Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Phase III”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 937 records · Page 52

GOTTCHA, Version2

One major challenge in the field of shotgun metagenomics is the accurate identification of the organisms present within the community, based on classification of short sequence reads. Though microbial community profiling methods have emerged to attempt to rapidly classify the millions of reads output from contemporary sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling tool with significantly smaller FDR, which is also capable of classifying never-before seen genomes into the appropriate parent taxa.The algorithm is based upon three primary computational phases: (I) genomic decomposition into bit vectors, (II) bit vector intersections to identify shared regions, and (III) bit vector subtractions to remove shared regions and reveal unique, signature regions. In the Decomposition phase, genomic data is first masked to highlight only the valid (non-ambiguous) regions and then decomposed into overlapping 24-mers. The k-mers are sorted along with their start positions, de-replicated, and then prefixed, to minimize data duplication. The prefixes are indexed and an identical data structure is created for the start positions to mimic that of the k-mer data structure. During the Intersection phase -- which is the most computationally intensive phase -- as an all-vs-all comparison is made, the number of comparisons is first reduced by four methods: (a) Prefix restriction, (b) Overlap detection, (c) Overlap restriction, and (d) Result recording. In Prefix restriction, only k-mers of the same prefix are compared. Within that group, potential overlap of k-mer suffixes that would result in a non-empty set intersection are screened for. If such an overlap exists, the region which intersects is first reduced by performing a binary search of the boundary suffixes of the smaller set into the larger set, which defines the limits of the zipper-based intersection process. Rather than recording the actual k-mers of the intersection, another data structure of identical "shape" is created which consists of only bit vectors so that only a 1 or 0 will be stored in the location of the k-mer suffix that was found in the intersection. This reduces the amount of data generated and stored considerably. During the Subtraction phase, relevant intersection bitmasks are first unionized together to form a single bitmask which is then applied over the original genome to reveal only those regions of the genome that are unique. These regions are then exported to disk in FASTA format and used in the application of determining the constituents of an unknown metagenomic community.

Freitas, Tracey↗

Advanced Modeling of Ions in Solutions, on Surfaces, and in Biological Environments (Final Scientific/Technical Report)

The research supported by this grant focused on modeling liquid water from basic microscopic theory and on developing advanced methodologies for molecular simulation and electronic structure calculation of large and disordered systems. Water is arguably the most important molecule on earth: without it there would be no life, as we know it. Water does not behave as a simple liquid. Understanding its unique and anomalous properties at the molecular level has been the focus of intense study during the entire last century and still is a major goal of research today. To address the problem we adopted a multipronged approach that included methodological and algorithmic developments as well as simulations of important model systems. We made progress on several key issues. (i) We implemented accurate electronic structure schemes for modeling water from quantum mechanical theory that make accessible in simulations processes driven by formation and breaking of chemical bonds. We studied in this way neat bulk water and simple solvated ions. We could understand, in particular, why hydronium, i.e. the positive water ion, diffuses faster than its negative counterpart, the hydroxyl, solving a 200-year-old ionic mystery of water, as reported in a news article featuring our study on Chemistry World, the magazine of the Royal Society of Chemistry (U.K.). (ii) Using advanced statistical mechanical techniques we studied water in the deeply undercooled regime, which may hold the clue to understanding many of the water anomalies. These conditions are currently only accessible to simulations based on empirical force fields. We found that deeply undercooled water, as described by the popular force field ST2, possesses a secondary critical point, below which it would spontaneously separate into two liquids, one of low-density (LDL) and one of high-density (HDL), much in the same way in which water and oil phase-separate at room temperature. The secondary critical point is supported indirectly by many experiments, but rapid ice nucleation has so far hindered direct observation. In related studies we gained new insight on the connection of the two metastable liquids with the two corresponding amorphous ice phases, LDA and HDA, which are observed experimentally. (iii) We developed and implemented several new algorithms for computing the electronic structure of large systems and to accelerate the calculation of electron exchange energies. We applied these methodologies to model nanomaterials, such as nanoribbons and nanoflakes, and to study water absorption and splitting on nanomaterials. (iv) We developed new local order descriptors. (v) In the last year of the project we developed a methodology based on deep neural networks to construct model interatomic potentials that can accurately reproduce ab-initio quantum mechanical simulations at the computational cost of empirical force fields. These potentials will make possible to access the size and time scales that are currently only accessible with empirical force fields without loosing the predictive power of ab-initio simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Constraints on superoxide mediated formation of manganese oxides

