A thesis submitted to the Faculty of Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy February 2013 / A thorough understanding of the optical properties of aerosols, their spatial and temporal distribution and their radiative effects in the atmosphere, is needed for the better assessment of the impacts of aerosols on regional climate systems. Monitoring of aerosol parameters and solar radiation fluxes has been conducted in southern Africa by the AERONET programme since the middle of the last decade. These valuable data, combined with model estimates products, plus the intensive field experiments such as SAFARI 2000, provided key information, contributing towards a better overall understanding of the main characteristics of tropospheric aerosols over southern Africa and how these aerosols impact the direct aerosol forcing in the region. Two long-term AERONET sites, at Mongu in Zambia and Skukuza in South Africa, formed the core sources of data in this study. Secondary sites in Saudi Arabia (Solar Village) and United Arad Emirates (Hamin and Dhadnah) were used for comparison purposes. Aerosol optical properties and the direct aerosol radiative forcing over southern Africa both change significantly from one season to another, following the strong seasonal cycle of aerosol optical thickness (AOT). Consequently, the evaluation of aerosol forcing using static values throughout the year is not suitable for describing the aerosol climate effects in this region. Results show that the seasonal variations of aerosol optical thicknesses at 500 nm over southern Africa can be defined into three periods:  December to May with relatively clean atmospheric conditions, with monthly averages AOT values at 500 nm between 0.1 to 0.2, mainly associated with air masses from which aerosols have been washed during the wet season, and minimal regional biomass burning;  followed by a transition period towards high AOT values, from June to August, with a moderately turbid atmosphere (0.2 – 0.3);  September to November, with high levels of AOT (0.3 – 0.5) –mainly associated with biomass burning. Within this region a reversal gradient of AOT can be observed along the annual timeline; the north has higher magnitudes than the south, i.e. a north–south gradient, during the biomass-burning season and the opposite applies in the non-biomass burning season, i.e. a south–north gradient. From the currently available aerosol data, no long-term discernible trends are observable in aerosol loadings over this region. Direct aerosol radiative forcing evaluations, in southern Africa, need to take into account the differences between both the non-biomass burning and the biomass burning seasons. Direct aerosol forcing magnitudes during the biomass burning period are almost double those of the non-biomass burning at BOA and TOA. The impact of biomass burning on the direct aerosol forcing is not limited to the bottom of atmosphere (BOA), but also influences the forcing at top of atmosphere (TOA). Direct aerosol radiative forcing values for all of southern Africa are estimated at -33 W m-2 for BOA and -6 W m-2 for TOA. However, seasonal values may differ considerably from these levels. Monthly averages of direct aerosol radiative forcing at BOA are frequently less than -30 W m-2 from December to May (non-biomass burning period) with a slightly south-north gradient. From July to October, a strong north-south gradient of direct aerosol radiative forcing is observed and forcing magnitudes are frequently recorded at -50 W m-2 (and, on occasion well above that level) during September, i.e. at the peak of biomass burning. June and November are regarded as transitional months when levels move towards the higher or and lower values of forcing respectively. At TOA monthly averages of direct aerosol radiative forcing from December to May are frequently less than -9 W m-2 and, during biomass burning, direct aerosol radiative forcing values almost double. From the seasonal perspective, it is also possible to depict the reversal gradient behaviour at TOA. This study has contributed to improving the understanding and knowledge about of the direct aerosol radiative effects in this region - necessary step towards addressing the indirect and semi-direct aerosol effects. This study also emphasises the need for obtaining further data for defining the aerosol optical characterisations by regions or sub regions as demonstrated by the identifiable overall differences in the aerosol optical properties between the southern Africa and Middle Eastern regions. This process will require improving the quantity and quality of aerosol measurements at regional scales.

