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Magnetic (Ga{sub x}Fe{sub 1-x}){sub 3}O{sub 4} nanoparticles with 5%-33% gallium doping (x = 0.05-0.33) were measured using x-ray absorption spectroscopy and x-ray magnetic circular dichroism to determine that the Ga dopant is substituting for Fe{sub 3+} as Ga{sub 3+} in the tetrahedral A-site of the spinel structure, resulting in an overall increase in the total moment of the material. Frequency-dependent alternating-current magnetic susceptibility measurements showed these particles to be weakly interacting with a reduction of the cubic anisotropy energy term with Ga concentration. The element-specific dichroism spectra show that the average Fe moment is observed to increase with Ga concentration, a result consistent with the replacement of A-site Fe by Ga.

We discuss a standard model of heavy ion collisions that has emerged both from experimental results of the RHIC program and associated theoretical developments. We comment briefly on the impact of early results of the LHC program on this picture. We consider how this standard model of heavy ion collisions could be solidified or falsified in future experiments at RHIC, the LHC and a future Electro-Ion Collider.

A series of forty experiments on the National Ignition Facility (NIF) [E. I. Moses et al., Phys. Plasmas 16, 041006 (2009)] to study energy balance and implosion symmetry in reduced- and full-scale ignition hohlraums was shot at energies up to 1.3 MJ. This paper reports the findings of the analysis of the ensemble of experimental data obtained that has produced an improved model for simulating ignition hohlraums. Last year the first observation in a NIF hohlraum of energy transfer between cones of beams as a function of wavelength shift between those cones was reported [P. Michel, et al, Phys of Plasmas, 17, 056305, (2010)]. Detailed analysis of hohlraum wall emission as measured through the laser entrance hole (LEH) has allowed the amount of energy transferred versus wavelength shift to be quantified. The change in outer beam brightness is found to be quantitatively consistent with LASNEX [G. B. Zimmerman and W. L. Kruer, Comments Plasma Phys. Control. Fusion 2, 51 (1975)] simulations using the predicted energy transfer when possible saturation of the plasma wave mediating the transfer is included. The effect of the predicted energy transfer on implosion symmetry is also found to be in good agreement with gated x-ray framing …

We describe a molecularly defined duplication kit for the X chromosome of Drosophila melanogaster. A set of 408 overlapping P[acman] BAC clones was used to create small duplications (average length 88 kb) covering the 22-Mb sequenced portion of the chromosome. The BAC clones were inserted into an attP docking site on chromosome 3L using C31 integrase, allowing direct comparison of different transgenes. The insertions complement 92% of the essential and viable mutations and deletions tested, demonstrating that almost all Drosophila genes are compact and that the current annotations of the genome are reasonably accurate. Moreover, almost all genes are tolerated at twice the normal dosage. Finally, we more precisely mapped two regions at which duplications cause diplo-lethality in males. This collection comprises the first molecularly defined duplication set to cover a whole chromosome in a multicellular organism. The work presented removes a long-standing barrier to genetic analysis of the Drosophila X chromosome, will greatly facilitate functional assays of X-linked genes in vivo, and provides a model for functional analyses of entire chromosomes in other species.

Reductions are commonly used in parallel programs to produce a global result from partial results computed in parallel. Currently, OpenMP only supports reductions for primitive data types and a limited set of base language operators. This is a significant limitation for those applications that employ user-defined data types (e. g., objects). Implementing manual reduction algorithms makes software development more complex and error-prone. Additionally, an OpenMP runtime system cannot optimize a manual reduction algorithm in ways typically applied to reductions on primitive types. In this paper, we propose new mechanisms to allow the use of most pre-existing binary functions on user-defined data types as User-Defined Reduction (UDR) operators. Our measurements show that our UDR prototype implementation provides consistently good performance across a range of thread counts without increasing general runtime overheads.

Radiochemistry-based techniques will be an important complement to x-ray implosion diagnostics. Simulations demonstrate the value of alpha-induced or deuteron-induced reactions as a direct measurement of static mix contamination in DT-filled ignition capsules. In this proceedings we examine to what extent neutron-induced reactions might be highly correlated with the energetically down-scattered neutron fraction which is, in turn, related to the critical quantity of fuel areal density, {rho}R. Although alpha and deuteron reactions are highly suppressed in HT/D-filled capsules, neutron-induced reactions produce robust abundances and 2% measurements of the relevant radiological ratios is achievable. We conclude that radiochemical data are strongly correlated with the down-scattered fraction and fuel areal density. Unknown physics, primarily uncertainties in the direct T-T fusion neutron cross section and, to a lesser extent, various radiochemical production cross sections are important but calibration shots can be used to reduce these errors. The primary advantage of radiochemistry remains - it is the only technique that samples down-scattered neutrons from the entire capsule during the burn. In particular radiochemistry correlated with other diagnostics can be used to minimize experimental uncertainties and thus maximize gain.

