Thesis (Ph. D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; 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. 185-193). / This thesis describes the physics of fully three-dimensional low frequency acoustic interaction with internal waves, bottom sediment waves and surface swell waves that are often observed in shallow waters and on continental slopes. A simple idealized model of the ocean waveguide is used to analytically study the properties of acoustic normal modes and their perturbations due to waves of each type. The combined approach of a semi-quantitative study based on the geometrical acoustics approximation and on fully three-dimensional coupled mode numerical modeling is used to examine the azimuthal dependence of sound wave horizontal reflection from, transmission through and ducting between straight parallel waves of each type. The impact of the natural crossings of nonlinear internal waves on horizontally ducted sound energy is studied theoretically and modeled numerically using a three-dimensional parabolic equation acoustic propagation code. A realistic sea surface elevation is synthesized from the directional spectrum of long swells and used for three-dimensional numerical modeling of acoustic propagation. As a result, considerable normal mode amplitude scintillations were observed and shown to be strongly dependent on horizontal azimuth, range and mode number. Full field numerical modeling of low frequency sound propagation through large sand waves located on a sloped bottom was performed using the high resolution bathymetry of the mouth of San Francisco Bay. Very strong acoustic ducting is shown to steer acoustic energy beams along the sand wave's curved crests. / by Alexey Alexandrovich Shmelev. / Ph.D.

Thesis: Ph. D., Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references. / In the spring and summer within the ablation zone of the Greenland Ice Sheet (GrIS), meltwater drains to the ice sheet bed through an evolving network of efficient channelized and inefficient distributed drainage systems. Distributed system drainage is a key component in stabilizing GrIS velocity on interannual time scales and controlling geochemical fluxes. During the spring and summer of 2011 and 2012, I conducted fieldwork at a large outlet glacier in southwest Greenland underlain by metamorphic silicate rocks. Data collected from a continuous 222Rn monitor in the proglacial river were used as a component of a mass balance model. I demonstrated that Jdis, the 222Rn fraction derived from the distributed system, was >90% of the 222Rn flux on average, and therefore, 222Rn can be used as a passive flow tracer of distributed system drainage. Supraglacial meltwater runoff estimated using two independent models was compared with ice velocity measurements across the glacier's catchment. Major spikes of Jdis, occurred after rapid supraglacial meltwater runoff inputs and during the expansion of the subglacial channelized system. While increases in meltwater runoff induced ice acceleration, they also resulted in the formation of efficient subglacial channels and increased drainage from the distributed system, mechanisms known to cause slower late summer to winter velocities. Sr, U, and Ra isotopes and major and trace element chemistry were used to investigate the impact of glacial hydrology on subglacial weathering. Analysis of partial and total digestions of the riverine suspended load (SSL) found that trace carbonates within the silicate watershed largely controlled the 'Sr/'Sr ratio in the dissolved load. Experiments and sampling transects downstream from the GrIS demonstrated that [delta]234U in the dissolved phase decreased with increasing interaction with the SSL. The (2 2 8Ra/2 26Ra) value of the dissolved load was significantly higher than that of the SSL and therefore, was not the result of the source rock material but of extensive mineral surface weathering and the faster ingrowth rate of 228Ra (t1 2=5.75 y) relative to 22 6Ra (t112=1600 y). In summary, extensive, repeated cycles of rapid supraglacial meltwater runoff to subglacial drainage networks leads to increased distributed system drainage and mineral weathering. / by Benjamin Shawn Linhoff. / Ph. D.