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The Earth’s atmosphere supports microorganisms and they include potential pathogens and microbial allergens. Whilst indoor environments have been well studied, relatively little is known of bio-aerosols in outdoor locations and their potential influence on human health, particularly with regard to urban development. Hong Kong provides an ideal model system for testing hypotheses related to the impact of urbanization on bio-aerosols, with a well-defined gradient of urbanization and large population. This thesis describes work to establish the biodiversity and spatio-temporal dynamics of outdoor bio-aerosols in Hong Kong. A comprehensive study of multi-domain microbial diversity and allergen levels in urban aerosols over a contiguous annual timescale and along a gradient of urbanization was carried out. A comprehensive suite of climatic and pollutant variables were also recorded during the sampling interval. Terminal restriction fragment length polymorphism (T-RFLP) was employed to investigate variations in bacterial and eukaryal assemblages, followed by phylogenetic assessment using high-throughput sequencing. The results revealed a strong seasonality in both bacterial and eukaryal assemblages, with Archaea forming a negligible part of the urban bio-aerosols. The most abundant bacteria were proteobacteria but community shifts were seen due to increases in algae in summer, and betaproteobacteria and cyanobacteria in winter. This was most parsimoniously explained by considering the backward trajectory analysis of air mass. A greater abundance of marine-associated phylotypes such as Bacillariophyta and Chlorophyta were identified when the dominant air mass arriving in Hong Kong in the summer originated from oceanic sources. In contrast, betaproteobacteria, which indicated soil sources were prevalent when the origin of air mass was from terrestrial sources. A trend in fungal phylotypes was also apparent, with summer samples dominated by basidiomycetous Agaricales, and winter samples by the ascomycete genus Cladosporium. This was likely due to favourable climatic conditions during wetter summer months enhancing release of fungal basidiospores. A range of airborne human pathogens was also detectable at low levels including pathogenic bacteria such as Acinetobacter baumannii, Clostridium perfringens, Escherichia coli O157:H7, and Ricinus communis, and the pathogenic fungus Aspergillus terreus. Microbial allergens including bacterial endotoxins and fungal glucans were also quantified with immunological assays. These generally followed variations in biomass, and during some months were recorded at levels that may impact human health upon chronic exposure. Carbon dioxide levels were the only climatic or pollutant variable that correlated with allergen levels. Conversely changes in microbial assemblages were strongly correlated to several climatic variables including temperature, rainfall, air pressure and relative humidity, but not with the degree of urbanization or airborne pollutants. This study highlights the importance of including microbial assessments in future bio-surveillance of urban aerosols. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

Aerosols are known to have a large, uncertain effect on air quality and climate. Chemical processing of organic material in aqueous aerosols is known to form secondary organic aerosols (SOA), which make up a significant portion of particulate mass in the atmosphere. However, lack of clarity surrounding the importance of each source of SOA to total aerosol mass contributes to the uncertainties in their environmental impact. Disagreements between chemical models and field measurements suggest that some processes are misrepresented or are missing in current models. This work considers three pathways of SOA formation using Gas-Aerosol Model for Mechanism Analysis (GAMMA), a photochemical box model developed by the McNeill group featuring coupled gas phase and detailed aqueous phase aerosol chemistry. Imidazole-2-carboxaldehyde (IC), a light-absorbing organic species, has been observed to contribute to SOA formation as a photosensitizer. Currently, the extent of photosensitized reactions in ambient aerosols remains poorly constrained. Reactive uptake coefficients were determined from experimental studies of IC-containing aerosols and scaled for ambient simulations in GAMMA. Results of remote ambient simulations show that IC is unlikely to be a significant source of SOA largely due to its lack of abundance in atmospheric aerosols. Humic-like substances (HULIS) have also been experimentally shown to catalyze SOA formation through photosensitizer chemistry. We use GAMMA to quantify the uptake kinetics of limonene in these photosensitizer experiments. Ambient GAMMA simulations of this SOA formation pathway show that limonene-HULIS photosensitizer chemistry can contribute up to 65% of total aqueous SOA at pH 4. Further laboratory studies are recommended for this SOA source to assess the need for its inclusion in aerosol models. Chemical processing of organic material in cloudwater is another known source of SOA. We use GAMMA to consider the impact of the coupled effect of processing in both aqueous aerosol and cloudwater on isoprene epoxydiol (IEPOX) SOA. Simulations show that cloudwater at pH 3 – 4 can also be a potentially significant source of IEPOX SOA, largely due to higher water content in cloudwater than in aerosols. Thus, cloud processing may be a significant contributor to IEPOX SOA formation and could account for differences between predicted SOA mass and ambient measurements where mass transfer limitations in aerosol particles can be expected. This work concludes with recommendations for future work in GAMMA. Parameterization of glyoxal reactive uptake could allow for more accurate predictions of glyoxal oxidation product distributions. The inclusion of online thermodynamic calculations of inorganic species in GAMMA can better constrain several multiphase chemical processes, such as the highly pH-dependent uptake of IEPOX and sulfate formation. Updated detailed mechanisms of transition metal ion chemistry would also improve predictions of sulfate formation.