Manganese (Mn) oxides are among the most reactive sorbents and oxidants within the environment, where they play a central role in the cycling of nutrients, metals, and carbon. Recent discoveries have identified superoxide (O$^–_2$) both of biogenic and abiogenic origin as an effective oxidant of Mn(II) leading to the formation of Mn oxides. Here we examined the conditions under which abiotically produced superoxide led to oxidative precipitation of Mn and the solid-phases produced. Oxidized Mn, as both aqueous Mn(III) and Mn(III/IV) oxides, was only observed in the presence of active catalase, indicating that hydrogen peroxide (H 2 O 2 ), a product of the reaction of O$^–_2$ with Mn(II), inhibits the oxidation process presumably through the reduction of Mn(III). Citrate and pyrophosphate increased the yield of oxidized Mn but decreased the amount of Mn oxide produced via formation of Mn(III)- ligand complexes. While complexing ligands played a role in stabilizing Mn(III), they did not eliminate the inhibition of net Mn(III) formation by H 2 O 2 . The Mn oxides precipitated were highly disordered colloidal hexagonal birnessite, similar to those produced by biotically generated superoxide.Yet, in contrast to the large particulate Mn oxides formed by biogenic superoxide, abiotic Mn oxides did not ripen to larger, more crystalline phases.This suggests that the deposition of crystalline Mn oxides within the environment requires a biological, or at least organic, influence.This work provides the first direct evidence that, under conditions relevant to natural waters, oxidation of Mn(II) by superoxide can occur and lead to formation of Mn oxides. For organisms that oxidize Mn(II) by producing superoxide, these findings may also point to other microbially mediated processes, in particular enzymatic hydrogen peroxide degradation and/or production of organic ligand metabolites, that allow for Mn oxide formation.

59 BASIC BIOLOGICAL SCIENCES↗

Constraining the Absolute Orientation of eta Carinae's Binary Orbit: A 3-D Dynamical Model for the Broad [Fe III] Emission

We present a three-dimensional (3-D) dynamical model for the broad [Fe III] emission observed in Eta Carinae using the Hubble Space Telescope/Space Telescope Imaging Spectrograph (HST/STIS). This model is based on full 3-D Smoothed Particle Hydrodynamics (SPH) simulations of Eta Car's binary colliding winds. Radiative transfer codes are used to generate synthetic spectro-images of [Fe III] emission line structures at various observed orbital phases and STIS slit position angles (PAs). Through a parameter study that varies the orbital inclination i, the PA(theta) that the orbital plane projection of the line-of-sight makes with the apastron side of the semi-major axis, and the PA on the sky of the orbital axis, we are able, for the first time, to tightly constrain the absolute 3-D orientation of the binary orbit. To simultaneously reproduce the blue-shifted emission arcs observed at orbital phase 0.976, STIS slit PA = +38deg, and the temporal variations in emission seen at negative slit PAs, the binary needs to have an i approx. = 130deg to 145deg, Theta approx. = -15deg to +30deg, and an orbital axis projected on the sky at a P A approx. = 302deg to 327deg east of north. This represents a system with an orbital axis that is closely aligned with the inferred polar axis of the Homunculus nebula, in 3-D. The companion star, Eta(sub B), thus orbits clockwise on the sky and is on the observer's side of the system at apastron. This orientation has important implications for theories for the formation of the Homunculus and helps lay the groundwork for orbital modeling to determine the stellar masses.

