The Focusing DIRC is considered for the Barrel PID at a possible Super-B factory. To reduce sensitivity to background, it would be desirable to reduce a size of the present BaBar photon detector. One way to do it is to replace it with a focusing optics and use smaller photon detector pixels. We have simulated the focusing optics with simulation software based on a 3D calculation performed with the Mathematica program. The software does not use Optica package, instead, it uses its own 3D algorithm. The advantage of the presented method is that it is transparent, fast and that it uses a full backing of the Mathematica graphics, and it does not require expertise to run Geat4 MC software.

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We propose a modification to the Levenberg-Marquardt minimization algorithm for a more robust and more efficient calibration of highly parameterized, strongly nonlinear models of multiphase flow through porous media. The new method combines the advantages of truncated singular value decomposition with those of the classical Levenberg-Marquardt algorithm, thus enabling a more robust solution of underdetermined inverse problems with complex relations between the parameters to be estimated and the observable state variables used for calibration. The truncation limit separating the solution space from the calibration null space is re-evaluated during the iterative calibration process. In between these re-evaluations, fewer forward simulations are required, compared to the standard approach, to calculate the approximate sensitivity matrix. Truncated singular values are used to calculate the Levenberg-Marquardt parameter updates, ensuring that safe small steps along the steepest-descent direction are taken for highly correlated parameters of low sensitivity, whereas efficient quasi-Gauss-Newton steps are taken for independent parameters with high impact. The performance of the proposed scheme is demonstrated for a synthetic data set representing infiltration into a partially saturated, heterogeneous soil, where hydrogeological, petrophysical, and geostatistical parameters are estimated based on the joint inversion of hydrological and geophysical data.

Diabetes mellitus results from an absolute or relative deficiency of insulin producing pancreatic beta-cells. The adult human beta-cell's turnover rate remains unknown. We employed novel techniques to examine adult human islet beta-cell turnover and longevity in vivo. Subjects enrolled in NIH clinical trials received thymidine analogues [iododeoxyuridine (IdU) or bromodeoxyuridine (BrdU)] 8-days to 4-years prior to death. Archival autopsy samples from ten patients (aged 17-74 years) were employed to assess beta-cell turnover by scoring nuclear analog labeling within insulin staining cells. Human adult beta-cell longevity was determined by estimating the cells genomic DNA integration of atmospheric carbon-14 ({sup 14}C). DNA was purified from pancreatic islets isolated from cadaveric donors; whole islet prep DNA was obtained from a 15 year old donor, and purified beta-cell DNA was obtained from two donors (age 48 and 80 years). {sup 14}C levels were then determined using accelerator mass spectrometry (AMS). Cellular 'birth date' was determined by comparing the subject's DNA {sup 14}C content relative to a well-established {sup 14}C atmospheric prevalence curve. In the two subjects less than age 20 years, 1-2% of the beta-cell nuclei co-stained for BrdU/IdU. No beta-cell nuclei co-stained in the eight patients more than 30 years old. Consistent with …

This paper is the final paper in a series of papers that discusses passive quench protection for high inductance solenoid magnets. This report describes how passive quench protection system may be applied to superconducting magnets that are connected in series but not inductively coupled. Previous papers have discussed the role of magnet sub-division and quench back from a conductive mandrel in reducing the hot-spot temperature and the peak coil voltages to ground. When magnets are connected in series, quench-back from a conductive mandrel can cause other magnets in a string to quench even without inductive coupling between magnets. The magnet mandrels must be well coupled to the magnet circuit that is being quenched. When magnet circuit sub-division is employed to reduce the voltages-to-ground within magnets, the resistance across the subdivision becomes the most important factor in the successful quenching of the magnet string.

