This thesis investigates the mechanism of denitrification o f the Arctic lower stratosphere and the impact o f denitrification on ozone loss using the SLIMCAT chemical transport model. The development of a new microphysical model for the simulation of growth and sedimentation of large nitric acid trihydrate particles is also described. Model simulations of Arctic denitrification were carried out using thermodynamic equilibrium schemes based on the sedimentation of either nitric acid trihydrate or ice using different meteorological analyses. The severity and extent of denitrification in ice-based model runs was found to be highly sensitive to the meteorological analyses used whereas nitric acid trihydrate denitrification schemes exhibited considerably less sensitivity. The response of thermodynamic equilibrium and microphysical NAT-based denitrification to meteorological conditions has been studied in a series of short idealised simulations. It was found that microphysical denitrification was considerably more sensitive to the relative orientation of the polar vortex flow and the region of cold temperatures. A concentric vortex and cold region are required to promote the long particle growth times required for strong denitrification in the microphysical model. Reduced rates of denitrification were evident in the microphysical model at the highest altitudes. Results from the microphyical denitrification scheme were compared with in-situ and remote observations of denitrification for two recent cold Arctic winters. There was remarkable agreement between model and observations of both the magnitude and location of denitrification despite the simple volume-averaged nucleation rate used in the model. The limited range of observations did not allow further constraints to be placed on the microphysical model. Denitrification was found to enhance Arctic ozone loss by up to 30% during 1999/2000. Sensitivity studies o f the impact of denitrification on Arctic ozone loss were performed using thermodynamic nitric acid trihydrate denitrification schemes. Cumulative ozone depletion was found to increase non-linearly with increasing denitrification. Enhanced recovery of chlorine radicals to hydrogen chloride in strongly denitrified model runs offset reduced recovery to chlorine nitrate, limiting the impact of denitrification to the equivalent of 20 days additional ozone loss.

Knowledge of distributions of aerosols is critical to human health, Earth's radiative budget, and air quality. However, the lack of sufficient direct measurements of aerosol type, number, mass concentrations and current limitations of satellite retrievals make it challenging to accurately model the aerosol variability. Such measurement gaps also hinder evaluation of aerosol source budget from emission inventories, modeling of aerosol chemistry, and sinks. In this context, the first study characterizes the potential of multivariate relationships between Aerosol Optical Depth (AOD), a quantity that represents light extinction by aerosols in the atmospheric column and a suite of surface and atmospheric parameters (e.g., vegetation, precipitation, fire characteristics) in order to assess trends in AOD anomalies for the U.S Southwest. This study covers the area that experiences North American Monsoon (NAM) and examines trends in AOD across different aerosol sources in this region such as dust storms, biomass burning, and anthropogenic emissions. We find that aerosols from anthropogenic processes and biomass burning exhibited a strong declining trend in AOD whereas trends along the NAM alley were obfuscated by the monsoon precipitation (sink) and convective dust storms (sources). In the second study, we develop constraints to improve characterization of anthropogenic apparent Elemental Carbon (ECa) using coemitted combustion products such as Carbon Monoxide (CO) and Nitrogen Oxides (NOx). We compare observational ratios of ECa vs CO and ECa vs NOx against those from emission inventories. We find that the observational ratios have increased at sites in the Urban-West due to increase in ECa from 2000-2007 to 2008-2015. Further, emission ratios do not match with observational ratios. We recommend that rigorous efforts are needed to better quantify and monitor the changes in these species in the Urban-West particularly for non-road and residential combustion sectors. The final study of this dissertation discusses a technique to produce forecasts of AOD by combining satellite retrievals and a chemical transport model in an analog based framework. We use model forecasts of AOD, particulate matter (PM) concentrations, and meteorological parameters from Weather Research and Forecasting model with Chemistry (WRF-Chem) to train the framework for choosing analogs (past forecasts similar to current simulations). MODIS Terra and Aqua satellite retrievals of AOD for analog days are then used in a Kalman Filter (KF) framework to determine the forecast error and referred to as KFAN. The analog based estimates better forecasts of AOD for the Western US compared to the East and the mean bias in AOD forecasts are reduced to the range of 0.001-0.1. The reduction in positive bias in AOD is drastic and the method captures the decrease in AOD from morning to afternoon. We find that higher root mean square error (RMSE) values in the East are due to the inability of KFAN to capture the AOD peaks during biomass burning episodes and AOD lows during days of high precipitation rates. A systematic statistical analysis using step-wise linear regression models also show that in the East, there is a stronger dependence of aerosol loading on meteorological factors such as air temperature, precipitation, and relative humidity. As a consequence, overall quality of the analogs in the East is impacted when uncertainties in the simulated meteorological fields are higher. Overall, this study shows that the correlative information from multi-satellite remote sensing retrievals and models provide additional constraints on aerosols using composition/source identification (e.g., aerosol type, landcover, emission sources, fuel consumption), coemitted gas phase species (e.g., CO and NOx), and meteorological parameters (e.g., wind speed, TPW). The synergy of information from these datasets can be beneficial for design of future remote sensing missions, deployment of ground networks, and studies related to feedbacks between meteorology and aerosols.

