Theoretical and computational investigations are presented of boundary plasma microturbulence that take into account important effects of the geometry of diverted tokamaks--in particular, the effect of x-point magnetic shear and the termination of field lines on divertor plates. We first generalize our previous 'heuristic boundary condition' which describes, in a lumped model, the closure of currents in the vicinity of the x-point region to encompass three current-closure mechanisms. We then use this boundary condition to derive the dispersion relation for low-beta flute-like modes in the divertor-leg region under the combined drives of curvature, sheath impedance, and divertor tilt effects. The results indicate the possibility of strongly growing instabilities, driven by sheath boundary conditions, and localized in either the private or common flux region of the divertor leg depending on the radial tilt of divertor plates. We re-visit the issue of x-point effects on blobs, examining the transition from blobs terminated by x-point shear to blobs that extend over both the main SOL and divertor legs. We find that, for a main-SOL blob, this transition occurs without a free-acceleration period as previously thought, with x-point termination conditions applying until the blob has expanded to reach the divertor plate. We also derive …

In this paper we describe the capabilities of the MINERvA experiment for the measurement of neutrino-nucleus coherent scattering.

The availability of whole-cell level metabolic networks of high quality has made it possible to develop a predictive understanding of bacterial metabolism. Using the optimization framework of flux balance analysis, I investigate metabolic response and activity patterns to variations in the availability of nutrient and chemical factors such as oxygen and ammonia by simulating 30,000 random cellular environments. The distribution of reaction fluxes is heavy-tailed for the bacteria H. pylori and E. coli, and the eukaryote S. cerevisiae. While the majority of flux balance investigations have relied on implementations of the simplex method, it is necessary to use interior-point optimization algorithms to adequately characterize the full range of activity patterns on metabolic networks. The interior-point activity pattern is bimodal for E. coli and S. cerevisiae, suggesting that most metabolic reaction are either in frequent use or are rarely active. The trimodal activity pattern of H. pylori indicates that a group of its metabolic reactions (20%) are active in approximately half of the simulated environments. Constructing the high-flux backbone of the network for every environment, there is a clear trend that the more frequently a reaction is active, the more likely it is a part of the backbone. Finally, I briefly …

Traditional security approaches do not adequately addressall the requirements of open, scientific computing facilities. Many ofthe methods used for more restricted environments, including almost allcorporate/commercial systems, do not meet the needs of today's science.Use of only the available "state of the practice" commercial methods willhave adverse impact on the ability of DOE to accomplish its sciencegoals, and impacts the productivity of the DOE Science community. Inparticular, NERSC and other high performance computing (HPC) centers havespecial security challenges that are unlikely to be met unless DOE fundsdevelopment and support of reliable and effective tools designed to meetthe cyber security needs of High Performance Science. The securitychallenges facing NERSC can be collected into three basic problem sets:network performance and dynamics, application complexity and diversity,and a complex user community that can have transient affiliations withactual institutions. To address these problems, NERSC proposes thefollowing four general solutions: auditing user and system activityacross sites; firewall port configuration in real time;cross-site/virtual organization identity management and access control;and detecting security issues in application middleware. Solutions arealsoproposed for three general long term issues: data volume,application complexity, and information integration.

Recent instrumental developments have enabled greatly improved resolution of scanning transmission electron microscopes (STEM) through aberration correction. An additional and previously unanticipated advantage of aberration correction is the greatly improved depth sensitivity that has led to the reconstruction of a three-dimensional (3D) image from a focal series. In this chapter the potential of aberration-corrected 3D STEM to provide major improvements in the imaging capabilities for biological samples will be discussed. This chapter contains a brief overview ofthe various high-resolution 3D imaging techniques, a historical perspective of the development of STEM, first estimates of the dose-limited axial and lateral resolution on biological samples and initial experiments on stained thin sections.