Madura, T. I.↗

Variability of Jupiter's Five-Micron Hot Spot Inventory

Global upheavals on Jupiter involve changes in the albedo of entire axisymmetric regions, lasting several years, with the last two occurring in 1989 and 2006. Against this backdrop of planetary-scale changes, discrete features such as the Great Red Spot (GRS), and other vortices exhibit changes on shorter spatial- and time-scales. We track the variability of the discrete equatorial 5-micron hot spots, semi-evenly spaced in longitude and confined to a narrow latitude band centered at 6.5degN (southern edge of the North Equatorial Belt, NEB), abundant in Voyager images. Tantalizingly similar patterns were observed in the visible (bright plumes and blue-gray regions), where reflectivity in the red is anti-correlated with 5-microns thermal radiance. Ortiz et al. (1998, GRL, 103) characterized the latitude and drift rates of the hot spots, including the descent of the Galileo probe at the southern edge of a 5-micron hot spot, as the superposition of equatorial Rossby waves, with phase speeds between 99 - 103m/s, relative to System III. We note that the high 5-micron radiances correlate well but not perfectly with high 8.57-micron radiances. Because the latter are modulated primarily by changes in the upper ammonia (NH3) ice cloud opacity, this correlation implies that changes in the ammonia ice cloud field may be responsible for the variability seen in the 5-~m maps. During the NEB fade (2011 - early 2012), however, these otherwise ubiquitous features were absent, an atmospheric state not seen in decades. The ongoing NEB revival indicates nascent 5-~m hot spots as early as April 2012, with corresponding visible dark spots. Their continuing growth through July 2012 indicates the possit.le re-establishment of Rossby waves. The South Equatorial Belt (SEB) and NEB revivals began similarly with an instability that developed into a major outbreak, and many similarities in the observed propagation of clear regions.

Yanamandra-Fisher, Padma A.↗

GOTTCHA, Version 1

One major challenge in the field of shotgun metagenomics is the accurate identification of the organisms present within the community, based on classification of short sequence reads. Though microbial community profiling methods have emerged to attempt to rapidly classify the millions of reads output from contemporary sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling tool with significantly smaller FDR, which is also capable of classifying never-before seen genomes into the appropriate parent taxa.The algorithm is based upon three primary computational phases: (I) genomic decomposition into bit vectors, (II) bit vector intersections to identify shared regions, and (III) bit vector subtractions to remove shared regions and reveal unique, signature regions. In the Decomposition phase, genomic data is first masked to highlight only the valid (non-ambiguous) regions and then decomposed into overlapping 24-mers. The k-mers are sorted along with their start positions, de-replicated, and then prefixed, to minimize data duplication. The prefixes are indexed and an identical data structure is created for the start positions to mimic that of the k-mer data structure. During the Intersection phase -- which is the most computationally intensive phase -- as an all-vs-all comparison is made, the number of comparisons is first reduced by four methods: (a) Prefix restriction, (b) Overlap detection, (c) Overlap restriction, and (d) Result recording. In Prefix restriction, only k-mers of the same prefix are compared. Within that group, potential overlap of k-mer suffixes that would result in a non-empty set intersection are screened for. If such an overlap exists, the region which intersects is first reduced by performing a binary search of the boundary suffixes of the smaller set into the larger set, which defines the limits of the zipper-based intersection process. Rather than recording the actual k-mers of the intersection, another data structure of identical "shape" is created which consists of only bit vectors so that only a 1 or 0 will be stored in the location of the k-mer suffix that was found in the intersection. This reduces the amount of data generated and stored considerably. During the Subtraction phase, relevant intersection bitmasks are first unionized together to form a single bitmask which is then applied over the original genome to reveal only those regions of the genome that are unique. These regions are then exported to disk in FASTA format and used in the application of determining the constituents of an unknown metagenomic community.