In this dissertation I have argued that the study of stars and gaseous planets has relied too heavily on simplifying assumptions. In particular, I have demonstrated that the assumptions of spherical symmetry, thermal equilibrium, dynamical equilibrium and turbulent anisotropy all hide interesting phenomena which make a true difference to the structure and evolution of these bodies. To begin I developed new theoretical tools for probing these phenomena, starting with a new model of turbulent motion which accounts for many different sources of anisotropy. Building on this I studied rotating convection zones and determined scaling relations for the magnitude of differential rotation. In slowly-rotating systems the differential rotation is characterised by a power law with exponent of order unity, while in rapidly-rotating systems this exponent is strongly suppressed by the rotation. This provides a full characterisation of the magnitude of differential rotation in gaseous convection zones, and is in reasonable agreement with a wide array of simulations and observations. I then focused on the convection zones of rotating massive stars and found them to exhibit significantly anisotropic heat fluxes. This results in significant deviations from spherical symmetry and ultimately in qualitatively enhanced circulation currents in their envelopes. Accordingly, these stars ought to live much longer and have a different surface temperature. This potentially resolves several outstanding questions such as the anomalously slow evolution of stars on the giant branch, the dispersion in the observed properties of giant stars and the difficulty stellar modelling has to form massive binary black holes. In the same vein I examined the convection zones of bloated hot Jupiters and discovered a novel feedback mechanism between non-equilibrium tidal dissipation and the thermal structure of their upper envelopes. This mechanism stabilises shallow radiative zones against the convective instability, which would otherwise take over early on in the planet's formation as it proceeds to thermal equilibrium. Hence tidal dissipation is dramatically enhanced, which serves to inject significant quantities of heat into the upper layers of the planet and causes it to inflate. This mechanism can explain most of the observed population of inflated planets. Finally, I studied material mixing in the outer layers of accreting stars and developed a method for relating the observed surface chemistry to the bulk and accreting chemistries. This enables the direct inference of properties of circumstellar material and accretion rates for a wide variety of systems.

The fate and transport of cyanide in groundwater was investigated at gasworks sites in southeastern Australia. Two gasworks sites were investigated during this research: one in Tasmania and the other in Adelaide. The research followed three principal methods of investigation: field work, laboratory work and numerical modelling. The field work was aimed at observing the behaviour of cyanide in highly contaminated groundwater environments. Measured field parameters and laboratory analytical results from groundwater sampling were used to describe the hydrodynamics and hydrochemistry of the groundwater environment, providing a framework for groundwater flow and solute transport modelling. Groundwater and soil samples were also collected for use in laboratory experiments. The results from both field sites indicate contrasting hydrogeological environments, however, inorganic (metallic and non-metallic) and organic contaminants were measured in solution at both sites. The maximum concentrations observed at both sites were up to 5,300 mg/L CN(Total) (Adelaide site) and 21 mg/L CN(Total) (Tasmanian site). Results from geochemical modelling of solutes in groundwater at the field sites indicate that cyanide was predominantly in its free form in solution, with metallo- and alkali-cyanides also present.

