This study examines the temporal variability of ocean heat uptake in observations and in climate models. Previous work suggests that coupled Atmosphere-Ocean General Circulation Models (A-OGCMs) may have underestimated the observed natural variability of ocean heat content, particularly on decadal and longer timescales. To address this issue, we rely on observed estimates of heat content from the 2004 World Ocean Atlas (WOA-2004) compiled by Levitus et al. (2005). Given information about the distribution of observations in WOA-2004, we evaluate the effects of sparse observational coverage and the infilling that Levitus et al. use to produce the spatially-complete temperature fields required to compute heat content variations. We first show that in ocean basins with limited observational coverage, there are important differences between ocean temperature variability estimated from observed and infilled portions of the basin. We then employ data from control simulations performed with eight different A-OGCMs as a test-bed for studying the effects of sparse, space- and time-varying observational coverage. Subsampling model data with actual observational coverage has a large impact on the inferred temperature variability in the top 300 and 3000 meters of the ocean. This arises from changes in both sampling depth and in the geographical areas sampled. Our …

Metal ions are essential for the folding of RNA into stable tertiary structures and for the catalytic activity of some RNA enzymes. To aid in the study of the roles of metal ions in RNA structural biology, we have created MeRNA (Metals in RNA), a comprehensive compilation of all metal binding sites identified in RNA three-dimensional structures available from the Protein Data Bank (PDB) and Nucleic Acid Database (NDB). Currently, our database contains information relating to binding of 9764 metal ions corresponding to 23 distinct elements; in 256 RNA structures. The metal ion locations were confirmed and ligands characterized using original literature references. MeRNA includes eight manually identified metal-ion binding motifs, which are described in the literature. MeRNA is searchable by PDB identifier, metal ion, method of structure determination, resolution and R-values for X-ray structure, and distance from metal to any RNA atom or to water. New structures with their respective binding motifs will be added to the database as they become available. The MeRNA database will further our understanding of the roles of metal ions in RNA folding and catalysis and have applications in structural and functional analysis, RNA design and engineering.

Storage of greenhouse gases, primarily CO2, in geologic formations has been proposed as a means by which atmospheric emissions of such gases may be reduced (Bachu et al., 1994; Orr, 2004). Possible storage reservoirs currently under consideration include saline aquifers, depleted or depleting oil and gas fields, and unmineable coal seams (Baines and Worden, 2004). The amount of CO2 emitted from fossil-fueled power plants is very large, of the order of 30,000 tons per day (10 million tons per year) for a large 1,000 MW coal-fired plant (Hitchon,1996). In order to make a significant impact on reducing emissions, very large amounts of CO2 would have to be injected into subsurface formations, resulting in CO2 disposal plumes with an areal extent of order 100 km2 or more (Pruess et al., 2003). It appears inevitable, then, that such plumes will encounter imperfections in caprocks, such as fracture zones or faults, that would allow CO2 to leak from the primary storage reservoir. At typical subsurface conditions of temperature and pressure, CO2 is always less dense than aqueous fluids; thus buoyancy forces will tend to drive CO2 upward, towards the land surface, whenever adequate (sub-)vertical permeability is available. Upward migration of CO2 could also …

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Uranium mining and processing for nuclear weapons and fuel have left thousands of sites with toxic levels of this actinide in soil and ground water. An emerging strategy for remediating such environments involves using organic carbon to promote microbially-mediated reduction and precipitation of insoluble U(IV) minerals. Although previous U bioreduction studies have shown promising results, they were of short duration (up to a few months). Our longer-term (20 months) laboratory study using historically contaminated sediment has alarmingly shown that microbial reduction of U was transient even under reducing (methanogenic) conditions. Uranium was reductively immobilized during the first 100 days, but later (150 to 600 days) reoxidized and mobilized, although a microbial community capable of reducing U(VI) remained through the end of the experiment. The formation of Ca{sub 2}UO{sub 2}(CO{sub 3}){sub 3} complexes (caused by the elevated carbonate concentration from microbial respiration and presence of calcium) drove the U(IV)/U(VI) reduction potential to much more reducing conditions. Fe(III) and Mn(IV) were found to be likely terminal electron acceptors (TEAs) for U reoxidation. Thus, U remediation by organic carbon based reductive precipitation is not sustainable in calcareous, neutral to alkaline soils and ground waters.

A screen for the systematic identification of cis-regulatory elements within large (>100 kb) genomic domains containing Hox genes was performed by using the basal chordate Ciona intestinalis. Randomly generated DNA fragments from bacterial artificial chromosomes containing two clusters of Hox genes were inserted into a vector upstream of a minimal promoter and lacZ reporter gene. A total of 222 resultant fusion genes were separately electroporated into fertilized eggs, and their regulatory activities were monitored in larvae. In sum, 21 separable cis-regulatory elements were found. These include eight Hox linked domains that drive expression in nested anterior-posterior domains of ectodermally derived tissues. In addition to vertebrate-like CNS regulation, the discovery of cis-regulatory domains that drive epidermal transcription suggests that C. intestinalis has arthropod-like Hox patterning in the epidermis.

