Matrix-assisted laser desorption/ionization(MALDI) mass spectrometry(MS) has been widely used for analysis of biological molecules, especially macromolecules such as proteins. However, MALDI MS has a problem in small molecule (less than 1 kDa) analysis because of the signal saturation by organic matrixes in the low mass region. In imaging MS (IMS), inhomogeneous surface formation due to the co-crystallization process by organic MALDI matrixes limits the spatial resolution of the mass spectral image. Therefore, to make laser desorption/ionization (LDI) MS more suitable for mass spectral profiling and imaging of small molecules directly from raw biological tissues, LDI MS protocols with various alternative assisting materials were developed and applied to many biological systems of interest. Colloidal graphite was used as a matrix for IMS of small molecules for the first time and methodologies for analyses of small metabolites in rat brain tissues, fruits, and plant tissues were developed. With rat brain tissues, the signal enhancement for cerebroside species by colloidal graphite was observed and images of cerebrosides were successfully generated by IMS. In addition, separation of isobaric lipid ions was performed by imaging tandem MS. Directly from Arabidopsis flowers, flavonoids were successfully profiled and heterogeneous distribution of flavonoids in petals was observed for …

Among the olivine-structured metal phosphate family, LiMnPO{sub 4} exhibits a high discharge potential (4V), which is still compatible with common electrolytes, making it interesting for use in the next generation of Li ion batteries. The extremely low electronic conductivity of this material severely limits its electrochemical performance, however. One strategy to overcome this limitation is to make LiMnPO{sub 4} nanoparticulate to decrease the diffusion distance. Another is to add a carbon or other conductive coating in intimate contact with the nanoparticles of the main phase, as is commonly done with LiFePO{sub 4}. The electrochemical performance of LiFePO{sub 4} is highly dependent on the quality of the carbon coatings on the particles [1-2], among other variables. Combustion synthesis allows the co-synthesis of nanoparticles coated with carbon in one step. Hydrothermal synthesis is used industrially to make LiFePO{sub 4} cathode materials [3] and affords a good deal of control over purity, crystallinity, and particle size. A wide range of olivine-structured materials has been successfully prepared by this technique [4], including LiMnPO{sub 4} in this study. In this paper, we report on the new synthesis of nano-LiMnPO{sub 4} by a combustion method. The purity is dependent upon the conditions used for synthesis, including …

We develop a Bayesian model to invert spectral induced polarization (SIP) data for Cole-Cole parameters using Markov chain Monte Carlo (MCMC) sampling methods. We compare the performance of the MCMC based stochastic method with an iterative Gauss-Newton based deterministic method for Cole-Cole parameter estimation through inversion of synthetic and laboratory SIP data. The Gauss-Newton based method can provide an optimal solution for given objective functions under constraints, but the obtained optimal solution generally depends on the choice of initial values and the estimated uncertainty information is often inaccurate or insufficient. In contrast, the MCMC based inversion method provides extensive global information on unknown parameters, such as the marginal probability distribution functions, from which we can obtain better estimates and tighter uncertainty bounds of the parameters than with the deterministic method. Additionally, the results obtained with the MCMC method are independent of the choice of initial values. Because the MCMC based method does not explicitly offer single optimal solution for given objective functions, the deterministic and stochastic methods can complement each other. For example, the stochastic method can first be used to obtain the means of the unknown parameters by starting from an arbitrary set of initial values and the deterministic …

