Implementation of a non-hydrostatic, adaptive-grid dynamics core in CAM3. Part I: comparison of dynamics cores in aqua-planet simulations

We report on our implementation of EULAG as a dynamical core in the Community Atmospheric Model (CAM). EULAG is a non-hydrostatic, parallel computational model for all-scale geophysical flows. EULAG’s name derives from its two computational options: EULerian (flux form) or semi-LAGrangian (advective form). The model combines nonoscillatory forward-in-time (NFT) numerical algorithms with a robust elliptic Krylov solver. A signature feature of EULAG is that it is formulated in generalized coordinates. In particular, this enables grid adaptivity. In total, these features give EULAG novel advantages over the existing dynamical cores in CAM. This paper uses a series of aqua-planet simulations to demonstrate that CAM-EULAG results compare favorably with those from CAM simulations at standard CAM resolution that use current finite volume or Eulerian-spectral dynamical core options. We also show that the grid adaptivity implemented in CAM3-EULAG allows higher resolution in selected regions without causing anomalous behavior such as spurious wave reflection.     

Stuart H. Perry's contributions to meteorite collection and research, 1927–1957

Abstract— Stuart H. Perry (1874–1957), an influential Michigan newspaper editor and publisher and a vice president of the Associated Press, developed a passionate interest in collecting and studying meteorites in the 1920s and 1930s. Firmly believing that meteorites belong in great museums where they can be properly investigated, he generously donated his meteorites to various museums after he finished his own study of them. He had a sincere interest in the National Collection of Meteorites, and donated 192 specimens–‐mostly irons–‐to the U.S. National Museum; these constituted some of the most important meteorites in its collection, and moved iron meteorites to center stage, a position still occupied. By applying current metallographic methods to the study of iron meteorites, Perry directed scientists to a powerful new research tool, which led to major advances in our understanding of meteoritic irons and helped give rise to a new field within planetary sciences. His groundbreaking monograph The metallography of meteoric iron served as a standard reference collection of metallographic photomicrographs of iron meteorites for more than 30 years. It remained an insightful and useful work on the structure of meteoritic iron until improved binary and ternary phase diagrams in the Fe‐Ni(‐P) system allowed a more detailed treatment of the formation of iron meteorites. Perry received many honors for his work, and held office in the Meteoritical Society, serving as a councilor from 1941–1950, and as a vice president from 1950–1957.     

Arsenite sequestration at the surface of nano-Fe(OH)2, ferrous-carbonate hydroxide, and green-rust after bioreduction of arsenic-sorbed lepidocrocite by Shewanella putrefaciens

X-ray Absorption Fine Structure (XAFS) spectroscopy was used in combination with high resolution transmission electron microscopy (HRTEM), electron energy loss spectroscopy (EELS), X-ray energy dispersive spectroscopy (XEDS), X-ray powder diffraction, and Mössbauer spectroscopy to obtain detailed information on arsenic and iron speciation in the products of anaerobic reduction of pure and As(V)- or As(III)-adsorbed lepidocrocite (γ-FeOOH) by Shewanella putrefaciens ATCC 12099. We found that this strain of S. putrefaciens is capable of using Fe(III) in lepidocrocite and As(V) in solution or adsorbed on lepidocrocite surfaces as electron acceptors. Bioreduction of lepidocrocite in the absence of arsenic resulted in the formation of hydroxycarbonate green rust 1 [Fe^II₄Fe^III₂(OH)₁₂CO₃: GR1(CO₃)], which completely converted into ferrous-carbonate hydroxide (Fe^II₂(OH)₂CO₃: FCH) over nine months. This study thus provides the first evidence of bacterial reduction of stoichiometric GR1(CO₃) into FCH. Bioreduction of As(III)-adsorbed lepidocrocite also led to the formation of GR1(CO₃) prior to formation of FCH, but the presence of As(III) slows down this transformation, leading to the co-occurrence of both phases after 22-month of aging. At the end of this experiment, As(III) was found to be adsorbed on the surfaces of GR1(CO₃) and FCH. After five months, bioreduction of As(V)-bearing lepidocrocite led directly to the formation of FCH in association with nanometer-sized particles of a minor As-rich Fe(OH)₂ phase, with no evidence for green rust formation. In this five-month experiment, As(V) was fully converted to As(III), which was dominantly sorbed at the surface of the Fe(OH)₂ nanoparticles as oligomers binding to the edges of Fe(OH)₆ octahedra at the edges of the octahedral layers of Fe(OH)₂. These multinuclear As(III) surface complexes are characterized by As-As pairs at a distance of 3.32 ± 0.02 Å and by As-Fe pairs at a distance of 3.50 ± 0.02 Å and represent a new type of As(III) surface complex. Chemical analyses show that the majority of As(III) produced in the experiments with As present is associated with iron-bearing hydroxycarbonate or hydroxide solids, reinforcing the idea that, at least under some circumstances, bacterial reduction can promote As(III) sequestration instead of mobilizing it into solution.     

