binding of either tyrosine or 6MPH4 alone does not change the coordination. However, when both tyrosine and 6MPH4 are bound, the active site becomes 5-coordinate, creating an open site for reaction with O2. Investigation of the kinetics of oxygen reactivity of TyrH complexes in the absence and presence of tyrosine and/or 6MPH4 indicated that there is a significant enhancement in reactivity in the 5-coordinate complex in comparison to the 6-coordinate form. Similar investigations with E332A TyrH showed that Glu332 residue plays a role in directing the protonation of the bridged complex that forms prior to the formation of Fe(IV)O. Rapid chemical quench analyses of DOPA formation showed a burst of product formation, suggesting a slow product release step. Steady-state viscosity experiments established a diffusional step as being significantly rate-limiting. Further studies with stopped-flow spectroscopy indicated that the rate of TyrH reaction is determined by a combination of a number of physical and chemical steps. Investigation of the NO complexes of TyrH by means of optical absorption, electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) techniques revealed the relative positions of the substrate and cofactor with respect to NO, an O2 mimic, and provided further insight into how the active site is tuned for catalytic reactivity upon substrate and cofactor binding. The second theory is that a decreased vertical temperature lapse rate, dT/dp, would slow cloud growth, creating a mode of cloud-top heights at the stable layer as clouds lose buoyancy. The signal for lapse rate changes in the AIRS data, however, is not as strong as the signal for RH differences. Near 600-400 hPa, roughly the region where congestus cloud-top heights are located, no significant difference in lapse rates is noted between congestus and deep clouds; in fact, the mean values suggest that congestus clouds appear in more unstable atmospheres than deep clouds. Only slight differences in temperature and lapse rate are noted in ERA data as well. These results suggest that drier air may play a greater role in limiting congestus cloud-top heights than increased atmospheric stability. Five years of relative humidity (RH) observations from the Atmospheric Infrared Sounder (AIRS) instrument aboard the Aqua satellite are then analyzed to identify areas of anomalously dry air between 600 and 400 hPa over deep convective regions of the tropical oceans. Back trajectories are then calculated for each observed parcel.

The thesis consists of three projects. Each of these projects is a diagnostic study of the interaction between strong convective events and the background atmosphere. In all projects, we use a satellite rainfall dataset to identify strong rain events. We then use radiosonde soundings to generate composite anomaly patterns of meteorological variables about the strong rain events. In Project 1, we examine temperature, relative humidity, and divergence anomalies about strong convective events in the Western Tropical Pacific. A low-level convergence coupled to a midlevel divergence develops prior to peak rainfall. A midlevel convergence coupled to a low-level divergence develops after peak rainfall. Strong surface cold pools develop in response to high rainfall. Observations were compared to models and reanalyses. In general, models and reanalyses do not fully represent the timing, strength, and altitude of the mid-level convergence and divergence features. The surface cold anomaly is also underestimated in models. These discrepancies suggest that the mesoscale downward transport of mid-level air into the boundary layer in models may be too weak. In Project 2, we investigate the impact of convection on the background distribution of a chemical tracer (ozone). Negative ozone anomalies and higher frequency of midlevel cloud tops occur in a layer between 3 and 8 km prior to peak rainfall. Negative ozone anomalies in the upper troposphere develop in response to high rainfall. Chemistry transport model simulations also exhibit negative ozone anomalies at upper and midlevels. However, the ozone anomalies in the model are symmetric about peak rainfall and are more persistent than observations. In Project 3, we identify regional variations in the interaction between convection and the background atmosphere. In all four regions, deep convection imposes cooling in the lower and warming in the upper troposphere. In mid-latitudes, convection is associated with stronger anomalies in surface pressure, geopotential height, and CAPE. Over land, a low-level warm anomaly develops prior to peak rainfall and the surface cold pool that develops during peak rainfall is more persistent. The PV generated prior to peak rainfall, is advected towards the surface after peak rainfall and may play a role in hurricane genesis.

