Numerical simulations of the seasonal/latitudinal variations of atomic oxygen and nitric oxide in the lower thermosphere and mesosphere

A 2-Dimensional zonally-averaged thermospheric model and the global University College London (UCL) thermospheric model have been used to investigate the seasonal, solar activity and geomagnetic variation of atomic oxygen and nitric oxide. The 2-dimensional model includes detailed oxygen and nitrogen chemistry, with appropriate completion of the energy equation, by adding the thermal infrared cooling by O and NO. This solution includes solar and auroral production of odd nitrogen compounds and metastable species. This model has been used for three investigations; firstly, to study the interactions between atmospheric dynamics and minor species transport and density; secondly, to examine the seasonal variations of atomic oxygen and nitric oxide within the upper mesosphere and thermosphere and their response to solar and geomagnetic activity variations; thirdly, to study the factor of 7 to 8 peak nitric oxide density increase as solar F sub 10.7 cm flux increases from 70 to 240 reported from the Solar Mesospheric Explorer. Auroral production of NO is shown to be the dominant source at high latitudes, generating peak NO densities a factor of 10 greater than typical number densities at low latitudes. At low latitudes, the predicted variation of the peak NO density, near 110 km, with the solar F sub 10.7 cm flux is rather smaller than is observed. This is most likely due to an overestimate of the soft X-ray flux at low solar activity, for times of extremely low support number, as occurred in June 1986. As observed on pressure levels, the variation of O density is small. The global circulation during solstice and periods of elevated geomagnetic activity causes depletion of O in regions of upwelling, and enhancements in regions of downwelling

Self-consistent modelling of the polar thermosphere and ionosphere to magnetospheric convection and precipitation (invited review)

It has recently been demonstrated that the dramatic effects of plasma precipitation and convection on the composition and dynamics of the polar thermosphere and ionosphere include a number of strong interactive, or feedback, processes. To aid the evaluation of these feedback processes, a joint three dimensional time dependent global model of the Earth's thermosphere and ionosphere was developed in a collaboration between University College London and Sheffield University. This model includes self consistent coupling between the thermosphere and the ionosphere in the polar regions. Some of the major features in the polar ionosphere, which the initial simulations indicate are due to the strong coupling of ions and neutrals in the presence of strong electric fields and energetic electron precipitation are reviewed. The model is also able to simulate seasonal and Universal time variations in the polar thermosphere and ionospheric regions which are due to the variations of solar photoionization in specific geomagnetic regions such as the cusp and polar cap

The Bacterial Photosynthetic Reaction Center as a Model for Membrane Proteins

Membrane proteins participate in many fundamental cellular processes. Until recently, an understanding of the function and properties of membrane proteins was hampered by an absence of structural information at the atomic level. A landmark achievement toward understanding the structure of membrane proteins was the crystallization (1) and structure determination (2-5) the photosynthetic reaction center (RC) from the purple bacteria Rhodopseudomonas viridis, followed by that of the RC from Rhodobacter sphaeroides (6-17). The RC is an integral membrane protein-pigment complex, which carries out the initial steps of photosynthesis (reviewed in 18). RCs from the purple bacteria Rps. viridis and Rb. sphaeroides are composed of three membrane-associated protein subunits (designated L, M, and H), and the following cofactors: four bacteriochlorophylls (Bchl or B), two bacteriopheophytins (Bphe or [phi]), two quinones, and a nonheme iron. The cofactors are organized into two symmetrical branches that are approximately related by a twofold rotation axis (2, 8). A central feature of the structural organization of the RC is the presence of 11 hydrophobic [alpha]-helixes, approximately 20-30 residues long, which are believed to represent the membrane-spanning portion of the RC (3, 9). Five membrane-spanning helixes are present in both the L and M subunits, while a single helix is in the H subunit. The folding of the L and M subunits is similar, consistent with significant sequence similarity between the two chains (19-25). The L and M subunits are approximately related by the same twofold rotation axis that relates the two cofactor branches. RCs are the first membrane proteins to be described at atomic resolution; consequently they provide an important model for discussing the folding of membrane proteins. The structure demonstrates that [alpha]-helical structures may be adopted by integral membrane proteins, and provides confirmation of the utility of hydropathy plots in identifying nonpolar membrane-spanning regions from sequence data. An important distinction between the folding environments of water-soluble proteins and membrane proteins is the large difference in water concentration surrounding the proteins. As a result, hydrophobic interactions (26) play very different roles in stabilizing the tertiary structures of these two classes of proteins; this has important structural consequences. There is a striking difference in surface polarity of membrane and water-soluble proteins. However, the characteristic atomic packing and surface area appear quite similar. A computational method is described for defining the position of the RC in the membrane (10). After localization of the RC structure in the membrane, surface residues in contact with the lipid bilayer were identified. As has been found for soluble globular proteins, surface residues are less well conserved in homologous membrane proteins than the buried, interior residues. Methods based on the variability of residues between homologous proteins are described (13); they are useful (a) in defining surface helical regions of membrane and water-soluble proteins and (b) in assigning the side of these helixes that are exposed to the solvent. A unifying view of protein structure suggests that water-soluble proteins may be considered as modified membrane proteins with covalently attached polar groups that solubilize the proteins in aqueous solution