Biogenic nanoparticulate UO2: Synthesis, characterization, and factors affecting surface reactivity

The surface reactivity of biogenic, nanoparticulate UO₂ with respect to sorption of aqueous Zn(II) and particle annealing is different from that of bulk uraninite because of the presence of surface-associated organic matter on the biogenic UO₂. Synthesis of biogenic UO₂ was accomplished by reduction of aqueous uranyl ions, by Shewanella putrefaciens CN32, and the resulting nanoparticles were washed using one of two protocols: (1) to remove surface-associated organic matter and soluble uranyl species (NAUO2), or (2) to remove only soluble uranyl species (BIUO2). A suite of bulk and surface characterization techniques was used to examine bulk and biogenic, nanoparticulate UO₂ as a function of particle size and surface-associated organic matter. The N₂-BET surface areas of the two biogenic UO₂ samples following the washing procedures are 128.63 m² g⁻¹ (NAUO2) and 92.56 m² g⁻¹ (BIUO2), and the average particle sizes range from 5-10 nm based on TEM imaging. Electrophoretic mobility measurements indicate that the surface charge behavior of biogenic, nanoparticulate UO₂ (both NAUO2 and BIUO2) over the pH range 3-9 is the same as that of bulk. The U L_III-edge EXAFS spectra for biogenic UO₂ (both NAUO2 and BIUO2) were best fit with half the number of second-shell uranium neighbors compared to bulk uraninite, and no oxygen neighbors were detected beyond the first shell around U(IV) in the biogenic UO₂. At pH 7, sorption of Zn(II) onto both bulk uraninite and biogenic, nanoparticulate UO₂ is independent of electrolyte concentration, suggesting that Zn(II) sorption complexes are dominantly inner-sphere. The maximum surface area-normalized Zn(II) sorption loadings for the three substrates were 3.00 ± 0.20 μmol m⁻² UO₂ (bulk uraninite), 2.34 ± 0.12 μmol m⁻² UO₂ (NAUO2), and 2.57 ± 0.10 μmol m⁻² UO₂ (BIUO2). Fits of Zn K-edge EXAFS spectra for biogenic, nanoparticulate UO₂ indicate that Zn(II) sorption is dependent on the washing protocol. Zn-U pair correlations were observed at 2.8 ± 0.1 Å for NAUO2 and bulk uraninite; however, they were not observed for sample BIUO2. The derived Zn-U distance, coupled with an average Zn-O distance of 2.09 ± 0.02 Å, indicates that Zn(O,OH)₆ sorbs as bidentate, edge-sharing complexes to UO₈ polyhedra at the surface of NAUO2 nanoparticles and bulk uraninite, which is consistent with a Pauling bond-valence analysis. The absence of Zn-U pair correlations in sample BIUO2 suggests that Zn(II) binds preferentially to the organic matter coating rather than the UO₂ surface. Surface-associated organic matter on the biogenic UO₂ particles also inhibited particle annealing at 90 °C under anaerobic conditions. These results suggest that surface-associated organic matter decreases the reactivity of biogenic, nanoparticulate UO₂ surfaces relative to aqueous Zn(II) and possibly other environmental contaminants.     

Structural controls on fractured coal reservoirs in the southern Appalachian Black Warrior foreland basin

Coal is a nearly impermeable rock type for which the production of fluids requires the presence of open fractures. Basin-wide controls on the fractured coal reservoirs of the Black Warrior foreland basin are demonstrated by the variability of maximum production rates from coalbed methane wells. Reservoir behavior depends on distance from the thrust front. Far from the thrust front, normal faults are barriers to fluid migration and compartmentalize the reservoirs. Close to the thrust front, rates are enhanced along some normal faults, and a new trend is developed. The two trends have the geometry of conjugate strike-slip faults with the same σ₁ direction as the Appalachian fold-thrust belt and are inferred to be the result of late pure-shear deformation of the foreland. Face cleat causes significant permeability anisotropy in some shallow coal seams but does not produce a map-scale production trend.     

