This thesis describes the undertaking of multiple studies designed to evaluate and reduce global modelled surface O3 biases in CTMs/ESMs. Specific focus is placed on the evaluation of rural surface O3 seasonal variability in a global CTM (GEOS-Chem). A major observational data collation is undertaken, processing 1,033,463,750 measurements of O3 and some of its major precursors, from 16,996 sites, through a number of rigorous data quality checks, to ensure data is of a high enough quality for global model evaluation. Through a model–measurement comparison, applying spectral analysis, substantial seasonal biases of surface O3 in GEOS-Chem are found, with a general overestimation of the seasonal amplitudes in North America and Europe (by up to 16 ppbv), together with delayed phase maxima by 1–5 months. The main cause of these biases is found to be homogenous overestimates of summertime O3 in all observed areas, by a minimum of 10 ppbv. An extensive global sensitivity study is undertaken to evaluate the sensitivity of modelled surface O3 biases to alterations of anthropogenic emissions, biogenic emissions, and the O3 dry deposition flux. Constraining model biases jointly by O3, NO and CO observations yields regional optimal monthly scaling factors. Driving GEOS-Chem with these derived factors results in the modelled summertime overestimates of surface O3 being removed almost entirely, across all regions. The removal of this bias is dominantly controlled through increases to the summertime O3 dry deposition flux (by factors of 2–4), with modifications to this term providing the only viable pathway for substantial reduction of modelled summertime biases, in all evaluated regions. Surface O3 is found to be NOx sensitive in all regions, with scalings of VOC emissions generally not imparting significant change on O3. General modelled winter underestimates of surface O3 are able to be removed through reductions of NOx emissions.

The existence of downward propagation mechanisms that couple stratospheric disturbances to the troposphere motivated the study of processes that can influence these stratospheric regimes. The dependence of the variability on the amplitude of the tropospheric wave forcing was studied on a stratosphere-mesosphere model, showing the atmosphere to be at a transition phase between the two regimes, with potential large amplification of the response to small perturbations. The recent discovery of transient luminous events (TLEs) such as sprites motivated the systematic study of the response of the middle atmosphere model to increasingly complex idealised ozone perturbation experiments. Within radioactively driven regions, the response of the middle atmosphere was found to be linear on the magnitude of the ozone reduction, within the location and time of the perturbation. In dynamically controlled regions, localised ozone perturbations (e.g. the ozone hole) could induce larger non-local responses compared to an equivalent uniform ozone change. Impulsive perturbations were found to be more capable of inducing changes to the variability compared to the equivalent forcing that was constant in time. The first estimates of the chemical impact of sprites were obtained using satellite data. Sprites were shown to cause no significant NOx or ozone changes at a global level, but to induce up to tens of percentage changes in NOx at 50 to 70 km height over active sprite-producing thunderstones, in reasonable agreement with ion-chemistry model estimates. Sprite ozone changes were found to be 3 to 4 orders of magnitude lower than the weakest ozone perturbation needed to induce significant responses in the model.

This thesis focuses on the photochemistry occuring in the troposphere over Europe. The use of the MRP C-130 Hercules aircraft fitted with instrumentation for the measurement of pertinent chemical and physical parameters in the study of the chemistry of the troposphere is described. The calibration and characterisation of the University of Leicester fixed band-width radiometer for the measurement of the photolysis rate coefficient of ozone is also described. This instrument was fitted to the research aircraft in order to provide a measurement of the production rate of reactive radical species in conjuction with the in-situ chemical measurements. Results from the Atmospheric Chemistry and the Transport of Ozone (ACTO) experiment are presented. The average chemical environment is shown along with the relationship between tracer correlations and air mass origins, and shows that the the region of the upper troposphere sampled during the ACTO experiment was perturbed by the lower stratosphere. The results show that influence of the stratosphere was detected as low as 5.5 km and resulted in perturbed ozone, carbon monoxide and NOy levels relative to the background troposphere. The European Export of Precursors and Ozone by Long-range Transport (EXPORT) experiment is described in detail. A study of the average altitude profiles of measured tracers shows the influence of the European continental boundary layer on the lower and middle troposphere. The origin of air masses sampled in EXPORT acertained using a back-trajectory analysis is presented. This analysis shows that the composition of the troposphere during EXPORT with respect to air mass composition and origin was highly varied. The chemical processing in these air masses was studied by the use of a chemical box model and the results are presented. The processing of HOx radicals and ozone is found to be tied to a large extent to the levels of nitrogen oxides present in the air mass. This in turn depends on the altitude and origin of the sampled air mass. A comparison of the production and loss of HOx radicals and ozone in the ACTO and EXPORT experiments is presented. The gross HOx radical production and loss rates are found to be larger in the EXPORT experiment than in the ACTO experiment. However the net production of HOx radicals is found to be similar in both experiments. Net production of HOx radicals is observed at all altitudes in both experiments, with the exception of the polluted European boundary layer sampled in the EXPORT experiment. The net ozone production in both experiments shows a similar trend with altitude: a "c" shape is observed with a net destruction observed in the lower to mid troposphere, and production at higher and lower altitudes. The effect of the polluted European boundary layer is observed in the EXPORT experiment as HOx radical levels are suppressed resulting in net loss of ozone. The influence of the stratosphere is observed in the highest altitudes sampled in the ACTO experiment. Large net destruction rates are observed as a direct result of the large ozone mixing fraction sampled in the stratospherically influenced air masses.

