Calculations suggest that experiments relating to disk heating, as well as beam deposition, focusing and transport can be performed within the context of current design proposals for accelerator test-facilities. Since the test-facilities have lower ion kinetic energy and beam pulse power as compared to reactor drivers, we achieve high-beam intensities at the focal spot by using short focal distance and properly designed beam optics. In this regard, the low beam emittance of suggested multi-beam designs are very useful. Possibly even higher focal spot brightness could be obtained by plasma lenses which involve external fields on the beam which is stripped to a higher charge state by passing through a plasma cell. Preliminary results suggest that intensities approx. 10/sup 13/ - 10/sup 14/ W/cm/sup 2/ are achievable. Given these intensities, deposition experiments with heating of disks to greater than a million degrees Kelvin (100 eV) are expected.

We report the construction of a cell-based fluorescent reporter for anthrax lethal factor (LF) protease activity using the principle of fluorescence resonance energy transfer (FRET). This was accomplished by engineering an Escherichia coli cell line to express a genetically encoded FRET reporter and LF protease. Both proteins were encoded in two different expression plasmids under the control of different tightly controlled inducible promoters. The FRET-based reporter was designed to contain a LF recognition sequence flanked by the FRET pair formed by CyPet and YPet fluorescent proteins. The length of the linker between both fluorescent proteins was optimized using a flexible peptide linker containing several Gly-Gly-Ser repeats. Our results indicate that this FRET-based LF reporter was readily expressed in E. coli cells showing high levels of FRET in vivo in the absence of LF. The FRET signal, however, decreased 5 times after inducing LF expression in the same cell. These results suggest that this cell-based LF FRET reporter may be used to screen genetically encoded libraries in vivo against LF.

This paper is organized in the following manner. In the second section we discussed absorption; the dependence of scattered light signatures of parametric instabilities occurring at n/sub e/ less than or equal to n/sub c//4 on corona size is shown in section three; and evidence for suprathermal electron production in these long-scale length plasmas is presented in section four. The results and conclusions are finally summarized in section five.

The new heavy ion synchrotron facility proposed by GSI will have two superconducting magnet rings in the same tunnel, with rigidities of 300 T-m and 100 T-m. Fast ramp times are needed, which can cause significant problems for the magnets, particularly in the areas of ac loss and magnetic field distortion. The development of the low loss Rutherford cable that can be used is described, together with a novel insulation scheme designed to promote efficient cooling. Measurements of contact resistance in the cable are presented and the results of these measurements are used to predict the ac losses, in the magnets during fast ramp operation. For the high energy ring, a lm model dipole magnet was built, based on the RHIC dipole design. This magnet was tested under boiling liquid helium in a vertical cryostat. The quench current showed very little dependence on ramp rate. The ac losses, measured by an electrical method, were fitted to straight line plots of loss/cycle versus ramp rate, thereby separating the eddy current and hysteresis components. These results were compared with calculated values, using parameters which had previously been measured on short samples of cable. Reasonably good agreement between theory and experiment was found, …

Advanced architectures can deliver dramatically increased throughput for genomics and proteomics applications, reducing time-to-completion in some cases from days to minutes. One such architecture, hybrid-core computing, marries a traditional x86 environment with a reconfigurable coprocessor, based on field programmable gate array (FPGA) technology. In addition to higher throughput, increased performance can fundamentally improve research quality by allowing more accurate, previously impractical approaches. We will discuss the approach used by Convey?s de Bruijn graph constructor for short-read, de-novo assembly. Bioinformatics applications that have random access patterns to large memory spaces, such as graph-based algorithms, experience memory performance limitations on cache-based x86 servers. Convey?s highly parallel memory subsystem allows application-specific logic to simultaneously access 8192 individual words in memory, significantly increasing effective memory bandwidth over cache-based memory systems. Many algorithms, such as Velvet and other de Bruijn graph based, short-read, de-novo assemblers, can greatly benefit from this type of memory architecture. Furthermore, small data type operations (four nucleotides can be represented in two bits) make more efficient use of logic gates than the data types dictated by conventional programming models.JGI is comparing the performance of Convey?s graph constructor and Velvet on both synthetic and real data. We will present preliminary results on …

