Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 87-92). / Observations, theoretical models, and a numerical model (ADCIRC) are used to investigate the effects of tides, waves, bay bathymetry, and changing inlet geometry on the hydrodynamics of the multiple-inlet Katama system, Martha's Vineyard, MA. Momentum fluxes from breaking waves drive water into the inlet, nearly stopping the 2 m/s ebb currents during a hurricane. The evolving morphology of Katama Inlet has a dominant effect on tidal distortion and bay circulation. As Katama inlet lengthened, narrowed, and shoaled between 2011 and 2014, the relative effects of friction (observed and simulated) increased greatly, resulting in reduced circulation energy, an increase in the M6 tidal constituent, and changes in velocity asymmetries that are consistent with an evolution from flood to ebb dominance. The effects of changing inlet parameters (e.g., inlet geometry, bay bathymetry, friction, tidal forcing) are quantified via a lumped element model that accounts for the presence of a shallow flood shoal that limits flow from the ocean into the bay. As the difference in depth between inlet and flood shoal increases, the amplitude and phase of the incoming tide are increasingly modified from predictions without a flood shoal, and flows into the bay are further hindered. / by Mara S. M. Orescanin. / Ph. D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Driven by increasingly heavy oil reserves and more efficient refining technologies, use of heavy fuel oils for power generation is rising. Unlike other refined products and crude oils, a large portion of these heavy oils is undetectable using the traditional gas chromatography-based techniques on which oil spill science has been based. In the current study, samples collected after the 2007 M/V Cosco Busan heavy fuel oil spill (San Francisco, CA) were analyzed using gas chromatography (GC)-based techniques, numerical modeling and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to examine natural weathering of the oil over a one and a half year period. Traditional GC techniques detected variable evidence of evaporation/ dissolution, biodegradation and photodegradation. Petroleum hydrocarbon compounds smaller than -n-C 16 were rapidly lost due to evaporation and dissolution. Significant biodegradation was not detected until one month post spill while photodegradation was only observed at one field site. To further examine the processes of evaporation and dissolution, samples were analyzed with comprehensive two-dimensional GC (GCxGC) and a physiochemical model developed to approximate quantitative apportionment of compounds lost to the atmosphere and water. Model results suggest temperature is the primary control of evaporation. Finally, to examine the prominent non-GC amenable component of the oil, samples were analyzed with FT-ICR MS. Results showed expected clustering of samples, with those samples collected sooner after the spill having the most compositional similarity to the unweathered oil. Analysis of dominant heteroatom classes within the oil showed losses of high molecular weight species and the formation of stable core structures with time. These results highlight the susceptibility to weathering of these higher molecular weight components, previously believed to be recalcitrant in the environment. Research findings indicate that environmental weathering results in removal or alteration of larger alkylated compounds as well as loss of lower molecular weight species through evaporation/dissolution, biodegradation and photodegradation, with a resultant fraction of stable compounds likely to remain in the environment years after the spill. This research demonstrates the advantages of combining multiple analytical and modeling approaches for a fuller understanding of oil spill chemistry. / by Karin Lydia Lemkau. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2006. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (p. 155-162). / The oceanic response to overflows is explored using a two-layer isopycnal model. Overflows are a major source of the dense water of the global deep ocean, originating from only a few marginal seas. They enter the open ocean as dense gravity currents down a continental slope and play a crucial role in the deep ocean circulation. To understand the dynamics of these overflows, previous studies simplified their dynamics by treating the overlying ocean as inactive. This simplification may be a first approximation for the overflow but not for the overlying ocean. The Mediterranean overflow, for example, entrains about 2 Sv of overlying Atlantic water when it enters the Atlantic through Gibraltar Strait. The upper ocean must balance the mass loss and vortex stretching associated with entrainment. Thus for the upper ocean, overflows represent a localized region of intense mass and PV forcing. The simulations in this study show that in the upper layer, entrainment forces a cyclonic circulation along bathymetric contours. This is a topographic [beta]-plume and its transport depends on the entrainment region size and the topographic slope. / (cont.) Baroclinic instability also develops and creates eddy thickness flux to the in-shore direction, forcing a double gyre topographic [beta]-plume near the strait due to eddy PV flux convergence on the in-shore side of the continental slope and divergence on the offshore side. When the upper oceanic response to overflows is examined specifically for the Mediterranean overflow, the upper ocean is found to establish two trans-Atlantic zonal jets, analogous to the Azores current and the Azores Counter current. These two zonal jets are an extension of the topographic [beta]-plume driven by the overflow. Because the eddies in the steep slope region near Cape St. Vincent drive a mean flow across the slope, the topographic [beta]-plume connects to the Atlantic Ocean to become a basin scale flow. This thesis shows that overflows can induce a significant circulation in the upper ocean, and for the Mediterranean overflow, this circulation is a basin scale flow. / by Shinichiro Kida. / Ph.D.