Freitas, Tracey↗

Vibrations and Phase Stability in Mixed Valence Antimony Oxide

α-Sb 2 O 4 (cervantite) and β-Sb 2 O 4 (clinocervantite) are mixed valence compounds with equal proportions of Sb III and Sb V as represented in the formula Sb III Sb V O 4 . Their structure and properties can be difficult to calculate owing to the Sb III lone-pair electrons. Here, we present a study of the lattice dynamics and vibrational properties using a combination of inelastic neutron scattering, Mössbauer spectroscopy, nuclear inelastic scattering, and density functional theory (DFT) calculations. DFT calculations that account for lone-pair electrons match the experimental densities of phonon states. Mössbauer spectroscopy reveals the β phase to be significantly harder than the α phase. Calculations with O vacancies reveal the possibility for nonstoichiometric proportions of Sb III and Sb V in both phases. An open question is what drives the stability of the α phase over the β phase, as the latter shows pronounced kinetic stability and lower symmetry despite being in the high-temperature phase. Since the vibrational entropy difference is small, it is unlikely to stabilize the α phase. In conclusion, our results suggest that the α phase is more stable only because the material is not fully stoichiometric.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multijunction GaInP/GaAs Solar Cells Grown by Hydride Vapor Phase Epitaxy

We report the development of GaInP/GaAs monolithic tandem solar cells grown by hydride vapor phase epitaxy (HVPE). HVPE is a route to reduced III-V growth costs because the technique takes advantage of low cost inputs (elemental metals and HCl) and high source utilization, and exhibits high growth rates (up to 5 Au/min). The tandem device consists of three main components: a 1.90 eV Ga0.5In0.5P top cell, a p-Ga0.5In0.5P/n-GaAs tunnel junction, and a 1.41 eV rear heterojunction GaAs cell. The open circuit voltage (VOC) of the tandem is 2.41 V, indicating high material quality in both subcells, and voltage addition through the tunnel junction. Electroluminescence measurements indicate that the individual VOC's of the top and bottom cells are 1.40 and 1.01 V, respectively, at short circuit. This yields a band gap (EG) voltage offset, WOC = EG/q-VOC = 0.50 and 0.40 V, respectively, where q is the elementary charge. The WOC of the top cell is higher in part because the structure contains an unpassivated front surface, and because the back surface field (BSF) consists of p+ GaInP rather than a higher- EG heterobarrier. The top cell limits the current of this series-connected device for these reasons, with a short-circuit current density, JSC, of 10.1+/- 0.2 mA/cm2. The overall efficiency is 20.3 +/- 0.4% (uncertified). We measured the device under concentration to look for signs of tunnel junction breakdown, which we did not observe up to ~1000x, which was the highest concentration tested. Importantly, our dynamic-HVPE reactor enables us to deposit this device, which requires multiple abrupt changes in composition and doping, in a short growth time. We discuss next steps to improve the current result, with a clear pathway towards 30% efficiency. The potential for terrestrial applications of this lower cost III-V technology is also discussed.

14 SOLAR ENERGY↗

Development of HVPE-Grown III-V Solar Cells Passivated with AlInP

We present the first AlInP-passivated solar cells grown by dynamic hydride vapor phase epitaxy (D-HVPE). Single junction (1J) GaAs and GaInP/GaAs (2J) tandems with AlInP passivation achieve AM1.5G efficiencies of 26.0% and 28.5%, respectively, which are the highest reported efficiencies for HVPE-grown devices of each type. 1J devices passivated with either AlInP or GaInP exhibit similar VOC and long wavelength current collection, indicating that both windows provide similar passivation. Adding AlInP passivation to the 2J solar cell improves the VOC by -50 mV relative to the device passivated by a GaInP emitter. These achievements remove one of the last barriers limiting parity of HVPE device efficiencies with state-of-the-art.

AlInP↗

The Clustering of Galaxies in the Completed SDSS-III Baryon Oscillation Spectroscopic Survey: Cosmic Flows and Cosmic Web from Luminous Red Galaxies

