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.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 185-213). / In this thesis, I use coastal measurements of dissolved O₂ and inert gases to provide insight into the chemical, biological, and physical processes that impact the oceanic cycles of carbon and dissolved gases. Dissolved O₂ concentration and triple isotopic composition trace net and gross biological productivity. The saturation states of inert gases trace physical processes, such as air-water gas exchange, temperature change, and mixing, that affect all gases. First, I developed a field-deployable system that measures Ne, Ar, Kr, and Xe gas ratios in water. It has precision and accuracy of 1 % or better, enables near-continuous measurements, and has much lower cost compared to existing laboratory-based methods. The system will increase the scientific community's access to use dissolved noble gases as environmental tracers. Second, I measured O₂ and five noble gases during a cruise in Monterey Bay, California. I developed a vertical model and found that accurately parameterizing bubble-mediated gas exchange was necessary to accurately simulate the He and Ne measurements. I present the first comparison of multiple gas tracer, incubation, and sediment trap-based productivity estimates in the coastal ocean. Net community production estimated from ¹⁵NO₃⁻ uptake and 02 /Ar gave equivalent results at steady state. Underway O₂/Ar measurements revealed submesoscale variability that was not apparent from daily incubations. Third, I quantified productivity by O₂ mass balance and air-water gas exchange by dual tracer (³He/SF₆ ) release during ice melt in the Bras d'Or Lakes, a Canadian estuary. The gas transfer velocity at >90 % ice cover was 6 % of the rate for nearly ice-free conditions. Rates of volumetric gross primary production were similar when the estuary was completely ice-covered and ice-free, and the ecosystem was on average net autotrophic during ice melt and net heterotrophic following ice melt. I present a method for incorporating the isotopic composition of H₂O into the O₂ isotope-based productivity calculations, which increases the estimated gross primary production in this study by 46-97 %. In summary, I describe a new noble gas analysis system and apply O₂ and inert gas observations in new ways to study chemical, biological, and physical processes in coastal waters. / by Cara Charlotte Marie Manning. / 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), 2004. / Includes bibliographical references. / Observations at mid-ocean ridges indicate that magmas are focused to the ridge axis by a network of porous dunites in near chemical isolation. This thesis investigates several of the outstanding questions regarding the mechanisms of melt transport and its effects on the shallow mantle. Chapter 1 details the current understanding of melt migration from observations at mid-ocean ridges and ophiolites. Chapter 2 uses the size distribution and abundance of dunites measured in the Oman ophiolite to place limits on the potential mechanisms by which dunites form and subsequently estimate the flux of chemically unequilibrated melt which a network of dunites can supply. Chapter 3 characterizes the chemical composition of dunites and harzburgites from Oman to further constrain the process by which dunites form and relates the observed trends within dunites to variations in the time-integrated melt/rock ratio. Chapter 4 examines the microstructures of peridotites in Oman to constrain the deformation mechanisms which determine the viscosity of shallow mantle. Chapter 5 is a numerical investigation of advection beneath ridges incorporating the rheology inferred from the observed microstructures. Chapter 6 integrates the conclusions of the previous chapters, reevaluating the potential melt flux through dunites and constraining the permeability of the shallow mantle. / by Michael Geoffrey Braun. / Ph.D.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (leaves 78-79). / The initial water impact of a free-falling object is primarily related to the fluid forces on the wetted surface of the object. The shape-dependent added-mass coefficients express the fluid forces integrated over the body, and thus physically represent the additional inertia of water accelerated with the body. The field of hydrodynamic impact has been primarily concerned with estimating the added-mass coefficients of various types of bodies for different water impact types, such as seaplane landings, torpedo drops, and ship slamming. In this study, a numerical model has been constructed to estimate the hydrodynamic impact loads of a REMUS dropped in free-fall from a helicopter in a low hover. Developed by von Alt and associates at Woods Hole Oceanographic Institution, the REMUS (Remote Environmental Monitoring UnitS) is a small, man-portable, torpedo shaped Autonomous Underwater Vehicle (AUV) that is normally operated from small boats for a variety of scientific, industrial, and military applications. Finite-element method software and computer aided drafting tools were used to create a simplified model of REMUS without fins, propeller, or transducers. / (cont.) This axisymmetric REMUS model was cut by a flat free surface at various pitch angles and submergence values, and a panel mesh of the wetted surface of the vehicle was created using an automatic mesh generator. Surface boundary conditions are enforced for the free surface by reflecting the body panels using the method of images. Each panel mesh was evaluated for its added- mass characteristics using a source collocation panel method developed by Dr. Yonghwan Kim, formerly of the Vortical Flow Research Laboratory (VFRL) at the Massachusetts Institute of Technology. Experimental impact tests were conducted with a specially-instrumented test vehicle to verify the initial impact accelerations. / by Stephen Michael Roe. / S.M.

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), 1997. / Includes bibliographical references (p. 411-422). / Pelagic sedimentation is the primary modifier of topography generated by ridge-associated volcanic and tectonic processes. This thesis represents an effort to understand the processes of, and the general distribution of, pelagic sedimentation on rough topography, particularly in the Atlantic Basin but with applications to the world ocean as a whole. This study utilizes a simple numerical model of sedimentation which, when applied to models of rough basement topography, allows us to study sedimentation effects in terms of commonly-measured stochastic parameters including seafloor RMS height, abyssal hill spacing, and slope distribution. We also address the effect of sediment compaction on seafloor morphology, and the impact of long-wavelength topography on stochastic measures of sedimented seafloor. Understanding gained allows the construction of inverse problems to obtain information about sediment distribution and basement morphology from multibeam bathymetric data in regimes where backscatter from rough, reflective basement highs obscures returns from wide-beam seismic systems. By using maximum likelihood estimation to compare slope distribution functions calculated from data to those from filtered model topographies, we estimate average sediment thickness L, basement RMS height H, and a measure of sediment mobility k. Using data from near-ridge surveys and off-axis transit lines, we invert for L, H, and K for 3-29 Ma seafloor from the western flank of the Mid-Atlantic Ridge (MAR) near 26* N, 2- 45 Ma seafloor from the western flank of the MAR near 260 S, 2-40 Ma seafloor from the eastern flank of the MAR near 25* S, and 1-38 Ma seafloor from the western flank of the MAR near 35* S. Variations in L with seafloor age allow us to constrain sediment rain rate and the corrosivity of bottom waters to calcite since the Oligocene. We hypothesize that sediment rain rates during much of the early and middle Miocene were only 10-50% of the average rate for the past -10 m.y. Variations in H suggest correlation between tectonic setting and topographic variability. A relatively narrow range of K is needed to describe intrahill sedimentation patterns. / by Helen Faith Webb. / Ph.D.