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Desulfovibrio vulgaris ATCC 29579 is a well studied sulfate reducer that has known capabilities of reducing heavy metals and radionuclides, like chromium and uranium. Cultures grown in a defined medium (i.e. LS4D) had a lag period of approximately 40 h when exposed to 50 μMof Cr(VI). Substrate analysis revealed that although chromium is reduced within the first 5 h, growth does not resume for another 35 h. During this time, small amounts of lactate are still utilized but the reduction of sulfate does not occur. Sulfate reduction occurs concurrently with the accumulation of acetate approximately 40 h after inoculation, when growth resumes. Similar amounts of hydrogen are produced during this time compared to hydrogen production by cells not exposed to Cr(VI); therefore an accumulation of hydrogen cannot account for the utilization of lactate. There is a significant decrease in the carbohydrate to protein ratio at approximately 25 h, and this result indicated that lactate is not converted to glycogen. Most probable number analysis indicated that cell viability decreased steadily after inoculation and reached approximately 6 x 104 cells/ml 20 h post-chromium exposure. Regeneration of reducing conditions during chromium exposure does not induce growth and in fact may make the growth …

We compare four algorithms from the latest LAPACK 3.1 release for computing eigenpairs of a symmetric tridiagonal matrix. These include QR iteration, bisection and inverse iteration (BI), the Divide-and-Conquer method (DC), and the method of Multiple Relatively Robust Representations (MR). Our evaluation considers speed and accuracy when computing all eigenpairs, and additionally subset computations. Using a variety of carefully selected test problems, our study includes a variety of today's computer architectures. Our conclusions can be summarized as follows. (1) DC and MR are generally much faster than QR and BI on large matrices. (2) MR almost always does the fewest floating point operations, but at a lower MFlop rate than all the other algorithms. (3) The exact performance of MR and DC strongly depends on the matrix at hand. (4) DC and QR are the most accurate algorithms with observed accuracy O({radical}ne). The accuracy of BI and MR is generally O(ne). (5) MR is preferable to BI for subset computations.

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Solid deuterium-tritium (D-T) fuel layers for inertial confinement fusion experiments were formed inside of a 2 mm diameter beryllium shell and were characterized using phase-contrast enhanced x-ray imaging. The solid D-T surface roughness is found to be 0.4 {micro}m for modes 7-128 at 1.5 K below the melting temperature. The layer roughness is found to increase with decreasing temperature, in agreement with previous visible light characterization studies. However, phase-contrast enhanced x-ray imaging provides a more robust surface roughness measurement than visible light methods. The new x-ray imaging results demonstrate clearly that the surface roughness decreases with time for solid D-T layers held at 1.5 K below the melting temperature.

Accelerator mass spectrometry (AMS) counts individual rare, usually radio-, isotopes such as radiocarbon at high efficiency and specificity in milligram-sized samples. AMS traces very low chemical doses ({micro}g) and radiative doses (100 Bq) of isotope labeled compounds in animal models and directly in humans for pharmaceutical, nutritional, or toxicological research. Absorption, metabolism, distribution, binding, and elimination are all quantifiable with high precision after appropriate sample definition.

We describe here research directed towards early (presyndromic) diagnosis of infection. By using a mouse model and a multi-component blood protein diagnostic tool we detected cowpox infection several days in advance of overt symptoms with high accuracy. We provide details of the experimental design and measurement technique and elaborate on the long-range implication of these results.

An atmospheric chemistry-transport model is used to assess the impacts of sea-spray chemistry on the particle composition in and downwind of a coastal city--Vancouver, British Columbia. Reactions in/on sea-spray affect the entire particle ensemble and particularly the size distribution of particle nitrate. Urban air quality, and particularly airborne particles, is a major concern in terms of human health impacts. Sea-spray is known to be a major component of the particle ensemble at coastal sites yet relatively few air quality models include the interaction of gases with sea-spray and the fate of the particles produced. Sea-spray is not an inert addition to the particle ensemble because heterogeneous chemistry in/on sea-spray droplets changes the droplets composition and the particle size distribution, which impacts deposition and the ion balance in different particle size fractions. It is shown that the ISOPART model is capable of simulating gas and particle concentrations in the coastal metropolis of Vancouver and the surrounding valley. It is also demonstrated that to accurately simulate ambient concentrations of particles and reactive/soluble gases in a coastal valley it is absolutely critical to include heterogeneous chemistry in/on sea-spray. Partitioning of total particle-NO{sub 3}{sup -} between sea-spray and NH{sub 4}NO{sub 3} is highly sensitive …