The geological storage of CO{sub 2} in deep saline formations is increasing seen as a viable strategy to reduce the release of greenhouse gases into the atmosphere. However, costs of capture and compression of CO{sub 2} from industrial waste streams containing small quantities of sulfur and nitrogen compounds such as SO{sub 2}, H{sub 2}S and N{sub 2} are very expensive. Therefore, studies on the co-injection of CO{sub 2} containing other acid gases from industrial emissions are very important. In this paper, numerical simulations were performed to study the co-injection of H{sub 2}S with CO{sub 2} in sandstone and carbonate formations. Results indicate that the preferential dissolution of H{sub 2}S gas (compared with CO{sub 2} gas) into formation water results in the delayed breakthrough of H{sub 2}S gas. Co-injection of H{sub 2}S results in the precipitation of pyrite through interactions between the dissolved H{sub 2}S and Fe{sup 2+} from the dissolution of Fe-bearing minerals. Additional injection of H{sub 2}S reduces the capabilities for solubility and mineral trappings of CO{sub 2} compared to the CO{sub 2} only case. In comparison to the sandstone (siliciclastic) formation, the carbonate formation is less favorable to the mineral sequestration of CO{sub 2}. Different from CO{sub 2} …

Comprehensive understanding of the transport and deposition of engineered nanoparticles (NPs) in subsurface is required to assess their potential negative impact on the environment. We studied the deposition behavior of functionalized quantum dot (QD) NPs (CdTe) in different types of sands (Accusand, ultrapure quartz, and iron-coated sand) at various solution ionic strengths (IS). The observed transport behavior in ultrapure quartz and iron-coated sand was consistent with conventional colloid deposition theories. However, our results from the Accusand column showed that deposition was minimal at the lowest IS (1 mM) and increased significantly as the IS increased. The effluent breakthrough occurred with a delay, followed by a rapid rise to the maximum normalized concentration of unity. Negligible deposition in the column packed with ultrapure quartz sand (100 mM) and Accusand (1 mM) rules out the effect of straining and suggests the importance of surface charge heterogeneity in QD deposition in Accusand at higher IS. Data analyses further show that only a small fraction of sand surface area contributed in QD deposition even at the highest IS (100 mM) tested. The observed delay in breakthrough curves of QDs was attributed to the fast diffusive mass transfer rate of QDs from bulk solution to …

Stimulated by an acetate-amendment field experiment conducted in 2007, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this experiment, planktonic biomass was sampled at various time points to quantitatively evaluate proteomes. In 2008, an acetate-amended field experiment was again conducted in a similar manner to the 2007 experiment. As there was no comprehensive metagenome sequence available for use in proteomics analysis, we systematically evaluated 12 different organism genome sequences to generate sets of aggregate genomes, or “pseudo-metagenomes”, for supplying relative quantitative peptide and protein identifications. Proteomics results support previous observations of the dominance of Geobacteraceae during biostimulation using acetate as sole electron donor, and revealed a shift from an early stage of iron reduction to a late stage of iron reduction. Additionally, a shift from iron reduction to sulfate reduction was indicated by changes in the contribution of proteome information contributed by different organism genome sequences within the aggregate set. In addition, the comparison of proteome measurements made between the 2007 field experiment and 2008 field experiment revealed differences in proteome profiles. These differences may be the result of alterations in abundance and population structure …

A pilot-scale system was established to examine the feasibility of in situ U(VI) immobilization at a highly contaminated aquifer (U.S. DOE Integrated Field Research Challenge site, Oak Ridge, TN). Ethanol was injected intermittently as an electron donor to stimulate microbial U(VI) reduction, and U(VI) concentrations fell to below the Environmental Protection Agency drinking water standard (0.03 mg liter{sup -1}). Microbial communities from three monitoring wells were examined during active U(VI) reduction and maintenance phases with GeoChip, a high-density, comprehensive functional gene array. The overall microbial community structure exhibited a considerable shift over the remediation phases examined. GeoChip-based analysis revealed that Fe(III)-reducing bacterial (FeRB), nitrate-reducing bacterial (NRB), and sulfate-reducing bacterial (SRB) functional populations reached their highest levels during the active U(VI) reduction phase (days 137 to 370), in which denitrification and Fe(III) and sulfate reduction occurred sequentially. A gradual decrease in these functional populations occurred when reduction reactions stabilized, suggesting that these functional populations could play an important role in both active U(VI) reduction and maintenance of the stability of reduced U(IV). These results suggest that addition of electron donors stimulated the microbial community to create biogeochemical conditions favorable to U(VI) reduction and prevent the reduced U(IV) from reoxidation and that …

