Unraveling the microbiological processes that occur as water travels from a river's mouth into the ocean is critical to understanding the role of river plumes in global biogeochemical cycles. Metranscriptomics, the gene expression of a whole community of organisms, was utilized to examine six stations along the Amazon River Plume (ARP) in 2010 to test thehypothesis that there were measurable differences in gene expression for key biogeochemical genes along the ARP. This body of work focuses on methods developed to identify which genes are biogeochemically important for a particular environment along extreme salinity, nutrient and community gradients in the ARP, and the interpretation of these data. The metatranscriptome of a marine algal bloom of Protoperidinium quinquecorne was collected, as a pilot study, and represented the first published eukaryotic marine algal bloom metatranscriptome. Of the 232 transcripts examined, over 70% were eukaryotic mRNAs, thus demonstrating the successful isolation of eukaryotic transcripts from ribosomal RNAs and prokaryotic RNAs. Transcripts for nutrient and carbon uptake were identified, and reinforced the theory that biogeochemically-relevant genes will be amongst the highly-expressed genes in eukaryotic phytoplankton populations. The final two sections of this dissertation detail two different ways to bioinformatically examine metatranscriptomes from the eukaryotic microbial populations of the ARP. The reproducibility of metatranscriptomes was confirmed with very similar patterns of gene expression between true replicates differing by up to 2 hours and 2.5 km. Similar communities, two diatom-diazatroph association (DDA) stations, also showed stability of expression patterns over 25 days and 238.3 km. A gene database of 31 biogeochemical genes was used to enumerate transcript counts for the six different stations along the ARP. Patterns of gene expression reflected the major physical, chemical and biological influences in those communities. DDA blooms exhibited high silicon transporter expression to acquire silicon for diatoms, and the photosystem II D1 protein replacement was high in these low-turbidity blooms. In a low salinity (salinity 20.7) diatom bloom, nitrate transport genes were highly expressed to account for high growth rates fueled by photosynthesis, and carbonic anhydrase helped counter the low pCO2 waters. The last chapter compares all the sequences to the entire protein family (pfam) library to annotate all possible transcripts for important processes missed with a 31-gene database approach. Pfams for chlorophyll A-B binding protein and bacteriorhodopsin-like proteins ranked among the most-expressed pfams. These two pfams together show evolutionary adaptations to maximize ATP generation in surface community algal blooms. Multidimensional scaling plots illustrated that the patterns of gene expression were unique to each station. This body of work will expand our understanding of river plume eukaryotic phytoplankton communities, and when these data are added to metagenome, prokaryote metatranscriptome and modeling data, modelers will be able to better forecast diversity, transcription and community evolution over broad space and time scales.

River plumes often develop in complex environments, where variable coastal and bottom topography, ambient currents, winds and tides may play important roles in shaping the plume evolution. When all these factors are present, the plume dynamics may become intricate and unclear. The objective of this study is to understand the processes controlling the dynamics of a large river plume that is affected by strong boundary currents, variable winds and complex topography. The Mississippi River (MR) plume is the study case of this dissertation work, and focus is given to the interactions between the plume and the offshore circulation of the Gulf of Mexico (GoM). A series of numerical experiments was designed to investigate the impact of different factors on the development of a large scale river plume in scenarios with variable degrees of complexity. First, a box-like model with an idealized estuary was designed to address the general development of a mid-latitude river plume and assess the variability of the plume with changes in the outflow conditions at the river mouth. The structure and development of the plume in the flat-bottom, receiving basin was highly dependent on the degree of freshwater mixing at the source. Larger freshwater mixing enhanced the estuarine gravitational circulation and modified the dynamical balance at the estuary mouth. Those changes effectively modified the shape of the bulge and length/transport scales of the coastal current. Sloping-bottom conditions further modified the development of the plume. Secondly, a Northern GoM model was designed and numerical experiments were conducted to investigate the specific dynamics of the MR plume, in the presence of both shelf and basin-wide circulation. In particular, buoyancy-driven (due to the MR and all other major Northern GoM rivers) and wind-driven currents were studied on the shelf, while the extension of the Loop Current and associated frontal eddies were considered as major factors in the shelf to offshore interactions; wind-driven, shelfbreak eddies were also considered. Process-oriented experiments demonstrate that westerly and southerly winds promoted the development of a surface Ekman layer that enhances the offshore advection of plume waters. The steep topography in the vicinity of the MR Delta was a favorable condition for that process. When the MR plume was subject to a full-blown scenario (realistically-forced experiment nested within a large-scale model), complex interactions between wind-driven and eddy-driven dynamics determined the fate of the plume waters. Offshore removal is a frequent plume pathway, and the offshore transport can be as large as the wind-driven shelf transport. The offshore pathways depend on the position of the eddies near the shelf edge, their life span and the formation of eddy pairs that generate coherent cross-shelf flows. Strong eddy-plume interactions were observed when the Loop Current (LC) system impinged against the shelfbreak, causing the formation of coherent, narrow low-salinity bands that extended toward the Gulf interior. The offshore transport of MR water is a year-round process, but the interactions between the MR plume and the LC system have large inter-annual variability. Plume to LC interactions are determined by episodic northward intrusions of the LC system in the NGoM. The interactions are dictated by the proximity of the LC system to the MR Delta and by wind effects. On average, plume to LC interactions correspond to ~ 12 % of the year-round, total freshwater transport near the MR Delta, but this percentage can go up to 30 % in individual years. At the time of the plume to LC interactions, an average value of LC freshwater entrainment was estimated to be ~ 4,150 m3 s-1. The findings presented here are a major contribution toward the understanding of the cross-marginal and basin-wide transport of MR waters by a large-scale current system, and the connectivity to remote regions, such as the South Florida region and the Florida Keys.