The Asian monsoon-affected area is one of the most vulnerable regions in the world facing hydroclimate changes. Anthropogenic climate change, particularly the emissions of greenhouse gases (GHGs) and aerosols, exerts significant impacts on monsoon rainfall and circulation. Understanding the effects of external forcing on monsoon rainfall is essential for improving the predictability, constraining the uncertainty, and assessing the climate risks. In this dissertation, I use a combination of observations, outputs from multiple Coupled Model Intercomparison Project - Phase 5 (CMIP5) models, and idealized atmospheric general circulation model (AGCM) experiments to examine the Asian summer monsoon variability and change. The main focus is understanding the responses to GHGs and anthropogenic aerosols and their differences for both the historical period and future projections. The Asian monsoon is an interactive system influenced by multiple natural and anthropogenic factors. GHGs and aerosols induce significantly different changes in monsoon rainfall through both thermodynamical and dynamical processes. These changes can be further separated into the fast adjustments related to radiation and cloud processes and the slow response due to changes in sea surface temperature (SST). This thesis provides a detailed analysis of the multiple physical processes entangled in the total response, advancing our mechanistic understanding of the effects of external forcing on the Asian monsoon system and the associated uncertainties. In Chapter 2, I first analyze the monsoon-ENSO (El Nino - Southern Oscillation) relationship in observations and CMIP5 models to determine the role of natural variability. Separating the natural and forced components shows that natural variability plays a dominant role in the 20th century, however enhanced monsoon rainfall associated with global warming may contribute to a weakened ENSO-monsoon relation in the 21st century. In Chapter 3, I examine the physical mechanisms causing the changes of the Asian summer monsoon during the 20th and 21st century using observations and CMIP5 models, attributing the rainfall changes to the relative roles of thermodynamic and dynamic processes. CMIP5 models show a distinct drying of the Asian summer monsoon rainfall during the historical period but strong wetting for future projections, which can be explained by the strong aerosol-induced dynamical weakening during the 20th century and the thermodynamic enhancement due to GHGs in the 21st century. In Chapters 4 and 5, I further use multiple AGCMs to separate the total monsoon response into a fast adjustment component independent of the sea surface temperature (SST) responses, and a slow response component associated with SST feedbacks. For GHGs (Chapter 4), the fast and slow monsoon circulation changes largely oppose each other, leading to an overall weak response and large inter-model spread. For aerosols (Chapter 5), the strongly weakened monsoon circulation over land due to aerosols is largely driven by the fast adjustments related to aerosol-radiation and aerosol-cloud interactions. Finally in Chapter 6, I design idealized AGCM experiments with prescribed SSTs using the Community Atmosphere Model (CAM5) and the Geophysical Fluid Dynamic Laboratory Model (GFDL-AM3) to investigate the relative roles of uniform SST warming/cooling as well as global and regional SST patterns in shaping the differing monsoon responses. While GHGs-induced SST changes affect the monsoon largely via the uniform warming effect, for aerosols the SST spatial pattern plays the dominant role through changes in atmospheric circulation.

Atmospheric aerosols are tiny particles suspended in the atmosphere. They affect global air quality, public health and climate (Boucher et al., 2013; Myhre et al., 2013; Seinfeld and Pandis, 2016), thus playing a key role in the Earth system. However, due to the complexity of aerosol processes and climate change feedbacks, our understanding of aerosols in a changing world is still limited (Boucher et al., 2013). To understand the impact of organic aerosol volatility on particle microphysics and global climate, I developed a new aerosol microphysics scheme, MATRIX-VBS, and its evaluation and application are presented in this dissertation. MATRIX-VBS couples the volatility-basis set (VBS, Donahue et al., 2006) framework with the aerosol microphysical scheme MATRIX (Multiconfiguration Aerosol TRacker of mIXing state, Bauer et al., 2008) that resolves aerosol mass and number concentrations, size, and mixing state. With the inclusion of organic partitioning and photochemical aging of semi-volatile organic aerosols, aerosols are able to grow via organic condensation, a process previously not available in the original model MATRIX, where organic aerosols were treated as nonvolatile. Both MATRIX and MATRIX-VBS can be used as stand-alone box models or within a global model. After the development of MATRIX-VBS in the box model framework, both model’s simulations were performed and assessed on the box and global scales. On the box model scale, idealized experiments were