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: …

In 2006, Honeywell Federal Manufacturing & Technologies (FM&T) announced an updatedvision statement for the organization. The vision is “To be the most admired team within the NNSA [National Nuclear Security Administration] for our relentless drive to convert ideas into the highest quality products and services for National Security by applying the right technology, outstanding program management and best commercial practices.” The challenge to provide outstanding program management was taken up by the Program Management division and the Program Integration Office (PIO) of the company. This article describes how Honeywell developed and deployed a program management maturity model to drive toward excellence.

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Corrosion of steel canisters, stored in a repository for spent fuel and high-level nuclear wastes, leads to the generation and accumulation of hydrogen gas in the backfilled emplacement tunnels, which may significantly affect long-term repository safety. Previous studies used H{sub 2} generation rates based on the volume of the waste or canister material and the stoichiometry of the corrosion reaction. However, iron corrosion and H{sub 2} generation rates vary with time, depending on factors such as amount of iron, water availability, water contact area, and aqueous and solid chemistry. To account for these factors and feedback mechanisms, we developed a chemistry model related to iron corrosion, coupled with two-phase (liquid and gas) flow phenomena that are driven by gas-pressure buildup associated with H{sub 2} generation and water consumption. Results indicate that by dynamically calculating H{sub 2} generation rates based on a simple model of corrosion chemistry, and by coupling this corrosion reaction with two-phase flow processes, the degree and extent of gas pressure buildup could be much smaller compared to a model that neglects the coupling between flow and reactive transport mechanisms. By considering the feedback of corrosion chemistry, the gas pressure increases initially at the canister, but later decreases …

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.

Amorphous titania (TiO{sub 2}) is an important precursor for synthesis of single-phase nanocrystalline anatase. We synthesized x-ray amorphous titania by hydrolysis of titanium ethoxide at the ice point. Transmission electron microscopy examination and nitrogen gas adsorption indicated the particle size of the synthesized titania is {approx} 2 nm. Synchrotron wide-angle x-ray scattering (WAXS) was used to probe the atomic correlations in this amorphous sample. Atomic pair-distribution function (PDF) derived from Fourier transform of the WAXS data was used for reverse Monte Carlo (RMC) simulations of the atomic structure of the amorphous TiO{sub 2} nanoparticles. Molecular dynamics simulations were used to generate input structures for the RMC. X-ray absorption spectroscopy (XAS) simulations were used to screen candidate structures obtained from the RMC by comparing with experimental XAS data. The structure model that best describes both the WAXS and XAS data shows that an amorphous TiO{sub 2} particle consists of a highly distorted shell and a small strained anatase-like crystalline core. The average coordination number of Ti is 5.3 and most Ti-O bonds are populated around 1.940 {angstrom}. Relative to bulk TiO{sub 2}, the reduction of the coordination number is primarily due to the truncation of the Ti-O octahedra at the amorphous …

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.

Assessments of bentonite barrier performance in waste management scenarios require an accurate description of the diffusion of water and solutes through the barrier. A two-compartment macropore/nanopore model (on which smectite interlayer nanopores are treated as a distinct compartment of the overall pore space) was applied to describe the diffusion of {sup 22}Na{sup +} in compacted, water-saturated Na-bentonites and then compared with the well-known surface diffusion model. The two-compartment model successfully predicted the observed weak ionic strength dependence of the apparent diffusion coefficient (D{sub a}) of Na{sup +}, whereas the surface diffusion model did not, thus confirming previous research indicating the strong influence of interlayer nanopores on the properties of smectite clay barriers. Since bentonite mechanical properties and pore water chemistry have been described successfully with two-compartment models, the results in the present study represent an important contribution toward the construction of a comprehensive two-compartment model of compacted bentonite barriers.

CO oxidation is one of the most studied heterogeneous reactions, being scientifically and industrially important, particularly for removal of CO from exhaust streams and preferential oxidation for hydrogen purification in fuel cell applications. The precious metals Ru, Rh, Pd, Pt, and Au are most commonly used for this reaction because of their high activity and stability. Despite the wealth of experimental and theoretical data, it remains unclear what is the active surface for CO oxidation under catalytic conditions for these metals. In this communication, we utilize in situ synchrotron ambient pressure X-ray photoelectron spectroscopy (APXPS) to monitor the oxidation state at the surface of Rh nanoparticles during CO oxidation and demonstrate that the active catalyst is a surface oxide, the formation of which is dependent on particle size. The amount of oxide formed and the reaction rate both increase with decreasing particle size.

There are two major science programs at the Relativistic Heavy Ion Collider (RHIC). These are the heavy ion program, which collides beams of fully stripped ions, and the polarized proton program. A wide variety of stripper foils and carbon targets are used throughout the RHIC accelerator chain to facilitate these collisions. Each stripper and target has unique properties and functions. Those characteristics will be discussed, as well as recent efforts to improve their performance.