The WARP code is a robust electrostatic particle-in-cell simulation package used to model charged particle beams with strong space-charge forces. A fundamental operation associated with seeding detailed simulations of a beam transport channel is to generate initial conditions where the beam distribution is matched to the structure of a periodic focusing lattice. This is done by solving for periodic, matched solutions to a coupled set of ODEs called the Kapchinskij-Vladimirskij (KV) envelope equations, which describe the evolution of low-order beam moments subject to applied lattice focusing, space-charge defocusing, and thermal defocusing forces. Recently, an iterative numerical method was developed (Lund, Chilton, and Lee, Efficient computation of matched solutions to the KV envelope equations for periodic focusing lattices, Physical Review Special Topics-Accelerators and Beams 9, 064201 2006) to generate matching conditions in a highly flexible, convergent, and fail-safe manner. This method is extended and implemented in the WARP code as a Python package to vastly ease the setup of detailed simulations. In particular, the Python package accommodates any linear applied lattice focusing functions without skew coupling, and a more general set of beam parameter specifications than its predecessor. Lattice strength iteration tools were added to facilitate the implementation of problems with …

To ensure inheritance by daughter cells, many low-copy number bacterial plasmids, including the R1 drug-resistance plasmid, encode their own DNA segregation systems. The par operon of plasmid R1 directs construction of a simple spindle structure that converts free energy of polymerization of an actin-like protein, ParM, into work required to move sister plasmids to opposite poles of rod-shaped cells. The structures of individual components have been solved, but little is known about the ultrastructure of the R1 spindle. To determine the number of ParM filaments in a minimal R1 spindle, we used DNA-gold nanocrystal conjugates as mimics of the R1 plasmid. Wefound that each end of a single polar ParM filament binds to a single ParR/parC-gold complex, consistent with the idea that ParM filaments bind in the hollow core of the ParR/parC ring complex. Our results further suggest that multifilament spindles observed in vivo are associated with clusters of plasmidssegregating as a unit.

Most prokaryotes of interest to DOE are poorly understood. Even when full genomic sequences are available, the function of only a small number of gene products are clear. The critical question is how to best infer the most probable network architectures in cells that are poorly characterized. The project goal is to create a computational hypothesis testing (CHT) framework that combines large-scale dynamical simulation, a database of bioinformatics-derived probable interactions, and numerical parallel architecture data-fitting routines to explore many “what if ?” hypotheses about the functions of genes and proteins within pathways and their downstream effects on molecular concentration profiles and corresponding phenotypes. From this framework we expect to infer signal transduction pathways and gene expression networks in prokaryotes. Detailed mechanistic models of E. Coli have been developed that directly incorporate DNA sequence information. The CHT framework is implemented in the NIEngine network inference software. NIEngine has been applied to recover gene regulatory networks in E. coli to assess performance. Application to Shewanel la oneidensi and other organism of interest DOE will be conducted in partnership with Jim Collin's Lab at Boston University and other academic partners. The CHT framework has also found broad application in the automated learning of …

A recent independent review led to uncertainty about the technical basis for characterizing the residual amount of tritium in polymer components used in the Savannah River Site Tritium Facilities that are sent for waste disposal. A review of a paper published in the open literature firmly establishes the basis of the currently used characterization, 10 Ci/cc. Information provided in that paper about exposure experiments performed at the DOE Mound Laboratory allows the calculation of the currently used characterization. These experiments involved exposure of high density polyethylene (HD-PE) to initially 1 atm tritium gas. In addition, a review of recent research at the Savannah River Site not only further substantiates this characterization, but also establishes its use for ultra-high molecular weight polyethylene (UHMW-PE), polytetrafluoroethylene (PTFE, a trade name is Teflon{reg_sign}), and Vespel{reg_sign} polyimide. 10 Ci/cc tritium is a representative characterization for any type of polymer components exposed at ambient temperature and at approximately 1 atm. tritium gas.

