Apollo applications program data archives

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Line Intensities and Molecular Opacities of the FeH F4Δi−X4ΔiF^4\Delta_i-X^4\Delta_i Transition

We calculate new line lists and opacities for the $F^4\Delta_i-X^4\Delta_i$ transition of FeH. The 0-0 band of this transition is responsible for the Wing-Ford band seen in M-type stars, sunspots and brown dwarfs. The new Einstein A values for each line are based on a high level ab initio calculation of the electronic transition dipole moment. The necessary rotational line strength factors (H\"onl-London factors) are derived for both the Hund's case (a) and (b) coupling limits. A new set of spectroscopic constants were derived from the existing FeH term values for v=0, 1 and 2 levels of the $X$ and $F$ states. Using these constants extrapolated term values were generated for v=3 and 4 and for $J$ values up to 50.5. The line lists (including Einstein A values) for the 25 vibrational bands with v$\leq$4 were generated using a merged list of experimental and extrapolated term values. The FeH line lists were use to compute the molecular opacities for a range of temperatures and pressures encountered in L and M dwarf atmospheres. Good agreement was found between the computed and observed spectral energy distribution of the L5 dwarf 2MASS-1507.Comment: 52 pages, 3 figures, many tables, accepted for publication in the Astrophysical Journal Supplement

Spectroscopic Constants, Abundances, and Opacities of the TiH Molecule

Using previous measurements and quantum chemical calculations to derive the molecular properties of the TiH molecule, we obtain new values for its ro-vibrational constants, thermochemical data, spectral line lists, line strengths, and absorption opacities. Furthermore, we calculate the abundance of TiH in M and L dwarf atmospheres and conclude that it is much higher than previously thought. We find that the TiH/TiO ratio increases strongly with decreasing metallicity, and at high temperatures can exceed unity. We suggest that, particularly for subdwarf L and M dwarfs, spectral features of TiH near $\sim$0.52 \mic, 0.94 \mic, and in the $H$ band may be more easily measureable than heretofore thought. The recent possible identification in the L subdwarf 2MASS J0532 of the 0.94 \mic feature of TiH is in keeping with this expectation. We speculate that looking for TiH in other dwarfs and subdwarfs will shed light on the distinctive titanium chemistry of the atmospheres of substellar-mass objects and the dimmest stars.Comment: 37 pages, including 4 figures and 13 tables, accepted to the Astrophysical Journa

Atomic and Molecular Opacities for Brown Dwarf and Giant Planet Atmospheres

We present a comprehensive description of the theory and practice of opacity calculations from the infrared to the ultraviolet needed to generate models of the atmospheres of brown dwarfs and extrasolar giant planets. Methods for using existing line lists and spectroscopic databases in disparate formats are presented and plots of the resulting absorptive opacities versus wavelength for the most important molecules and atoms at representative temperature/pressure points are provided. Electronic, ro-vibrational, bound-free, bound-bound, free-free, and collision-induced transitions and monochromatic opacities are derived, discussed, and analyzed. The species addressed include the alkali metals, iron, heavy metal oxides, metal hydrides, $H_2$, $H_2O$, $CH_4$, $CO$, $NH_3$, $H_2S$, $PH_3$, and representative grains. [Abridged]Comment: 28 pages of text, plus 22 figures, accepted to the Astrophysical Journal Supplement Series, replaced with more compact emulateapj versio