The West African Monsoon onset marks a vital point in the seasonal monsoon cycle over the region with direct implications for local farmers and other stakeholders. In this work, valuable insight into the exact definition of the monsoon onset, its level of spatial consistency and cause of inter-annual variability of onsets has been presented. Criteria are presented to determine the value of monsoon onset definitions. There exist over seventeen unique onset definitions in publication. In this work, a representative sub-set of definitions have been compared to assess the relative value and suitability of onset definitions. It is found that the length scale over which a definition is defined determines the relevance to certain users. Local farmers require knowledge on local onset definitions which often have no similarity to regional onset definitions. Local onset dates are shown to have a pragmatic level of spatial homogeneity. Local Onset Regions (LORs) are presented over which local onset variability can be studied using a representative time series of onset dates. Using LORs, it is found that the seasonal progression of the Inter-Tropical Front and the phase of the Madden-Julian Oscillation drive the inter-annual variability of local onsets. The late passage of the Inter-Tropical Front past a LOR is linked to later onset in that region. Furthermore, when the Madden-Julian Oscillation inhibits convection across the Guinea Coast, local onset dates tend to be earlier than climatology. Further research into predicting drivers of local onset variability are suggested. Finally, seasonal forecast models tend to under-predict the variability of onset dates across West Africa. There is little significant correlation between observed onset dates (regional or local) and forecasts. It is concluded that seasonal onset forecasts are currently of little value to forecast users in West Africa. Suggestions as to the cause of this limitation are discussed.

This thesis discusses the mesospheric retrievals from high spectral resolution infrared limb measurements data as measured by the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS). Altough MIPAS was designed for stratospheric studies, since April 2007, MIPAS measures the entire mesosphere at least every ten days using a special viewing mode. Retrieving geophysical properties at such high altitudes requires careful attention due to signal to noise limitations as well as the intrusion of non Local Thermodynamic Equilibrium (nonLTE) effects. The three main parts of this thesis are: (1) The evaluation of the Oxford MIPAS middle atmosphere dataset (profiles of pressure, temperature, H2O, O3, HNO3, CH4, N2O, NO2 and CO) as retrieved by the iterative algorithm MORSE. Comparisons of daily zonal means, daily zonal sections and comparisons of pairs of profiles against several mesospheric instruments are shown. (2) The description and validation of a new linear (non-iterative) retrieval algorithm. This algorithm exploits the linearity of an optically thin path which allows to use all the available spectral points of the target parameter rather than just subset of the spectra. (3) The validation of the modelled vibrational temperatures used either in the MORSE or in the linear retrieval to estimate the influence of the nonLTE effects upon the measured radiaces. This thesis also briefly investigates the potential of the HIgh Resolution Dynamic Limb Sounder (HIRDLS) instrument to provide valuable mesospheric information, as well as the detection of polar mesospheric clouds using MIPAS radiances.