<p>Nuclear reactors release small amounts of radioactivity during their normal operations. The most common method of calculating the dose to the public that results from such releases uses Gaussian Plume models. We are investigating these methods using CAP88-PC, a computer code developed for the Environmental Protection Agency (EPA) in the USA that calculates the concentration of radionuclides released from a stack using Pasquill stability classification. A buoyant or momentum driven part is also included. The uptake of the released radionuclide by plants, animals and humans, directly and indirectly, is then calculated to obtain the doses to the public. This method is well established but is known to suffer from many approximations and does not give answers that are accurate to be better than 50% in many cases. More accurate, though much more computer-intensive methods have been developed to calculate the movement of gases&nbsp / using fluid dynamic models. Such a model, using the code FLUENT can model complex terrains and will also be investigated in this work. This work is a preliminary study to compare the results of the traditional Gaussian plume model and a fluid dynamic model for a simplified case. The results indicate that Computational Fluid Dynamics calculations give qualitatively similar results with the possibility of including much more effects than the simple Gaussian plume model.</p>

This thesis dealt with the techniques that could be used for the pre-assessment of contaminated sites. The goals of the thesis were based on a simple fact that every contaminated site possesses certain potential to degrade natural resources, specifically groundwater and land resources. The thesis focused on using mathematical and statistical techniques to predict the maximum length of contaminated plumes or Lmax, which it considered as a key parameter that could be used for the site assessment. As the first thesis work, data from KORA sites were compiled and analysed. From the analyses, it was found that the Lmax for BTEX plumes are in average under 150 m long. Further, for this work, Analytical Models that can be used to estimate Lmax were reviewed and, examples comparing model and fifield Lmax were presented. The second work for the thesis focused on a development and analysis of a new 3D-analytical model for a fifinite planar and fully penetrating source. An implicit expression for predicting Lmax was obtained. The analysis of the developed model suggested that the longest Lmax will result if the source takes an approximately square shape. The last part of the thesis improved the 3D-analytical model obtained in the second work by presenting an expression for a fifinite planar source that only partially penetrates the aquifer. For this work, a very simple numerical technique was developed that not only simplififies numerical analysis of the scenarios considered in this thesis but it also bears potentials to be used for very complex subsurface reaction transport scenarios. This thesis has been successful in narrowing research-gaps on problems related to contaminated sites management. / Diese Doktorarbeit befasste sich mit Methoden, welche für eine Vorabbewertung von kontaminierten Standorten genutzt werden können. Die Ziele der Arbeit basierten auf dem einfachen Fakt, dass jeder kontaminierte Standort ein bestimmtes Potential besitzt, natürliche Ressourcen, speziell Grundwasser- und Bodenressourcen, in ihrer Qualität negativ zu beeinträchtigen. Die Arbeit war auf die Nutzung mathematischer und statistischer Techniken zur Abschätzung der maximalen Schadstofffahnenlänge, auch Lmax, fokussiert, welche als entscheidender Parameter für die Standortbewertung genutzt werden kann. Der erste Teil der Doktorarbeit beinhaltete die Zusammenstellung und Analyse von Daten einer Vielzahl von KORA-Standorten. Anhand dieser Untersuchungen konnte festgestellt werden, dass Lmax von BTEX-Fahnen im Mittel unterhalb von 150 m liegt. Des Weiteren wurden für diese Arbeit analytische Modelle, welche für die Abschätzung von Lmax genutzt werden können, kritisch bewertet und vergleichende Beispiele zwischen mit Modellierung bestimmter und im Feld ermittelter Lmax präsentiert. Der zweite Teil der Doktorarbeit zielte auf die Entwicklung und Analyse eines neuen dreidimensionalen, analytischen Models für eine finite, planare und über die komplette Mächtigkeit vorherrschende Quelle ab. Es konnte ein impliziter mathematischer Ausdruck zur Vorhersage von Lmax gewonnen werden. Die Analyse des Models wies darauf hin, dass maximale Lmax erreicht werden, wenn die Quelle eine annähernd quadratische Form aufweist. Der letzte Teil der Doktorarbeit diente der Weiterentwicklung des dreidimensionalen, analytischen Modells aus dem zweiten Teil durch die Entwicklung eines Ausdrucks für eine finite, planare Quelle, welche jedoch nur teilweise die Mächtigkeit des Grundwasserleiters kontaminiert. Für diese Arbeit wurde ein sehr einfacher numerischer Ansatz entwickelt, welcher die numerische Analyse der in dieser Arbeit berücksichtigten Szenarien nicht einfach nur erleichtert, sondern auch das Potential beinhaltet diesen auf komplexe, reaktive Transportszenarien im Untergrund anzuwenden. Abschließend kann gesagt werden, dass diese Arbeit erfolgreich zur Verringerung von Forschungslücken in der Problematik des Managements kontaminierter Standorte beigetragen hat.