The research effort in the Waychunas group is focused on the characterization and measurement of processes at the mineral-water interfaces specifically related to the onset of precipitation. This effort maps into one of the main project groups with the Penn State University EMSI (CEKA) known as PIG (Precipitation Interest Group), and involves collaborations with several members of that group. Both synchrotron experimentation and technique development are objectives, with the goals of allowing precipitation from single molecule attachment to sub-monolayer coverage to be detected and analyzed. The problem being addressed is the change in reactivity of mineral interfaces due to passivation or activation by precipitates or sorbates. In the case of passivation, fewer active sites may be involved in reactions with environmental fluids, while in the activated case the precipitate may be much more reactive than the substrate, or result in the creation of a higher density of active sites. We approach this problem by making direct measurements of several types of precipitation reactions: iron-aluminum oxide formation on quartz and other substrates from both homogeneous (in solution) nucleation, and heterogeneous (on the surface) nucleation; precipitation and sorption of silicate monomers and polymers on Fe oxide surfaces; and development of grazing-incidence small …

A complete, isostructural series of lanthanide complexes (except Pm) with the ligand TREN-1,2-HOIQO has been synthesized and structurally characterized by means of single-crystal X-ray analysis. All complexes are 1D-polymeric species in the solid state, with the lanthanide being in an eight-coordinate, distorted trigonal-dodecahedral environment with a donor set of eight unique oxygen atoms. This series constitutes the first complete set of isostructural lanthanide complexes with a ligand of denticity greater than two. The geometric arrangement of the chelating moieties slightly deviates across the lanthanide series, as analyzed by a shape parameter metric based on the comparison of the dihedral angles along all edges of the coordination polyhedron. The apparent lanthanide contraction in the individual Ln-O bond lengths deviates considerably from the expected quadratic decrease that was found previously in a number of complexes with ligands of low denticity. The sum of all bond lengths around the trivalent metal cation, however, is more regular, showing an almost ideal quadratic behavior across the entire series. The quadratic nature of the lanthanide contraction is derived theoretically from Slater's model for the calculation of ionic radii. In addition, the sum of all distances along the edges of the coordination polyhedron show exactly the same …

Electrical conductivity of the lower-mantle ferropericlase-(Mg{sub 0.75},Fe{sub 0.25})O has been studied using designer diamond anvils to pressures over one megabar and temperatures up to 500 K. The electrical conductivity of (Mg{sub 0.75},Fe{sub 0.25})O gradually rises by an order of magnitude up to 50 GPa but decreases by a factor of approximately three between 50 to 70 GPa. This decrease in the electrical conductivity is attributed to the electronic high-spin to low-spin transition of iron in ferropericlase. That is, the electronic spin transition of iron results in a decrease in the mobility and/or density of the charge transfer carriers in the low-spin ferropericlase. The activation energy of the low-spin ferropericlase is 0.27 eV at 101 GPa, similar to that of the high-spin ferropericlase at relatively low temperatures. Our results indicate that low-spin ferropericlase exhibits lower electrical conductivity than high-spin ferropericlase, which needs to be considered in future geomagnetic models for the lower mantle. The extrapolated electrical conductivity of the low-spin ferropericlase, together with that of silicate perovskite, at the lower mantle pressure-temperature conditions is consistent with the model electrical conductivity profile of the lower mantle.

Phenotype microarrays provide a technology to simultaneouslysurvey the response of an organism to nearly 2,000 substrates, includingcarbon, nitrogen and potassium sources; varying pH; varying saltconcentrations; and antibiotics. In order to more quickly and easily viewand compare the large number of growth curves produced by phenotypemicroarray experiments, we have developed software to produce and displaycolor images, each of which corresponds to a set of 96 growth curves.Using color images to represent growth curves data has proven to be avaluable way to assess experiment quality, compare replicates, facilitatecomparison of the responses of different organisms, and identifysignificant phenotypes. The color images are linked to traditional plotsof growth versus time, as well as to information about the experiment,organism, and substrate. In order to share and view information and dataproject-wide, all information, plots, and data are accessible using onlya Web browser.

The nuclear pore complex (NPC) provides the sole aqueous conduit for macromolecular exchange between the nucleus and cytoplasm of cells. Its conduit contains a size-selective gate and is populated by a family of NPC proteins that feature long natively-unfolded domains with phenylalanine-glycine repeats. These FG nucleoporins play key roles in establishing the NPC permeability barrier, but little is known about their dynamic structure. Here we used molecular modeling and biophysical techniques to characterize the dynamic ensemble of structures of a representative FG domain from the yeast nucleoporin Nup116. The results show that its FG motifs function as intra-molecular cohesion elements that impart order to the FG domain. The cohesion of coils mediated by FG motifs in the natively unfolded domain of Nup116 supports a type of tertiary structure, a native pre-molten globule, that could become quaternary at the NPC through recruitment of neighboring FG nucleoporins, forming one cohesive meshwork of intertwined filaments capable of gating protein diffusion across the NPC by size exclusion.

A variety of laser-material interaction experiments have been conducted at Lawrence Livermore National Laboratory (LLNL) utilizing the solid-state heat capacity laser (SSHCL). For these series of experiments, laser output power is 25kW, on-target laser spot sizes of up to 16 cm by 16 cm square, with air speeds of approximately 100 meters per second flowing across the laser-target interaction surface as shown in Figure 1. The empirical results obtained are used to validate our simulation models.

