No description available.

Thesis (Ph.D.)--University of Western Australia, 2007.

Thesis (Ph. D.)--Florida State University, 2005. / Advisor: Dr. James J. O'Brien, Florida State University, College of Arts and Sciences, Dept. of Oceanography. Title and description from dissertation home page (viewed June 8, 2005). Document formatted into pages; contains xiii, 87 pages. Includes bibliographical references.

Thesis (M. S.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009. / Committee Chair: Janata, Jiri; Committee Member: Lyon, Andrew; Committee Member: Weissburg, Marc.

Thesis (Ph. D.)--Aerospace Engineering, Georgia Institute of Technology, 2007. / Yeung, Pui-Kuen, Committee Member ; Lieuwen, Tim, Committee Member ; Menon, Suresh, Committee Chair ; Seitzman, Jerry, Committee Member ; Syed, Saadat, Committee Member.

We investigate flows generated by bacteria near boundaries which are ubiquitous in biological systems. A bacterium such as \textit{Escherichia coli} is equipped with a number of rotary motors on its surface. Every motor has a helical flagellum attached to it and by rotating these motors the bacterium can move the fluid. We consider these flows in four different systems. Firstly, we explore a chiral flow which is always in the clockwise direction (when viewed from above) ahead of a dense suspension of bacteria on a moist surface. We quantitatively test a hypothesis that this flow is due to the action of cells stalled at the edge of a colony which extend their flagella outwards, moving fluid over a substrate. The model provides insight on the flagella orientations and their spatial distributions. Secondly, inspired by experiments which proposed to use confined bacteria in order to generate flows near surfaces, we develop a theoretical model of this fluid transport using a superposition of fundamental flow singularities. The rotation of a helical bacterial flagellum induces both a force and a torque on the surrounding fluid, both of which lead to a net flow along the surface. We investigate the optimal helical shapes to be used as micropumps near surfaces and show that bacterial flagella are nearly optimal. Thirdly, we build a theoretical model on a reorientation of peritrichous bacteria at the edge of a liquid drop on a Petri dish. Bacteria are more likely to turn clockwise because of the interaction between counterclockwise rotating flagella and boundaries which causes them to self-organise and circle clockwise (when viewed from above) around the outer edge of the colony. Finally, motivated by problems in biological physics occurring near corners, we derive the asymptotic behaviour for the Stokeslet (a flow due to a point force at low Reynolds number) both near and far from a corner geometry by using complex analysis on a known double integral solution for corner flows. We analyse flows in acute, obtuse and salient three-dimensional corners. We also use experiments on beads sedimenting in corn syrup to qualitatively test our results. The fundamental understanding of Stokes flows near boundaries is important for future developments in biophysics and bioengineering including applications to bacterial micropumps, steering microswimmers near corners, and preventing biofilm formation.

Recent efforts in understanding the variability inherent in coastal and offshore waters have highlighted the need for higher resolution sampling at finer spatial and temporal resolutions. Gliders are increasingly used in these transitional waters due to their ability to provide these finer resolution data sets in areas where satellite coverage may be poor, ship-based surveys may be impractical, and important processes may occur below the surface. Since no single instrument platform provides coverage across all needed spatial and temporal scales, Ocean Observation systems are using multiple types of instrument platforms for data collection. However, this results in increasingly large volumes of data that need to be processed and analyzed and there is no current “best practice” methodology for combining these instrument platforms. In this study, high resolution glider data, High Frequency Radar (HFR), and satellite-derived data products (MERRA_2 and ARMOR3D NRT Eddy Tracking) were used to quantify: 1) dominant scales of variability of the central Red Sea, 2) determine the minimum sampling frequency required to adequately characterize the central Red Sea, 3) discriminate whether the fine scale persistency of oceanographic variables determined from the glider data are comparable to those identified using HFR and satellite-derived data products, and 4) determine additional descriptive information regarding eddy occurrence and strength in the Red Sea from 2018-2019. Both Integral Time Scale and Characteristic Length Scale analysis show that the persistence time frame from glider data for temperature, salinity, chlorophyll-α, and dissolved oxygen is 2-4 weeks and that these temporal scales match for HFR and MERRA_2 data, matching a similar description of a ”weather-band” level of temporal variability. Additionally, the description of eddy activity in the Red Sea also supports this 2-4-week time frame, with the average duration of cyclonic and anticyclonic eddies from 2018-2019 being 22 and 27 days, respectively. Adoption of scale-based methods across multiple ocean observation areas can help define “best practice” methodologies for combining glider, HFR, and satellite-derived data to better understand the naturally occurring variability and improve resource allocation.

No description available.

