Thesis (Ph.D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science; and the Woods Hole Oceanographic Institution), 2012. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from student submitted PDF version of thesis. / Includes bibliographical references (p. 91-98). / This thesis presents a system for automatically building 3-D optical and bathymetric maps of underwater terrain using autonomous robots. The maps that are built improve the state of the art in resolution by an order of magnitude, while fusing bathymetric information from acoustic ranging sensors with visual texture captured by cameras. As part of the mapping process, several internal relationships between sensors are automatically calibrated, including the roll and pitch offsets of the velocity sensor, the attitude offset of the multibeam acoustic ranging sensor, and the full six-degree of freedom offset of the camera. The system uses pose graph optimization to simultaneously solve for the robot's trajectory, the map, and the camera location in the robot's frame, and takes into account the case where the terrain being mapped is drifting and rotating by estimating the orientation of the terrain at each time step in the robot's trajectory. Relative pose constraints are introduced into the pose graph based on multibeam submap matching using depth image correlation, while landmark-based constraints are used in the graph where visual features are available. The two types of constraints work in concert in a single optimization, fusing information from both types of mapping sensors and yielding a texture-mapped 3-D mesh for visualization. The optimization framework also allows for the straightforward introduction of constraints provided by the particular suite of sensors available, so that the navigation and mapping system presented works under a variety of deployment scenarios, including the potential incorporation of external localization systems such as long-baseline acoustic networks. Results of using the system to map the draft of rotating Antarctic ice floes are presented, as are results fusing optical and range data of a coral reef. / by Clayton Gregory Kunz. / Ph.D.

Thesis (S.M.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 99-100). / Signal detection and synchronization in the time varying ocean environment is a difficult endeavor. The current common methods include using a linear frequency modulated chirped pulse or maximal length sequence as a detection pulse, then match filtering to that signal. In higher signal to noise ratio (SNR) environments (- 0 dB and higher) this has been a suitable solution. As the SNR drops lower however, this solution no longer provides an acceptable probability of detection for a given tolerable probability of false alarm. The issue derives from the inherent coherence issues in the ocean environment which limit the useful matched filter length. This thesis proposes an alternative method of detection based on a recursive least squares linearly adaptive equalizer which we term the Adaptive Linear Equalizer Detector (ALED). This detectors performance has demonstrated reliable probability of detection with minimal interfering false alarms with SNR as low as -20 dB. Additionally this thesis puts forth a computationally feasible method for implementing the detector. / by Ryan Thomas Gieleghem. / 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), 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / As the only low-latitude connection between ocean basins, the Indonesian Throughflow allows the direct transmission of heat and salinity between the Pacific and Indian Oceans. Despite its potential importance, the role of the Indonesian Throughflow in global ocean circulation and regional climate is still not clear due to sparse measurements and the relative difficulty of modeling the region. The Mg/Ca and [delta]¹⁸0 of calcite of the calcitic planktic foraminifera Globigerinoides ruber (G. ruber) were used to estimate the sea surface temperature and [delta]¹⁸0 of water, an indicator of hydrologic conditions, over the past 20,000 years. I also attempted to estimate thermocline structure using the foraminifera, Pulleniatina obliquiloculata, but the Mg/Ca and [delta]¹⁸0 of calcite data yield conflicting interpretations, indicating further work on this proxy is required. The G. ruber Mg/Ca results suggest that the sea surface temperature of the outflow passages was influenced by high latitude Southern Hemisphere temperature. This connection is likely via intermediate waters that upwell in the Banda Sea. At approximately 10,000 years before present, there was a warming in the Makassar Strait. This local warming was coincident with the flooding of the Sunda Shelf, which opened a connection between the South China Sea and the Indonesian Throughflow. Regional [delta]¹⁸0 of seawater reconstructions show that during the last glacial maximum the [delta]¹⁸0 of seawater pattern was very similar to modern, but there were relatively enriched values over the equatorial IndoPacific during high latitude Northern Hemisphere cold events (Heinrich Stadial 1 and the Younger Dryas). From these results we postulate that the mean position of the Intertropical Convergence Zone was approximately the same as modern at the last glacial maximum and was likely displaced to the south during the Younger Dryas and Heinrich Stadial 1, suggesting the Intertropical Convergence Zone primarily responds to changes in the interhemispheric temperature gradient. These results shed light on the primary controls of the temperature and hydrology of Indonesian Throughflow region. / by Fern Tolley Gibbons. / Ph.D.

