Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling (GOS) sequences. The GOS dataset covers nearly all known prokaryotic protein families. A total of 3,995 medium- and large-sized clusters consisting of only GOS sequences are identified, out of which 1,700 have no detectable homology to known families. The GOS-only clusters contain a higher than expected proportion of sequences of viral origin, thus reflecting a poor sampling of viral diversity until now. Protein domain distributions in the GOS dataset and current protein databases show distinct biases. Several protein domains that were previously categorized as kingdom specific are shown to have GOS examples in other kingdoms. About 6,000 sequences (ORFans) from the literature that heretofore lacked similarity to known proteins have matches in the GOS data. The GOS dataset is also used to improve remote homology detection. Overall, besides nearly doubling the number of current proteins, the predicted GOS proteins also add a great deal of diversity to known protein families and shed …

Thermal damage experiments were conducted on LX-04, LX-10, and LX-17 at high temperatures. Both pristine and damaged samples were characterized for their material properties. A pycnometer was used to determine sample true density and porosity. Gas permeability was measured in a newly procured system (diffusion permeameter). Burn rate was measured in the LLNL strand burner. Weight losses upon thermal exposure were insignificant. Damaged pressed parts expanded, resulting in a reduction of bulk density by up to 10%. Both gas permeabilities and burn rates of the damaged samples increased by several orders of magnitude due to higher porosity and lower density. Moduli of the damaged materials decreased significantly, an indication that the materials became weaker mechanically. Damaged materials were more sensitive to shock initiation at high temperatures. No significant sensitization was observed when the damaged samples were tested at room temperature.

Remediation by soil-vapor extraction has been used for over a decade at Lawrence Livermore National Laboratory (LLNL). We have found that natural changes in environmental conditions affect the rate of soil-vapor extraction. Data on flow rate observations collected over this time are compared to in-situ measurements of several different environmental parameters (soil-gas pressure, soil-temperature, soil-moisture, Electrical Resistance Tomography (ERT), rainfall and barometric pressure). Environmental changes that lead to increased soil-moisture are associated with reduced soil-vapor extraction flow rates. We have found that the use of higher extraction vacuums combined with dual-phase extraction can help to increase pneumatic conductivity when vadose zone saturation is a problem. Daily changes in barometric pressure and soil-gas temperature were found to change flow rate measurements by as much as 10% over the course of a day.

We report the magnetic and transport properties of Ga{sub 1-x}Mn{sub x}P synthesized via ion implantation followed by pulsed laser melting over a range of x, namely 0.018 to 0.042. Like Ga{sub 1-x}Mn{sub x}As, Ga{sub 1-x}Mn{sub x}P displays a monotonic increase of the ferromagnetic Curie temperature with x associated with the hole-mediated ferromagnetic phase while thermal annealing above 300 C leads to a quenching of ferromagnetism that is accompanied by a reduction of the substitutional fraction of Mn. However, contrary to observations in Ga{sub 1-x}Mn{sub x}As, Ga{sub 1-x}Mn{sub x}P is non-metallic over the entire composition range. At the lower temperatures over which the films are ferromagnetic, hole transport occurs via hopping conduction in a Mn-derived band; at higher temperatures it arises from holes in the valence band which are thermally excited across an energy gap that shrinks with x.

We present the results of a study of the performance of InGaAs detectors conducted for the SuperNova Acceleration Probe (SNAP) dark energy mission concept. Low temperature data from a nominal 1.7um cut-off wavelength 1kx1k InGaAs photodiode array, hybridized to a Rockwell H1RG multiplexer suggest that InGaAs detector performance is comparable to those of existing 1.7um cut-off HgCdTe arrays. Advances in 1.7um HgCdTe dark current and noise initiated by the SNAP detector research and development program makes it the baseline detector technology for SNAP. However, the results presented herein suggest that existing InGaAs technology is a suitable alternative for other future astronomy applications.

