transmittance condition, but used slightly more electric lighting with it than they did when window transmittance was fixed.

The injection and storage of anthropogenic CO{sub 2} in deep geologic formations is a potentially feasible strategy to reduce CO{sub 2} emissions and atmospheric concentrations. While the purpose of geologic carbon storage is to trap CO{sub 2} underground, CO{sub 2} could migrate away from the storage site into the shallow subsurface and atmosphere if permeable pathways such as well bores or faults are present. Large-magnitude releases of CO{sub 2} have occurred naturally from geologic reservoirs in numerous volcanic, geothermal, and sedimentary basin settings. Carbon dioxide and natural gas have also been released from geologic CO{sub 2} reservoirs and natural gas storage facilities, respectively, due to influences such as well defects and injection/withdrawal processes. These systems serve as natural and industrial analogues for the potential release of CO{sub 2} from geologic storage reservoirs and provide important information about the key features, events, and processes (FEPs) that are associated with releases, as well as the health, safety, and environmental consequences of releases and mitigation efforts that can be applied. We describe a range of natural releases of CO{sub 2} and industrial releases of CO{sub 2} and natural gas in the context of these characteristics. Based on this analysis, several key conclusions can …

The goal is to examine the dependence of the plastic flow direction as a function of strain increment for a generalized quadratic flow potential; and from that, extract a scheme for constructing a plastic flow direction for a more general class of yield and flow surfaces.

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The main objectives of the project were to monitor, characterize, and quantify in situ the rates of formation and dissociation of methane hydrates at and near the seafloor in the northern Gulf of Mexico, with a focus on the Bush Hill seafloor hydrate mound; to record the linkages between physical and chemical parameters of the deposits over the course of one year, by emphasizing the response of the hydrate mound to temperature and chemical perturbations; and to document the seafloor and water column environmental impacts of hydrate formation and dissociation. For these, monitoring the dynamics of gas hydrate formation and dissociation was required. The objectives were achieved by an integrated field and laboratory scientific study, particularly by monitoring in situ formation and dissociation of the outcropping gas hydrate mound and of the associated gas-rich sediments. In addition to monitoring with the MOSQUITOs, fluid flow rates and temperature, continuously sampling in situ pore fluids for the chemistry, and imaging the hydrate mound, pore fluids from cores, peepers and gas hydrate samples from the mound were as well sampled and analyzed for chemical and isotopic compositions. In order to determine the impact of gas hydrate dissociation and/or methane venting across the seafloor …

The radiolysis of water in contact with spent nuclear fuel (SNF) will produce oxidants and reductants that can affect the dissolution of the fuel in a geologic disposal site. These products are created by initial radiolytic species which are a function of the type of radiation being emitted by the SNF, i.e. alpha, beta and/or gamma, as well as the energy of this radiation, the fuel grain size (and resulting surface-to-volume ratio) and the fuel-to-water ratio. These products interact with the surface of the fuel, creating new species and ultimately affecting the dissolution rate. The objective of the work reported here is to develop a systematic dosimetry model to determine the dose to water from the SNF as a function of these variables. This dose is calculated for different radiation types as a function of decay for the average fuel composition expected at Yucca Mountain. From these dose calculations the production rate of initial radiolytic products can be estimated. This data provides the basis for subsequent determination of the resulting chemical interactions at the fuel/water interface predicted by published theoretical and experimental data.