The Near-Infrared and Optical Spectra of Methane Dwarfs and Brown Dwarfs

We identify the pressure--broadened red wings of the saturated potassium resonance lines at 7700 \AA as the source of anomalous absorption seen in the near-infrared spectra of Gliese 229B and, by extension, of methane dwarfs in general. This conclusion is supported by the recent work of Tsuji {\it et al.} 1999, though unlike them we find that dust need not be invoked to explain the spectra of methane dwarfs shortward of 1 micron. We find that a combination of enhanced alkali abundances due to rainout and a more realistic non-Lorentzian theory of resonant line shapes may be all that is needed to properly account for these spectra from 0.5 to 1.0 microns. The WFPC2 $I$ measurement of Gliese 229B is also consistent with this theory. Furthermore, a combination of the blue wings of this K I resonance doublet, the red wings of the Na D lines at 5890 \AA, and, perhaps, the Li I line at 6708 \AA can explain in a natural way the observed WFPC2 $R$ band flux of Gliese 229B. Hence, we conclude that the neutral alkali metals play a central role in the near-infrared and optical spectra of methane dwarfs and that their lines have the potential to provide crucial diagnostics of brown dwarfs. We speculate on the systematics of the near-infrared and optical spectra of methane dwarfs, for a given mass and composition, that stems from the progressive burial with decreasing \teff of the alkali metal atoms to larger pressures and depths.Comment: Revised and accepted to Ap.J. volume 531, March 1, 2000, also available at http://jupiter.as.arizona.edu/~burrows/papers/BMS.p

Dynamic clamp with StdpC software

Dynamic clamp is a powerful method that allows the introduction of artificial electrical components into target cells to simulate ionic conductances and synaptic inputs. This method is based on a fast cycle of measuring the membrane potential of a cell, calculating the current of a desired simulated component using an appropriate model and injecting this current into the cell. Here we present a dynamic clamp protocol using free, fully integrated, open-source software (StdpC, for spike timing-dependent plasticity clamp). Use of this protocol does not require specialist hardware, costly commercial software, experience in real-time operating systems or a strong programming background. The software enables the configuration and operation of a wide range of complex and fully automated dynamic clamp experiments through an intuitive and powerful interface with a minimal initial lead time of a few hours. After initial configuration, experimental results can be generated within minutes of establishing cell recording

Alginate inhibits iron absorption from ferrous gluconate in a randomized controlled trial and reduces iron uptake into Caco-2 cells

Previous in vitro results indicated that alginate beads might be a useful vehicle for food iron fortification. A human study was undertaken to test the hypothesis that alginate enhances iron absorption. A randomised, single blinded, cross-over trial was carried out in which iron absorption was measured from serum iron appearance after a test meal. Overnight-fasted volunteers (n=15) were given a test meal of 200g cola-flavoured jelly plus 21 mg iron as ferrous gluconate, either in alginate beads mixed into the jelly or in a capsule. Iron absorption was lower from the alginate beads than from ferrous gluconate (8.5% and 12.6% respectively, p=0.003). Sub-group B (n=9) consumed the test meals together with 600 mg calcium to determine whether alginate modified the inhibitory effect of calcium. Calcium reduced iron absorption from ferrous gluconate by 51%, from 11.5% to 5.6% (p=0.014), and from alginate beads by 37%, from 8.3% to 5.2% (p=0.009). In vitro studies using Caco-2 cells were designed to explore the reasons for the difference between the previous in vitro findings and the human study; confirmed the inhibitory effect of alginate. Beads similar to those used in the human study were subjected to simulated gastrointestinal digestion, with and without cola jelly, and the digestate applied to Caco-2 cells. Both alginate and cola jelly significantly reduced iron uptake into the cells, by 34% (p=0.009) and 35% (p=0.003) respectively. The combination of cola jelly and calcium produced a very low ferritin response, 16.5% (p<0.001) of that observed with ferrous gluconate alone. The results of these studies demonstrate that alginate beads are not a useful delivery system for soluble salts of iron for the purpose of food fortification

Genome landscapes and bacteriophage codon usage

Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns of codon usage across 74 diverse bacteriophages that infect E. coli, P. aeruginosa and L. lactis as their primary host. We introduce the concept of a `genome landscape,' which helps reveal non-trivial, long-range patterns in codon usage across a genome. We develop a series of randomization tests that allow us to interrogate the significance of one aspect of codon usage, such a GC content, while controlling for another aspect, such as adaptation to host-preferred codons. We find that 33 phage genomes exhibit highly non-random patterns in their GC3-content, use of host-preferred codons, or both. We show that the head and tail proteins of these phages exhibit significant bias towards host-preferred codons, relative to the non-structural phage proteins. Our results support the hypothesis of translational selection on viral genes for host-preferred codons, over a broad range of bacteriophages.Comment: 9 Color Figures, 5 Tables, 53 Reference