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2011. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 63-65). / Remote sensing and in situ observations are used to investigate the ocean response to the Tokar Wind Jet in the Red Sea. The wind jet blows down the pressure gradient through the Tokar Gap on the Sudanese coast, at about 18°N, during the summer monsoon season. It disturbs the prevailing along-sea (southeastward) winds with strong cross-sea (northeastward) winds that can last from days to weeks and reach amplitudes of 20-25 m/s. By comparing scatterometer winds with along-track and gridded sea level anomaly observations, it is shown that an intense dipolar eddy spins up in less than seven days in response to the wind jet. The eddy pair has a horizontal scale of 140 km. Maximum ocean surface velocities can reach 1 m/s and eddy currents extend at least 200 m into the water column. The eddy currents appear to cover the width of the sea, providing a pathway for rapid transport of marine organisms and other drifting material from one coast to the other. Interannual variability in the strength of the dipole is closely matched with variability in the strength of the wind jet. The dipole is observed to be quasi-stationary, although there is some evidence for slow eastward propagation-simulation of the dipole in an idealized high-resolution numerical model suggests that this is the result of self-advection. These and other recent in situ observations in the Red Sea show that the upper ocean currents are dominated by mesoscale eddies rather than by a slow overturning circulation. / by Ping Zhai. / S.M.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2003. / Includes bibliographical references. / Sorption is a key factor in determining the fate of polycyclic aromatic hydrocarbons (PAHs) in the environment. Here, PAH sorption is proposed as the sum of two mechanisms: absorption into a biogenic, organic carbon (OC) fraction and adsorption onto a combustion-derived, black carbon (BC) fraction. To study BC adsorption, a 375ʻC thermal oxidation method was employed to remove OC and isolate the BC fraction. Test studies showed that nitrogen-containing macromolecules charred during this pretreatment causing a positive bias to the BC measurement. Meanwhile, the oxidation of relatively small BC particles underestimated the total BC content in non-charring samples. Models based on carbon oxidation were then proposed to estimate reasonably the total BC and OC contents of sediment samples. The adsorption of pyrene onto isolated BC particles was then studied by constructing a nonlinear isotherm, which was characterized with a BC-normalized distribution coefficient and a Freundlich exponent. Pyrene sorption to Boston Harbor sediment was then modeled as the sum of OC absorption and BC adsorption using the measured adsorption parameters and literature absorption values. Finally, literature reports of high PAH distribution coefficients from the field and nonlinear PAH isotherms from the laboratory were re-explained by considering BC adsorption. / by AmyMarie Accardi-Dey. / Ph.D.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2010. / Includes bibliographical references (p. 54-56). / This paper begins to explore a previously neglected mechanism for abyssal ocean mixing using bottom boundary layer dynamics. Abyssal mixing and the associated upward buoyancy fluxes are necessary to balance the sinking of dense waters at high latitudes and to close the global overturning circulation. Previous studies have concentrated on the hypothesis that the primary mechanism for this mixing is breaking internal waves generated by tidal flows over rough topography. However, intriguing observations, particularly from the Brazil Basin Tracer Release Experiment, suggest that mixing in the flank canyons of the Mid-Atlantic Ridge generated when strong mean flows interact with the many sills and constrictions within the canyons may represent a dynamically important amount of abyssal mixing. The energy pathways and mechanisms of this mixing are much less clear than in the case of breaking internal waves. This study attempts to clarify this by suggesting an analogy with an idealized diffusive boundary layer over a sloping bottom. This boundary layer is characterized by up-slope flows powered by the buoyancy flux in the fluid far from the boundary. Here we explore the energy budget of the boundary layer, and find that the diffusive boundary layer provides flows that are generally consistent with those observed in submarine canyons. In addition, we derive the vertical velocity in the far-field fluid, analogous to an Ekman pumping velocity, that these boundary layers can induce when the bottom slope is not constant. Finally, we present both theoretical and numerical models of exchange flows between the bottom boundary and the far-field flow when the bottom slope is not constant. These exchange flows provide a mechanism by which boundary-driven mixing can affect the overall stratification and buoyancy fluxes of the basin interior. / by Rebecca Walsh Dell. / S.M.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2006. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references. / Cetacean blubber is a primary site for lipid storage, which the animal utilizes during periods of energetic stress. It is important to understand how the blubber responds to factors such as ontogeny, water temperature, reproductive status, and nutritional state because blubber is also the primary bioaccumulation site for persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs). During periods of lipid mobilization such as lactation, PCBs from the blubber are mobilized into the circulatory system and may cause toxic effects. One particular toxic mechanism may include the induction of cytochrome P450 enzymes in the integument and liver, which could enhance the biotransformation of PCBs to hydroxylated metabolites (OH-PCBs). OH-PCBs may then interfere with thyroid hormone dependent neurodevelopment. The goals of these studies were to investigate the relationships between lipid dynamics and PCB effects and to devise a quantitative approach to assess neurodevelopment in delphinid cetaceans. Blubber morphology, cytochrome P450 1A1 (CYP1A1) expression in the skin-blubber biopsy, blubber and plasma PCBs, and plasma OH-PCBs were assessed in bottlenose dolphins (Tursiops truncatus). / (cont.) In addition, magnetic resonance (MR) images of the post-mortem brain in situ were obtained from Atlantic white-sided dolphin (Lagenorhynchus acutus) specimens. These results showed that: 1) Factors such as ontogeny, water temperature, and reproductive status affected blubber morphology in bottlenose dolphins. In response to warmer water, the lipid content of the blubber decreased and this appeared to involve loss of lipids from adipocytes in the middle blubber layer. Similar to the effects of starvation on blubber morphology, lactation decreased adipocyte size predominantly in the deeper blubber, 2) CYP1A1 levels in the deep blubber were significantly related to the total plasma TEQ98 concentrations, adipocyte shrinkage, and plasma OH-PCB levels, 3) Through in situ MR imaging of stranded, Atlantic white-sided dolphin specimens, the size of brain structures that depend on thyroid hormones for maturation could be measured accurately. Future studies can use this technique, coupled with chemical analysis of brain regions, to determine if thyroid hormone disrupting chemicals in delphinid cetaceans are associated with changes in the size of brain structures. / by Eric Wilson Montie. / Ph.D.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 68-74). / Coastal barriers are particularly susceptible to the predicted effects of accelerated of sea-level rise and the potential for increased impacts of intense storms. Over centennial scales, barriers are maintained via overtopping during storms, causing deposition of washover fans on their landward sides. This study examines three washover fans on the south shore of Martha's Vineyard using a suite of data including vibracores, ground penetrating radar, high resolution dGPS, and LiDAR data. From these data, the volumes of the deposits were determined and range from 2.1-2.4 x 10⁴ m³. Two overwashes occurred during Hurricane Bob in 1991. The water levels produced by this storm have a return interval of ~28 years, resulting in an onshore sediment flux of 2.4-3.4 m³/m/yr. The third washover was deposited by a nor'easter in January 1997, which has a water level return interval of ~6 years, resulting in a flux of 8.5 m³/m/yr. These fluxes are smaller than the flux of sediment needed to maintain a geometrically stable barrier estimated from shoreline retreat rates, suggesting that the barrier is not in long-term equilibrium, a result supported by the thinning of the barrier over this time interval. / by Emily A. Carruthers. / S.M.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / Includes bibliographical references (p. 54-59). / (cont) An increased understanding of heterotrophic bacterial strategies for acquiring nutrients and trace elements is critical for elucidating their impact on biogeochemical cycling in the ocean. It is estimated that iron is a limiting nutrient for phytoplankton growth in over 30% of the open ocean, but still little is known about bacterial strategies for iron acquisition. Siderophore (Fe ligand) production by bacteria may play a major role in influencing the bioavailability of iron in the ocean. Despite the importance of siderophores in the environment, only limited information from a select group of bacteria is available. On a cruise through the Costa Rica Dome (CRD) upwelling region in July 2005, a library of 867 isolates from five depth profiles inside and outside of the dome was obtained and screened for siderophore production using the Chrome Azurol-S (CAS) assay. Phylogenetic affiliation of 134 isolates was determined by sequencing the 16s rDNA gene, and determined that gamma proteobacteria such as Alteromonas, Pseudoalteromonas, Halomonas, and Marinobacter dominated the collection, while alpha-proteobacteria such as Roseobacter were also represented. The isolates obtained from stations in the CRD showed greater siderophore-producing capabilities between 55m and 100m while strains isolated from outside the CRD had shallower peak (-8-35m) production. Functional group determination showed that hydroxamate production dominated from 50-150m, while hydroxamate and catechol production is roughly equal in shallower waters. By characterizing the siderophores produced by these isolates and determining the genetic make-up of the population, these findings further our understanding of how heterotrophic microbes affect biogeochemical processes and the competitive nature of nutrient acquisition. / by Whitney B. Krey. / S.M.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), February 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 327-334). / In the present work, we study the statistics of wavefields obtained from non-linear phase-resolved simulations. The numerical model used to generate the waves models wave-wave interactions based on the fully non-linear Zakharov equations. We vary the simulated wavefield's input spectral properties: directional spreading function, Phillips parameter and peak shape parameter. We then investigate the relationships between a wavefield's input spectral properties and its output physical properties via statistical analysis. We investigate surface elevation distribution, wave definition methods in a nonlinear wavefield with a two-dimensional wavenumber, defined waves' distributions, and the occurrence and spacing of large wave events. / by Legena Albertha Henry. / S.M.