Midlevel clouds are observed globally and impact the general circulation through their influence on the radiation budget and their precipitation production. However, because midlevel clouds occur less frequently than high and low clouds they are relatively understudied. Satellite observations from the MODIS, CALIPSO, and CloudSat instruments onboard the A-Train are combined to study midlevel cloud characteristics in the Tropical Western Pacific (TWP) between January 2007 and December 2010. Characteristic cloud and microphysical properties including cloud top height (CTH), geometric thickness, optical depth, effective radius, and liquid or ice water path (LWP or IWP), and environmental properties, including temperature and specific humidity profiles, are determined for precipitating and non-precipitating midlevel clouds. In the study region, approximately 14% of all cloudy scenes are classified as midlevel clouds (4 km < CTH < 8 km). These are concentrated in areas of deeper convection associated with the Pacific warm pool, ITCZ, and SPCZ. Non-precipitating clouds dominate the region, accounting for approximately 70% of all single and two-layer midlevel clouds scenes. Midlevel clouds occur most frequently in three different scenarios: high over midlevel clouds (~65%), single-layer (~25%), and midlevel over mid- or low-level clouds (~10%). Environmental moisture appears to play a larger role than temperature in determining midlevel cloud distributions due to large variations in moisture between the different cloud scenarios. In all scenes, a trimodal distribution in CTH frequency is found within the midlevel. Two of these peaks have been identified in previous studies; however a third midlevel mode is recognized here. CTHs occur most frequently in peaks between 5-6 km, 6-6.25 km, and 6.5-7.5 km. Although the past studies have only noted two midlevel peaks, this third mode is a robust feature in this dataset. Two types of clouds dominate these peaks: non-precipitating altostratus or altocumulus-like clouds less than 1 km thick and geometrically thick precipitating cumulus congestus clouds. Environmental temperature stable layers and dry maxima are found at each one of these peak frequency heights. Again, moisture seems to play a more dominant role in determining the height of the midlevel clouds due to larger variances between the moisture gradients associated with each peak. Microphysical properties (optical depth, effective radius, and LWP or IWP) are characterized for single-layer clouds. Approximately 30% of all single-layer midlevel clouds are precipitating and these clouds tend to occur on the edges of the deep tropics. In general, precipitating clouds have greater optical depths, effective radii, and water path. This research implies that some past studies at single point locations can be representative of the broader tropics, whereas others are not.

This thesis deals with tropical intraseasonal variation (TISV) having time scales in 20-80 day range. Variations on this time scale have been observed to have profound influence on the weather and climate of the entire globe, and hence its study forms an important area of current research. A large number of studies have been carried out on this topic since the pioneering work of Madden and Julian in 1971. However, the observational studies are biased towards using the outgoing longwave radiation (OLR) as the variable of interest, and other variables, pressure in particular, have received less attention. The present thesis explores features of intraseasonal variations in sea level pressure (SLP) with the following main objectives. 1. Compare and contrast wavenumber – frequency spectra of OLR, zonal winds and SLP. 2. Quantify temporal and spatial variations of different tropical modes observed in the above variables. 3. Investigate intraseasonal variations in sea level pressure in the tropics and its meridional connections. 4. Document the movement of cloud bands during the periods of high and low TISV activity during different seasons. 5. Explore the relations between intraseasonal variations in SLP and monsoon rainfall over India. The study considered global data for a time period of 25 years from 1979 to 2003. Spectral analysis and correlations are the main tools of analysis. A combined FFT-wavelet spectral method, which uses FFT in longitude and wavelet transform in time, was developed for this purpose. This method provided an effective way of obtaining wavenumber - frequency spectra as well as in quantifying temporal variations of different modes. The transform gives spectral intensity as a function of wavenumber, frequency and time. The analysis is applied to OLR, zonal wind and SLP to understand spectral characteristics of different modes and their temporal variations. The thesis shows that the nature of spectra for OLR, SLP and wind is different although these variables are physically connected. OLR spectrum shows many of the equatorial modes observed from the previous studies for an equivalent depth of 40 m. Spectra of zonal winds at three vertical levels (850 mb, 500 mb and 200 mb) shows peaks corresponding to MJO, Kelvin modes at an equivalent depth of 75 m and Rossby Haurwitz modes. SLP spectrum is different from others. It has peaks at wavenumber zero and at MJO and Rossby Haurwitz modes. Another important new result of the thesis is the spatial and temporal behavior of SLP on intraseasonal time scales. It is shown that the the global atmosphere exhibits quasi-periodic oscillations in SLP with variations in the tropics and high latitudes strongly correlated but in opposite phases. Importantly, the strength of TISV is correlated with sea surface temperature (SST) anomalies in the equatorial Pacific Ocean. This may have some predictive value for predicting the active and weak TISV activity.