SATB1 is an important regulator of nuclear architecture that anchors specialized DNA sequences onto its cage-like network and recruits chromatin remodeling/modifying factors to control gene transcription. We studied the role of SATB1 in regulating the coordinated expression of Il5, Il4, and Il13 from the 200kb cytokine gene cluster region of mouse chromosome 11 during T-helper 2 (Th2)-cell activation. We show that upon cell activation, SATB1 is rapidly induced to form a unique transcriptionally-active chromatin structure that includes the cytokine gene region. Chromatin is folded into numerous small loops all anchored by SATB1, is histone H3 acetylated at lysine 9/14, and associated with Th2-specific factors, GATA3, STAT6, c-Maf, the chromatin-remodeling enzyme Brg-1, and RNA polymerase II across the 200kb region. Before activation, the chromatin displays some of these features, such as association with GATA3 and STAT6, but these were insufficient for cytokine gene expression. Using RNA interference (RNAi), we show that upon cell activation, SATB1 is not only required for chromatin folding into dense loops, but also for c-Maf induction and subsequently for Il4, Il5, and Il13 transcription. Our results show that SATB1 is an important determinant for chromatin architecture that constitutes a novel higher-order, transcriptionally-active chromatin structure upon Th2-cell activation.

PETN is widely recognized as an example of nearly ideal detonation performance. The chemical composition is such that little or no carbon is produced in the detonation products. The reaction zone width is less than currently detectable. (<1 ns) Observations on PETN have thus become a baseline for EOS model predictions. It has therefore become important to characterize the detonation parameters as accurately as possible in order to provide the most exacting comparisons of EOS predictions with experimental results. We undertook a painstaking review of the detonation pressure measurements reported in an earlier work that was presented at the Fifth Detonation Symposium and found that corrections were required in determining the shock velocity in the PMMA witness material. We also refined the impedance calculation to account for the difference between the usual ''acoustic'' method and the more accurate Riemann integral. Our review indicates that the CJ pressures previously reported for full density PETN require an average lowering of about 6 percent. The lower densities require progressively smaller corrections. We present analysis of the records, supporting hydrodynamic simulations, the Riemann integral results, and EOS parameter values derived from the revised results.

We investigated the valence and spin state of iron in an Al-bearing ferromagnesian silicate perovskite sample, (Mg{sub 0.88}Fe{sub 0.09})(Si{sub 0.94}Al{sub 0.10})O{sub 3}, at 300 K and up to 100 GPa, using diamond-anvil cells and synchrotron Moessbauer spectroscopy techniques. Under elevated pressures, our Moessbauer time spectra are sufficiently fitted by a ''three-doublet'' model, which assumes two ferrous (Fe{sup 2+}) iron types and one ferric (Fe{sup 3+}) iron type with distinct hyperfine parameters. At pressures above 20 GPa, the fraction of the ferric iron, Fe{sup 3+}/{Sigma}Fe, is about 75% and remains unchanged to the highest pressure, indicating a fixed valence state of iron within this pressure range. Between 20 and 100 GPa, the quadruple splittings of all three iron types do not change with pressure, while the isomer shift between the Fe{sup 3+} types and the Fe{sup 2+} type increases continuously with increasing pressure. In conjunction with previous x-ray emission data on the same sample, the unchanging quadruple splittings and increasing isomer shift suggest that Fe{sup 2+} undergoes a broad spin crossover towards the low-spin state at 100 GPa, while Fe{sup 3+} remains in the high-spin state. The essentially constant quadruple splittings of Fe{sup 2+} can also be taken as an indication …

We calculate {Delta}I = 3/2 kaon decay matrix elements using domain wall fermions and the DBW2 gauge action at one coarse lattice spacing corresponding to a{sup -1} = 1.3 GeV. We employ the Lellouch and Luescher formula and its extension for non-zero total momentum to extract the infinite volume, center-of-mass frame decay amplitudes. The decay amplitudes obtained from the methods correspond to those from the indirect method with full order chiral perturbation theory. We confirm that the result is consistent with the previous result calculated with H-parity (anti-periodic) boundary condition by investigating the relative momentum dependence. We evaluate the decay amplitude ReA{sub 2} at the physical point by a chiral extrapolation with a polynomial function of m{sub {pi}}{sup 2} and the relative momentum as well as the {Delta}I = 3/2 electroweak penguin contributions to {var_epsilon}{prime}/{var_epsilon}. We found that the result of ReA{sub 2} reasonably agrees with the experiment.

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We report on our study of QCD thermodynamics with 2 + 1 flavors of dynamical quarks. In this proceeding we present several thermodynamic quantities and our recent calculation of the critical temperature. In order to investigate the thermodynamic properties of QCD near the continuum limit we adopt improved staggered (p4) quarks coupled with tree-level Symanzik improved glue on N{sub t} = 4 and 6 lattices. The simulations are performed with a physical value of the strange quark mass and light quark masses which are in the range of m{sub q}/m{sub s} = 0.05 - 0.4. The lightest quark mass corresponds to a pion mass of about 150 MeV.