Conventional and high resolution electron microscopy havebeen applied for studying lattice defects in nonpolar a-plane GaN grownon a 4H-SiC substrate with an AlN buffer layer. Samples in plan-view andcross-section configurations have been investigated. Basal and prismaticstacking faults together with Frank and Shockley partial dislocationswere found to be the main defects in the GaN layers. High resolutionelectron microscopy in combination with image simulation supported Drum smodel for the prismatic stacking faults. The density of basal stackingfaults was measured to be ~;1.6_106cm-1. The densities of partialdislocations terminating I1 and I2 types of intrinsic basal stackingfaults were ~;4.0_1010cm-2 and ~;0.4_1010cm-2, respectively. The energyof the I2 stacking fault in GaN was estimated to be (40+-4) erg/cm2 basedon the separation of Shockley partial dislocations. To the best of ourknowledge, the theoretically predicted I3 basal stacking fault in GaN wasobserved experimentally for the first time.

The combustion of fossil fuels is profoundly altering the chemical composition of the atmosphere. Beginning with the Industrial Revolution, the concentration of carbon dioxide in the atmosphere has increased from approximately 280 to 370 {micro}l l{sup -1} in 2004, and it is expected to exceed 550 {micro}l l{sup -1} by 2050. Tropospheric ozone has risen even more rapidly than CO{sub 2} and average summer concentrations in the Northern Hemisphere are expected to continue to increase by 0.5-2.5% per year over the next 30 years. Although elevated CO{sub 2} stimulates photosynthesis and productivity of terrestrial ecosystems, ozone (O{sub 3}) is deleterious. In addition to directly affecting the physiology and productivity of crops, increased concentrations of tropospheric CO{sub 2} and O{sub 3} are predicted to lower the nutritional quality of leaves, which has the potential to increase herbivory as insects eat more to meet their nutritional demands. We tested the hypothesis that changes in tropospheric chemistry affect the relationship between plants and insect herbivores by changing leaf quality. The susceptibility to herbivory of soybean grown in elevated CO{sub 2} or O{sub 3} was examined using free air gas concentration enrichment (SoyFACE). FACE technology has the advantage that plants are cultivated under realistic …

We show that changes in the orientation of the inner accretion disk of Cygnus X-1 affect the shape of the broad Fe K{alpha} emission line emitted from this object, in such a way that eV-level spectral resolution observations (such as those that will be carried out by the ASTRO-E2 satellite) can be used to analyze the dynamics of the disk. We here present a new diagnosis tool, supported by numerical simulations, by which short observations of Cygnus X-1, separated in time, can determine whether its accretion disk actually processes, and if so, determine its period and precession angle. Knowing the precession parameters of Cygnus X-1 would result in a clarification of the origin of such precession, distinguishing between tidal and spin-spin coupling. This approach could also be used for similar studies in other microquasar systems.

The Solid-State, Heat-Capacity Laser (SSHCL) program at Lawrence Livermore National Laboratory is a multigeneration laser development effort scalable to the megawatt power levels. Wavefront quality is a driving metric of its performance. A deformable mirror with over 100 degrees of freedom situated within the cavity is used to correct both the static and dynamic aberrations sensed with a Shack-Hartmann wavefront sensor. The laser geometry is an unstable, confocal resonator with a clear aperture of 10 cm x 10 cm. It operates in a pulsed mode at a high repetition rate (up to 200 Hz) with a correction being applied before each pulse. Wavefront information is gathered in real-time from a low-power pick-off of the high-power beam. It is combined with historical trends of aberration growth to calculate a correction that is both feedback and feed-forward driven. The overall system design, measurement techniques and correction algorithms are discussed. Experimental results are presented.

We summarize four of our group's high-risk/high-payoff research projects funded by the Intelligence Technology Innovation Center (ITIC) in conjunction with our DHS-funded pathogen informatics activities. These are (1) quantitative assessment of genomic sequencing needs to predict high quality DNA and protein signatures for detection, and comparison of draft versus finished sequences for diagnostic signature prediction; (2) development of forensic software to identify SNP and PCR-RFLP variations from a large number of viral pathogen sequences and optimization of the selection of markers for maximum discrimination of those sequences; (3) prediction of signatures for the detection of virulence, antibiotic resistance, and toxin genes and genetic engineering markers in bacteria; (4) bioinformatic characterization of virulence factors to rapidly screen genomic data for potential genes with similar functions and to elucidate potential health threats in novel organisms. The results of (1) are being used by policy makers to set national sequencing priorities. Analyses from (2) are being used in collaborations with the CDC to genotype and characterize many variola strains, and reports from these collaborations have been made to the President. We also determined SNPs for serotype and strain discrimination of 126 foot and mouth disease virus (FMDV) genomes. For (3), currently >1000 probes …