designed to simulate different environments, clean, polluted, urban, and rural. I investigated the evolution of organic aerosol mass concentration and volatility distribution among gas and aerosol phases, and results show that semi-volatile primary organic aerosols evaporate almost completely in the intermediate-volatility range and stay in the particle phase in the low volatility range. I also concluded that the volatility distribution of organics relies on emission, oxidation, and temperature, and the inclusion of organic aerosol volatility changes aerosol mixing state. Comparing against parallel simulations with the original model MATRIX, which treats organic aerosols as nonvolatile, I assessed the effect of gas-particle partitioning and photochemical aging of semi-volatile organics on particle growth, composition, size distribution and mixing state. Results also show that the new model produces different mixing states, increased number concentrations and decreased aerosol sizes for organic-containing aerosol populations. Monte-Carlo type experiments were performed and they offered a more in-depth look at the impact of organic aerosol volatility on activated number concentration, which is the number concentration of aerosols that are activated but has not yet formed into a cloud droplet. By testing multiple parameters such as aerosol composition, mass concentration and number concentration, as well as particle size, I examined the impact of partitioning organic aerosols on activated aerosol number concentration. I found that the new model MATRIX-VBS produces fewer activated particles compared to the original model MATRIX, except in environments with low cloud updrafts, in clean regions at above freezing temperatures, and in polluted areas at high temperature (310K) and extremely low humidity conditions. I concluded that such change is caused by the differences in aerosol number concentration and size between the two models, which would determine how many particles could activate. On the global scale, MATRIX-VBS was implemented in the NASA GISS ModelE Earth systems model. I assessed and evaluated the new model by comparing aerosol mass and number concentrations, activated cloud number concentration, and AOD against output from the original MATRIX model. Further, I evaluate the two models against observations of organic aerosol mass concentration from the aircraft campaign ATom (Atmospheric Tomography Mission), and aerosol optical depth from ground measurement stations from AERONET (Aerosol Robotic Network) as well as satellite retrievals from MODIS (MODerate resolution Imaging Spectroradiometer) and CALIPSO (Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations). Results show that organics in MATRIX-VBS experience more distant long-range transport, and their mass concentration increase aloft and decrease at the surface as compared to those in MATRIX. There are still underestimations in the vertical profiles of mass concentration in both models, especially in the high latitudes in the Northern Hemisphere and South Pacific Ocean basin, possibly due to the application of universal distribution of mass-based emission factors among different volatilities that perhaps is not realistic in all climate zones, thus affecting organic aerosol lifetime and transport. Just as the box model results, there are more particles and generally more activated ones (except for rare cases such as the highly polluted Eastern China) in MATRIX-VBS than in MATRIX. As for AOD comparisons, MATRIX-VBS have generally lower AOD than MATRIX, which can be due to smaller aerosols and different aerosol composition in the new model, which is also underestimating biomass burning in the Amazon and Congo basins. Compared to satellite retrievals from MODIS and ground measurements from AERONET, both models overestimate aerosol optical depth over anthropogenic polluted regions and biomass regions such as central Africa. Overall, both models also underestimate AOD as compared to AERONET in the winter (DJF), whereas they generally overestimate or estimate it well in other seasons. Even though during its initial evaluation, MATRIX-VBS does not seem to have improved from MATRIX on the global scale in representing the real world, it made the first key step in improving our understanding of organic aerosols on the process level. Changes in mass, number concentration, size distribution, and mixing state (composition) have great implications and impact on climate. Further studies are needed in examining and improving factors linked to the new representation of semi-volatiles in an aerosol microphysics model, including but not limited to the treatment of mass-based emission factor distribution among different organic volatilities and the size distribution of tiny organic particles that have evaporated but not completely. Challenges in evaluations of organic aerosol against measurements remain in that remote regions of significant interest lack available measurements, and additional field campaigns will be important for us to better understand real world conditions and shed light on model performance.