The last decade has witnessed a rapid proliferation of superscalar cache-based microprocessors to build high-end computing (HEC) platforms, primarily because of their generality, scalability, and cost effectiveness. However, the growing gap between sustained and peak performance for full-scale scientific applications on conventional supercomputers has become a major concern in high performance computing, requiring significantly larger systems and application scalability than implied by peak performance in order to achieve desired performance. The latest generation of custom-built parallel vector systems have the potential to address this issue for numerical algorithms with sufficient regularity in their computational structure. In this work we explore applications drawn from four areas: magnetic fusion (GTC), plasma physics (LBMHD3D), astrophysics (Cactus), and material science (PARATEC). We compare performance of the vector-based Cray X1, X1E, Earth Simulator, NEC SX-8, with performance of three leading commodity-based superscalar platforms utilizing the IBM Power3, Intel Itanium2, and AMD Opteron processors. Our work makes several significant contributions: a new data-decomposition scheme for GTC that (for the first time) enables a breakthrough of the Teraflop barrier; the introduction of a new three-dimensional Lattice Boltzmann magneto-hydrodynamic implementation used to study the onset evolution of plasma turbulence that achieves over 26Tflop/s on 4800 ES processors; the …

Nucleic acid aptamers have found steadily increased utility and application steadily over the last decade. In particular, aptamers have been touted as a valuable complement to and in some cases replacement for antibodies due to their structural and functional robustness as well as their ease in generation and synthesis. They are thus attractive for biosecurity applications, e.g. pathogen detection, and are especially well suited since their in vitro generation process does not require infection of any host systems. Herein we provide a brief overview of the aptamers generated against biopathogens over the last few years. In addition, a few recently described detection platforms using aptamers (aptasensors) and potentially suitable for biosecurity applications will be discussed.

Simulation of ductile fracture at the atomic scale reveals many aspects of the fracture process including specific mechanisms associated with void nucleation and growth as a precursor to fracture and the plastic deformation of the material surrounding the voids and cracks. Recently we have studied void coalescence in ductile metals using large-scale atomistic and continuum simulations. Here we review that work and present some related investigations. The atomistic simulations involve three-dimensional strain-controlled multi-million atom molecular dynamics simulations of copper. The correlated growth of two voids during the coalescence process leading to fracture is investigated, both in terms of its onset and the ensuing dynamical interactions. Void interactions are quantified through the rate of reduction of the distance between the voids, through the correlated directional growth of the voids, and through correlated shape evolution of the voids. The critical inter-void ligament distance marking the onset of coalescence is shown to be approximately one void radius based on the quantification measurements used, independent of the initial separation distance between the voids and the strain-rate of the expansion of the system. No pronounced shear flow is found in the coalescence process. We also discuss a technique for optimizing the calculation of fine-scale information …

In acidic aqueous solutions, gluconate protonation is coupled with lactonization of gluconic acid. With the decrease of pC{sub H}, two lactones ({delta}/{gamma}) are sequentially formed. The {delta}-lactone forms more readily than the {gamma}-lactone. In 0.1 M gluconate solutions, if pC{sub H} is above 2.5, only the {delta}-lactone is generated. When pC{sub H} is decreased below 2.0, the formation of the {gamma}-lactone is observable although the {delta}-lactone predominates. At I = 0.1 M NaClO{sub 4} and room temperature, the deprotonation constant of the carboxylic group, using the NMR technique, was determined to be log K{sub a} = 3.30 {+-} 0.02; the {delta}-lactonization constant, by the batch potentiometric titrations, was obtained to be log K{sub L} = - (0.54 {+-} 0.04). Using ESI-MS, the rate constants of the {delta}-lactonization and the hydrolysis at pC{sub H} {approx} 5.0 were estimated to be k{sub 1} = 3.2 x 10{sup -5} s{sup -1} and k{sup -1} = 1.1 x 10{sup -4} s{sup -1}, respectively.

This manuscript discusses the multilayer coating results for the primary and secondary mirrors of the Micro Exposure Tool (MET): a 0.30-numerical aperture (NA) lithographic imaging system with 200 x 600 {micro}m{sup 2} field of view at the wafer plane, operating in the extreme ultraviolet (EUV) wavelength region. Mo/Si multilayers were deposited by DC-magnetron sputtering on large-area, curved MET camera substrates, and a velocity modulation technique was implemented to consistently achieve multilayer thickness profiles with added figure errors below 0.1 nm rms to achieve sub-diffraction-limited performance. This work represents the first experimental demonstration of sub-diffraction-limited multilayer coatings for high-NA EUV imaging systems.