[Truncated abstract] The study of eastern ocean boundary currents has been principally restricted to the Pacific and Atlantic ocean regions. The traditional view of the circulation near eastern ocean boundaries is that upwelling-favourable winds force surface waters offshore, leading to upwelling of cold, nutrient-rich subsurface water at the coast, the formation and offshore advection of a coastal front, and the generation of alongshore currents, generally having an equatorward surface flow and a poleward undercurrent. The eastern ocean boundary system of the southern Indian Ocean, off the west coast of Australia, is unique compared with these regions because a warm, poleward surface flow, known as the Leeuwin Current, dominates the dynamics over the continental shelf. Satellite imagery has shown the Leeuwin Current consists of a complex system of meanders, jet-like streams, and eddies, and has a seasonal and interannual variability. The oceanic circulation of the region between Carnarvon (latitude 25°S) and Jurien Bay (latitude 31°S) was examined using observational and remotely sensed data in conjunction with a detailed numerical modelling study. The model was validated using in situ ADCP and CTD data, and the horizontal eddy viscosity parameterization was tested against field observations. ... The resulting offshore meander grew laterally, shallowed, and closed to form an anticlockwise eddy to the original clockwise eddy’s south, forming a characteristic LC eddy pair (dipole). The model demonstrated the LC and Leeuwin Undercurrent (LUC) coupling played an important role in the onset of eddies at both sites. When an energy diagnostic scheme was used, the dominant instability process linked to the anticlockwise eddy’s development at site 1 was a mixed mode barotropic and baroclinic instability. The baroclinic instability’s source was the available potential energy stored within the mean lateral density gradient. The LC’s meandering southerly flow interacting with the LUC’s northerly subsurface flow generated the horizontal shear that sourced the barotropic instability. The dominant instability process at site 2 was baroclinic in origin. Possible links between the eddy field dynamics and the shelfslope region’s alongshore topographic variability were considered. The results of a suite of five model runs, differing only in the specification of bottom topography, were contrasted to investigate the effects. Except for the expected alongshore variability, delay in the onset of instabilities, varying growth rates, and some differences in the dominant wavebands’ mesoscale patterns, the overall impression was the response was similar.

A partir d'un ensemble de données d'observation ainsi qu'un modèle couplé physiquebiogéochimique à haute résolution (CROCO-PISCES), cette thèse explore les processus biophysiques associés à l’une des plus grandes floraisons phytoplanctoniques de l’océan global, au Sud-Est de Madagascar, et le possible rôle des tourbillons sur ces blooms. L’étude montre que ce phénomène se produit dans une région caractérisée par une couche de mélange peu profonde, avec des eaux de surface moins salées probablement associées au courant Sud-Est de Madagascar (SEMC), et avec une structure dipolaire dans la circulation moyenne. Les observations ont révélé une diminution des remontées d’eaux froides (upwelling) le long des côtes sud-est de Madagascar pendant les mois de bloom. Dans le modèle, les nitrates provenant des niveaux de subsurface (advection verticale ; upwelling) ainsi que de la côte malgache (advection horizontale) favorisent la production phytoplanctonique simulée. Une expérience lagrangienne de particules montre une plus forte advection de ces dernières dans la zone de floraison pendant les périodes de bloom alors qu’elles sont déviées vers le sud de Madagascar vers le continent Africain pendant les années sans floraison. Une étude est réalisée à partir d’un jeu de données de suivi des tourbillons co-localisés avec des flotteurs de profilage Argo, pour mieux comprendre des tourbillons intensifiés en surface et subsurface. Une méthode d’identification des structures tourbillonnaires de subsurface a été mise en place en se basant sur l’anomalie de la hauteur dynamique stérique. Ces tourbillons, appelés ‘SIDDIES’ (South Indian ocean eDDIES), se produisent en tant que tourbillon intensifié en surface (surfSIDDIES) et en subsurface (subSIDDIES). Ils se déplacent le long d’une bande de latitude située entre 15°S et 35°S appelée « couloir SIDDIES ». Au cours de leurs déplacements, les subSIDDIES cycloniques (anticycloniques) transportent via les processus d’advection, des masses d’eaux chaudes et peu salées de l’Est vers l’Ouest de l’Océan Indien, contribuant ainsi à environ 58% (32%) du flux total de chaleur par tourbillons dans le sud de l'océan Indien. / Using observational datasets and a high resolution coupled biophysical model (CROCOPISCES), the main aims of this thesis is to study the biophysical processes associated with one of the largest phytoplankton blooms in global ocean, southeast of Madagascar, and the possible role of mesoscale eddies.The study has shown that the bloom occurs in a region of shallow-stratified mixed layer water, with low-salinity waters at the surface possibly associated with the South-East Madagasacar Current (SEMC), and dipole structure in the mean circulation. Observations show that curren-driven upwelling south of Madagascar is reduced during bloom months. It is shown in the model that nitrate from subsurface levels (upwelling) as well as from the Madagascan coast (advection) fertilize the simulated bloom. A Lagrangian analysis shows dispersion of higher percentages of particles in the bloom region during bloom years and south of Madagascar during non-bloom years.Using co-located Argo profiles and an eddy detected algorithm dataset, surface and subsurface-intensified eddies are studied. Subsurface eddies are identified using a detection method based on their steric dynamic height anomaly. Referred to as `SIDDIES’ (South Indian ocean eDDIES), they occur as surface (surfSIDDIES) or subsurface (subSIDDIES) and propagate along a latitudinal band (15°S-35°S) termed as `SIDDIES Corridor’. Advecting warm and fresh water during their propagation, cyclonic (anticyclonic) subSIDDIES contribute about 58% (32%) of the total eddy-heat flux in the South Indian Ocean.