This thesis consists of three distinct parts of CAST, CONTRAST and ATTREX, which were aircraft and field campaigns in the West Pacific in January-March 2014. The first section comprises of ozonesonde measurements from Manus Island, Papua New Guinea. A contamination issue affected the first 14 ozonesondes, and so particular care was required to characterize the background current, and as a result, a 'hybrid' background current correction was developed, which combines a constant correction with a pressure dependent correction. Collocated measurements with the CONTRAST aircraft - the NCAR Gulfsteam V - suggests the new hybrid correction produces better ozonesonde profiles than the other corrections that are found in the literature. The results of the ozonesonde measurements revealed a low-ozone event, with minimum ozone concentrations of ~12 ppbv, which was coincident with an easterly jet, and traced back to an area of deep convection: clean marine boundary layer air was uplifted into the tropical tropopause layer (TTL) and then advected in the easterly jet across to Manus Island. The second section attempted to find more examples of low-ozone conditions in the TTL from the aircraft data. The ATTREX aircraft - the NASA Northrop Grumman Global Hawk - observed ozone concentrations of ~10 ppbv in the Southern Hemisphere in proximity of tropical storm Lusi. Whole air samples from all three aircraft suggests the low-ozone air had recently encountered the boundary layer, with enhanced concentrations of surface-generated very short lived substances (VSLSs) compared to air with higher ozone concentrations. No low-ozone events were found in the Northern Hemisphere, even in the vicinity of tropical cyclone Faxai. The third section explores the low-ozone events in the WRF-Chem (Weather Research and Forecasting - with chemistry) in order to see whether the model was capable of recreating the low-ozone event measured by the ozonesondes on 21-23 February as a case study. The WRF-Chem simulation did correctly reproduce the large convective storm in a similar area to that observed by satellites, and surface tracers were uplifted in large quantities as hypothesized. However, no evidence of injection of air into the stratosphere was found in the simulation, and, rather than uplift directly from the surface, mixing of air in the boundary layer followed by uplift into the TTL was the main mechanism for producing the low-ozone event.

The Community Multiscale Air Quality (CMAQ) system is the Environmental Protection Agency's main modeling tool for atmospheric pollution studies. CMAQ-ADJ, the adjoint model of CMAQ, offers new analysis capabilities such as receptor-oriented sensitivity analysis and chemical data assimilation. This thesis presents the construction, validation, and properties of new adjoint modules in CMAQ, and illustrates their use in sensitivity analyses and data assimilation experiments. The new module of discrete adjoint of advection is implemented with the aid of automatic differentiation tool (TAMC) and is fully validated by comparing the adjoint sensitivities with finite difference values. In addition, adjoint sensitivity with respect to boundary conditions and boundary condition scaling factors are developed and validated in CMAQ. To investigate numerically the impact of the continuous and discrete advection adjoints on data assimilation, various four dimensional variational (4D-Var) data assimilation experiments are carried out with the 1D advection PDE, and with CMAQ advection using synthetic and real observation data. The results show that optimization procedure gives better estimates of the reference initial condition and converges faster when using gradients computed by the continuous adjoint approach. This counter-intuitive result is explained using the nonlinearity properties of the piecewise parabolic method (the numerical discretization of advection in CMAQ). Data assimilation experiments are carried out using real observation data. The simulation domain encompasses Texas and the simulation period is August 30 to September 1, 2006. Data assimilation is used to improve both initial and boundary conditions. These experiments further validate the tools developed in this thesis. / Master of Science