Efforts during this second year focused on four areas: (1) continued searching and summarizing of published Fischer-Tropsch synthesis (FTS) mechanistic and kinetic studies of FTS reactions on iron catalysts; (2) investigation of CO adsorption/desorption and temperature programmed hydrogenation (TPH) of carbonaceous species after FTS on unsupported iron and alumina-supported iron catalysts; (3) activity tests of alumina-supported iron catalysts in a fixed bed reactor; (4) sequential design of experiments, for the collection of rate data in a Berty CSTR reactor, and nonlinear-regression analysis to obtain kinetic parameters. Literature sources describing mechanistic and kinetic studies of Fischer-Tropsch synthesis on iron catalysts were compiled in a review. Temperature-programmed desorption/reaction methods (the latter using mass-spectrometry detection and also thermogravimetric analyzer (TGA)) were utilized to study CO adsorption/-desorption on supported and unsupported iron catalysts. Molecular and dissociative adsorptions of CO occur on iron catalysts at 25-150 C. The amounts adsorbed and bond strengths of adsorption are influenced by supports and promoters. That CO adsorbs dissociatively on polycrystalline Fe at temperatures well below those of FT reaction indicates that CO dissociation is facile and unlikely to be the rate-limiting step during FTS. Carbonaceous species formed after FT reaction for only 5 minutes at 200 C were …

The goal of the Biomolecular Simulation of Base Excision Repair and Protein Signaling project is to enhance our understanding of the mechanism of human polymerase-, one of the key enzymes in base excision repair (BER) and the cell-signaling enzymes cyclic-AMP-dependent protein kinase. This work used molecular modeling and simulation studies to specifically focus on the • dynamics of DNA and damaged DNA • dynamics and energetics of base flipping in DNA • mechanism and fidelity of nucleotide insertion by BER enzyme human polymerase-β • mechanism and inhibitor design for cyclic-AMP-dependent protein kinase. Molecular dynamics simulations and electronic structure calculations have been performed using the computer resources at the Molecular Science Computing Facility at the Environmental Molecular Sciences Laboratory.

An international team comprising SLAC, KEK, FNAL, JLAB and DESY is collaborating on the design, fabrication and test of a low loss, 1.3 GHz 9-cell SRF structure as a potential improvement for the ILC main linac. The advantages of this structure over the TESLA structure include lower cryogenic loss, shorter rise time, and less stored energy. Among the issues to be addressed in this design are HOM damping, Lorentz force detuning and multipacting. We will report on HOM damping calculations using the parallel finite element eigenmode solver Omega3P and the progress made towards an optimized design. Studies on multipacting and estimates of the Lorentz force detuning will also be presented.

It has been empirically observed in both experiments and particle-in-cell simulations that space-charge-dominated beams suffer strong growth in statistical phase-space area (degraded quality) and particle losses in alternating gradient quadrupole transport channels when the undepressed phase advance {sigma}{sub 0} increases beyond about 85{sup o} per lattice period. Although this criterion has been used extensively in practical designs of strong focusing intense beam transport lattices, the origin of the limit has not been understood.We propose a mechanism for the transport limit resulting from classes of halo particle resonances near the core of the beam that allow near-edge particles to rapidly increase in oscillation amplitude when the space-charge intensity and the utter of the matched beam envelope are both sufficiently large. When coupled with a diffuse beam edge and/or perturbations internal to the beam core that can drive particles outside the edge, this mechanism can result in large and rapid halo-driven increases in the statistical phase-space area of the beam, lost particles, and degraded transport. A core-particle model is applied to parametrically analyze his process. Extensive self-consistent particle in cell simulations are employed to better quantify space-charge limit and verify core-particle model predictions.

Critical experiments were conducted at the Oak Ridge Critical Experiment Facility (ORCEF) to determine the critical concentration for an unreflected 69.2-cm-diameter sphere of UO{sub 2}F{sub 2}, at an enrichment of {approx}37 percent U{sup 235}, by weight. These experiments were a continuation of previous efforts to determine critical dimensions for fissile materials in simple geometry. Some of the earlier experiments in this vessel have been published as part of the OECD handbook. The reports concerning these experiments have only recently become available. Until August 2005, Refs. 2 and 3 were still classified. These documents, along with experimental logbooks and unclassified papers available on the experimental campaign and facility are being used to generate a computer model for this critical experiment.