Model heterogeneous catalysts have been synthesized and studied to better understand how the surface structure of noble metal nanoparticles affects catalytic performance. In this project, monodisperse rhodium and platinum nanoparticles of controlled size and shape have been synthesized by solution phase polyol reduction, stabilized by polyvinylpyrrolidone (PVP). Model catalysts have been developed using these nanoparticles by two methods: synthesis of mesoporous silica (SBA-15) in the presence of nanoparticles (nanoparticle encapsulation, NE) to form a composite of metal nanoparticles supported on SBA-15 and by deposition of the particles onto a silicon wafer using Langmuir-Blodgett (LB) monolayer deposition. The particle shapes were analyzed by transmission electron microscopy (TEM) and high resolution TEM (HRTEM) and the sizes were determined by TEM, X-ray diffraction (XRD), and in the case of NE samples, room temperature H2 and CO adsorption isotherms. Catalytic studies were carried out in homebuilt gas-phase reactors. For the nanoparticles supported on SBA-15, the catalysts are in powder form and were studied using the homebuilt systems as plug-flow reactors. In the case of nanoparticles deposited on silicon wafers, the same systems were operated as batch reactors. This dissertation has focused on the synthesis, characterization, and reaction studies of model noble metal heterogeneous catalysts. …

This is the final report of the ATLAS Simulation Optimization Task Force, establishedin June of 2007. This note justifies the selected Geant4 version, physics list, and range cuts to be used by the default ATLAS simulation for initial data taking and beyond. The current status of several projects, including detector description, simulation validation, studies of additional Geant4 parameters, and cavern background, are reported.

We present the extension of a deterministic fractal geometric procedure aimed at representing the complexity of the spatio-temporal patterns encountered in environmental applications. The original procedure, which is based on transformations of multifractal distributions via fractal functions, is extended through the introduction of nonlinear perturbations to the underlying iterated linear maps. We demonstrate how the nonlinear perturbations generate yet a richer collection of patterns by means of various simulations that include evolutions of patterns based on changes in their parameters and in their statistical and multifractal properties. It is shown that the nonlinear extensions yield structures that closely resemble complex hydrologic temporal data sets, such as rainfall and runoff time series, and width-functions of river networks as a function of distance from the basin outlet. The implications of this nonlinear approach for environmental modeling and prediction are discussed.

Storage of large amounts of carbon dioxide (CO{sub 2}) in deep geological formations for greenhouse gas mitigation is gaining momentum and moving from its conceptual and testing stages towards widespread application. In this work we explore various optimization strategies for characterizing surface leakage (seepage) using near-surface measurement approaches such as accumulation chambers and eddy covariance towers. Seepage characterization objectives and limitations need to be defined carefully from the outset especially in light of large natural background variations that can mask seepage. The cost and sensitivity of seepage detection are related to four critical length scales pertaining to the size of the: (1) region that needs to be monitored; (2) footprint of the measurement approach, and (3) main seepage zone; and (4) region in which concentrations or fluxes are influenced by seepage. Seepage characterization objectives may include one or all of the tasks of detecting, locating, and quantifying seepage. Each of these tasks has its own optimal strategy. Detecting and locating seepage in a region in which there is no expected or preferred location for seepage nor existing evidence for seepage requires monitoring on a fixed grid, e.g., using eddy covariance towers. The fixed-grid approaches needed to detect seepage are expected …

In conventional models of gauge-mediated supersymmetry breaking, the lightest supersymmetric particle (LSP) is invariably the gravitino. However, if the supersymmetry breaking sector is strongly coupled, conformal sequestering may raise the mass of the gravitino relative to the remaining soft supersymmetry-breaking masses. In this letter, we demonstrate that such conformal dynamics in gauge-mediated theories may give rise to satisfactory neutralino dark matter while simultaneously solving the flavor and {mu}/B{mu} problems.