Palaeoleptus burmanicus n. gen., n. sp., an Early Cretaceous shore bug (Hemiptera: Palaeoleptidae n. fam.) in Burmese amber

Palaeoleptus burmanicus gen. et sp. nov. (Hemiptera: Leptopodomorpha: Palaeoleptidae fam. nov.) is described from Early Cretaceous Burmese amber. The fossil is characterized by nearly completely coreaceous wings with only a small membranous area at the distal tip, and a unique wing venation consisting of eight closed cells, including four obliquely orientated toward the embolar wing margin and two large vertically-positioned cells extending nearly to the apical wing margin. Additional characters are large, compound eyes, three pairs of cephalic trichobothria, four antennal segments all similar in texture, spines on the profemur, ocelli positioned on a tubercle and a rostrum extending to the mesocoxae, with the second segment bearing four pairs of spines. The female fossil contains an asymmetrical subgenital plate orientated toward the left side of the body, indicating a side-by-side mating behavior as occurs in extant Leptopodomorpha.     

Petrologic and textural diversity among the PCA 02 howardite group,one of the largest pieces of the Vestan surface

Abstract— Nine howardites and two diogenites were recovered from the Pecora Escarpment Icefield (PCA) in 2002. Cosmogenic radionuclide abundances indicate that the samples are paired and that they constituted an approximately 1 m (diameter) meteoroid prior to atmospheric entry. At about 1 m in diameter, the PCA 02 HED group represents one of the largest single pre‐atmospheric pieces of the Vestan surface yet described. Mineral and textural variations were measured in six of the PCA 02 howardites to investigate meter‐scale diversity of the Vestan surface. Mineral compositions span the range of known eucrite and diogenite compositions. Additional non‐diogenitic groups of Mg‐ and Fe‐rich olivine are observed, and are interpreted to have been formed by exogenic contamination and impact melting, respectively. These howardites contain olivine‐rich impact melts that likely formed from dunite‐ and harzburgite‐rich target rocks. Containing the first recognized olivine‐rich HED impact melts, these samples provide meteoritic evidence that olivine‐rich lithologies have been exposed on the surface of Vesta. Finally, we present a new method for mapping distributions of lithologies in howardites using 8 elemental X‐ray maps. Proportions of diogenite and eucrite vary considerably among the PCA 02 howardites, suggesting they originated from a heterogeneous portion of the Vestan surface. While whole sample modes are dominated by diogenite, the finer grain size fractions are consistently more eucritic. This discrepancy has implications for near‐infrared spectral observations of portions of Vesta’s surface that are similar to the PCA 02 howardites, as the finer grained eucritic material will disproportionately dominate the spectra.     

Comparison of Line-of-Sight Magnetograms Taken by the Solar Dynamics Observatory/Helioseismic and Magnetic Imager and Solar and Heliospheric Observatory/Michelson Doppler Imager

We compare line-of-sight magnetograms from the Helioseismic and Magnetic Imager (HMI) onboard the Solar Dynamics Observatory (SDO) and the Michelson Doppler Imager (MDI) onboard the Solar and Heliospheric Observatory (SOHO). The line-of-sight magnetic signal inferred from the calibrated MDI data is greater than that derived from the HMI data by a factor of 1.40. This factor varies somewhat with center-to-limb distance. An upper bound to the random noise for the 1′′ resolution HMI 720-second magnetograms is 6.3 Mx?cm^?2, and 10.2 Mx?cm^?2 for the 45-second magnetograms. Virtually no p-mode leakage is seen in the HMI magnetograms, but it is significant in the MDI magnetograms. 12-hour and 24-hour periodicities are detected in strong fields in the HMI magnetograms. The newly calibrated MDI full-disk magnetograms have been corrected for the zero-point offset and underestimation of the flux density. The noise is 26.4 Mx?cm^?2 for the MDI one-minute full-disk magnetograms and 16.2 Mx?cm^?2 for the five-minute full-disk magnetograms observed with four-arcsecond resolution. The variation of the noise over the Sun’s disk found in MDI magnetograms is likely due to the different optical distortions in the left- and right-circular analyzers, which allows the granulation and p-mode to leak in as noise. Saturation sometimes seen in sunspot umbrae in MDI magnetograms is caused by the low intensity and the limitation of the onboard computation. The noise in the HMI and MDI line-of-sight magnetic-field synoptic charts appears to be fairly uniform over the entire map. The noise is 2.3 Mx?cm^?2 for HMI charts and 5.0 Mx?cm^?2 for MDI charts. No evident periodicity is found in the HMI synoptic charts.     

Image Quality of the Helioseismic and Magnetic Imager (HMI) Onboard the Solar Dynamics Observatory (SDO)

We describe the imaging quality of the Helioseismic and Magnetic Imager (HMI) onboard the Solar Dynamics Observatory (SDO) as measured during the ground calibration of the instrument. We describe the calibration techniques and report our results for the final configuration of HMI. We present the distortion, modulation transfer function, stray light, image shifts introduced by moving parts of the instrument, best focus, field curvature, and the relative alignment of the two cameras. We investigate the gain and linearity of the cameras, and present the measured flat field.