Les interactions entre la convection humide et la dynamique de grande échelle sont au cœur du climat tropical et de sa variabilité. Les processus associés aux nuages convectifs, tels que la condensation, l'évaporation, les processus radiatifs, et le transport d'énergie à petite échelle associé, génèrent des gradients de température dans l'atmosphère. Ces derniers engendrent des circulations de grande échelle qui contrôlent les distributions spatio-temporelles d'énergie et d'humidité, et donc en retour celle de la convection. Ces interactions forment probablement l'un des problèmes scientifiques majeurs de la modélisation de l'atmosphère. L'objectif de cette thèse est d'analyser la représentation de ces interactions dans le modèle de climat ARPEGE-Climat Version 6 et de comprendre le rôle qu'elles peuvent jouer dans les principaux biais du modèle sous les tropiques, notamment un biais froid de plusieurs degrés en moyenne et haute troposphère et un biais sec vers 850 hPa. Les impacts des processus convectifs sur la grande échelle sont souvent caractérisés par deux quantités, la source de chaleur apparente Q1 et le puits d'humidité apparent Q2 . Bien que difficilement observables, ces deux quantités peuvent être estimées en déployant un réseau de radiosondages permettant de déterminer les différents termes des bilans d'eau et d'énergie sur un quadrilatère donné. Un tel dispositif a été mis en œuvre d'octobre à décembre 2011 pendant la campagne CINDY2011/DYNAMO au cœur de l'Océan Indien. Les observations collectées et les données de Q1 et Q2 dérivées ont été utilisées dans cette thèse pour (i) caractériser le cycle de vie de la convection et (ii) mettre en place une configuration unicolonne du modèle ARPEGE-Climat sur les quadrilatères Nord et Sud du domaine CINDY2011/DYNAMO. Les résultats ont montré que le modèle ARPEGE-Climat est capable de reproduire de manière satisfaisante les transitions entre régimes de convection peu profonde, profonde et stratiforme, malgré une nette sous-estimation du flux d'évaporation en surface et de l'activité convective sur le domaine nord. Le modèle reproduit plus difficilement l'humidification de la troposphère pendant les phases de cumulus peu profonds. Les résultats obtenus dans ce cadre unicolonne ont ensuite été confrontés à des configurations 3D du modèle ARPEGE-Climat, à la fois en mode AMIP où le modèle est seulement forcé par les températures de la mer observées, et en mode "Transpose-AMIP" où le modèle est de plus initialisé à partir d'états réalistes de l'atmosphère. L'analyse de la dérive systématique du modèle dans ces simulations Transpose-AMIP a permis de montrer que les biais obtenus en mode AMIP étaient associés à des processus rapides (quelques jours). Ces biais sont généralement aussi très similaires à ceux documentés dans le cadre unicolonne. L'origine des biais thermodynamiques est analysée plus en détail, soulignant un rôle important des régimes de convection profonde, notamment dans sa phase stratiforme, pour le biais froid de la haute troposphère, et des défauts importants dans les régimes de cumulus peu profond et de congestus pour les biais d'humidité. Ces régimes mériteront une attention particulière dans les prochains développements de la physique d'ARPEGE-Climat. / The tropical climate and its variability at multiple timescales are dominated by interactions between moist convection and the large-scale atmospheric circulation. Small-scale processes associated with convective clouds such as condensation and evaporation, radiation, and vertical mixing all contribute to atmospheric temperature gradients which generate large-scale circulations. Such circulations exert a control on the spatio-temporal distribution of energy and humidity within the tropical atmosphere and, in turn, on moist convection. These twoway interactions represent one of the most difficult scientific challenge for global atmospheric modelling. The main objective of the present thesis is to analyse the representation of these interactions in Version 6 of the ARPEGE-Climat atmospheric general circulation model and to understand their possible contribution to the main model biases in the tropics, especially a cold bias in the mid and upper troposphere and a dry bias around 850 hPa. The large-scale impacts of moist convection are often characterized by two quantities, the apparent heat source, Q1, and the apparent moisture sink, Q2. Although difficult to observe, these two quantities can be estimated by deploying a sounding array of sufficient density to compute the different terms of the water and energy budgets over a selected domain. Such a strategy was implemented between October and December 2011 during the CINDY2011/DYNAMO field campaign in the middle of the tropical Indian Ocean. The collected observations and the derived Q1 and Q2 estimates are used in the present thesis to (i) characterize the life cycle of the tropical convection and (ii) set up a single column configuration of the ARPEGE-Climat model on the northern and southern domains of the campaign. Results show that the model is able to capture satisfactorily the transitions between different convective regimes, from shallow to deep and stratiform, despite a strong undestimation of surface evaporation and of the overall convective activity over the northern domain. The model however shows some difficulties at simulating the troposphere moistening during the shallow cumulus regime. The single column model results are then compared to 3D configurations of the ARPEGEClimat model, both in AMIP mode where the model is only driven by observed sea surface temperatures, and in " Transpose-AMIP " mode where the model is also initialized from realistic atmospheric conditions. Through the analysis of the systematic atmospheric drift across these Transpose-AMIP integrations, the dominant contribution of fast (within a few days) processes to the model biases found in AMIP mode is highlighted. Such biases also show some similarity with the errors simulated in the single-column framework. A more detailed analysis of the model systematic errors reveals a strong contribution of deep convection, especially in its stratiform regime, to the cold bias in the upper troposphere, and of deficiencies in the shallow cumulus regime to the moisture biases. These regimes will therefore deserve a particular attention during the next phase of development of the ARPEGE-Climat model.