The Indian Ocean Experiment (INDOEX) had as a primary objective determining the radiative forcing due to anthropogenic aerosols over climatologically significant space and time scales: the Indian Ocean during the winter monsoon, January-March. During the winter monsoon, polluted, low-level air from the Asian subcontinent blows over the Arabian Sea and Indian Ocean. As part of INDOEX, aerosol optical depths were derived from Advanced Very High Resolution Radiometer (AVHRR) data for the cloud-free ocean regions. The AVHRR radiances were first calibrated using the interior zone of the Antarctic and Greenland ice sheets, which proved to be radiometrically stable calibration targets. Optical depths were derived by matching the observed radiances to radiances calculated for a wide range of optical depths and viewing geometry. Optical depths derived with the AVHRR were compared with those derived with NASA's Aerosol Robotic Network (AERONET) CIMEL instrument at the Center for Clouds, Chemistry, and Climate's Kaashidhoo Observatory, as well as with other surface and shipboard observations taken in the INDOEX region. The retrieved and surface-based optical depths agreed best for a new 2-channel, 2- aerosol model scheme in which the AVHRR observations at O·64 and O·84 microns were used to determine relative amounts of marine and polluted continental aerosol and then the resulting aerosol mixture was used to derive the optical depths. Broadband radiative transfer calculations for the mixture of marine and polluted continental aerosols were combined with the 0·64 and 0·84-micron AVHRR radiances to determine the radiative forcing due to aerosols in the INDOEX region. Monthly composites of aerosol optical depth and top of the atmosphere, surface, and atmospheric radiative forcing were derived from calibrated AVHRR radiances for January-March 1996-2000. An inter-annual variability in the magnitude and spatial extent of high value regions is noted for derived optical depths and radiative forcing, with highest values reached in 1999, particularly in the Bay of Bengal which during the IFP was covered by plumes from Indochina. Frequency distributions of the optical depth for 1⁰ x 1⁰ latitude-longitude regions are well represented by gamma distribution functions. The day-to-day and year-to-year variability of the optical depth for such regions is correlated with the long term average optical depth. Interannual variability of the monthly mean optical depths for such regions is found to be as large as the day to day. / Graduation date: 2001

Cloud reflectivity is a function of cloud liquid water content and droplet number concentration. Since cloud droplets form around pre-existing aerosol particles, cloud droplet number concentration depends on the availability of particles that can serve as cloud condensation nuclei. Given constant liquid water amount, increased availability of cloud condensation nuclei leads to clouds with a greater droplet number concentration, greater total droplet surface area and consequently, greater reflectivity. The change in cloud reflectivity resulting from the increased availability of condensation nuclei is known as the aerosol indirect effect. The aerosol indirect effect ranks as one of the largest sources of uncertainty in current estimates of global climate change, largely due to difficulties in measurement. Changes in cloud reflectivity resulting from the aerosol indirect effect are typically much smaller than the natural background variability observed in clouds. As a result, the modification signal is very difficult to detect against the background noise. Additionally, since atmospheric aerosols are ubiquitous, it is difficult to find polluted and nonpolluted clouds that are sufficiently alike for reasonable comparison. However, ship tracks seen in satellite images present one opportunity to study the aerosol indirect effect in relative isolation. Ship tracks are regions of enhanced reflectivity in marine stratus, resulting from the addition of aerosols from ship exhaust plumes to preexisting clouds. Ship tracks are a common feature of satellite images of the North Pacific. Since the marine atmosphere has comparatively low background aerosol concentrations, the addition of ship exhaust particles can lead to distinct increases in cloud reflectivity. Ship tracks allow for sampling of polluted and nonpolluted clouds from adjacent regions with similar solar and viewing geometry, cloud temperatures and surface properties, and consequently provide a unique opportunity to study the effects of aerosol modification of cloud reflectivity. Using satellite images of the North Pacific in July 1999, over 1000 ship tracks were identified, logged and analyzed, yielding 504 sets of radiance data matching polluted clouds with nearby nonpolluted clouds. It was expected that increasing the size of the region for selection of nonpolluted clouds would increase the variability in observed reflectivity, and make detection of the modification signal more difficult. In order to study this potential effect of domain size for selection of nonpolluted clouds on measurements of the aerosol indirect effect, three data sets were collected, using domain sizes for selection of nonpolluted clouds of 15, 50 and 100 km. Analysis of retrieved optical depth and droplet effective radius for modified and control pixels shows evidence of a 1-5% increase in visible optical depth of marine stratus following modification by addition of ship exhaust particles, but unexpectedly, shows only slight increases in uncertainty with increasing domain size. A subsequent study revealed that autocorrelation lengths of radiances and retrieved cloud properties were only 8-15 km. This indicates that even the 15 km control domain captured much of the background variability present. Domain sizes smaller than 15 km are difficult to sample automatically while avoiding the inclusion of polluted clouds in the nonpolluted cloud sample. As a result, it remains necessary to analyze large numbers of ship tracks to separate the aerosol modification signal from the background variability. / Graduation date: 2003

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