We present a new spatial discretization of the discrete-ordinates transport equation in two-dimensional Cartesian (X-Y) geometry for arbitrary polygonal meshes. The discretization is a discontinuous finite element method (DFEM) that utilizes piecewise bi-linear (PWBL) basis functions, which are formally introduced in this paper. We also present a series of numerical results on quadrilateral and polygonal grids and compare these results to a variety of other spatial discretizations that have been shown to be successful on these grid types. Finally, we note that the properties of the PWBL basis functions are such that the leading-order piecewise bi-linear discontinuous finite element (PWBLD) solution will satisfy a reasonably accurate diffusion discretization in the thick diffusion limit, making the PWBLD method a viable candidate for many different classes of transport problems.

A series of bis(3-hydroxy-N-methyl-pyridin-2-one) ligands was synthesized, and their respective uranyl complexes were characterized by single crystal X-ray diffraction analyses. These structures were inspected for high-energy conformations and evaluated using a series of metrics to measure co-planarity of chelating moieties with each other and the uranyl coordination plane, as well as to measure coordinative crowding about the uranyl dication. Both very short (ethyl, 3,4-thiophene and o-phenylene) and very long ({alpha},{alpha}{prime}-m-xylene and 1,8-fluorene) linkers provide optimal ligand geometries about the uranyl cation, resulting in planar, unstrained molecular arrangements. The planarity of the rigid linkers also suggests there is a degree of pre-organization for a planar coordination mode that is ideal for uranyl-selective ligand design. Comparison of intramolecular N{sub amide}-O{sub phenolate} distances and {sup 1}H NMR chemical shifts of amide protons supports earlier results that short linkers provide the optimal geometry for intramolecular hydrogen bonding.

A neutron source for neutron resonance spectroscopy (NRS) has been developed using high intensity, short pulse lasers. This measurement technique will allow for robust measurements of interior ion temperature of laser-shocked materials and provide insight into equation of state (EOS) measurements. The neutron generation technique uses protons accelerated by lasers off of Cu foils to create neutrons in LiF, through (p,n) reactions with {sup 7}Li and {sup 19}F. The distribution of the incident proton beam has been diagnosed using radiochromic film (RCF). This distribution is used as the input for a (p,n) neturon prediction code which is compared to experimentally measured neutron yields. From this calculation, a total fluence of 1.8 x 10{sup 9} neutrons is infered, which is shown to be a reasonable amount for NRS temperature measurement.

Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence determinants such as quantitative scores of promoters and terminators? Are translation efficiency measures, e.g. codon adaptation index and RBS score related to gene expression? We used the whole transcriptome shotgun sequencing of a bacterial pathogen Bacillus anthracis to assess correlation of gene expression level with promoter, terminator and RBS scores, codon adaptation index, as well as with a new measure of gene translational efficiency, average translation speed. We compared computational predictions of operon topologies with the transcript borders inferred from RNA-Seq reads. Transcriptome mapping may also improve existing gene annotation. Upon assessment of accuracy of current annotation of protein-coding genes in the B. anthracis genome we have shown that the transcriptome data indicate existence of more than a hundred genes missing in the annotation though predicted by an ab initio gene finder. Interestingly, we observed that many pseudogenes possess not only a sequence with detectable coding potential but also promoters that maintain transcriptional activity.

New chemical kinetic reaction mechanisms are developed for two of the five major components of biodiesel fuel, methyl stearate and methyl oleate. The mechanisms are produced using existing reaction classes and rules for reaction rates, with additional reaction classes to describe other reactions unique to methyl ester species. Mechanism capabilities were examined by computing fuel/air autoignition delay times and comparing the results with more conventional hydrocarbon fuels for which experimental results are available. Additional comparisons were carried out with measured results taken from jet-stirred reactor experiments for rapeseed methyl ester fuels. In both sets of computational tests, methyl oleate was found to be slightly less reactive than methyl stearate, and an explanation of this observation is made showing that the double bond in methyl oleate inhibits certain low temperature chain branching reaction pathways important in methyl stearate. The resulting detailed chemical kinetic reaction mechanism includes more approximately 3500 chemical species and more than 17,000 chemical reactions.

Using X-ray microprobe analysis of samples from comet Wild 2 returned by the Stardust mission, we determine that the crystalline Fe-bearing silicate fraction in this Jupiter-family comet is greater than 0.5. Assuming this mixture is a composite of crystalline inner solar system material and amorphous cold molecular cloud material, we deduce that more than half of Wild 2 has been processed in the inner solar system. Several models exist that explain the presence of crystalline materials in comets. We explore some of these models in light of our results.