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File system designers continue to look to new architectures to improve scalability. Object-based storage diverges from server-based (e.g. NFS) and SAN-based storage systems by coupling processors and memory with disk drives, delegating low-level allocation to object storage devices (OSDs) and decoupling I/O (read/write) from metadata (file open/close) operations. Even recent object-based systems inherit decades-old architectural choices going back to early UNIX file systems, however, limiting their ability to effectively scale to hundreds of petabytes. We present Ceph, a distributed file system that provides excellent performance and reliability with unprecedented scalability. Ceph maximizes the separation between data and metadata management by replacing allocation tables with a pseudo-random data distribution function (CRUSH) designed for heterogeneous and dynamic clusters of unreliable OSDs. We leverage OSD intelligence to distribute data replication, failure detection and recovery with semi-autonomous OSDs running a specialized local object storage file system (EBOFS). Finally, Ceph is built around a dynamic distributed metadata management cluster that provides extremely efficient metadata management that seamlessly adapts to a wide range of general purpose and scientific computing file system workloads. We present performance measurements under a variety of workloads that show superior I/O performance and scalable metadata management (more than a quarter million metadata …

We discuss wakefields excited by short bunches in accelerators. In particular, we review some of what has been learned in recent years concerning diffraction wakes, roughness impedance, coherent synchrotron radiation wakes, and the resistive wall wake, focusing on analytical solutions where possible. As examples, we apply formulas for these wakes to various parts of the Linac Coherent Light Source (LCLS) project. The longitudinal accelerator structure wake of the SLAC linac is an important ingredient in the LCLS bunch compression process. Of the wakes in the undulator region, the dominant one is the resistive wall wake of the beam pipe.

The attenuation of very high energy gamma rays by pair production on the Galactic interstellar radiation field has long been thought of as negligible. However, a new calculation of the interstellar radiation field consistent with multi-wavelength observations by DIRBE and FIRAS indicates that the energy density of the Galactic interstellar radiation field is higher, particularly in the Galactic center, than previously thought. We have made a calculation of the attenuation of very high energy gamma rays in the Galaxy using this new interstellar radiation field which takes into account its nonuniform spatial and angular distributions. We find that the maximum attenuation occurs around 100 TeV at the level of about 25% for sources located at the Galactic center, and is important for both Galactic and extragalactic sources.

The authors report a study of D*{sub sJ}(2317){sup +} and D{sub sJ}(2460){sup +} meson production in B decays. They observe and measure branching fractions for the decays B{sup +} {yields} D{sub sJ}{sup (*)+} {bar D}{sup (*)0} and B{sup 0} {yields} D{sub sJ}{sup (*)+} {bar D}{sup (*)-} with the subsequent decays D*{sub sJ}(2317){sup +} {yields} D{sub s}{sup +} {pi}{sup 0}, D{sub sJ}(2460){sup +} {yields} D*{sub s}{sup +}{pi}{sup 0}, and D{sub sJ}(2460){sup +} {yields} D{sub s}{sup +}{gamma}. In addition, they perform an angular analysis of D{sub sJ}(2460){sup +} {yields} D{sub s}{sup +}{gamma} decays to test the different D{sub sJ}(2460){sup +} spin hypotheses.

The addition of inexpensive high-speed oscilloscopes has enabled higher Te Thomson scattering measurements on the SSPX spheromak. Along with signal correlation techniques, the scopes allow new analyses based on the shape of the scattered laser pulse to discriminate against fluctuating background plasma light that often make gated-integrator measurements unreliable. A 1.4 J Nd:YAG laser at 1064 nm is the scattering source. Spatial locations are coupled by viewing optics and fibers to 4-wavelength-channel filter polychrometers. Ratios between the channels determine Te while summations of the channels determine density. Typically, the channel that provides scattered signal at higher Te is contaminated by fluctuating background light. Individual channels are correlated with either a modeled representation of the laser pulse or a noise-free stray light signal to extract channel amplitudes.

In recently developed laser-driven shockless compression experiments an ablatively driven shock in a primary target is transformed into a ramp compression wave in a secondary target via unloading followed by stagnation across an intermediate vacuum gap. Current limitations on the achievable peak pressures are limited by the ability of shaping the temporal profile of the ramp compression pulse. We report on new techniques using graded density reservoirs for shaping the loading profile and extending these techniques to high peak pressures.

The BABAR experiment at SLAC successfully collects physics data since 1999. One of the major parts of its on-line system is the configuration database which provides other parts of the system with the configuration data necessary for data taking. Originally the configuration database was implemented in the Objectivity/DB ODBMS. Recently BABAR performed a successful migration of its event store from Objectivity/DB to ROOT and this prompted a complete phase-out of the Objectivity/DB in all other BABAR databases. It required the complete redesign of the configuration database to hide any implementation details and to support multiple storage technologies. In this paper we describe the process of the migration of the configuration database, its new design, implementation strategy and details.

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