Ultra supercritical (USC) power plants offer the promise of higher efficiencies and lower emissions. Current goals of the U.S. Department of Energy’s Advanced Power Systems Initiatives include coal generation at 60% efficiency, which would require steam temperatures of up to 760°C. This research examines the steamside oxidation of alloys for use in USC systems, with emphasis placed on applications in high- and intermediate-pressure turbines. The list of alloys being examined is discussed, including the addition of new alloys to the study. These include alloy 625, selected because of its use as one of the two alloys used for turbine rotors, valves, casings, blading and bolts in the European AD700 full-scale demonstration plant (Scholven Unit F). The other alloy, alloy 617, is already one of the alloys currently being examined by this project. Other new alloys to the study are the three round robin alloys in the UK-US collaboration: alloys 740, TP347HFG, and T92. Progress on the project is presented on cyclic oxidation in 50% air – 50% water vapor, furnace exposures in moist air, and thermogravimetric analysis in argon with oxygen saturated steam. An update on the progress towards obtaining an apparatus for high pressure exposures is given.

The elemental (non-volatile) composition of five Stardust impact tracks and terminal particles left from capture of Comet 81P/Wild 2 dust were mapped in a synchrotron x-ray scanning microprobe with full fluorescence spectra at each pixel. Because aerogel includes background levels of several elements of interest, we employ a novel 'dual threshold' approach to discriminate against background contaminants: an upper threshold, above which a spectrum contains cometary material plus aerogel and a lower threshold below which it contains only aerogel. The difference between normalized cometary-plus-background and background-only spectra is attributable to cometary material. The few spectra in between are discarded since misallocation is detrimental: cometary material incorrectly placed in the background spectrum is later subtracted from the cometary spectrum, doubling the loss of reportable cometary material. This approach improves precision of composition quantification. We present the refined whole impact track and terminal particle elemental abundances for the five impact tracks. One track shows mass increases in Cr and Mn (1.4x), Cu, As and K (2x), Zn (4x) and total mass (13%) by dual thresholds compared to a single threshold. Major elements Fe and Ni are not significantly affected. The additional Cr arises from cometary material containing little Fe. We exclude Au …

Gasifiers are containment vessels used to react carbon-containing materials with oxygen and water, producing syngas (CO and H2) that is used in chemical and power production. It is also a potential source of H2 in a future hydrogen economy. Air cooled slagging gasifiers are one type of gasifier, operating at temperatures from 1275-1575º C and at pressures of 400 psi or higher. They typically use coal or petroleum coke as the carbon source, materials which contain ash impurities that liquefy at the gasification temperatures, producing liquid slag in quantities of 100 or more tons/day, depending on the carbon fed rate and the percent ash present in the feedstock. The molten slag is corrosive to refractory linings, causing chemical dissolution and spalling. The refractory lining is composed of chrome oxide, alumina, and zirconia; and is replaced every 3-24 months. Gasifier users would like greater on-line availability and reliability of gasifier liners, something that has impacted gasifier acceptance by industry. Research is underway at NETL to improve refractory service life and to develop a no-chrome or low-chrome oxide alternative refractory liner. Over 250 samples of no- or low-chrome oxide compositions have been evaluated for slag interactions by cup testing; with potential candidates …

Recognizing the role that semiconductor suppliers can playin meeting energy-efficiency regulations and voluntary specifications,this paper provides an overview of Chinese policies and implementingbodies; a discussion of current programs, their goals, and effectiveness;and possible steps that can be taken tomeet these energy-efficiencyrequirements while also meeting products' high performance and costgoals.

In general, the Linux 2.6 scheduler can ensure fairness and provide excellent interactive performance at the same time. However, our experiments and mathematical analysis have shown that the current Linux interactivity mechanism tends to incorrectly categorize non-interactive network applications as interactive, which can lead to serious fairness or starvation issues. In the extreme, a single process can unjustifiably obtain up to 95% of the CPU! The root cause is due to the facts that: (1) network packets arrive at the receiver independently and discretely, and the 'relatively fast' non-interactive network process might frequently sleep to wait for packet arrival. Though each sleep lasts for a very short period of time, the wait-for-packet sleeps occur so frequently that they lead to interactive status for the process. (2) The current Linux interactivity mechanism provides the possibility that a non-interactive network process could receive a high CPU share, and at the same time be incorrectly categorized as 'interactive.' In this paper, we propose and test a possible solution to address the interactivity vs. fairness problems. Experiment results have proved the effectiveness of the proposed solution.