Several contemporary proton-recoil detectors are described and compared. These detectors have been used for neutron-spectrum measurements over various portions of the 10-keV-to-20-MeV energy range. Several factors which limit the accuracy of the results are compared quantitatively. General suggestions are given for setting and using standard cross sections and for future developments using the n,p scattering reaction.

The authors present the detection of volatile organic compounds directly in their vapor phase by surface-enhanced Raman scattering (SERS) substrates based on lithographically-defined two-dimensional rectangular array of nanopillars. The type of nanopillars is known as the tapered pillars. For the tapered pillars, SERS enhancement arises from the nanofocusing effect due to the sharp tip on top. SERS experiments were carried out on these substrates using various concentrations of toluene vapor. The results show that SERS signal from a toluene vapor concentration of ppm level can be achieved, and the toluene vapor can be detected within minutes of exposing the SERS substrate to the vapor. A simple adsorption model is developed which gives results matching the experimental data. The results also show promising potential for the use of these substrates in environmental monitoring of gases and vapors.

A 'proof-of-principle' Nb{sub 3}Sn superconducting dual-bore dipole magnet was built from racetrack coils, as a first step in a program to develop an economical, 15 Tesla, accelerator-quality magnet. The mechanical design and magnet fabrication procedures are discussed. No training was required to achieve temperature-dependent plateau currents, despite several thermal cycles that involved partial magnet disassembly and substantial pre-load variations. Subsequent magnets are expected to approach 15 Tesla with substantially improved conductor.

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.

Micro-Raman spectroscopy has been demonstrated to be a viable tool for nondestructive determination of the crystal phase of relevant minerals. Collecting spectra on particles down to 5 microns in size was completed. Some minerals studied were weak scatterers and were better studied with the other techniques. A decent graphical software package should easily be able to compare collected spectra to a spectral library as well as subtract out matrix vibration peaks. Due to the success and unequivocal determination of the most common mineral false positive (zircon), it is clear that Raman has a future for complementary, rapid determination of unknown particulate samples containing actinides.

Energy efficiency resource standards (EERS) are a prominent strategy to potentially achieve rapid and aggressive energy savings goals in the U.S. As of December 2010, twenty-six U.S. states had some form of an EERS with savings goals applicable to energy efficiency (EE) programs paid for by utility customers. The European Union has initiated a similar type of savings goal, the Energy End-use Efficiency and Energy Services Directive, where it is being implemented in some countries through direct partnership with regulated electric utilities. U.S. utilities face significant financial disincentives under traditional regulation which affects the interest of shareholders and managers in aggressively pursuing cost-effective energy efficiency. Regulators are considering some combination of mandated goals ('sticks') and alternative utility business model components ('carrots' such as performance incentives) to align the utility's business and financial interests with state and federal energy efficiency public policy goals. European countries that have directed their utilities to administer EE programs have generally relied on non-binding mandates and targets; in the U.S., most state regulators have increasingly viewed 'carrots' as a necessary condition for successful achievement of energy efficiency goals and targets. In this paper, we analyze the financial impacts of an EERS on a large electric utility …

A series of laser wake field accelerator experiments leading to electron energy exceeding 1 GeV are described. Theoretical concepts and experimental methods developed while conducting experiments using the 10 TW Ti:Sapphire laser at UCLA were implemented and transferred successfully to the 100 TW Callisto Laser System at the Jupiter Laser Facility at LLNL. To reach electron energies greater than 1 GeV with current laser systems, it is necessary to inject and trap electrons into the wake and to guide the laser for more than 1 cm of plasma. Using the 10 TW laser, the physics of self-guiding and the limitations in regards to pump depletion over cm-scale plasmas were demonstrated. Furthermore, a novel injection mechanism was explored which allows injection by ionization at conditions necessary for generating electron energies greater than a GeV. The 10 TW results were followed by self-guiding at the 100 TW scale over cm plasma lengths. The energy of the self-injected electrons, at 3 x 10{sup 18} cm{sup -3} plasma density, was limited by dephasing to 720 MeV. Implementation of ionization injection allowed extending the acceleration well beyond a centimeter and 1.4 GeV electrons were measured.