The Plutonium Finishing Plant at the Department of Energy's Hanford Site in southeastern Washington State began operations in 1949 to process plutonium and plutonium products. Its primary mission was to produce plutonium metal, fabricate weapons parts, and stabilize reactive materials. These operations, and subsequent activities, were performed in production lines, consisting primarily of hundreds of gloveboxes. Over the years, these gloveboxes and attendant processes have been continuously modified. The plant is currently inactive and Fluor Hanford has been tasked with cleaning out contaminated equipment and gloveboxes from the facility so it can be demolished in the near future. Approximately 100 gloveboxes at PFP have been cleaned out in the past four years and about 90 gloveboxes remain to be cleaned out. Because specific commitment dates for this work have been established with the State of Washington and other entities, it is important to adopt work practices that increase the safety and speed of this effort. The most recent work practice to be adopted by Fluor Hanford D and D workers is the use of 3-D models to make the process of cleaning out the radioactive gloveboxes more efficient. The use of 3-D models has significantly improved the work-planning process by …

The GGF Student Scholar program enabled GGF the opportunity to bring over sixty qualified graduate and under-graduate students with interests in grid technologies to its three annual events over the three-year program.

The 'Criticality HazOp' technique, as developed at Hanford's Plutonium Finishing Plant (PFP), has allowed for efficiencies enabling shortening of the time necessary to complete new or revised criticality safety evaluation reports (CSERs). For example, in the last half of 2007 at PFP, CSER revisions undergoing the 'Criticality HazOp' process were completed at a higher rate than previously achievable. The efficiencies gained through use of the 'Criticality HazOp' process come from the preliminary narrowing of potential scenarios for the Criticality analyst to fully evaluate in preparation of the new or revised CSER, and from the use of a systematized 'Criticality HazOp' group assessment of the relevant conditions to show which few parameter/condition/deviation combinations actually require analytical effort. The 'Criticality HazOp' has not only provided efficiencies of time, but has brought to criticality safety evaluation revisions the benefits of a structured hazard evaluation method and the enhanced insight that may be gained from direct involvement of a team in the process. In addition, involved personnel have gained a higher degree of confidence and understanding of the resulting CSER product.

Crosswell seismic acquisition provides an ideal geometry for monitoring travel time changes in the subsurface. Analysis of delay time in terms of a characteristic frequency allows us to estimate optimal acquisition parameters (frequency and distance). We have deployed standard data acquisition equipment for continuous monitoring of crosswell travel time in two separate field experiments, with well spacing of 3 and 30 m. The acquisition hardware used for the field experiments is described, along with environmental effects (such as temperature) that influence the measurements. Two field experiments are described that correlate changes in travel time (and therefore velocity) with changes in barometric pressure. The results from the two field sites show a pressure sensitivity for velocity of 10{sup -6}/Pa to 10{sup -8}/Pa.

Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42 C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. Conclusions: …

Although electrokinetic effects are not new, only recently have they been investigated for possible use in energy conversion devices. We have recently reported the electrokinetic generation of molecular hydrogen from rapidly flowing liquid water microjets [Duffin et al. JPCC 2007, 111, 12031]. Here, we describe the use of liquid water microjets for direct conversion of electrokinetic energy to electrical power. Previous studies of electrokinetic power production have reported low efficiencies ({approx}3%), limited by back conduction of ions at the surface and in the bulk liquid. Liquid microjets eliminate energy dissipation due to back conduction and, measuring only at the jet target, yield conversion efficiencies exceeding 10%.

The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of …

The Real Time System Operations (RTSO) 2006-2007 project focused on two parallel technical tasks: (1) Real-Time Applications of Phasors for Monitoring, Alarming and Control; and (2) Real-Time Voltage Security Assessment (RTVSA) Prototype Tool. The overall goal of the phasor applications project was to accelerate adoption and foster greater use of new, more accurate, time-synchronized phasor measurements by conducting research and prototyping applications on California ISO's phasor platform - Real-Time Dynamics Monitoring System (RTDMS) -- that provide previously unavailable information on the dynamic stability of the grid. Feasibility assessment studies were conducted on potential application of this technology for small-signal stability monitoring, validating/improving existing stability nomograms, conducting frequency response analysis, and obtaining real-time sensitivity information on key metrics to assess grid stress. Based on study findings, prototype applications for real-time visualization and alarming, small-signal stability monitoring, measurement based sensitivity analysis and frequency response assessment were developed, factory- and field-tested at the California ISO and at BPA. The goal of the RTVSA project was to provide California ISO with a prototype voltage security assessment tool that runs in real time within California ISO?s new reliability and congestion management system. CERTS conducted a technical assessment of appropriate algorithms, developed a prototype incorporating state-of-art …