This dissertation presents a series of laboratory experiments to study flow and mixing properties of multiphase plumes. The particle image velocimetry (PIV) and laserinduced fluorescence (LIF) techniques are developed to measure two-dimensional velocity and concentration fields of multiphase plumes. The developed measurement techniques are applied to bubble plumes in different ambient conditions. The problems and errors in the two-phase PIV application to a bubble plume case are addressed through a comparative study between the optical separation method using fluorescent particles and a new phase separation method using vector postprocessing. The study shows that the new algorithm predicts well the instantaneous and time-averaged velocity profiles and has errors comparable to those for image masking techniques. The phase separation method developed in the previous section is applied to study the mean flow characteristics of a bubble plume in quiescent and unstratified condition. The entrainment coefficients representing the mixing properties of a bubble plume are calculated to lie between 0.08 near the plume source and 0.05 in the upper region, and to depend on the non-dimensional quantity us/(B/z)1/3, where us is the bubble slip velocity, B is the initial buoyancy flux, and z is the height from the diffuser. Further, the LIF technique is investigated to measure the scalar concentration field around a bubble plume in quiescent, unstratified condition. This new application to bubble plumes accounts for light scattering by bubbles using an attenuation coef- ficient that is proportional to the local void fraction. Measured scalar concentration fields show similar trend in concentration fluctuation to turbulent plume cases. Finally, the velocity and concentration field measurements using the developed two-phase PIV and LIF methods are applied for a bubble plume in a density-stratified ambient. The turbulent flow characteristics induced by a bubble plume in a stratified ambient water are studied. The plume fluctuation frequency is measured as about 0.1 Hz and compares well to plume wandering frequency measured in unstratified plume cases.

The Nil&uuml / fer Unit of the Karakaya Complex at the pre-Liassic basement of the Sakarya Composite Terrane is composed mainly of metabasaltic lithologies with limestones, and minor cherts and mudstones. These metabasic assemblages show OIB- and E-MORB-type geochemical signatures with variable enrichment in the most incompatible elements relative to N-MORB. The Eymir Unit consists of variably deformed metaclastics, and constitutes the matrix in which the Nil&uuml / fer-type blocks are embedded. In the Ankara region, the Eymir Unit is intruded by metadiabase dikes that display intra-oceanic SSZ-type signatures with a marked negative Nb anomaly combined with a slightly depleted HFSE budget relative to N-MORB. The wide range in trace element ratios displayed by the Nil&uuml / fer metabasic rocks can be explained by melt-mixing processes that has taken place within the spinel-garnet transition zone. Pb-Nd-Hf radiogenic isotope systematics reveal that the Nil&uuml / fer samples has been derived from enriched mantle sources, and a multi-component source mixing is required to explain their genesis. The Eymir metadiabases, however, require contribution from a sediment component that mixes with a depleted mantle source. The geochemical data when combined with the geological and petrographical observations suggest that the Nil&uuml / fer metabasic rocks represent ancient oceanic islands that were created by a heterogeneous mantle plume rising beneath the Palaeotethyan oceanic lithosphere. During the latest Triassic, these oceanic islands were incorporated into a subduction/accretion prism, where they mixed with the continental-derived assemblages of diverse origin, creating the Karakaya Complex. The intrusion of the SSZ-type metadiabases postdates the formation and deformation of the Complex.