Next Generation sequencing is producing ever larger data sizes with a growth rate outpacing Moore's Law. The data deluge has made many of the current sequenceanalysis tools obsolete because they do not scale with data. Here we present BioPig, a collection of cloud computing tools to scale data analysis and management. Pig is aflexible data scripting language that uses Apache's Hadoop data structure and map reduce framework to process very large data files in parallel and combine the results.BioPig extends Pig with capability with sequence analysis. We will show the performance of BioPig on a variety of bioinformatics tasks, including screeningsequence contaminants, Illumina QA/QC, and gene discovery from metagenome data sets using the Rumen metagenome as an example.

The Image Content Engine (ICE) is being developed to provide cueing assistance to human image analysts faced with increasingly large and intractable amounts of image data. The ICE architecture includes user configurable feature extraction pipelines which produce intermediate feature vector and match surface files which can then be accessed by interactive relational queries. Application of the feature extraction algorithms to large collections of images may be extremely time consuming and is launched as a batch job on a Linux cluster. The query interface accesses only the intermediate files and returns candidate hits nearly instantaneously. Queries may be posed for individual objects or collections. The query interface prompts the user for feedback, and applies relevance feedback algorithms to revise the feature vector weighting and focus on relevant search results. Examples of feature extraction and both model-based and search-by-example queries are presented.

At the Berkeley Structural Genomics Center (BSGC), our goalis to obtain a near-complete structural complement of proteins in theminimal organisms Mycoplasma genitalium and M. pneumoniae, two closelyrelated pathogens. Current targets for structure determination have beenselected in six major stages, starting with those predicted to be mosttractable to high throughput study and likely to yield new structuralinformation. We report on the process used to select these proteins, aswell as our target deselection procedure. Target deselection reducesexperimental effort by eliminating targets similar to those recentlysolved by the structural biology community or other centers. We measurethe impact of the 69 structures solved at the BSGC as of July 2004 onstructure prediction coverage of the M. pneumoniae and M. genitaliumproteomes. The number of Mycoplasma proteins for which thefold couldfirst be reliably assigned based on structures solved at the BSGC (24 M.pneumoniae and 21 M. genitalium) is approximately 25 percent of the totalresulting from work at all structural genomics centers and the worldwidestructural biology community (94 M. pneumoniae and 86M. genitalium)during the same period. As the number of structures contributed by theBSGC during that period is less than 1 percent of the total worldwideoutput, the benefits of a focused target selection strategy are apparent.If the …

The A-01 NPDES outfall at the Savannah River Site receives process wastewater discharges and stormwater runoff from the Savannah River National Laboratory. Routine monitoring indicated that copper concentrations were regularly higher than discharge permit limit, and water routinely failed toxicity tests. These conditions necessitated treatment of nearly one million gallons of water per day plus storm runoff. Washington Savannah River Company personnel explored options to bring process and runoff waters into compliance with the permit conditions, including source reduction, engineering solutions, and biological solutions. A conceptual design for a constructed wetland treatment system (WTS) was developed and the full-scale system was constructed and began operation in 2000. The overall objective of our research is to better understand the mechanisms of operation of the A-01 WTS in order to provide better input to design of future systems. The system is a vegetated surface flow wetland with a hydraulic retention time of approximately 48 hours. Copper, mercury, and lead removal efficiencies are very high, all in excess of 80% removal from water passing through the wetland system. Zinc removal is 60%, and nickel is generally unaffected. Dissolved organic carbon in the water column is increased by the system and reduces toxicity of …