An Isomorphous Replacement Method for Phasing Twinned Structures

A linear least-squares formulation of the method of isomorphous replacement is presented. With data from untwinned crystals, this approach is shown to be equivalent to the phasing representation developed by Hendrickson & Lattman [Acta Cryst. (1970). B26, 136-143]. A general method for calculating the most probable phase is described and applied to the higher- dimensional problem of phase determination for twinned structures. A method for calculating the best phase with intensity data from twinned crystals is also presented. The dependences of these phasing procedures on the number of derivatives and accuracy of the data sets are evaluated in test calculations

Post-harvest handling practices and associated food losses and limitations in the sweetpotato value chain of southern Ethiopia

Household food insecurity is a chronic problem in Ethiopia; the situation is being exacerbated by high population growth rates and recurring droughts in the country. The interest to address post-harvest value chain (VC) constraints leading to food losses has increased significantly to provide adequate nutrition to the growing population. In this study, mapping of sweetpotato VC not only quantifies the degree of losses but establish links between distinct VC constraints and respective food losses and limitations. Harvest and handling at farm level and shelf life issues at distribution were identified as vulnerable hot-spots of the sweetpotato food losses. Apart from physical and biological factors, demand and supply mismatch during the main harvest season at the wet markets leads to food (up to 25%) and economic losses (33–75%) followed by deficiencies in the lean season. A multi-stakeholder cooperation is required to mitigate food losses, which can have a high impact on the nutritional and financial status of the producers, market operators, and the consumers

Spectropolarimetric observations of the Ca II 8498 A and 8542 A lines in the quiet Sun

The Ca II infrared triplet is one of the few magnetically sensitive chromospheric lines available for ground-based observations. We present spectropolarimetric observations of the 8498 A and 8542 A lines in a quiet Sun region near a decaying active region and compare the results with a simulation of the lines in a high plasma-beta regime. Cluster analysis of Stokes V profile pairs shows that the two lines, despite arguably being formed fairly close, often do not have similar shapes. In the network, the local magnetic topology is more important in determining the shapes of the Stokes V profiles than the phase of the wave, contrary to what our simulations show. We also find that Stokes V asymmetries are very common in the network, and the histograms of the observed amplitude and area asymmetries differ significantly from the simulation. Both the network and internetwork show oscillatory behavior in the Ca II lines. It is stronger in the network, where shocking waves, similar to those in the high-beta simulation, are seen and large self-reversals in the intensity profiles are common.Comment: 23 pages, 17 figures, accepted to ApJ some figures are low-res, for high-res email [email protected]

Radiative Shock-Induced Collapse of Intergalactic Clouds

Accumulating observational evidence for a number of radio galaxies suggests an association between their jets and regions of active star formation. The standard picture is that shocks generated by the jet propagate through an inhomogeneous medium and trigger the collapse of overdense clouds, which then become active star-forming regions. In this contribution, we report on recent hydrodynamic simulations of radiative shock-cloud interactions using two different cooling models: an equilibrium cooling-curve model assuming solar metallicities and a non-equilibrium chemistry model appropriate for primordial gas clouds. We consider a range of initial cloud densities and shock speeds in order to quantify the role of cooling in the evolution. Our results indicate that for moderate cloud densities (>1 cm^{-3}) and shock Mach numbers (<20), cooling processes can be highly efficient and result in more than 50% of the initial cloud mass cooling to below 100 K. We also use our results to estimate the final H_2 mass fraction for the simulations that use the non-equilibrium chemistry package. This is an important measurement, since H_2 is the dominant coolant for a primordial gas cloud. We find peak H_2 mass fractions of >0.01 and total H_2 mass fractions of >10^{-5} for the cloud gas. Finally, we compare our results with the observations of jet-induced star formation in ``Minkowski's Object.'' We conclude that its morphology, star formation rate (~ 0.3M_solar/yr) and stellar mass (~ 1.2 x 10^7 M_solar) can be explained by the interaction of a 90,000 km/s jet with an ensemble of moderately dense (~ 10 cm^{-3}), warm (10^4 K) intergalactic clouds in the vicinity of its associated radio galaxy at the center of the galaxy cluster.Comment: 30 pages, 7 figures, submitted to Astrophysical Journa