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), 2013. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from student-submitted PDF version of thesis. / Includes bibliographical references. / Seafloor digital imagery and bathymetric data are used to evaluate the volcanic characteristics of the 85°E segment of the ultraslow spreading Gakkel Ridge (9 mm yr-¹). Imagery reveals that ridges and volcanic cones in the axial valley are covered by numerous, small-volume lava flows, including a few flows fresh enough to have potentially erupted during the 1999 seismic swarm at the site. The morphology and distribution of volcaniclastic deposits observed on the seafloor at depths of ~3800 m, greater than the critical point for steam generation, are consistent with having formed by explosive discharge of magma and CO² from source vents. Microearthquakes recorded on a 200 m aperture seismometer network deployed on the Trans-Atlantic Geotraverse active mound, a seafloor massive sulfide on the Mid-Atlantic Ridge at 26°N, are used to image subsurface processes at the hydrothermal system. Over nine-months, 32,078 local microearthquakes (ML = -1) with single-phase arrivals cluster on the southwest flank of the deposit at depths <125 m. Microearthquakes characteristics are consistent with reaction-driven cracking driven by anhydrite deposition in the shallow secondary circulation system. Exit fluid temperatures recorded at diffuse vents on the mound during the microearthquake study are used to explore linkages between seismicity and venting. / by Claire Willis Pontbriand. / Ph.D.

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), 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Despite widespread concerns about the effects of anthropogenic noise on baleen whales (suborder Mysticeti), we lack basic information about their auditory physiology for comprehensive risk assessments. Hearing ranges and sensitivities could be measured if customized equipment and methods were developed based on how baleen whales receive sound. However, sound reception pathways in baleen whales are currently unknown. This thesis presents an integrative approach to understanding hearing in baleen whales through dissections, biomedical imaging, biochemical analyses, and modeling sound propagation through a whale head using the Finite Element Method (FEM). We focused on the minke whale (Balaenoptera acutorostrata) because it is one of the smallest and most abundant mysticete species, reducing logistical difficulties for dissections and experiments. We discovered a large, well-formed fat body extending from the blubber region to the ears and contacting the ossicles. Although odontocetes, or toothed whales, are thought to use specialized "acoustic fats" for sound reception, no such tissues had been described for mysticetes to date. Our study indicates that the basic morphology and biochemical composition of the minke whale "ear fats" are very different from those of odontocete acoustic fats. However, the odontocete and mysticete fatty tissues share some characteristics, such as being conserved even during starvation, containing fewer dietary signals compared to blubber, and having well-defined attachments to the tympano-periotic complex, which houses the middle and inner ears. FE models of the whale head indicated that the ear fats caused a slight increase in the total pressure magnitude by the ears, and this focusing effect could be attributed to the low density and low sound speed of the ear fats in the models. Fatty tissues are known to have lower densities and sound speeds than other types of soft tissues, which may explain why they are an important component of the auditory system of odontocetes, and perhaps mysticete cetaceans as well. In an aquatic habitat where the pinna and air-filled ear canal are no longer effective at collecting and focusing so'und towards the ears, we propose that both odontocete and mysticete cetaceans have incorporated fatty tissues into their auditory systems for underwater sound reception. / by Maya Yamato. / Ph.D.

Thesis: S.M., Joint Program in Applied Ocean Physics and Engineering (Massachusetts Institute of Technology, Department of Aeronautics and Astronautics; and the Woods Hole Oceanographic Institution), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 99-103). / The recent success of object detection systems motivates object-based representations for robot navigation; i.e. semantic simultaneous localization and mapping (SLAM), in which we aim to jointly estimate the pose of the robot over time as well as the location and semantic class observed objects. A solution to the semantic SLAM problem necessarily addresses the continuous inference problems where am I? and where are the objects?, but also the discrete inference problem what are the objects?. We consider the problem of semantic SLAM under non-Gaussian uncertainty. The most prominent case in which this arises is from data association uncertainty, where we do not know with certainty what objects in the environment caused the measurement made by our sensor. The semantic class of an object can help to inform data association; a detection classified as a door is unlikely to be associated to a chair object. / However, detectors are imperfect, and incorrect classification of objects can be detrimental to data association. While previous approaches seek to eliminate such measurements, we instead model the robot and landmark state uncertainty induced by data association in the hopes that new measurements may disambiguate state estimates, and that we may provide representations useful for developing decisionmaking strategies where a robot can take actions to mitigate multimodal uncertainty. The key insight we leverage is that the semantic SLAM problem with unknown data association can be refrained as a non-Gaussian inference problem. We present two solutions to the resulting problem: we first assume Gaussian measurement models, and non-Gaussianity only due to data association uncertainty. We then relax this assumption and provide a method that can cope with arbitrary non-Gaussian measurement models. / We show quantitatively on both simulated and real data that both proposed methods have robustness advantages as compared to traditional solutions when data associations are uncertain. / "Supported by the Office of Naval Research under grants N00014-18-1-2832 and N00014-16-2628, as well as the National Science Foundation (NSF) Graduate Research Fellowship"--Page 5 / by Kevin J. Doherty. / S.M. / S.M. Joint Program in Applied Ocean Physics and Engineering (Massachusetts Institute of Technology, Department of Aeronautics and Astronautics; and the Woods Hole Oceanographic Institution)