Analogues were developed for Interplanetary Dust Particles (IDPs) and Meteoric Smoke Particles (MSPs). Candidate materials were characterised and compared to the present understanding of the nature of IDPs and MSPs. Knowledge and understanding from meteoritics was used to inform open questions in atmospheric chemistry. The elemental composition, structural, surface and size distribution properties of the candidates was compared to micrometeorites and remote measurements of MSPs. Both relatively rare carbonaceous and the more common ordinary chondritic meteorites and terrestrial minerals were shown to be useful analogues for IDPs, whilst synthetic materials were identified as analogues for MSPs. Uptake of HNO3 and HO2, based on laboratory experiments, was implemented in a global modelling study. The uptake processes were assessed to determine the region(s) and season(s) in which they would affect atmospheric chemistry. This heterogeneous chemistry augmented previous understanding of gas-phase chemistry, with a view to understanding all sources and sinks of atmospheric species. Whole Atmosphere Community Climate Model (WACCM) runs including uptake were compared to control runs with only gas-phase chemistry. Uptake of both HNO3 and HO2 was shown to alter chemistry in the polar vortex, including effects on many secondary species and feedbacks on each other. Heterogeneous nucleation kinetics of nitric acid hydrates in Polar Stratospheric Clouds (PSCs) was investigated in the laboratory. SiO2 particles were used as analogues for MSPs processed in acidic solution and the phase which formed was investigated. A newly developed drop freeze assay capable of quantifying heterogeneous nucleation kinetics was used. Nucleation events observed in μl droplets were parameterised using current theoretical models and the results compared to atmospheric observations. The measured heterogeneous nucleation kinetics of the Dihydrate, which then readily converts to the Trihydrate, on SiO2 were shown to be capable of explaining the concentrations of crystals observed in the atmosphere.

Ionospheric modification by means of high-power electromagnetic (EM) waves can result in the excitation of a diverse range of plasma waves and instabilities. This thesis presents the development and application of a GPU-accelerated finite-difference time-domain (FDTD) code designed to simulate the time-explicit response of an ionospheric plasma to incident EM waves. Validation tests are presented in which the code achieved good agreement with the predictions of plasma theory and the computations of benchmark software. The code was used to investigate the mechanisms behind several recent experimental observations which have not been fully understood, including the effect of 2D density inhomogeneity on the O-mode to Z-mode conversion process and thus the shape of the conversion window, and the influence of EM wave polarisation and frequency on the growth of density irregularities. The O-to-Z-mode conversion process was shown to be responsible for a strong dependence of artificially-induced plasma perturbation on both the EM wave inclination angle and the 2D characteristics of the background plasma. Allowing excited Z-mode waves to reflect back towards the interaction region was found to cause enhancement of the electric field and a substantial increase in electron temperature. Simulations of O-mode and X-mode polarised waves demonstrated that both are capable of exciting geomagnetic field-aligned density irregularities, particularly at altitudes where the background plasma frequency corresponds to an electron gyroharmonic. Inclusion of estimated electrostatic fields associated with irregularities in the simulation algorithm resulted in an enhanced electron temperature. Excitation of these density features could address an observed asymmetry in anomalous absorption and recent unexplained X-mode heating results reported at EISCAT. Comparing simulations with ion motion allowed or suppressed indicated that a parametric instability was responsible for irregularity production. Simulation of EM wave fields confirmed that X-mode waves are capable of exceeding the threshold for parametric instability excitation under certain conditions.

The variation between surface and air temperature within a city and its surrounding area is a result of variations in surface cover, thermal capacity and 3-dimensional geometry. This study examines the spatiotemporal formation of the daytime Surface Urban Cool Island (SUCI) and night-time Surface Urban Heat Island (SUHI) effect in Erbil, Iraq, as a case study for cities in semi-arid climates more generally. It furthermore quantifies the influence of rapid urban expansion on the urban heat/cool island effect over a 20 year period. Satellite images acquired by Landsat 4, 5, 7 and 8 between 1992 and 2013 are used to retrieve Land Surface Temperature (LST). Normalised Ratio Scale (NRS) is applied to the multi-mission Landsat data, which is used to adjust the temperature range for different acquisition times of images within the same temporal range. In addition, LST data from the Moderate Resolution Imaging Spectroradiometer (MODIS) on board Aqua and Terra from January 2003 to December 2014 are analysed. In order to establish the drivers of the observed patterns of LST and SUCI/SUHI, the relationships of LST with wetness, greenness, NDVI, soil moisture and other variables are assessed. The results indicate that during the daytime in summer, autumn and winter, densely built-up areas had lower LST acting as cool islands (SUCI) compared to the non-urbanised area around the city. In contrast, at night-time, Erbil experienced higher LST and demonstrated a significant SUHI effect. The mean LST of the newly urbanised and vegetated areas between 1992 and 2013 decreased by 2.28°C and 7.29°C respectively. Soil moisture (wetness) is the main marker of the SUCI/SUHI effect, whilst urban expansion may cause a decrease of daytime LST in dry climate zones. The NRS method is appropriate for detecting temperature trends greater than 2°C in Landsat data.