There are currently great needs to develop low-cost inorganic materials that can efficiently perform solar water splitting as photoelectrolysis of water into hydrogen and oxygen has significant potential to provide clean energy. We investigate the Si/TiO2 nanowire heterostructures to determine their potential for the photooxidation of water. We observed that highly dense Si/TiO2 core/shell nanowire arrays enhanced the photocurrent by 2.5 times compared to planar Si/TiO2 structure due to their low reflectance and high surface area. We also showed that n-Si/n-TiO2 nanowire arrays exhibited a larger photocurrent and open circuit voltage than p-Si/n-TiO2 nanowires due to a barrier at the heterojunction.

Possible means of reducing atmospheric CO{sub 2} emissions include injecting CO{sub 2} in petroleum reservoirs for Enhanced Oil Recovery or storing CO{sub 2} in deep saline aquifers. Large-scale injection of CO{sub 2} into subsurface reservoirs would induce a complex interplay of multiphase flow, capillary trapping, dissolution, diffusion, convection, and chemical reactions that may have significant impacts on both short-term injection performance and long-term fate of CO{sub 2} storage. Reactive Transport Modeling is a promising approach that can be used to predict the spatial and temporal evolution of injected CO{sub 2} and associated gas-fluid-rock interactions. This presentation will summarize recent advances in reactive transport modeling of CO{sub 2} storage and review key technical issues on (1) the short- and long-term behavior of injected CO{sub 2} in geological formations; (2) the role of reservoir mineral heterogeneity on injection performance and storage security; (3) the effect of gas mixtures (e.g., H{sub 2}S and SO{sub 2}) on CO{sub 2} storage; and (4) the physical and chemical processes during potential leakage of CO{sub 2} from the primary storage reservoir. Simulation results suggest that CO{sub 2} trapping capacity, rate, and impact on reservoir rocks depend on primary mineral composition and injecting gas mixtures. For example, models …

Growth in renewable energy in the U.S. over the past decade has been propelled by a number of forces, including rising fossil fuel prices, environmental concerns, and policy support at the state and federal levels. In this article, we review and discuss what are arguably the two most important types of state policies for supporting electricity generation from geothermal and other forms of renewable energy: renewables portfolio standards and utility integrated resource planning requirements. Within the Western U.S., where the vast majority of the nation's readily-accessible geothermal resource potential resides, these two types of state policies have been critical to the growth of renewable energy, and both promise to continue to play a fundamental role for the foreseeable future. In its essence, a renewables portfolio standard (RPS) requires utilities and other retail electricity suppliers to produce or purchase a minimum quantity or percentage of their generation supply from renewable resources. RPS purchase obligations generally increase over time, and retail suppliers typically must demonstrate compliance on an annual basis. Mandatory RPS policies are backed by various types of compliance enforcement mechanisms, although most states have incorporated some type of cost-containment provision, such as a cost cap or a cap on retail …

Sr3(Ru1-xMnx)2O7, in which 4d-Ru is substituted by the more localized 3d-Mn, is studied by x-ray dichroism and spin-resolved density functional theory. We find that Mn impurities do not exhibit the same 4+ valence of Ru, but act as 3+ acceptors; the extra eg electron occupies the in-plane 3dx2-y2 orbital instead of the expected out-of-plane 3d3z2-r2. We propose that the 3d-4d interplay, via the ligand oxygen orbitals, is responsible for this crystal-field level inversion and the material's transition to an antiferromagnetic, possibly orbitally ordered, low-temperature state.

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The construction of a host of interesting patterns over one and two dimensions, as transformations of multifractal measures via fractal interpolating functions related to simple affine mappings, is reviewed. It is illustrated that, while space-filling fractal functions most commonly yield limiting Gaussian distribution measures (bells), there are also situations (depending on the affine mappings parameters) in which there is no limit. Specifically, the one-dimensional case may result in oscillations between two bells, whereas the two-dimensional case may give rise to unexpected circle map dynamics of an arbitrary number of two-dimensional circular bells. It is also shown that, despite the multitude of bells over two dimensions, whose means dance making regular polygons or stars inscribed on a circle, the iteration of affine maps yields exotic kaleidoscopes that decompose such an oscillatory pattern in a way that is similar to the many cases that converge to a single bell.

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.

Large inter-individual variation in the composition of the intestinal microbiota between unrelated individuals has made it challenging to identify specific aspects of dysbiosis that lead to Crohn's disease. To reduce variations in exposure during establishment of the gut flora and influence of genotype, we studied the mucosaassociated microbiota of monozygotic twin pairs that were discordant (n=6) or concordant (n=4) for Crohn's disease. DNA was extracted from biopsies collected from 5 locations between the ileum and rectum. Bacterial 16S ribosomal RNA genes were amplified and community composition assessed by terminal-restriction fragment length polymorphism, cloning and sequencing and quantitative real-time PCR. The microbial compositions at all biopsy locations for each individual were similar, regardless of disease state, but there were differences between individuals. In particular, individuals with predominantly ileal Crohn's had a dramatically lower abundance (P<0.001) of Faecalibacterium prausnitzii and increased abundance (P<0.03) of Escherichia coli compared to healthy co-twins and those with Crohn's localized in the colon. This dysbiosis was significantly correlated to the disease phenotype rather than genotype. The reduced abundance of F. prausnitzii and increased abundance of E. coli are indicative of an ileal Crohn's disease phenotype, distinct from colonic Crohn's disease and the relative abundances of these specific …