Monodisperse sub-10 nm (6.5 nm) sized Rh nanocrystals with (111) and (100) surface structures were synthesized by a seedless polyol reduction in ethylene glycol, with poly(vinylpyrrolidone) as a capping ligand. When using [Rh(Ac){sub 2}]{sub 2} as the metal precursor, (111)-oriented Rh nanopolyhedra containing 76% (111)-twined hexagons (in 2D projection) were obtained; whereas, when employing RhCl{sub 3} as the metal precursor in the presence of alkylammonium bromide, such as tetramethylammonium bromide and trimethyl(tetradecyl)ammonium bromide, (100)-oriented Rh nanocubes were obtained with 85% selectivity. The {l_brace}100{r_brace} faces of the Rh nanocrystals are stabilized by chemically adsorbed Br{sup -} ions from alkylammonium bromides, which led to (100)-oriented nanocubes. Monolayer films of the (111)-oriented Rh nanopolyhedra and (100)-oriented Rh nanocubes were deposited on silicon wafers in a Langmuir-Blodgett trough to make model 2D nanoarray catalysts. These nanocatalysts were active for CO oxidation by O{sub 2}, and the turnover frequency was independent of nanoparticle shape, consistent with that previously observed for Rh(111) and Rh(100) single crystals.

For elastically noninteracting vertical-fracture sets at arbitrary orientation angles to each other, a detailed model is presented in which the resulting anisotropic fractured medium generally has orthorhombic symmetry overall. Some of the analysis methods and ideas of Schoenberg are emphasized, together with their connections to other similarly motivated and conceptually related methods by Sayers and Kachanov, among others. Examples show how parallel vertical-fracture sets having HTI (horizontal transversely isotropic) symmetry transform into orthotropic fractured media if some subsets of the vertical fractures are misaligned with the others, and then the fractured system can have VTI (vertical transversely isotropic) symmetry if all of the fractures are aligned randomly or half parallel and half perpendicular to a given vertical plane. An orthotropic example having vertical fractures in an otherwise VTI earth system (studied previously by Schoenberg and Helbig) is compared with the other examples treated and it is finally shown how fluids in the fractures affect the orthotropic poroelastic system response to seismic waves. The key result is that fracture-influence parameters are multiplied by a factor of (1-B), where 0 {le} B < 1 is Skempton's second coefficient for poroelastic media. Skempton's B coefficient is itself a measurable characteristic of fluid-saturated porous …

Natural hexagonal birnessite is a poorly-crystalline layer type Mn(IV) oxide precipitated by bacteria and fungi which has a particularly high adsorption affinity for Pb(II). X-ray spectroscopic studies have shown that Pb(II) forms strong inner-sphere surface complexes mainly at two sites on hexagonal birnessite nanoparticles: triple corner-sharing (TCS) complexes on Mn(IV) vacancies in the interlayers and double edge-sharing (DES) complexes on lateral edge surfaces. Although the TCS surface complex has been well characterized by spectroscopy, some important questions remain about the structure and stability of the complexes occurring on the edge surfaces. First-principles simulation techniques such as density functional theory (DFT) offer a useful way to address these questions by providing complementary information that is difficult to obtain by spectroscopy. Following this computational approach, we used spin-polarized DFT to perform total-energy-minimization geometry optimizations of several possible Pb(II) surface complexes on model birnessite nanoparticles similar to those that have been studied experimentally. We first validated our DFT calculations by geometry optimizations of (1) the Pb-Mn oxyhydroxide mineral, quenselite (PbMnO{sub 2}OH), and (2) the TCS surface complex, finding good agreement with experimental structural data while uncovering new information about bonding and stability. Our geometry optimizations of several protonated variants of the DES surface …

The goal of modern high explosive slow heat cookoff modeling is to understand the level of mechanical violence. This requires understanding the coupled thermal-mechanical-chemical system that such an environment creates. Recent advances have improved our ability to predict the time to event, and we have been making progress on predicting the mechanical response. By adding surface tension to the product gas pores in the high explosive, we have been able to reduce the current model's tendency to over-pressurize confinement vessels. We describe the model and demonstrate how it affects a LX-10 STEX experiment. Issues associated with current product gas equations of state are described and examined.