We present a Bayesian phase-space reconstruction of the cosmic large-scale matter density and velocity fields from the Sloan Digital Sky Survey-III Baryon Oscillations Spectroscopic Survey Data Release 12 CMASS galaxy clustering catalogue. We rely on a given Λ cold dark matter cosmology, a mesh resolution in the range of 6-10 h -1 Mpc, and a lognormal-Poisson model with a redshift-dependent non-linear bias. The bias parameters are derived from the data and a general renormalized perturbation theory approach. We use combined Gibbs and Hamiltonian sampling, implemented in the ARGO code, to iteratively reconstruct the darkmatter density field and the coherent peculiar velocities of individual galaxies, correcting hereby for coherent redshift space distortions. Our tests relying on accurate N-body-based mock galaxy catalogues show unbiased real space power spectra of the non-linear density field up to k ~ 0.2 h Mpc -1 , and vanishing quadrupoles down to r ~ 20 h -1 Mpc. We also demonstrate that the non-linear cosmic web can be obtained from the tidal field tensor based on the Gaussian component of the reconstructed density field. We find that the reconstructed velocities have a statistical correlation coefficient compared to the true velocities of each individual lightcone mock galaxy of r ~ 0.68 including about 10 per cent of satellite galaxies with virial motions (about r = 0.75 without satellites). The power spectra of the velocity divergence agree well with theoretical predictions up to k ~ 0.2 h Mpc -1 . This work will be especially useful to improve, for example, baryon acoustic oscillation reconstructions, kinematic Sunyaev- Zeldovich, integrated Sachs-Wolfe measurements or environmental studies.

Ata, Metin↗

X-ray structure and investigation of molecular motions by dielectric, vibrational and 1H NMR methods for two organic-inorganic hybrid piperazinium compounds: (C4H12N2)2[Sb2Cl10]·2H2O and (C4H12N2)2[Sb2Br10]·2H2O

Highlights: • Bis(piperazine-1,4-diium) decabromodiantimonate(III) (PSB) dihydrate has been synthesized and characterized. • The structural phase transition for PSB at ca. 50 K has been confirmed by the dielectric and {sup 1}H NMR spectroscopy results. • The molecular motion parameters of the organic cations and water molecules have been evaluated and compared for PSB and PSC. - Abstract: Bis(piperazine-1,4-diium) decabromodiantimonate(III) dihydrate, (C{sub 4}H{sub 12}N{sub 2}){sub 2}[Sb{sub 2}Br{sub 10}]·2H{sub 2}O, (abbreviated as PSB) has been synthesized and characterized by single-crystal X-ray diffraction studies. The obtained results indicate that PSB is isostructural with a recently described chloride analogue, (C{sub 4}H{sub 12}N{sub 2}){sub 2}[Sb{sub 2}Cl{sub 10}]⋅2H{sub 2}O (PSC), crystallizing with R{sub 2}MX{sub 5}·nH{sub 2}O stoichiometry and characterized by the discrete zero-dimensional anionic species. The crystal structure of PSB is described by monoclinic symmetry in a P2{sub 1}/n space group. Dielectric measurements (down to 25 K) and IR spectral analyses (measured over a broad temperature range) suggested a much more complicated phase situation below 80 K than for that of PSC. To verify and compare the molecular motions of the organic cations in both analogues, a proton magnetic resonance ({sup 1}H NMR) technique was also applied.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Fe-bearing phases in modern lacustrine microbialites from Mexico