A lack of quality data on high clouds has led to inadequate representations within global weather and climate models. Recent advances in spaceborne measurements of the Earth’s atmosphere have provided complementary information on the interior of these clouds. This study demonstrate how an array of space-borne measurements can be used and combined, by close co-located comparisons in space and time, to form a more complete representation of high cloud processes and properties. High clouds are found in the upper atmosphere, where sub-zero temperatures frequently result in the formation of cloud particles that are composed of ice. Weather and climate models characterise the bulk properties of these ice particles to describe the current state of the cloud-sky atmosphere. By directly comparing measurements with simulations undertaken at the same place and time, this study demonstrates how improvements can be made to the representation of cloud properties. The results from this study will assist in the design of future cloud missions to provide a better quality input. These improvements will also help improve weather predictions and lower the uncertainty in cloud feedback response to increasing atmospheric temperature. Most clouds are difficult to monitor by more than one instrument due to continuous changes in: large-scale and sub-cloud scale circulation features, microphysical properties and processes and characteristic chemical signatures. This study undertakes co-located comparisons of high cloud data with a cloud ice dataset reported from the Microwave Limb Sounder (MLS) instrument onboard the Aura satellite that forms part of the A-train constellation. Data from the MLS science team include vertical profiles of temperature, ice water content (IWC) and the mixing ratios of several trace gases. Their vertical resolutions are 3 to 6 km. Initial investigations explore the link between cloud-top properties and the longwave radiation budget, developing methods for estimating cloud top heights using; longwave radiative fluxes, and IWC profiles. Synergistic trios of direct and indirect high cloud measurements were used to validate detections from the MLS by direct comparisons with two different A-train instruments; the NASA Moderate-resolution Imaging Spectroradiometer (MODIS) and the Clouds and the Earth’s Radiant Energy System (CERES) onboard on the Aqua satellite. This finding focuses later studies on two high cloud scene types that are well detected by the MLS; deep convective plumes that form from moist ascent, and their adjacent outflows that emanate outwards several hundred kilometres. The second part of the thesis identifies and characterises two different high cloud scenes in the tropics. Direct observational data is used to refine calculations of the climate sensitivity to upper tropospheric humidity and high cloud in different conditions. The data reveals several discernible features of convective outflows are identified using a large sample of MLS data. The key finding, facilitated by the use of co-location, reveals that deep convective plumes exert a large longwave warming effect on the local climate of 52 ± 28Wm−2, with their adjacent outflows presenting a more modest warming of 33 ± 20Wm−2.

A method of inferring tropospheric gravity wave source characteristics from middle atmosphere observations has been adapted from previous studies for use with MF radar observations of the equatorial mesosphere-lower thermosphere at Christmas Island in the central Pacific. The nature of the techniques applied also permitted an analysis of the momentum flux associated with the characterised sources and its effects on the equatorial mean flow and diurnal solar thermal tide. An anisotropic function of gravity wave horizontal phase speed was identified as being characteristic of convectively generated source spectra. This was applied stochastically to a ray-tracing model to isolate numerical estimates of the function parameters. The inferred spectral characteristics were found to be consistent with current theories relating convective gravity wave spectra to tropospheric conditions and parameters characterising tropical deep convection. The results obtained provide observational constraints on the model spectra used in gravity wave parameterisations in numerical weather prediction and general circulation models. The interaction of gravity waves with the diurnal solar thermal tide was found to cause an amplification of the tide in the vicinity of the mesopause. The gravity wave-tidal interactions were highly sensitive to spectral width and amplitude. Estimates were made of the high frequency gravity wave contribution to forcing the MSAO with variable results. The data used in the analysis are part of a large archive which now has the potential to provide tighter constraints on wave spectra through the use of the methods developed here. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1352362 / Thesis (Ph.D.) -- University of Adelaide, School of Chemistry and Physics, 2009