We present updated results on time-dependent CP asymmetries in fully reconstructed B{sup 0} {yields} D{sup (*){+-}}{pi}{sup {-+}} and B{sup 0} {yields} D{sup {+-}}{rho}{sup {-+}} decays in approximately 232 million {Upsilon}(4S) {yields} B{bar B} events collected with the BABAR detector at the PEP-II asymmetric-energy B factory at SLAC. From a time-dependent maximum likelihood fit we obtain for the parameters related to the CP violation angle 2{beta} + {gamma}: a{sup D{pi}} = -0.010 {+-} 0.023 {+-} 0.007, c{sub lep}{sup D{pi}} = -0.033 {+-} 0.042 {+-} 0.012, a{sup D*{pi}} = -0.040 {+-} 0.023 {+-} 0.010, C{sub lep}{sup D*{pi}} = 0.049 {+-} 0.042 {+-} 0.015, a{sup D{rho}} = -0.024 {+-} 0.031 {+-} 0.009, c{sub lep}{sup D{rho}} = -0.098 {+-} 0.055 {+-} 0.018, where the first error is statistical and the second is systematic. Using other measurements and theoretical assumptions, we interpret the results in terms of the angles of the Cabibbo-Kobayashi-Maskawa unitarity triangle and find |sin(2{beta}+{gamma})| > 0.64 (0.40) at 68% (90%) confidence level.

This document describes the implementation of the topological vertex finding algorithm ZVTOP within the org.lcsim reconstruction and analysis framework. At the present date, Java vertexing tools allow users to perform topological vertexing on tracks that have been obtained from a Fast MC simulation. An implementation that will be able to handle fully reconstructed events is being designed from the ground up for longevity and maintainability.

PEP-II is an e{sup +}e{sup -} asymmetric B-Factory Collider located at SLAC operating at the Upsilon 4S resonance (3.1 GeV x 9 GeV). It has reached a luminosity of 9.21 x 10{sup 33}/cm{sup 2}/s and has delivered an integrated luminosity of 710 pb{sup -1} in one day. PEP-II has delivered, over the past six years, an integrated luminosity to the BaBar detector of over 262 fb{sup -1}. PEP-II operates in continuous injection mode for both beams boosting the integrated luminosity. The peak positron current has reached 2.45 A in 1588 bunches. Steady progress is being made in reaching higher luminosity. The goal over the next several years is to reach a luminosity of 2.1 x 10{sup 34}/cm{sup 2}/s. The accelerator physics issues being addressed in PEP-II to reach this goal include the electron cloud instability, beam-beam effects, parasitic beam-beam effects, high RF beam loading, shorter bunches, lower {beta}*{sub y} interaction region operation, and coupling control. Figure 1 shows the PEP-II tunnel.

A unique electronics system has been built and tested for reading signals from the silicon-strip detectors of the Gamma-ray Large Area Space Telescope mission. The system amplifies and processes signals from 884,736 36-cm long silicon strips in a 4 x 4 array of tower modules. An aggressive mechanical design fits the readout electronics in narrow spaces between the tower modules, to minimize dead area. This design and the resulting departures from conventional electronics packaging led to several fabrication challenges and lessons learned. This paper describes the fabrication processes and how the problems peculiar to this design were overcome.

We show how the string amplitude {Phi}(z) defined on the fifth dimension in AdS{sub 5} space can be precisely mapped to the light-front wavefunctions of hadrons in physical spacetime. We find an exact correspondence between the holographic variable z and an impact variable {zeta}, which represents the measure of transverse separation of the constituents within the hadrons. In addition, we derive effective four dimensional Schroedinger equations for the bound states of massless quarks and gluons which exactly reproduce the AdS/CFT results and give a realistic description of the light-quark meson and baryon spectrum as well as the form factors for spacelike Q{sup 2}. Only one parameter which sets the mass scale, {Lambda}{sub QCD}, is introduced.

This document describes a groundwater assessment plan for the single-shell tank systems in Waste Management Area A-AX at the Hanford Site.