The complete sequences of the mitochondrial genomes of theoomycetes of Phytophthora ramorum and P. sojae were determined during thecourse of their complete nuclear genome sequencing (Tyler, et al. 2006).Both are circular, with sizes of 39,314 bp for P. ramorum and 42,975 bpfor P. sojae. Each contains a total of 37 identifiable protein-encodinggenes, 25 or 26 tRNAs (P. sojae and P. ramorum, respectively)specifying19 amino acids, and a variable number of ORFs (7 for P. ramorum and 12for P. sojae) which are potentially additional functional genes.Non-coding regions comprise approximately 11.5 percent and 18.4 percentof the genomes of P. ramorum and P. sojae, respectively. Relative to P.sojae, there is an inverted repeat of 1,150 bp in P. ramorum thatincludes an unassigned unique ORF, a tRNA gene, and adjacent non-codingsequences, but otherwise the gene order in both species is identical.Comparisons of these genomes with published sequences of the P. infestansmitochondrial genome reveals a number of similarities, but the gene orderin P. infestans differs in two adjacent locations due to inversions.Sequence alignments of the three genomes indicated sequence conservationranging from 75 to 85 percent and that specific regions were morevariable than others.

The Entiat 4-mile Wells (Entiat 4-mile) project is located in the Entiat subbasin and will benefit Upper Columbia steelhead, spring Chinook and bull trout. The goal of this project is to prevent juvenile fish from being diverted into an out-of-stream irrigation system and to eliminate impacts due to the annual maintenance of an instream pushup dam. The objectives include eliminating a surface irrigation diversion and replacing it with two wells, which will provide Bonneville Power Administration (BPA) and the Bureau of Reclamation (Reclamation) with a Federal Columbia River Power System (FCRPS) BiOp metric credit of one. Wells were chosen over a new fish screen based on biological benefits and costs. Long-term biological benefits are provided by completely eliminating the surface diversion and the potential for fish entrainment in a fish screen. Construction costs for a new fish screen were estimated at $150,000, which does not include other costs associated with implementing and maintaining a fish screening project. Construction costs for a well were estimated at $20,000 each. The diversion consisted of a pushup dam that diverted water into an off-channel pond. Water was then pumped into a pressurized system for irrigation. There are 3 different irrigators who used water from …

Dose-response curves for induction of micro-nuclei (MN) was measured in Chinese hamster V79 and xrs6 (Ku80-) cells and in human mammary epithelial MCF10A cells in the dose range of 0.05-1 Gy. The Chinese Hamster cells were exposed to 1 GeV/u Fe ions, 600 MeV/u Fe ions, and 300 MeV/u Fe ions (LETs of 151, 176 and 235 keV/{micro}m respectively) as well as with 320 kVp X-rays as reference. Second-order polynomials were fitted to the induction curves and the initial slopes (the alpha values) were used to calculate RBE. For the repair proficient V79 cells the RBE at these low doses increased with LET. The values obtained were 3.1 (LET=151 keV/{micro}m), 4.3 (LET = 176 keV/{micro}m) and 5.7 (LET = 235 keV/{micro}m), while the RBE was close to 1 for the repair deficient xrs6 cells regardless of LET. For the MCF10A cells the RBE was determined for 1 GeV/u Fe ions and found to be 5.4, slightly higher than for V79 cells. To test the effect of shielding, the 1 GeV/u Fe ion beam was intercepted by various thickness of high-density polyethylene plastic absorbers, which resulted in energy loss and fragmentation. It was found that the MN yield for V79 cells …

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Trivalent bismuth luminescence is reported in three Sillenbismuth oxyhalide phases, SrBiO2Cl, BaBiO2Cl, and BaBiO2Br. Thesecompounds exhibit Bi 6s6->6 s2 emission under UV and X-ray radiation.At room temperature, BaBiO2Cl shows the most intense light emission, withspectral and decay properties similar to those found in Bi4Ge3O12 (BGO).At low temperatures, each phase show an increase in the photoluminescenceintensities and a narrowing of the emission peaks. In contrast to thetemperature dependence of BGO, X-ray excited luminescence intensities ofall three phases remain relatively constant throughout the temperaturerange 10 - 295 K. This result indicates that the Sillen phases undergoless thermal quenching than BGO. The low temperature and room temperatureradio-luminescence decay times were determined from pulsed x-raymeasurements. At room temperature, SrBiO2Cl exhibits faster decays thanBGO, while, BaBiO2Cl and BaBiO2Br have decay times similar toBGO.