The accuracy and representativeness of flux measurements from a tall tower in a complex landscape was assessed by examining the vertical and sector variability of the ratio of wind speed to momentum flux and the ratio of vertical advective to eddy flux of heat. The 30-60 m ratios were consistent with theoretical predictions which indicate well mixed flux footprints. Some variation with sector was observed that were consistent with upstream roughness. Vertical advection was negligible compared with vertical flux except for a few sectors at night. This implies minor influence from internal boundary layers. Flux accuracy is a function of sector and stability but 30-60 m fluxes were found to be generally representative of the surrounding landscape. This paper will study flux data from a 300 m tower, with 4 levels of instruments, in a complex landscape. The surrounding landscape will be characterized in terms of the variation in the ratio of mean wind speed to momentum flux as a function of height and wind direction. The importance of local advection will be assessed by comparing vertical advection with eddy fluxes for momentum and heat.

The National Spherical Torus Experiment (NSTX) will be upgraded to provide increased toroidal field, plasma current and pulse length. This involves the replacement of the so-called center stack, including the inner legs of the Toroidal Field (TF) coil, the Ohmic Heating (OH) coil, and the inner Poloidal Field (PF) coils. In addition the increased performance of the upgrade requires qualification of remaining existing components for higher loads. Initial conceptual design efforts were based on worst-case combinations of possible currents that the power supplies could deliver. This proved to be an onerous requirement and caused many of the outer coils support structures to require costly heavy reinforcement. This has led to the planned implementation of a Digital Coil Protection System (DCPS) to reduce design-basis loads to levels that are more realistic and manageable. As a minimum, all components must be qualified for the increase in normal operating loads with headroom. Design features and analysis efforts needed to meet the upgrade loading are discussed. Mission and features of the DCPS are presented.

To enable detailed investigations of early stage hydrothermal plume formation and abiotic and biotic plume processes we developed a new oceanographic tool. The Suspended Particulate Rosette sampling system has been designed to collect geochemical and microbial samples from the rising portion of deep-sea hydrothermal plumes. It can be deployed on a remotely operated vehicle for sampling rising plumes, on a wire-deployed water rosette for spatially discrete sampling of non-buoyant hydrothermal plumes, or on a fixed mooring in a hydrothermal vent field for time series sampling. It has performed successfully during both its first mooring deployment at the East Pacific Rise and its first remotely-operated vehicle deployments along the Mid-Atlantic Ridge. It is currently capable of rapidly filtering 24 discrete large-water-volume samples (30-100 L per sample) for suspended particles during a single deployment (e.g. >90 L per sample at 4-7 L per minute through 1 {mu}m pore diameter polycarbonate filters). The Suspended Particulate Rosette sampler has been designed with a long-term goal of seafloor observatory deployments, where it can be used to collect samples in response to tectonic or other events. It is compatible with in situ optical sensors, such as laser Raman or visible reflectance spectroscopy systems, enabling in situ …

We present a detailed analysis of the structural and magnetic properties of solution-grown PtCo-CdS hybrid structures in comparison to similar free-standing PtCo alloy nanoparticles. X-ray absorption spectroscopy is utilized as a sensitive probe for identifying subtle differences in the structure of the hybrid materials. We found that the growth of bimetallic tips on a CdS nanorod substrate leads to a more complex nanoparticle structure composed of a PtCo alloy core and thin CoO shell. The core-shell architecture is an unexpected consequence of the different nanoparticle growth mechanism on the nanorod tip, as compared to free growth in solution. Magnetic measurements indicate that the PtCo-CdS hybrid structures are superparamagnetic despite the presence of a CoO shell. The use of X-ray spectroscopic techniques to detect minute differences in atomic structure and bonding in complex nanosystems makes it possible to better understand and predict catalytic or magnetic properties for nanoscale bimetallic hybrid materials.