In the subtropical oligotrophic ocean, nitrogen fixation is an important source of new nitrogen (N) for supporting biological production. Previous studies have found that nitrogen-fixing Diatom-Diazotroph Associations (DDAs) are in high abundance in the intermediate salinity zone of large river plumes such as the Amazon and Mekong rivers, while Trichodesmium spp. becomes more abundant at higher salinities. This recurring pattern in the Amazon River plume suggests that strong salinity and nutrient gradients within the river plumes may lead to a cascade in diazotroph communities. I hypothesized that the Mississippi River, a major source of freshwater, nutrients and sediments to the northern Gulf of Mexico, creates a similar distribution of diazotroph communities. The relationship between large diazotrophs and salinity was examined in samples collected in July 2011 during a flood outflow from the Mississippi River. The dominant DDA, Hemiaulus spp. – Richelia spp., was at greatest abundance (≈31,000 cells L-1) west of the birdfoot delta on the periphery of the plume (≈29 salinity) where bottom water hypoxia was also observed. Trichodesmium spp., a cyanobacterium genus that occurs in both colonial and free trichome morphologies, was abundant at both high (≈35) salinities east of the delta reaching 20+ colonies L-1, as well as in the fresher (≈28) waters of the plume where it reached 3,500 trichomes L-1. Diazotroph distributions were separated east and west of the Mississippi River outflow, with DDAs being most abundant over bottom water hypoxic regions to the west and Trichodesmium spp. in high abundance to the east. The diazotroph – salinity gradient relationships present within the Amazon River plume were not present within the Gulf of Mexico. This study suggests that environmental factors other than salinity, such as nutrients or hypoxia, are influencing the distribution of diazotrophs around the Mississippi River plume. The seasonal hypoxia seen in the Gulf of Mexico with the co-occurring DDA increase could appear in other river systems. / text

When a lander approaches a dusty surface, the plume from the descent engine impinges on the ground and entrains loose regolith into a high velocity spray. This problem exhibits a wide variety of complex phenomena such as highly under-expanded plume impingement, transition from continuum to free molecular flow, erosion, coupled gas-dust motions, and granular collisions for a polydisperse distribution of aerosolized particles. The focus of this work is to identify and model the important physical phenomena and to characterize the dust motion that would result during typical lunar landings. A hybrid continuum-kinetic solver is used, but most of the complex physics are simulated using the direct simulation Monte Carlo method. A descent engine of comparable size and thrust to the Lunar Module Descent Engine is simulated because it allows for direct comparison to Apollo observations. Steady axisymmetric impingement was first studied for different thrust engines and different hovering altitudes. The erosion profiles are obtained from empirically derived scaling relationships and calibrated to closely match the net erosion observed during the Apollo missions. Once entrained, the dust motion is strongly influenced by particle-particle collisions and the collision elasticity. The effects of two-way coupling between the dust and gas motions are also studied. Small particles less than 1 µm in diameter are accelerated to speeds that exceed 1000 m/s. The larger particles have more inertia and are accelerated to slower speeds, approximately 350 m/s for 11 µm grains, but all particle sizes tend obtain their maximum speed within approximately 40 m from the lander. The maximum particle speeds and erosion rates tend to increase as the lander approaches the lunar surface. The erosion rates scale linearly with engine thrust and the maximum particle speed increases for higher thrust engines. Dust particles are able to travel very far from the lander because there is no background atmosphere on the moon to inhibit their motion. The far field deposition is obtained by using a staged calculation, where the first stages are in the near field where the flow is quasi-steady and the outer stages are unsteady. A realistic landing trajectory is approximated by a set of discrete hovering altitudes which range from 20 m to 3 m. Larger particles are accelerated to slower speeds and are deposited closer to the lander than smaller particles. Many of the gas molecules exceed lunar escape speed, but some gas molecules become trapped within the dust cloud and remain on the moon. The high velocity particulate sprays can be damaging to nearby structures, such as a lunar outpost. One way of mitigating this damage is to use a berm or fence to shield nearby structures from the dust spray. This work attempts to predict the effectiveness of such a fence. The effects of fence height, placement, and angle as well as the model sensitivity to the fence restitution coefficient are discussed. The expected forces exerted on fences placed at various locations are computed. The pressure forces were found to be relatively small at fences placed at practical distances from the landing site. The trajectories of particles that narrowly avoid the fence were not significantly altered by the fence, suggesting that the dust motion is weakly coupled to the gas in the near vicinity of the fence. Future landers may use multi-engine configurations that can form 3-dimensional gas and dust flows. There are multiple plume-plume and plume-surface interactions that affect the erosion rates and directionality of the dust sprays. A 4-engine configuration is simulated in this work for different hovering altitudes. The focusing of dust along certain trajectories depends on the lander hovering altitude, where at lower altitudes the dust particles focus along symmetry planes while at higher altitudes the sprays are more uniform. The surface erosion and trenching behavior for a 4-engine lander are also discussed. / text