There is compelling empirical [1] and theoretical [2] evidence that the global confinement of H-mode discharges increases as the pedestal pressure or temperature increases. Therefore, confidence in the performance of future machines requires an ability to predict the pedestal conditions in those machines. At this time, both the theoretical and empirical understanding of transport in the pedestal are incomplete and are inadequate to predict pedestal conditions in present or future machines. Recent empirical results might be evidence of a fundamental relation between the electron temperature T{sub e} and electron density n{sub e} profiles in the pedestal. A data set from the ASDEX-Upgrade tokamak has shown that {eta}{sub e}, the ratio between the scale lengths of the n{sub e} and T{sub e} profiles, exhibits a value of about 2 throughout the pedestal, despite a large range of the actual density and temperature values [3]. Data from the DIII-D tokamak show that over a wide range of pedestal density, the width of the steep gradient region for the T{sub e} profile is about 1-2 times the corresponding width for the n{sub e} profile, where both widths are measured from the plasma edge [4]. Thus, the barrier in the density might form a …

A brief review of BRAHMS measurements of bulk particle production in RHIC Au+Au collisions at {radical}s{sub NN} 200GeV is presented, together with some discussion of baryon number transport. Intermediate p{sub T} measurements in different collision systems (Au+Au, d+ Au and p+p) are also discussed in the context of jet quenching and saturation of the gluon density in Au ions at RHIC energies. This report also includes preliminary results for identified particles at forward rapidities in d+Au and Au+Au collisions.

Understanding the stability physics of the H-mode pedestal in tokamak devices requires an accurate measurement of plasma current in the pedestal region with good spatial resolution. Theoretically, the high pressure gradients achieved in the edge of H-mode plasmas should lead to generation of a significant edge current density peak through bootstrap and Pfirsh-Schlueter effects. This edge current is important for the achievement of second stability in the context of coupled magneto hydrodynamic (MHD) modes which are both pressure (ballooning) and current (peeling) driven [1]. Many aspects of edge localized mode (ELM) behavior can be accounted for in terms of an edge current density peak, with the identification of Type 1 ELMs as intermediate-n toroidal mode number MHD modes being a natural feature of this model [2]. The development of a edge localized instabilities in tokamak experiments code (ELITE) based on this model allows one to efficiently calculate the stability and growth of the relevant modes for a broad range of plasma parameters [3,4] and thus provides a framework for understanding the limits on pedestal height. This however requires an accurate assessment of the edge current. While estimates of j{sub edge} can be made based on specific bootstrap models, their validity …

We have developed a 3D wavelet-based filter for visualizing structural features in volumetric data. The only variable parameter is a characteristic linear size of the feature of interest. The filtered output contains only those regions that are correlated with the characteristic size, thus denoising the image. We demonstrate the use of the filter by applying it to 3D data from a variety of electron microscopy samples including low contrast vitreous ice cryogenic preparations, as well as 3D optical microscopy specimens.

Understanding the evolution of microstructure in welds is an important goal of welding research because of the strong correlation between weld microstructure and weld properties. To achieve this goal it is important to develop a quantitative measure of phase transformations encountered during welding in order to ultimately develop methods for predicting weld microstructures from the characteristics of the welding process. To aid in this effort, synchrotron radiation methods have been developed at Lawrence Livermore National Laboratory (LLNL) for direct observation of microstructure evolution during welding. Using intense, highly collimated synchrotron radiation, the atomic structure of the weld heat affected and fusion zones can be probed in real time. Two synchrotron-based techniques, known as spatially resolved (SRXRD) and time resolved (TRXRD) x-ray diffraction, have been developed for these investigations. These techniques have now been used to investigate welding induced phase transformations in titanium alloys, low alloy steels, and stainless steel alloys. This paper will provide a brief overview of these methods and will discuss microstructural evolution during the welding of low carbon (AISI 1005) and medium carbon (AISI 1045) steels where the different levels of carbon influence the evolution of microstructures during welding.

Artificially creviced Alloy 22 (N06022) is susceptible to crevice corrosion in presence of high chloride aqueous solution when high temperatures and high anodic potentials are applied. The presence of oxyanions in the electrolyte, especially nitrate, inhibits the nucleation and growth of crevice corrosion. Crevice corrosion may initiate when a constant potential above the crevice repassivation potential is applied. The occurrence of crevice corrosion can be divided into three characteristic domains: (1) nucleation, (2) growth and (3) stifling and arrest. That is, crevice corrosion reaches a critical stage after which growth stops and the specimens start to regain the passive behavior displayed prior to localized attack.