The paper presents a comparison of hydrologic issues and technical approaches used in deep-well injection and disposal of liquid wastes, and those issues and approaches associated with injection and storage of CO{sub 2} in deep brine formations. These comparisons have been discussed in nine areas: (1) Injection well integrity; (2) Abandoned well problems; (3) Buoyancy effects; (4) Multiphase flow effects; (5) Heterogeneity and flow channeling; (6) Multilayer isolation effects; (7) Caprock effectiveness and hydrogeomechanics; (8) Site characterization and monitoring; and (9) Effects of CO{sub 2} storage on groundwater resources There are considerable similarities, as well as significant differences. Scientifically and technically, these two fields can learn much from each other. The discussions presented in this paper should help to focus on the key scientific issues facing deep injection of fluids. A substantial but by no means exhaustive reference list has been provided for further studies into the subject.

During the construction and operational phases of a high-level radioactive waste (HLW) repository constructed in a clay formation, ventilation of underground drifts will cause desaturation and oxidation of the rock. The Ventilation Experiment (VE) was performed in a 1.3 m diameter unlined horizontal microtunnel on Opalinus clay at Mont Terri underground research laboratory in Switzerland to evaluate the impact of desaturation on rock properties. A multiphase flow and reactive transport model of VE is presented here. The model accounts for liquid, vapor and air flow, evaporation/condensation and multicomponent reactive solute transport with kinetic dissolution of pyrite and siderite and local-equilibrium dissolution/precipitation of calcite, ferrihydrite, dolomite, gypsum and quartz. Model results reproduce measured vapor flow, liquid pressure and hydrochemical data and capture the trends of measured relative humidities, although such data are slightly overestimated near the rock interface due to uncertainties in the turbulence factor. Rock desaturation allows oxygen to diffuse into the rock and triggers pyrite oxidation, dissolution of calcite and siderite, precipitation of ferrihydrite, dolomite and gypsum and cation exchange. pH in the unsaturated rock varies from 7.8 to 8 and is buffered by calcite. Computed changes in the porosity and the permeability of Opalinus clay in the unsaturated …

In this paper a method for the estimation of the curvature along a condensed phase interface is presented. In a previous paper in this journal [1] a mathematical relationship was established between this curvature and a template disk located at a given point along the interface. The portion of the computed area of the template disk covering one of the phases was shown to be asymptotically linear in the mean curvature. Instead of utilizing this relationship, an empirical approach was proposed in [1] in order to compensate for discrete uncertainties. In this paper, we show that this linear relationship can be used directly along the interface avoiding the empirical approach proposed earlier. Modifications of the algorithm are however needed, and with good data smoothing techniques, our method provides good quantitative curvature estimates.

The wind power industry in the U.S. has been on a growth binge in recent years, and the rapid pace of development has made it difficult to keep up with trends in the marketplace. Yet the need for timely, objective information on the wind industry and its progress has never been greater. This article, excerpted from a longer report from the U.S. Department of Energy, attempts to fill this need by providing a comprehensive, yet detailed, overview of key developments in the U.S. wind power market, with a particular focus on 2007. This summary includes information on wind project installation trends, industry developments, and, perhaps most interestingly, project-level installed cost and pricing information that has not otherwise been widely reported. The article concentrates on larger-scale wind applications, defined here as projects utilizing turbines that exceed 50 kW in size. In many cases, the data reported here represent only a sample of all wind projects installed in the United States; furthermore, the data vary in quality. As such, emphasis should be placed on overall trends in the data, rather than on individual data points.

Motor vehicle emissions of ammonia have been measured at a California highway tunnel in the San Francisco Bay area. Between 1999 and 2006, light-duty vehicle ammonia emissions decreased by 38 {+-} 6%, from 640 {+-} 40 to 400 {+-} 20 mg kg{sup -1}. High time resolution measurements of ammonia made in summer 2001 at the same location indicate a minimum in ammonia emissions correlated with slower-speed driving conditions. Variations in ammonia emission rates track changes in carbon monoxide more closely than changes in nitrogen oxides, especially during later evening hours when traffic speeds are highest. Analysis of remote sensing data of Burgard et al. (Environ Sci. Technol. 2006, 40, 7018-7022) indicates relationships between ammonia and vehicle model year, nitrogen oxides, and carbon monoxide. Ammonia emission rates from diesel trucks were difficult to measure in the tunnel setting due to the large contribution to ammonia concentrations in a mixed-traffic bore that were assigned to light-duty vehicle emissions. Nevertheless, it is clear that heavy-duty diesel trucks are a minor source of ammonia emissions compared to light-duty gasoline vehicles.