Single-well injection-withdrawal (SWIW) tracer tests involve injection of traced fluid and subsequent tracer recovery from the same well, usually with some quiescent time between the injection and withdrawal periods. SWIW are insensitive to variations in advective processes that arise from formation heterogeneities, because upon withdrawal, fluid parcels tend to retrace the paths taken during injection. However, SWIW are sensitive to diffusive processes, such as diffusive exchange of conservative or reactive solutes between fractures and rock matrix. This paper focuses on SWIW tests in which temperature itself is used as a tracer. Numerical simulations demonstrate the sensitivity of temperature returns to fracture-matrix interaction. We consider thermal SWIW response to the two primary reservoir improvements targeted with stimulation, (1) making additional fractures accessible to injected fluids, and (2) increasing the aperture and permeability of pre-existing fractures. It is found that temperature returns in SWIW tests are insensitive to (2), while providing a strong signal of more rapid temperature recovery during the withdrawal phase for (1).

It is well known in computational fluid dynamics that grid quality affects the accuracy of numerical solutions. When assessing grid quality, properties such as aspect ratio, orthogonality of coordinate surfaces, and cell volume are considered. Mesoscale atmospheric models generally use terrain-following coordinates with large aspect ratios near the surface. As high resolution numerical simulations are increasingly used to study topographically forced flows, a high degree of non-orthogonality is introduced, especially in the vicinity of steep terrain slopes. Numerical errors associated with the use of terrainfollowing coordinates can adversely effect the accuracy of the solution in steep terrain. Inaccuracies from the coordinate transformation are present in each spatially discretized term of the Navier-Stokes equations, as well as in the conservation equations for scalars. In particular, errors in the computation of horizontal pressure gradients, diffusion, and horizontal advection terms have been noted in the presence of sloping coordinate surfaces and steep topography. In this work we study the effects of these spatial discretization errors on the flow solution for three canonical cases: scalar advection over a mountain, an atmosphere at rest over a hill, and forced advection over a hill. This study is completed using the Weather Research and Forecasting (WRF) model. …

This work aims to characterize microbial tolerance to 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), ionic liquid that has emerged as a novel biomass pretreatment for lignocellulosic biomass. Enrichment experiments performed using inocula treated with [C2mim][OAc] under solid and liquid cultivation yielded fungal populationsdominated by Aspergilli. Ionic liquid-tolerant Aspergillus isolates from these enrichments were capable of growing in a radial plate growth assay in the presence of 10% [C2mim][OAc]. When a [C2mim][OAc]-tolerant Aspergillus fumigatus strain was grown in the presence of switchgrass, endoglucanases and xylanases were secreted that retained residual enzymatic activity in the presence of 20% [C2mim][OAc]. The results of the study suggest tolerance to ionic liquids is a general property of Aspergilli. Tolerance to an industrially important ionic liquid was discovered in a fungal genera that is widely used in biotechnology, including biomass deconstruction.

This article uses an analytical approach to determine the dilution of an unsteadily-generated solute in an unsteady solvent stream, under cyclic temporal boundary conditions. The goal is to find a simplified way of showing equivalence of such a process to a reference case where equivalent dilution is defined as a weighted average concentration. This derivation has direct applications to the ventilation of indoor spaces where indoor air quality and energy consumption cannot in general be simultaneously optimized. By solving the equation we can specify how much air we need to use in one ventilation pattern compared to another to obtain same indoor air quality. Because energy consumption is related to the amount of air exchanged by a ventilation system, the equation can be used as a first step to evaluate different ventilation patterns effect on the energy consumption. The use of the derived equation is demonstrated by representative cases of interest in both residential and non-residential buildings.

The decay heat from radioactive waste that is to be disposed in the once proposed geologic repository at Yucca Mountain (YM) will significantly influence the moisture conditions in the fractured rock near emplacement tunnels (drifts). Additionally, large-scale convective cells will form in the open-air drifts and will serve as an important mechanism for the transport of vaporized pore water from the fractured rock in the drift center to the drift end. Such convective processes would also impact drift seepage, as evaporation could reduce the build up of liquid water at the tunnel wall. Characterizing and understanding these liquid water and vapor transport processes is critical for evaluating the performance of the repository, in terms of water-induced canister corrosion and subsequent radionuclide containment. To study such processes, we previously developed and applied an enhanced version of TOUGH2 that solves for natural convection in the drift. We then used the results from this previous study as a time-dependent boundary condition in a high-resolution seepage model, allowing for a computationally efficient means for simulating these processes. The results from the seepage model show that cases with strong natural convection effects are expected to improve the performance of the repository, since smaller relative humidity …