An extensive study of helium isotopes in fluids collectedfrom surface springs, fumaroles and wells across the northern Basin andRange Province reveals a systematic trend of decreasing 3He/4He ratiosfrom west to east. The western margin of the Basin and Range ischaracterized by mantle-like ratios (6-8 Ra) associated with active orrecently active crustal magma systems (e.g. Coso, Long Valley, Steamboat,and the Cascade volcanic complex). Moving towards the east, the ratiosdecline systematically to a background value of ~;0.1 Ra. The regionaltrend is consistent with extensive mantle melting concentrated along thewestern margin and is coincident with an east-to-west increase in themagnitude of northwest strain. The increase in shear strain enhancescrustal permeability resulting in high vertical fluid flow rates thatpreserve the high helium isotope ratios at the surface. Superimposed onthe regional trend are "helium spikes", local anomalies in the heliumisotope composition. These "spikes" reflect either local zones of mantlemelting or locally enhanced crustal permeability. In the case of theDixie Valley hydrothermal system, it appears to be a combination ofboth.

A controller for the third generation, 6 degree-of-freedom (DOF) piezoelectric translation stage shown in Figure 1 is presented. This was tested by monitoring all six coordinate motions using an orthogonal array of six, high-resolution capacitance gages. The full 6 DOF matrix transformations and controller block diagrams for this system have been measured and the system operated under closed loop control. Results of early experiments to determine the 21 open loop response functions as well as preliminary results showing the closed loop response for the 3 linear translations are presented in this abstract. The ultimate goal of this project is to incorporate this 6 DOF stage within a long range X-Y scanning system for nanometer pick-and-place capability over an area of 50 x 50 mm. The control strategy and early results from this system will be presented.

Spontaneous mixing of materials at unstably stratified interfaces occurs in a wide variety of atmospheric, oceanic, geophysical and astrophysical flows. The Rayleigh-Taylor instability, in particular, plays key roles in the death of stars, planet formation and the quest for controlled thermonuclear fusion. Despite its ubiquity, fundamental questions regarding Rayleigh-Taylor instability persist. Among such questions are: Does the flow forget its initial conditions? Is the flow self-similar? What is the value of the scaling constant? How does mixing influence the growth rate? Here we show results from a 3072{sup 3} grid-point Direct Numerical Simulation in an attempt to answer these and other questions. The data indicate that the scaling constant cannot be found by fitting a curve to the width of the mixing region (as is common practice) but can only be accurately obtained by recourse to the similarity equation for the growth rate. The data further establish that the ratio of kinetic energy to released potential energy is not constant, as has heretofore been assumed. The simulated flow reaches a Reynolds number of 32,000, far exceeding that of all previous simulations. The latter stages of the simulation reveal a weak Reynolds number dependence, which may have profound consequences for modeling …

This paper discusses the use of computational fluid dynamics (CFD) methods to understand and characterize erosion of the floor and internal structures in the slurry mixing vessels in the Defense Waste Processing Facility. An initial literature survey helped identify the principal drivers of erosion for a solids laden fluid: the solids content of the working fluid, the regions of recirculation and particle impact with the walls, and the regions of high wall shear. A series of CFD analyses was performed to characterize slurry-flow profiles, wall shear, and particle impingement distributions in key components such as coil restraints and the vessel floor. The calculations showed that the primary locations of high erosion resulting from abrasion were at the leading edge of the coil guide, the tank floor below the insert plate of the coil guide support, and the upstream lead-in plate. These modeling results based on the calculated high shear regions were in excellent agreement with the observed erosion sites in both location and the degree of erosion. Loss of the leading edge of the coil guide due to the erosion damage during the slurry mixing operation did not affect the erosion patterns on the tank floor. Calculations for a lower …

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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.

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.

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.