This dissertation presents a scientific framework that facilitates enhanced understanding of aerosol source - receptor (S/R) relationships and their impact on the local, regional and global air quality by employing a complementary suite of modeling methods. The receptor - oriented Positive Matrix Factorization (PMF) technique is combined with Potential Source Contribution Function (PSCF), a trajectory ensemble model, to characterize sources influencing the aerosols measured at Gosan, Korea during spring 2001. It is found that the episodic dust events originating from desert regions in East Asia (EA) that mix with pollution along the transit path, have a significant and pervasive impact on the air quality of Gosan. The intercontinental and hemispheric transport of aerosols is analyzed by a series of emission perturbation simulations with the Sulfur Transport and dEposition Model (STEM), a regional scale Chemical Transport Model (CTM), evaluated with observations from the 2008 NASA ARCTAS field campaign. This modeling study shows that pollution transport from regions outside North America (NA) contributed ∼ 30 and 20% to NA sulfate and BC surface concentration. This study also identifies aerosols transported from Europe, NA and EA regions as significant contributors to springtime Arctic sulfate and BC. Trajectory ensemble models are combined with source region tagged tracer model output to identify the source regions and possible instances of quasi-lagrangian sampled air masses during the 2006 NASA INTEX-B field campaign. The impact of specific emission sectors from Asia during the INTEX-B period is studied with the STEM model, identifying residential sector as potential target for emission reduction to combat global warming. The output from the STEM model constrained with satellite derived aerosol optical depth and ground based measurements of single scattering albedo via an optimal interpolation assimilation scheme is combined with the PMF technique to characterize the seasonality and regional distribution of aerosols in Asia. This innovative analysis framework that combines the output from source - oriented chemical transport models with receptor models is shown to reduce the uncertainty in aerosol distributions, which in turn leads to better estimates of source - receptor relationships and impact assessments of aerosol radiative forcing and health effects due to air pollution.

Ozone (O3) and particulate matter (PM) existing in the atmosphere have adverse effects to human and environment. Southeast Texas experiences high O3 and PM events due to special meteorological conditions and high emission rates of volatile organic compounds (VOCs) and nitrogen oxides (NOx). Quantitative knowledge of the contributions of different emissions sources to O3 and PM is helpful to better understand their formation mechanisms and develop effective control strategies. Tagged reactive tracer techniques are developed and coupled into two chemical transport models (UCD/CIT model and CMAQ) to conduct source apportionment of O3, primary PM, secondary inorganic PM, and secondary organic aerosol (SOA) and aging distribution of elemental carbon (EC) and organic carbon (OC). Ozone (O3) and particulate matter (PM) existing in the atmosphere have adverse effects to human and environment. Southeast Texas experiences high O3 and PM events due to special meteorological conditions and high emission rates of volatile organic compounds (VOCs) and nitrogen oxides (NOx). Quantitative knowledge of the contributions of different emissions sources to O3 and PM is helpful to better understand their formation mechanisms and develop effective control strategies. Tagged reactive tracer techniques are developed and coupled into two chemical transport models (UCD/CIT model and CMAQ) to conduct source apportionment of O3, primary PM, secondary inorganic PM, and secondary organic aerosol (SOA) and aging distribution of elemental carbon (EC) and organic carbon (OC). Models successfully reproduce the concentrations of gas phase and PM phase species. Vehicles, natural gas, industries, and coal combustion are important O3 sources. Upwind sources have non-negligible influences (20-50%) on daytime O3, indicating that regional NOx emission controls are necessary to reduce O3 in Southeast Texas. EC is mainly from diesel engines while majority of primary OC is from internal combustion engines and industrial sources. Open burning, road dust, internal combustion engines and industries are the major sources of primary PM2.5. Wildfire dominates primary PM near fire locations. Over 80% of sulfate is produced in upwind areas and coal combustion contributes most. Ammonium ion is mainly from agriculture sources. The SOA peak values can be better predicted when the emissions are adjusted by a factor of 2. 20% of the total SOA is due to anthropogenic sources. Solvent and gasoline engines are the major sources. Oligomers from biogenic SOA account for 30-58% of the total SOA, indicating that long range transport is important. PAHs from anthropogenic sources can produce 4% of total anthropogenic SOA. Wild fire, vehicles, solvent and industries are the major sources. EC and OC emitted within 0-3 hours contribute approximately 70-90% in urban Houston and about 20-40% in rural areas. Significant diurnal variations in the relative contributions to EC are predicted. Fresh particles concentrations are high at morning and early evening. The concentrations of EC and OC that spend more than 9 hours in the air are low over land but almost accounts for 100% of the total EC and OC over the ocean.