Drosophila melanogaster cell lines are important resources for cell biologists. Here, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. Unannotated transcription is substantial (typically 19% of euchromatic signal). Conservatively, we identify 1405 novel transcribed regions; 684 of these appear to be new exons of neighboring, often distant, genes. Sixty-four percent of genes are expressed detectably in at least one line, but only 21% are detected in all lines. Each cell line expresses, on average, 5885 genes, including a common set of 3109. Expression levels vary over several orders of magnitude. Major signaling pathways are well represented: most differentiation pathways are ‘‘off’’ and survival/growth pathways ‘‘on.’’ Roughly 50% of the genes expressed by each line are not part of the common set, and these show considerable individuality. Thirty-one percent are expressed at a higher level in at least one cell line than in any single developmental stage, suggesting that each line is enriched for genes characteristic of small sets of cells. Most remarkable is that imaginal discderived lines can generally be assigned, on the basis of expression, to small territories within developing discs. These mappings reveal unexpected stability of even fine-grained spatial determination. No two …

We present the Genomic Standards Consortium's (GSC) 'Minimum Information about an ENvironmental Sequence' (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

Recently a Resistive Magnetohydrodynamics (MHD) package has been added to the KULL code. In order to be compatible with the underlying hydrodynamics algorithm, a new sub-zonal magnetics discretization was developed that supports arbitrary polygonal and polyhedral zones. This flexibility comes at the cost of many more unknowns per zone - approximately ten times more for a hexahedral mesh. We can eliminate some (or all, depending on the dimensionality) of the extra unknowns from the global matrix during assembly by using a Schur complement approach. This trades expensive global work for cache-friendly local work, while still allowing solution for the full system. Significant improvements in the solution time are observed for several test problems.

We prove a general theorem on the relation between the bulk topological quantum number and the edge states in two dimensional insulators. It is shown that whenever there is a topological order in bulk, characterized by a non-vanishing Chern number, even if it is defined for a non-conserved quantity such as spin in the case of the spin Hall effect, one can always infer the existence of gapless edge states under certain twisted boundary conditions that allow tunneling between edges. This relation is robust against disorder and interactions, and it provides a unified topological classification of both the quantum (charge) Hall effect and the quantum spin Hall effect. In addition, it reconciles the apparent conflict between the stability of bulk topological order and the instability of gapless edge states in systems with open boundaries (as known happening in the spin Hall case). The consequences of time reversal invariance for bulk topological order and edge state dynamics are further studied in the present framework.

We report hole-doping dependence of the in-plane resistivity {rho}{sub ab} in a cuprate superconductor La{sub 2-x}Sr{sub x}CuO{sub 4}, carefully examined using a series of high-quality single crystals. Our detailed measurements find a tendency towards charge ordering at particular rational hole doping fractions of 1/16, 3/32, 1/8, and 3/16. This observation appears to suggest a specific form of charge order and is most consistent with the recent theoretical prediction of the checkerboard-type ordering of the Cooper pairs at rational doping fractions x = (2m + 1)/2{sup n}, with integers m and n.

At present, the only solid material believed to be a viable option for plasma-facing components (PFCs) in a fusion reactor is tungsten. Operated at the lower temperatures typical of present-day fusion experiments, tungsten is known to suffer from surface degradation during long-term exposure to helium-containing plasmas, leading to reduced thermal conduction to the bulk, and enhanced erosion. Existing alloys are also quite brittle at temperatures under 700oC. However, at a sufficiently high operating temperature (700 - 1000 oC), tungsten is selfannealing and it is expected that surface damage will be reduced to the point where tungsten PFCs will have an acceptable lifetime in a reactor environment. The existence of only one potentially viable option for solid PFCs, though, constitutes one of the most significant restrictions on design space for DEMO and follow-on fusion reactors. In contrast, there are several candidates for liquid metal-based PFCs, including gallium, tin, lithium, and tin-lithium eutectics. We will discuss options for liquid metal walls in tokamaks, looking at both high and low recycling materials. We will then focus in particular on one of the candidate liquids, lithium. Lithium is known to have a high chemical affinity for hydrogen, and has been shown in test stands1 …