Thesis: S.M., 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), 2020 / Cataloged from student-submitted PDF of thesis. / Includes bibliographical references. / Arctic marine and lacustrine systems are experiencing rapid warming due to climate change. These changes are especially important at the interface between sediments and surface waters because they are hotspots for biogeochemical transformations such as redox reactions, nutrient consumption and regeneration, organic matter leaching and degradation, and mineral weathering. Radium isotopes (²²³Ra, ²²⁴Ra, ²²⁶Ra, ²²⁸Ra) and radon-222, naturally occurring radioactive isotopes produced in sediments, are well-suited as tracers of nutrients, trace metals, and organic matter cycling processes at the sediment-water interface. In this thesis, I have applied radon-222 and the quartet of radium isotopes to study fundamental processes in subarctic lakes and on the Arctic continental shelf. First, radon-222 is used to quantify groundwater discharge into a shallow, tundra lake on the Yukon-Kuskokwim Delta in Alaska in summer of 2017. / Radon-derived groundwater fluxes were then paired with methane (CH₄) measurements to determine delivery rates of methane into the lake via groundwater. Groundwater CH₄ fluxes significantly exceeded diffusive air-water fluxes from the lake to the atmosphere, suggesting that groundwater is an important source of CH₄ to Arctic lakes and may drive observed CH₄ emissions. Higher CH₄ emissions were observed compared to those reported previously in high latitude lakes, like due to higher CH₄ concentrations in groundwater. These findings indicate that deltaic lakes across warmer permafrost regions may act as important hotspots for methane release across Arctic landscapes. Then, the quartet of radium isotopes is used to study the impacts of storms and sea ice formation as drivers of sediment-water interaction on the Alaskan Beaufort shelf. / The timeseries presented in this study is among the first to document the combined physical and chemical signals of winter water formation in the Beaufort Sea, made possible by repeat occupations of the central Beaufort shelf. Radium measurements are combined with inorganic nitrogen and hydrographic measurements to elucidate the episodic behavior of winter water formation and its ability to drive exchange with bottom sediments during freeze-up. / by Jessica Stephanie Dabrowski. / S.M. / S.M. 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)