This thirty-month project was successful in attaining its ambitious objectives of demonstrating a radically novel 'remote-phosphor' LED light source that can out-perform conventional conformal coated phosphor LED sources. Numerous technical challenges were met with innovative techniques and optical configurations. This product development program for a new generation of solid-state light sources has attained unprecedented luminosity (over 1 kilo-lumen) and efficacy (based on the criterion lumens per 100mw radiant blue). LPI has successfully demonstrated its proprietary technology for optical synthesis of large uniform sources out of the light output of an array of separated LEDs. Numerous multiple blue LEDs illuminate single a phosphor patch. By separating the LEDs from the phosphor, the phosphor and LEDs operate cooler and with higher efficiency over a wide range of operating conditions (from startup to steady state). Other benefits of the system include: better source uniformity, more types of phosphor can be used (chemical interaction and high temperatures are no longer an issue), and the phosphor can be made up from a pre-manufactured sheet (thereby lowering cost and complexity of phosphor deposition). Several laboratory prototypes were built and operated at the expected high performance level. The project fully explored two types of remote phosphor system: …

A linear scaling approach for general and accurate pseudopotential Density Functional Theory calculations is presented. It is based on a Finite Difference discretization. Effective O(N) scaling is achieved by confining the orbitals in spherical localization regions. To improve accuracy and flexibility while computing the smallest possible number of orbitals, we propose an algorithm to adapt localization regions during computation. Numerical results for a polyacethylene chain and a magnesium oxide ring are presented.

We continue to utilize the oligonucleotide microarrays that were constructed through funding with this project to characterize growth responses of Desulfovibrio vulgaris relevant to metal-reducing conditions. To effectively immobilize heavy metals and radionuclides via sulfate-reduction, it is important to understand the cellular responses to adverse factors observed at contaminated subsurface environments (e.g., nutrients, pH, contaminants, growth requirements and products). One of the major goals of the project is to construct whole-genome microarrays for Desulfovibrio vulgaris. First, in order to experimentally establish the criteria for designing gene-specific oligonucleotide probes, an oligonucleotide array was constructed that contained perfect match (PM) and mismatch (MM) probes (50mers and 70mers) based upon 4 genes. The effects of probe-target identity, continuous stretch, mismatch position, and hybridization free energy on specificity were examined. Little hybridization was observed at a probe-target identity of <85% for both 50mer and 70mer probes. 33 to 48% of the PM signal intensities were detected at a probe-target identity of 94% for 50mer oligonucleotides, and 43 to 55% for 70mer probes at a probe-target identity of 96%. When the effects of sequence identity and continuous stretch were considered independently, a stretch probe (>15 bases) contributed an additional 9% of the PM signal intensity …

Recent CO{sub 2} sequestration pilot projects have implemented novel approaches to well-based subsurface monitoring aimed at increasing the amount and quality of information available from boreholes. Some of the drivers for the establishment of new well-based technologies and methodologies arise from: (1) the need for data to assess physical and geochemical subsurface processes associated with CO{sub 2} emplacement; (2) the high cost of deep boreholes and need to maximize data yield from each; (3) need for increased temporal resolution to observe plume evolution; (4) a lack of established processes and technologies for integrated permanent sensors in the oil and gas industry; and (5) a lack of regulatory guidance concerning the amount, type, and duration of monitoring required for long-term performance confirmation of a CO{sub 2} storage site. In this paper we will examine some of the latest innovations in well-based monitoring and present examples of integrated monitoring programs.