A comparison of two-dimensional and three-dimensional high-resolution numerical large-eddy simulations of planar, miscible Rayleigh-Taylor instability flows are presented. The resolution of the three-dimensional simulation is sufficient to attain a fully turbulent state. A number of different statistics from the mixing region (e.g., growth rates, PDFs, mixedness measures, and spectra) are used to demonstrate that two-dimensional flow simulations differ substantially from the three-dimensional one. It is found that the two-dimensional flow grows more quickly than its three-dimensional counterpart at late times, develops larger structures, and is much less well mixed. These findings are consistent with the concept of inverse cascade in two-dimensional flow, as well as the influence of a reduced effective Atwood number on miscible flow.

Due to the recent explosion of interest in studying the electromagnetic behavior of large (truncated) periodic structures such as phased arrays, frequency-selective surfaces, and metamaterials, there has been a renewed interest in efficiently modeling such structures. Since straightforward numerical analyses of large, finite structures (i.e., explicitly meshing and computing interactions between all mesh elements of the entire structure) involve significant memory storage and computation times, much effort is currently being expended on developing techniques that minimize the high demand on computer resources. One such technique that belongs to the class of fast solvers for large periodic structures is the GIFFT algorithm (Green's function interpolation and FFT), which is first discussed in [1]. This method is a modification of the adaptive integral method (AIM) [2], a technique based on the projection of subdomain basis functions onto a rectangular grid. Like the methods presented in [3]-[4], the GIFFT algorithm is an extension of the AIM method in that it uses basis-function projections onto a rectangular grid through Lagrange interpolating polynomials. The use of a rectangular grid results in a matrix-vector product that is convolutional in form and can thus be evaluated using FFTs. Although our method differs from [3]-[6] in various respects, …

The stable spin direction in the RHIC rings is vertical. With one or two partial helical Siberian snakes in the AGS, the stable spin direction at extraction is not vertical. Interleaved vertical and horizontal bends in the transport line between AGS and the RHIC rings also tend to tip the spin away from the vertical. In order to maximize polarization in RHIC, we examined several options to improve the matching of the stable spin direction during beam transfer from the AGS to each of the RHIC rings. While the matching is not perfect, the most economical method appears to be a lowering of the injection energy by one unit of G{gamma} from 46.5 to 45.5.

Rapid cycling synchrotrons (RCSs) are used in many high power facilities like spallation neutron sources and proton drivers to accumulate and accelerate proton beams. In such accelerators, beam collimation plays a crucial role in reducing the uncontrolled beam loss. Furthermore, injection and extraction sections often need to reside in dispersion-free regions to avoid couplings; sizeable drift space is needed to house the RF accelerating cavities; long, uninterrupted straights are desired to ease injection tuning and to raise collimation efficiency. Finally, the machine circumference needs to be small to reduce construction costs. In this paper, we present a lattice satisfying these needs. The lattice contains a drift created by a missing dipole near the peak dispersion to facilitate longitudinal collimation. The compact FODO arc allows easy orbit, tune, coupling, and chromatic correction. The doublets provide long uninterrupted straights. The four-fold lattice symmetry separates injection, extraction, and collimation to different straights. This lattice is adopted for the China Spallation Neutron Source (CSNS) synchrotron [1].

Simulations show that luminosity of the PEP-II B-factory can be doubled from its present peak value of 1 x 10{sup 34}cm{sup -2}s{sup -1}. The particle simulation code BBI developed for studying beam-beam interaction was used to perform the simulations. It was first found that the parasitic collisions significantly degrade the simulated luminosity as the beam currents are increased from 3A and 1.7A to 4A and 2.2A in the low and high energy rings, respectively. The effect of changes in various accelerator parameters on luminosity was then studied in detail from a rough starting point based on analytic estimates and in the process we systematically optimized the luminosity and showed that a luminosity of over 2 x 10{sup 34}cm{sup -2}s{sup -1} is achievable within feasible limits.

We report on a successful test of bunch-beam stochastic cooling in RHIC at 100 GeV. The cooling system is designed for heavy ions but was tested in the recent RHIC run which operated only with polarized protons. To make an analog of the ion beam a special bunch was prepared with very low intensity. This bunch had {approx}1.5 x 10{sup 9} protons, while the other 100 bunches contained {approx}1.2 x 10{sup 11} protons each. With this bunch a cooling time on the order 1 hour was observed through shortening of the bunch length and increase in the peak bunch current, together with a narrowing of the spectral line width of the Scottky power at 4 GHz. The low level signal processing electronics and the isolated-frequency kicker cavities are described.