Understanding the influence of past land use changes on climate is needed to improve regional projections of future climate change and inform debates about the tradeoffs associated with land use decisions. The effects of rapid expansion of irrigated area in the 20th century has remained unclear relative to other land use changes, such as urbanization, that affected a similar total land area. Using spatial and temporal variations in temperature and irrigation extent observed in California, we show that irrigation expansion has had a large cooling effect on summertime average daily daytime temperatures (-0.15 to -0.25 C.decade{sup -1}), which corresponds to a cooling estimated at -2.0 - -3.3 C since the introduction of irrigation practice. Irrigation has negligible effects on nighttime temperatures, leading to a net cooling effect of irrigation on climate (-0.06 to -0.19 C.decade{sup -1}). Stabilization of irrigated area has occurred in California since 1980 and is expected in the near future for most irrigated regions. The suppression of past human-induced greenhouse warming by increased irrigation is therefore likely to slow in the future, and a potential decrease in irrigation may even contribute to a more rapid warming. Changes in irrigation alone are not expected to influence broadscale temperatures, …

The purpose of this study was to determine if the alpha energy spectrum in a Passive Implanted Planar Silicon (PIPS) detector, as modeled by MCNPX [1], can be used to design a radon stripping algorithm for a continuous air monitor (CAM). This stripping algorithm would be employed to discriminate naturally occurring radioisotopes from the anthropogenic for nuclear safety -related applications. It is hoped that using an algorithm based on MCNPX simulations, the CAM will not be prone to false alarms when radon levels are dynamic as identified in other CAM systems [2,3]. This work is focused on the design of the next generation air particulate detector (NGAPD) for the United States Navy. The primary isotope of interest is Co-60. This radionuclide emits a beta with an average energy of 96 keV. Therefore, once deposited on the CAM filter, it will produce a beta continuum seen by the PIPS detector. In addition, as radon progeny is deposited on the air filter, these will give rise to characteristic alpha peaks and a beta continuum. This is primarily an issue in port-or land-based applications. Ultimately, measurement of a radon alpha spectrum is desired to predict the amount of beta activity which would be …

Technologies for introducing molecules into living cells are vital for probing the physical properties and biochemical interactions that govern the cell's behavior. Here we report the development of a nanoscale cell injection system-termed the nanoinjector-that uses carbon nanotubes to deliver cargo into cells. A single multi-walled carbon nanotube attached to an atomic force microscope tip was functionalized with cargo via a disulfide-based linker. Penetration of cell membranes with this 'nanoneedle', followed by reductive cleavage of the disulfide bonds within the cell's interior, resulted in the release of cargo inside the cells. The capability of the nanoinjector was demonstrated by injection of protein-coated quantum dots into live human cells. Single-particle tracking was employed to characterize the diffusion dynamics of injected quantum dots in the cytosol. This new technique causes no discernible membrane or cell damage, and can deliver a discrete number of molecules to the cell's interior without the requirement of a carrier solvent.

Most expert analyses of the projected world energy needs show utilization of nuclear energy will be essential for the next few decades, and hence the need to support this technology grows. But as one measure of the supporting science base of this field, as of December 2006, only 25 Pu containing structures were in the Cambridge Structural Database, as compared to 21,807 for Fe. A comparison of the rate of addition to this knowledge base reveals that approximately 500 Fe structures are registered with the Cambridge Structural Database every year, while in the same period only two or three Pu crystal structures are published. A continuing objective of this laboratory has been the development of new sequestering agents for actinide decorporation and selective extractions. This effort has been based on similarities in the properties of Pu(IV) and Fe(III), and the chelating groups in microbial Fe(III) sequestering agents, siderophores. The HOPO ligands (Figure 1) are one such class of chelating group which have been investigated as selective actinide extractants.