The modeling of dielectric and magnetic materials in the time domain is required for pulse power applications, pulsed induction accelerators, and advanced transmission lines. For example, most induction accelerator modules require the use of magnetic materials to provide adequate Volt-sec during the acceleration pulse. These models require hysteresis and saturation to simulate the saturation wavefront in a multipulse environment. In high voltage transmission line applications such as shock or soliton lines the dielectric is operating in a highly nonlinear regime, which require nonlinear models. Simple 1-D models are developed for fast parameterization of transmission line structures. In the case of nonlinear dielectrics, a simple analytic model describing the permittivity in terms of electric field is used in a 3-D finite difference time domain code (FDTD). In the case of magnetic materials, both rate independent and rate dependent Hodgdon magnetic material models have been implemented into 3-D FDTD codes and 1-D codes.

Alloy 22 (N06022) has been extensively tested for general and localized corrosion behavior both in the wrought and annealed condition and in the as-welded condition. The specimens for testing were mostly prepared from flat plates of material. It was important to determine if the process of fabricating a full diameter Alloy 22 container will affect the corrosion performance of the alloy. Specimens were prepared directly from a fabricated container and tested for corrosion resistance. Results show that both the anodic corrosion behavior and the localized corrosion resistance of specimens prepared from a welded fabricated container was the same as from flat welded plates.

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It has been suggested that x-ray free electron lasers will enable single-particle diffraction imaging of biological molecules. In this paper we present a model to estimate the required pulse parameters based on a trade-off between minimizing image degradation due to damage and maximizing the image signal-to-noise ratio. We discuss several means to alleviate the photon requirements, and compare the requirements with existing or planned x-ray sources such as short-pulse x-ray free-electron lasers.

The High Performance Storage System (HPSS) provides scalable hierarchical storage management (HSM), archive, and file system services. Its design, implementation and current dominant use are focused on HSM and archive services. It is also a general-purpose, global, shared, parallel file system, potentially useful in other application domains. When HPSS design and implementation began over a decade ago, scientific computing power and storage capabilities at a site, such as a DOE national laboratory, was measured in a few 10s of gigaops, data archived in HSMs in a few 10s of terabytes at most, data throughput rates to an HSM in a few megabytes/s, and daily throughput with the HSM in a few gigabytes/day. At that time, the DOE national laboratories and IBM HPSS design team recognized that we were headed for a data storage explosion driven by computing power rising to teraops/petaops requiring data stored in HSMs to rise to petabytes and beyond, data transfer rates with the HSM to rise to gigabytes/s and higher, and daily throughput with a HSM in 10s of terabytes/day. This paper discusses HPSS architectural, implementation and deployment experiences that contributed to its success in meeting the above orders of magnitude scaling targets. We also discuss …

Rockfishes (Sebastes spp.) support one of the most economically important fisheries of the Pacific Northwest and it is essential for sustainable management that age estimation procedures be validated for these species. Atmospheric testing of thermonuclear devices during the 1950s and 1960s created a global radiocarbon ({sup 14}C) signal in the ocean environment that scientists have identified as a useful tracer and chronological marker in natural systems. In this study, we first demonstrated that fewer samples are necessary for age validation using the bomb-generated {sup 14}C signal by emphasizing the utility of the time-specific marker created by the initial rise of bomb-{sup 14}C. Second, the bomb-generated {sup 14}C signal retained in fish otoliths was used to validate the age and age estimation methodology of the quillback rockfish (Sebastes maliger) in the waters of southeast Alaska. Radiocarbon values from the first year's growth of quillback rockfish otoliths were plotted against estimated birth year producing a {sup 14}C time series spanning 1950 to 1985. The initial rise of bomb-{sup 14}C from pre-bomb levels ({approx} -90 {per_thousand}) occurred in 1959 {+-} 1 year and {sup 14}C levels rose relatively rapidly to peak {Delta}{sup 14}C values in 1967 (+105.4 {per_thousand}), with a subsequent declining trend …

Dielectric Wall Accelerator (DWA) technology incorporates the energy storage mechanism, the switching mechanism, and the acceleration mechanism for electron beams. Electromagnetic simulations of DWA structures includes these effects and also details of the switch configuration and how that switch time affects the electric field pulse which accelerates the particle beam. DWA structures include both bi-linear and bi-spiral configurations with field gradients on the order of 20MV/m and the simulations include the effects of the beampipe, the beampipe walls, the DWA High Gradient Insulator (HGI) insulating stack, wakefield impedance calculations, and test particle trajectories with low emittance gain. Design trade-offs include the transmission line impedance (typically a few ohms), equilibration ring optimization, driving switch inductances, and layer-to-layer coupling effects and the associated affect on the acceleration pulse's peak value.