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X-ray fluorescence microCT (computed tomography) is a novel technique that allows non-destructive determination of the 3D distribution of chemical elements inside a sample. This is especially important in samples for which sectioning is undesirable either due to the risk of contamination or the requirement for further analysis by different characterization techniques. Developments made by third generation synchrotron facilities and laboratory X-ray focusing systems have made these kinds of measurements more attractive by significantly reducing scan times and beam size. First results from the x-ray fluorescence microCT experiments performed at SSRL beamline 6-2 are reported here. Beamline 6-2 is a 54 pole wiggler that uses a two mirror optical system for focusing the x-rays onto a virtual source slit which is then reimaged with a set of KB mirrors to a (2 x 4) {micro}{sup 2} beam spot. An energy dispersive fluorescence detector is located in plane at 90 degrees to the incident beam to reduce the scattering contribution. A PIN diode located behind the sample simultaneously measures the x-ray attenuation in the sample. Several porous micrometeorite samples were measured and the reconstructed element density distribution including self-absorption correction is presented. Ultimately, this system will be used to analyze particles from …

Novel applications of gamma ray spectroscopy for D&D process development, inventory reduction, safety analysis and facility management are discussed in this paper. These applications of gamma spectroscopy were developed and implemented during the Risk Reduction Program (RPP) to successfully downgrade the Heavy Element Facility (B251) at Lawrence Livermore National Laboratory (LLNL) from a Category II Nuclear Facility to a Radiological Facility. Non-destructive assay in general, gamma spectroscopy in particular, were found to be important tools in project management, work planning, and work control (''Expect the unexpected and confirm the expected''), minimizing worker dose, and resulted in significant safety improvements and operational efficiencies. Inventory reduction activities utilized gamma spectroscopy to identify and confirm isotopics of legacy inventory, ingrowth of daughter products and the presence of process impurities; quantify inventory; prioritize work activities for project management; and to supply information to satisfy shipper/receiver documentation requirements. D&D activities utilize in-situ gamma spectroscopy to identify and confirm isotopics of legacy contamination; quantify contamination levels and monitor the progress of decontamination efforts; and determine the point of diminishing returns in decontaminating enclosures and glove boxes containing high specific activity isotopes such as {sup 244}Cm and {sup 238}Pu. In-situ gamma spectroscopy provided quantitative comparisons of several …

The large scale application of non-evaporable getter coating in RHIC has been effective in reducing the electron cloud. Since beams with higher intensity and smaller bunch spacing became possible in operation, the emittance growth is of concern. Study results are reported together with experiences of machine improvements: saturated NEG coatings, anti-grazing ridges in warm sections, and the pre-pumping in cryogenic regions.

For long-term tracking, it is important to have symplectic maps for the various electromagnetic elements in an accelerator ring. While many standard elements are handled well by modern tracking programs, new magnet configurations (e.g., a helical dipole with a superimposed solenoid [1]) are being used in real accelerators. Transport matrices and higher terms may be calculated by numerical integration through model-generated or measured field maps. The resulting matrices are most likely not quite symplectic due to numerical errors in the integrators as well as the fieldmaps. In his thesis [2], Healy presented a simple algorithm to symplectify a matrix. While the method is quite robust, this paper presents a discussion of its limitations.

In the past, an increase of beam intensity in RHIC has caused several decades of pressure rises in the warm sections during operation. This has been a major factor limiting the RHIC luminosity. About 430 meters of NEG coated beam pipes have been installed in the warm sections to ameliorate this problem. Beam ion induced desorption is one possible cause of pressure rises. A series beam studies in RHIC has been dedicated to estimate the desorption rate of various beam pipes (regular and NEG coated) at various warm sections. Correctors were used to generate local beam losses and consequently local pressure rises. The experimental results are presented and analyzed in this paper.

The authors develop a plane-wave-based transfer matrix method in curvilinear coordinates to study the guided modes in curved nanoribbon waveguides. The problem of a curved structure is transformed into an equivalent one of a straight structure with spatially dependent tensors of dielectric constant and magnetic permeability. The authors investigate the coupling between the eigenmodes of the straight part and those of the curved part when the waveguide is bent. The authors show that curved sections can result in strong oscillations in the transmission spectrum similar to the recent experimental results of Lawet al.