In 2009, NASA's LCROSS mission impacted Cabeus Crater near the Lunar South Pole with the spent Centaur upper stage rocket. The impact was observed by the trailing sheperding spacecraft (S-S/C) that impacted the moon 250 seconds after the Centaur impact. The main objective of the LCROSS mission was to verify the existence of water ice in the lunar regolith---the subsequent analysis of the data confirmed water ice present in the crater. The analysis of the S-S/C instrument data suggested that the plume consisted of two components: a central "spike" component and a thin, outward "cone" component. A model has been developed at The University of Texas at Austin improve the analysis of the data obtained by the S-S/C. This model is created with a free-molecular ballistic grain code that involves simulating individual regolith grains in the debris plume through grain-heating and grain-movement models and then modeling the spectral radiance properties of the grains as observed by the S-S/C. Mie scattering theory is used to model scattering and absorption of incoming solar radiation by the particles in the plume assuming they are perfect spheres. The UT LCROSS code was utilized in a parametric study that evaluated the effect of variations in assumed model plume parameters on the modeling of S-S/C UV-VIS instrument observations. The plume parameters were chosen based on the assumption that the dust plume was split into two components: a central spike and a surrounding high angle cone. The following parameters were varied: the spike and cone angles, the spike and cone grain radius distributions, and the spike mass fraction. The following parameters could be varied but were given fixed values: ice fraction between plume components, ice grain purity, albedo, and ice fraction in plume. The impact of these plume parameters upon plume brightness and blue/red color ratio was determined. Two grain models were used. In the initial grain species model all grains have a soil core surrounded by a thin ice shell. In the second, two species model two grain types were utilized: a pure ice grain component and a pure soil grain component. / text

The phenomenon of plume persistence was observed for five federal Superfund sites by analysis of historical groundwater-withdrawal and contaminant-concentration data collected from long-term pump-and-treat operations. The potential factors contributing to plume persistence are generally recognized to include incomplete isolation of the source zone, permeability heterogeneity, well-field hydraulics, and non-ideal (rate-limited, nonlinear) desorption. However, the significance of each factor, especially the site-specific contribution is undetermined, which is very important for site development and management. One objective of this study is to quantify the impacts of different factors on mass-removal efficiency. Three-dimensional (3D) numerical models were used to simulate the impact of different well-field configurations on pump-and-treat mass removal. The relationship between reduction in contaminant mass discharge (CMDR) and mass removal (MR) was used as the metric to examine remediation efficiency. Results indicate that (1) even with effort to control the source, residual impact of source can still be a factor causing plume persistence, (2) the well-field configuration has a measurable impact on mass-removal efficiency, which can be muted by the influence of permeability heterogeneity, (3) in terms of permeability heterogeneity, both variance and correlation scale influence the overall mass-removal behavior, (4) the CMDR-MR relationship can be used to quantify the impacts of different factors on mass-removal efficiency at the plume scale. It has been recognized that the use of pump and treat for groundwater remediation will require many decades to attain site closure at most complex sites. Thus, monitored natural attenuation (MNA) and enhanced attenuation (EA) have been widely accepted as alternatives because of their lower cost and sustainable management for large, complex plumes. However, the planning and evaluation of MNA/EA applications require greater levels of characterization data than typically collected. Advanced, innovative methods are required to characterize specific attenuation processes and associated rates to evaluate the feasibility of MNA/EA. Contaminant elution and tracer (CET) tests have been proposed as one such advanced method. Another objective of this study is to investigate the use of modified well-field configurations to enhance the performance of CET tests to collect critical site-specific data that can be used to better delineate attenuation processes and quantify the associated rate coefficients. Three-dimensional numerical models were used to simulate the CET test with specific well-field configurations under different conditions. The results show that the CET test with a nested (two-couplet) well-field configuration can be used to characterize transport and attenuation processes by eliminating the impact of the surrounding plume. The results also show that applying select analytical mass-removal functions can be an efficient method for parameter estimation, as it does not require the use of mathematical transport modeling and does not require the attendant input data that are costly and time-consuming to obtain.