Iron biominerals can form in neutral pH microaerophilic environments where microbes both catalyze iron oxidation and create polymers that localize mineral precipitation. In order to classify the microbial polymers that influence FeOOH mineralogy, we studied the organic and mineral components of biominerals using scanning transmission X-ray microscopy (STXM), micro X-ray fluorescence ({mu}XRF) microscopy, and high-resolution transmission electron microscopy (HRTEM). We focused on iron microbial mat samples from a creek and abandoned mine; these samples are dominated by iron oxyhydroxide-coated structures with sheath, stalk, and filament morphologies. In addition, we characterized the mineralized products of an iron-oxidizing, stalk-forming bacterial culture isolated from the mine. In both natural and cultured samples, microbial polymers were found to be acidic polysaccharides with carboxyl functional groups, strongly spatially correlated with iron oxyhydroxide distribution patterns. Organic fibrils collect FeOOH and control its recrystallization, in some cases resulting in oriented crystals with high aspect ratios. The impact of polymers is particularly pronounced as the materials age. Synthesis experiments designed to mimic the biomineralization processes show that the polysaccharide carboxyl groups bind dissolved iron strongly but release it as mineralization proceeds. Our results suggest that carboxyl groups of acidic polysaccharides are produced by different microorganisms to create a …

The speciation of Cr(VI) in Cromite Ore Processing Residue was investigated by means of bulk XRD, and a combination of micro-XRF, -XAS and -XRD at the Advanced Light Source (ALS), Berkeley, CA, U.S.A.. Bulk XRD yielded one group of phases that contained explicitly Cr(VI) in their structure, Calcium Aluminum Chromium Oxide Hydrates, accounting for 60% of the total Cr(VI). Micro-analyses at ALS yielded complimentary information, confirming that hydrogarnets and hydrotalcites, two mineral groups that can host Cr(VI) in their structure by substitution, were indeed Cr(VI) sinks. Chromatite (CaCrO4) was also identified by micro-XRD, which was not possible with bulk methods due to its low content. The acquisition of micro-XRF elemental maps enabled not only the identification of Cr(VI)-binding phases, but also the understanding of their location within the matrix. This information is invaluable when designing Cr(VI) treatment, to optimize release and availability for reduction.

This paper presents an approach to accomplish synthetic aperture radar (SAR) image segmentation, which are corrupted by speckle noise. Some ordinary segmentation techniques may require speckle filtering previously. Our approach performs radar image segmentation using the original noisy pixels as input data, eliminating preprocessing steps, an advantage over most of the current methods. The algorithm comprises a statistical region growing procedure combined with hierarchical region merging to extract regions of interest from SAR images. The region growing step over-segments the input image to enable region aggregation by employing a combination of the Kolmogorov-Smirnov (KS) test with a hierarchical stepwise optimization (HSWO) algorithm for the process coordination. We have tested and assessed the proposed technique on artificially speckled image and real SAR data containing different types of targets.

We study the universality of the transverse momentum dependent parton distributions at small-x, by comparing the initial/final state interaction effects in dijet-correlation in pA collisions with that in deep inelastic lepton nucleus scattering. We demonstrate the non-universality by an explicit calculation in a particular model where the multiple gauge boson exchange contributions are summed up to all orders. We furthercomment on the implications of our results on the theoretical interpretation of di-hadron correlation in dA collisions in terms of the saturation phenomena in deep inelastic lepton nucleus scattering.

Measured energy performance data are essential to national efforts to improve building efficiency, as evidenced in recent benchmarking mandates, and in a growing body of work that indicates the value of permanent monitoring and energy information feedback. This paper presents case studies of energy information systems (EIS) at four enterprises and university campuses, focusing on the attained energy savings, and successes and challenges in technology use and integration. EIS are broadly defined as performance monitoring software, data acquisition hardware, and communication systems to store, analyze and display building energy information. Case investigations showed that the most common energy savings and instances of waste concerned scheduling errors, measurement and verification, and inefficient operations. Data quality is critical to effective EIS use, and is most challenging at the subsystem or component level, and with non-electric energy sources. Sophisticated prediction algorithms may not be well understood but can be applied quite effectively, and sites with custom benchmark models or metrics are more likely to perform analyses external to the EIS. Finally, resources and staffing were identified as a universal challenge, indicating a need to identify additional models of EIS use that extend beyond exclusive in-house use, to analysis services.

CgWind is a high-fidelity large eddy simulation (LES) tool designed to meet the modeling needs of wind turbine and wind park engineers. This tool combines several advanced computational technologies in order to model accurately the complex and dynamic nature of wind energy applications. The composite grid approach provides high-quality structured grids for the efficient implementation of high-order accurate discretizations of the incompressible Navier-Stokes equations. Composite grids also provide a natural mechanism for modeling bodies in relative motion and complex geometry. Advanced algorithms such as matrix-free multigrid, compact discretizations and approximate factorization will allow CgWind to perform highly resolved calculations efficiently on a wide class of computing resources. Also in development are nonlinear LES subgrid-scale models required to simulate the many interacting scales present in large wind turbine applications. This paper outlines our approach, the current status of CgWind and future development plans.

This article reports an interdisciplinary effort that combines the geospatial informatics approach with a bioinformatics approach to form an improved understanding on the transmission mechanisms of H5N1 virus.