The objective of this thesis is to evaluate the sources of the differences between the NO2 satellite retrieval products provided by the Royal Dutch Meteorological Institute (KNMI) and the National Aeronautics and Space Administration (NASA). Ground studies have shown that although both products use the same satellite, these products yield different observations for NO2 tropospheric columns concentrations. This study does not validate either retrieval product, but rather indentifies the main sources for the discrepancy. There are several parameters which allow successful retrieval of NO2 vertical columns. For this study, only the difference between the radiative models and the a priori NO2 chemical transport models were considered relevant. All other parameters, such as cloud properties, slant columns, stratospheric serration and their assumptions, were held constant. Here, the models are referred to by their proprietor's acronym: "TOMRAD" refers to the radiative model used by NASA, "DAK" refers to the radiative model used by KNMI, "TM4" refers to the a priori chemical transport model used by KNMI, and "REAM" refers to the a priori chemical transport model maintained by the School of Earth and Atmospheric Sciences at the Georgia Institute of Technology. Mixing these parameters creates four retrievals for comparison. Many significant differences were identified after comparing these four retrievals. First, there are viewing geometry biases between the port side and the starboard side of the satellite retrieval for each swath. These viewing geometry biases lead to artificial periodicities in the retrievals of NO2 tropospheric vertical columns over a specific coordinate or site, such as a city. Furthermore, there were significant differences found after using different a priori NO2 chemical transport models. The low horizontal resolution of TM4 and the satellite retrieval/TM4 coupling effect compared to REAM leads to considerable questioning of the near real time application of the KNMI NO2 retrieval product. Though the TM4 model performs poorly, TM4 retrievals do perform nearly as well as REAM retrievals at capturing day-to-day variability and the spatial variability of the cities used as examples here. The retrievals using TOMRAD outperformed the retrievals using DAK when compared to the high resolution, hourly REAM a priori chemical transport model. In sum, these findings should lead to better optimizations of both the KNMI and NASA retrievals, and thus make their publicly available data products more reliable and accurate for general use.

In this thesis, a new aerosol module is developed for the STEM model (the Sulfur Transport and dEposition Model) to better understand the chemical aging of dust during long range transport and assess the impact of heterogeneous reactions on tropospheric chemistry. The new aerosol module is verified and first applied in a box model, and then coupled into the 3-Dimentional STEM model. In the new aerosol model, a non-equilibrium (dynamic or kinetic) approach to treat gas-to-particular conversion is employed to replace the equilibrium method in STEM model. Meanwhile, a new numerical method solving the aerosol dynamics equation is introduced into the dynamic aerosol model for its improved computational efficiency and high accuracy. Compared with the equilibrium method, the new dynamic approach is found to provide better results on predicating the different hygroscopicity and chemical aging patterns as a function of size. The current modeling study also takes advantage of new findings from laboratory experiments about heterogeneous reactions on mineral oxides and dust particles, in order to consider the complexity of surface chemistry (such as surface saturation, coating and relative humidity). Modeling results show that the impacts of mineralogy and relative humidity on heterogeneous reactions are significant and should be considered in atmospheric chemistry modeling with first priority. Finally, the upgraded 3-D STEM model is utilized to explore the observations from the Intercontinental Chemical Transport Experiment - Phase B (INTEX-B). The new dynamic approach for gas-to-particular conversion and RH-dependent heterogeneous uptake of HNO3 improve the model performance in term of aerosol predictions under different conditions. It is shown that these improvements change the modeled nitrate and sulfate concentrations, but also modify their size distributions significantly.