Parameters are being studied for a high luminosity e{sup +}e{sup -} collider operating at the Upsilon 4S that would deliver a luminosity in the range of 7 to 10 x 10{sup 35}/cm{sup 2}/s. Particle physics studies dictate that a much higher luminosity collider than the present B-Factory accelerators will be needed to answer future new key physics questions. The success of the present B-Factories, PEP-II and KEKB, in producing unprecedented luminosity with very short commissioning times has taught us about the accelerator physics of asymmetric e{sup +}e{sup -} colliders in a new parameter regime. Such a collider could produce an integrated luminosity of 10,000 fb{sup -1} (10 ab{sup -1}) in a running year. A Super-B-Factory [1-8] with 30 to 50 times the performance of the present PEP-II accelerator would incorporate a higher frequency RF system, lower impedance vacuum chambers, higher power synchrotron radiation absorbers, and stronger bunch-by-bunch feedback systems. The present injector based on the SLAC linac needs no improvements and is ready for the Super-B-Factory.

Galactosylceramide (GalCer), a glycosphingolipid, is believed to exist in the extracellular leaflet of cell membranes in nanometer sized domains or rafts. The local clustering of GalCer within rafts is thought to facilitate the initial adhesion of certain viruses, including HIV-1 and bacteria to cells through multivalent interactions between receptor proteins (gp120 for HIV-1) and GalCer. Here we use atomic force microscopy (AFM) to study the effects of cholesterol on solid-phase GalCer domain microstructure and miscibility with a fluid lipid 1,2-Dilauroyl-sn-Glycero-3-Phosphocholine (DLPC), in supported lipid bilayers. Using ''slow cooled vesicle fusion'' to prepare the supported lipid bilayers, we were able to overcome the nonequilibrium effects of the substrate (verified by comparison to results for giant unilamellar vesicles, GUVs) and accurately quantify the dramatic effect of cholesterol on the GalCer domain surface area to perimeter ratio (AD/P) and DLPC-GalCer miscibility. We compare these results to a supported lipid bilayer system in which the bilayer is rapidly cooled (nonequilibrium conditions), ''quenched vesicle fusion'' and find that the microstructures are remarkably similar above a cholesterol mole fraction of approximately 0.06. We determined that GalCer domains were contained in one leaflet distal to the mica substrate through qualitative binding experiments with Trichosanthes kirilowii agglutinin (TKA), …

Design of the first generation LCLS injector is nearing completion. Fabrication has begun and component installation is planned for 2006. We discuss the last modifications made on both the 1.6 cell S-Band RF gun and the SLAC S-Band accelerating structures to minimize irreversible emittance growth. The mode separation between the 0 and {pi} modes was increased from 3.4 MHz to 15 MHz. Dual feed and racetrack shapes have been incorporated in the full cell of the new gun. The linac sections were also modified to accommodate dual feeds and racetrack shapes in their input cells. PARMELA simulations indicating the need for these modifications are presented.

The LCLS injector is required to provide a 1-nC, 10-ps bunch with a normalized rms transverse projected emittance of less than 1 micron. The LCLS beam is generated and accelerated in a 1.6-cell S-band RF gun at 120 MV/m up to 6 MeV. The gun is followed by two SLAC 3-m S-band accelerator structures to further accelerate the beam to 135 MeV which moves the beam out of the space-charge dominated regime. In the SLAC S-band structures, the RF power feed is through a single coupling-hole (single-feed coupler) which results in a field asymmetry. The time dependent multipole fields in the coupler induce a transverse kick along the bunch and cause the emittance to increase above the LCLS specification. To meet the stringent emittance requirements for the injector, the single-feed couplers will be replaced by a dual-feed racetrack design to minimize the multipole field effects. We will present detailed studies of the multipole fields in the SLAC linac RF coupler and the improvements with the dual-feed ractrack design using the parallel finite element S-parameter solver S3P.