Transition metal ions impurities in microbialites have been previously suggested as paleoenvironmental and/or paleobiological proxies. However, how metals are incorporated into microbialites remains poorly known. Here, in order to assess the distribution and speciation of Fe in modern microbialites, we conducted bulk X-ray diffraction, infrared spectroscopy, X-ray absorption near-edge structure (XANES) spectroscopy, electron microscopy and X-ray microscopy analyses on samples collected from shallow depths in five alkaline lakes in Mexico: Lake Alchichica, Lake La Preciosa, Lake Atexcac, Lake La Alberca de Los Espinos and Lake Pátzcuaro. A range of Fe contents were measured in these microbialites, from low (~0.12 wt.%) to relatively high (~2.2 wt.%). Fe was distributed heterogeneously in microbialites, mostly localized as hotspots or sometimes arranged as discrete laminae. Fe was mostly trivalent in all microbialites and was incorporated into diverse authigenic phases, the proportion of which varied among microbialites. Authigenic phases included Fe-bearing Mg-phyllosilicates such as kerolite and/or stevensite, i.e. (Mg,Fe(II),Fe(III)) 3 Si 4 O 10 (OH) 2 ·nH 2 O and Fe-Mg layered double hydroxides (LDH), i.e. pyroaurite [Mg(II) 6 Fe(III) 2 (CO 3 )(OH) 16 ·4H 2 O] and/or iowaite [Mg(II) 6 Fe(III) 2 Cl 2 (OH) 16 ·4H 2 O], together with Fe-(oxyhydr)oxides. Carbonate phases were negligible carriers of Fe in all lakes. Iowaite/pyroaurite phases, which have often been found as low temperature alteration products in serpentinites, were surprisingly observed in Lake Alchichica, whereas Fe-bearing kerolite/stevensite was present in Lake La Preciosa, Lake Atexcac, Lake La Alberca de Los Espinos and Lake Pátzcuaro. Fe present in these shallow water microbialites may be originated from groundwater seepage derived from adjacent Fe-rich volcanic rocks. We suggest that the occurence of iowaite/pyroaurite vs authigenic Fe-bearing kerolite/stevensite depends on the orthosilicic acid concentration in the lakes. Pyroaurite/iowaite may form and stay preserved in Lake Alchichica because of the low [H 4 SiO 4 ] as well as high alkalinity, [Mg 2+ ], [CO 3 2- ], [Cl-] and pH (~9) prevailing in this lake, while in other lakes, where [H 4 SiO 4 ] is higher (above ~0.4 mM), Fe-bearing kerolite or smectite phases are formed. Overall, the message carried by the Fe-bearing mineral phases in these modern microbialites is multifold: Fe-bearing phases within microbialites may contain some information on environmental conditions (e.g., [H 4 SiO 4 ]) as well as on geochemical processes implicated during their formation (e.g., seepage of anoxic Fe-bearing groundwater). Considering the reactivity of pyroaurite/iowaite and kerolite/stevensite and their possible transformation into diverse mineral phases upon microbial activity, burial and diagenesis, a careful appraisal of Fe speciation using a similar combination of bulk and microscopy analyses is required in order to better assess the origin of Fe in ancient microbialites.

58 GEOSCIENCES↗

Analysis of navigation and guidance requirements for commercial VTOL operations

The paper presents some results of a program undertaken to define navigation and guidance requirements for commercial VTOL operations in the takeoff, cruise, terminal and landing phases of flight in weather conditions up to and including Category III. Quantitative navigation requirements are given for the parameters range, coverage, operation near obstacles, horizontal accuracy, multiple landing aircraft, multiple pad requirements, inertial/radio-inertial requirements, reliability/redundancy, update rate, and data link requirements in all flight phases. A multi-configuration straw-man navigation and guidance system for commercial VTOL operations is presented. Operation of the system is keyed to a fully automatic approach for navigation, guidance and control, with pilot as monitor-manager. The system is a hybrid navigator using a relatively low-cost inertial sensor with DME updates and MLS in the approach/departure phases.

Hoffman, W. C.↗

MEANDERING SHALLOW ATMOSPHERIC JET AS A MODEL OF SATURN'S NORTH-POLAR HEXAGON

The Voyager flybys of Saturn in 1980–1981 revealed a circumpolar Hexagon at ∼78° north planetographic latitude that has persisted for over 30 Earth years, more than one Saturn year, and has been observed by ground-based telescopes, Hubble Space Telescope and multiple instruments on board the Cassini orbiter. Its average phase speed is very slow with respect to the System III rotation rate, defined by the primary periodicity in the Saturn Kilometric Radiation during the Voyager era. Cloud tracking wind measurements reveal the presence of a prograde jet-stream whose path traces the Hexagon’s shape. Previous numerical models have produced large-amplitude, n = 6, wavy structures with westward intrinsic phase propagation (relative to the jet). However, the observed net phase speed has proven to be more difficult to achieve. Here we present numerical simulations showing that instabilities in shallow jets can equilibrate as meanders closely resembling the observed morphology and phase speed of Saturn’s northern Hexagon. We also find that the winds at the bottom of the model are as important as the winds at the cloud level in matching the observed Hexagon’s characteristics.

79 ASTRONOMY AND ASTROPHYSICS↗