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), 2003. / 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. 299-310). / Inertial terms dominate the single-gyre ocean model and prevent western-intensification when the viscosity is small. This occurs long before the oceanically-appropriate parameter range. It is demonstrated here that the circulation is controlled if a mechanism for ultimate removal of vorticity exists, even if it is active only in a narrow region near the boundary. Vorticity removal is modeled here as a viscosity enhanced very near the solid boundaries to roughly parameterize missing boundary physics like topographic interaction and three dimensional turbulence over the shelf. This boundary-enhanced viscosity allows western-intensified mean flows even when the inertial boundary width is much wider than the frictional region because eddies flux vorticity from within the interior streamlines to the frictional region for removal. Using boundary-enhanced viscosity, western-intensified calculations are possible with lower interior viscosity than in previous studies. Interesting behaviors result: a boundary-layer balance novel to the model, calculations with promise for eddy param- eterization, eddy-driven gyres rotating opposite the wind, and temporal complexity including basin resonances. / (cont.) I also demonstrate that multiple-gyre calculations have weaker mean circulation than single-gyres with the same viscosity and subtropical forcing. Despite traditional understanding, almost no inter-gyre flux occurs if no-slip boundary conditions are used. The inter-gyre eddy flux is in control only with exactly symmetric gyres and free slip boundaries. Even without the inter-gyre flux, the multiple-gyre circulation is weak because of sinuous instabilities on the jet which are not present in the single-gyre model. These modes efficiently flux vorticity to the boundary and reduce the circulation without an inter-gyre flux, postponing inertial domination to much smaller viscosities. / by Baylor Fix-Kemper. / Ph.D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2013. / Pages 181 and 182 blank. Cataloged from PDF version of thesis. / Includes bibliographical references. / Steroidal estrogens are potent endocrine disrupting chemicals that are naturally excreted by vertebrates (e.g., humans and fish) and can enter natural waters through the discharge of treated and raw sewage. Because estrogens are detrimental to aquatic organisms at picomolar concentrations, many studies have measured so-called "free" estrogen concentrations in wastewater effluents, rivers, and lakes. Yet, to our knowledge, no studies have characterized the broader range of estrogens that includes free, conjugated, and halogenated forms. Conjugated estrogens are important because they can be easily converted to potent free forms by bacteria in wastewater treatment plants and receiving waters. And halogenated estrogens, produced during wastewater disinfection, are only slightly less potent than free estrogens but much more likely to bioaccumulate. We have developed a tandem mass spectrometry method that is capable of simultaneously quantifying free, conjugated, and halogenated estrogens at picomolar levels in wastewater effluent and coastal seawater. The method was validated using treated effluent from the greater Boston metropolitan area, where we found that halogenated estrogens represented over 50 % of the total estrogen discharge flux. A kinetic model of estrogen halogenation was used to predict the distribution of free and halogenated forms in wastewater effluent and suggested that chlorinated estrogens may be formed en route to the wastewater treatment plant. In the receiving waters of Massachusetts Bay, we detected a range of conjugated, free, and halogenated forms at concentrations that were well-predicted by dilution near the sewage outfall. Farther downstream, we found significantly higher estrone concentrations which points to large inputs of estrogens from sources other than sewage. Finally, we have used compound-specific measurements of 13C and 14C in commercial and pharmaceutical estrogen preparations to evaluate the potential for using carbon isotopes to distinguish between synthetic and endogenous steroids in wastewater and other environmental matrices. Our results show that synthetic estrogens and progestogens exhibit significantly depleted [delta]13 C values (~30 0/00) compared to endogenous steroids (-16 0/00 to -26 0/00). This isotopic difference should make it possible to apportion synthetic and endogenous hormone sources in complex environments. / by David R. Griffith. / Ph. D.

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. / Organic carbon (OC) preserved in marine sediments acts as a reduced carbon sink that balances the global carbon cycle. Understanding the biogeochemical mechanisms underpinning the balance between OC preservation and degradation is thus critical both to quantifying this carbon reservoir and to estimating the extent of life in the deep subsurface biosphere. This work utilizes bulk and spatially-resolved X-ray absorption spectroscopy to characterize the OC content and composition of various environmental systems in order to identify the role of minerals and surrounding geochemistry in organic carbon preservation in sediments. Biogenic manganese (Mn) oxides formed either in pure cultures of Mn-oxidizing microorganisms, in incubations of brackish estuarine waters, or as ferromanganese deposits in karstic cave systems rapidly associate with OC following precipitation. This association is stable despite Mn oxide structural ripening, suggesting that mineral-associated OC could persist during early diagenetic reactions. OC associated with bacteriogenic Mn oxides is primarily proteinaceous, including intact proteins involved in Mn oxidation and likely oxide nucleation and aggregation. Pelagic sediments from 16 sites underlying the South Pacific and North Atlantic gyres and spanning a gradient of sediment age and redox state were analyzed in order to contrast the roles of oxygen exposure, OC recalcitrance, and mineral-based protection of OC as preservation mechanisms. OC and nitrogen concentrations measured at these sites are among the lowest globally (<0.1%) and, to a first order, scale with sediment oxygenation. In the deep subsurface, however, molecular recalcitrance becomes more important than oxygen exposure time in protecting OC against remineralization. Deep OC consists of primarily amide and carboxylic carbon in a scaffolding of aliphatic and O-alkyl moieties, corroborating the extremely low C/N values observed. These findings suggest that microbes in oxic pelagic sediments are carbon-limited and may preferentially remove carbon relative to nitrogen from the organic matter pool. As a whole, this work documents how interactions with mineral surfaces and exposure to oxygen generate a reservoir of OC stabilized in sediments on at least 25-million year time scales. / by Emily Racz Estes. / Ph. D.