The TOMCAT 3-D chemical transport model (CTM) has been used to investigate the cause of recent variations in global atmospheric methane (CH4), focusing on examining changes in the balance of sources and sinks of the species. The chemical loss, transport and emissions of methane have been studied and a new 4D-Var inverse version of TOMCAT has been created. The accuracy of the TOMCAT model transport was investigated by simulating the distribution of the long-lived species SF6. A range of model grid resolutions, boundary layer schemes and advection schemes were tested. New retrievals from the Atmospheric Chemistry Experiment (ACE) satellite instrument were used to test the model in the upper troposphere and lower stratosphere. The standard CTM simulated the observed distribution and growth of SF6 well. However, based on comparison with ground-based data, the interhemispheric transport in the TOMCAT model was found to be approximately 20% too slow, with too little temporal variation in southern hemisphere transport. On the whole, however, tracer transport in the CTM using its standard set-up was accurate. As a basis for the inverse model simpler advection and boundary layer (BL) schemes were tested. The advection scheme which conserved only up to first-order moments (rather than secondorder moments) did not significantly reduce the accuracy of the model transport. However, use of a local boundary layer mixing scheme rather than a non-local scheme did degrade the quality of the transport by reducing the speed of vertical mixing out of the BL. A number of currently used CH4 emission inventories were used with the forward TOMCAT model in order to examine the effect they have on the global CH4 budget, and two different estimates of the OH sink were also tested. A published OH field derived from global CH3CCl3 and a chemical box model was found to be more consistent with OH observations than the field from the full chemistry TOMCAT model. Although both OH fields produced global CH4 lifetimes consistent with published estimates, the TOMCAT OH field yielded model CH4 which was up to 100 ppb higher than observations at the surface. Data assimilation was used to improve the estimate of the stratospheric sink of CH4. Although this sink is small overall, it needs to be represented realistically in order to accurately reproduce global CH4 to within 10 ppbv. A new adjoint version of the TOMCAT model was produced by explicit coding, and was thoroughly tested. This was incorporated into a new 4D-Var inverse model which can be used to produce updated CH4 surface flux estimates which are constrained to agree with atmospheric observations. The inverse model was used to investigate emissions in the Arctic where the forward TOMCAT model and standard emissions revealed a seasonal cycle out of phase with surface CH4 observations. It was found that northern hemisphere summertime wetland emissions were overestimated in the GISS inventory by up to 100% for the period 2000-2006, and that this was likely due to the estimates of emission rates and thaw period used when producing that inventory. It was also found that increased Asian emissions suggested in the EDGAR V4.0 inventory are not consistent with observations unless mitigated by a corresponding drop in emissions elsewhere.

Over the past two decades the growth rate of methane has shown large variability on multi-year timescales, the reasons for which are not well understood. The JULES land surface model, TOMCAT 3-D chemical transport model and observations have been used to investigate causes for these variations, with a specific focus on wetland emissions and atmospheric loss. The role of atmospheric variability in the recent methane trends was investigated using TOMCAT, driven by variations in global mean hydroxyl concentrations derived from methyl chloroform observations. Results show that between 1999 and 2006, a stall in the atmospheric methane growth rate was, in part, caused by changes in the atmospheric loss. This was due largely to relatively small changes in global mean hydroxyl concentrations over time, with minor contributions from variations in atmospheric transport and temperature. Methane emissions from various wetland inventories were evaluated using TOMCAT and observations, and recent trends in emissions were investigated. Emissions calculated by JULES were spatially and temporally similar to a top-down emission inventory and produced good agreement with satellite observations when used in TOMCAT (R = 0.84). Emissions derived for the period 1993 – 2012 show a statistically significant (95%-level) positive trend of 0.43 Tg/yr. This suggests a long-term positive trend in wetland emissions that may continue. During the stall in methane growth (1999-2006) modelled wetland emissions were 0.4 Tg/yr lower than average. This suggests that a decrease in wetland emissions contributed to the observed stall in methane growth. The wetland methane processes within JULES were developed to include transport, oxidation, sulphate suppression, unsaturated production and methane storage pools. The parameters required for the additional processes were derived using a perturbed parameter ensemble to optimise the fit with observed fluxes. This slightly increased model performance at flux sites from R = 0.32 in the standard model to R = 0.34 in the updated model. The new version of JULES was tested using TOMCAT and satellite observations, and model agreement improved from R = 0.84 to R = 0.87, additionally the root-mean-squared-error reduced from 17.17 ppb to 15.09 ppb. This suggests the optimised additional model processes slightly improved model performance.