Thesis: Ph. D., Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 283-314). / Animal movement is motivated in part by energetic constraints, where fitness is maximized by minimizing energy consumption. The energetic cost of movement depends on the resistive forces acting on an animal; changes in this force balance can occur naturally or unnaturally. Fishing gear that entangles large whales adds drag, often altering energy balance to the point of terminal emaciation. An analog to this is drag from tags attached to cetaceans for research and monitoring. This thesis quantifies the effects of drag loading from these two scenarios on fine-scale movements, behaviors and energy consumption. I measured drag forces on fishing gear that entangled endangered North Atlantic right whales and combined these measurements with theoretical estimates of drag on whales' bodies. Entanglement in fishing gear increased drag forces by up to 3 fold. Bio-logging tags deployed on two entangled right whales recorded changes in the diving and fine-scale movement patterns of these whales in response to relative changes in drag and buoyancy from fishing gear and through disentanglement: some swimming patterns were consistently modulated in response. Disentanglement significantly altered dive behavior, and can affect thrust production. Changes in the force balance and swimming behaviors have implications for the survival of chronically entangled whales. I developed two bioenergetics approaches to estimate that chronic, lethal entanglements cost approximately the same amount as the cost of pregnancy and supporting a calf to near-weaning. I then developed a method to estimate drag, energy burden and survival of an entangled whale at detection. This application is essential for disentanglement response and protected species management. Experiments with tagged bottlenose dolphins suggest similar responses to added drag: I determined that instrumented animals slow down to avoid additional energetic costs associated with drag from small bio-logging tags, and incrementally decrease swim speed as drag increases. Metabolic impacts are measurable when speed is constrained. I measured the drag forces on these tags and developed guidelines depending on the relative size of instruments to study-species. Together, these studies quantify the magnitude of added drag in complementary systems, and demonstrate how animals alter their movement to navigate changes in their energy landscape associated with increased drag. / by Julie M. van der Hoop. / Ph. D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 1987. / Includes bibliographical references (leaves 181-185). / This thesis presents an application of the Grant-Madsen-Glenn bottom boundary layer model (Grant and Madsen, 1979; Glenn and Grant, 1987) to predictions of sediment transport on the continental shelf. The analysis is a two-stage process. Via numerical experiment, we explore the sensitivity of sediment transport to variations in model parameters and assumptions. A notable result is the enhancement of suspended sediment stratification due to wave boundary layer effects. When sediment stratification is neglected under conditions of large wave bottom velocities (i.e. ,... ), concentration predictions can be more than an order of magnitude higher than any observed during storm conditions on the continental shelf. A number of limitations to application emerged from the analysis. Solutions to the stratified model are not uniquely determined under a number of cases of interest, potentially leading to gross inaccuracies in the prediction of sediment load and transport. Load and sediment transport in the outer Ekman Layer, beyond the region of emphasis for the model, can be as large or larger than the near-bottom estimates in some cases; such results suggest directions for improvements in the theoretical model. In the second step of the analysis, we test the ability of the model to make predictions of net sediment transport that are consistent with observed sediment depositional patterns. Data from the Mid-Atlantic Bight and the Northern California coast are used to define reasonable model input to represent conditions on two different types of shelves. In these examples, the results show how the intensification of wave bottom velocities with decreasing depth can introduce net transport over a region. The patterns of erosion/deposition are shown to be strongly influenced by sediment stratification and moveable bed roughness. Also predicted by the applications is a rapid winnowing out of fine grain size components when there is even a small variation of bed grain size texture in the along-flow direction. / by Margaret Redding Goud. / Ph.D.

Thesis (Ph. D. in Geophysics)--Joint Program in Marine Geology and Geophysics (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2013. / Page 176 blank. Cataloged from PDF version of thesis. / Includes bibliographical references. / In this thesis we present results from inversion of data using dense arrays of collocated seismic and magnetotelluric stations located in the Cascadia subduction zone region of central Washington. In the migrated seismic section, we clearly image the top of the slab and oceanic Moho, as well as a velocity increase corresponding to the eclogitization of the hydrated upper crust. A deeper velocity increase is interpreted as the eclogitization of metastable gabbros, assisted by fluids released from the dehydration of upper mantle chlorite. A low velocity feature interpreted as a fluid/melt phase is present above this transition. The serpentinized wedge and continental Moho are also imaged. The magnetotelluric image further constrains the fluid/melt features, showing a rising conductive feature that forms a column up to a conductor indicative of a magma chamber feeding Mt. Rainier. This feature also explains the disruption of the continental Moho found in the migrated image. Exploration of the assumption of smoothness implicit in the standard MT inversion provides tools that enable us to generate a more accurate MT model. This final MT model clearly demonstrates the link between slab derived fluids/melting and the Mt. Rainier magma chamber. / by R. Shane McGary. / Ph.D.in Geophysics

Thesis (Ph.D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science; and the Woods Hole Oceanographic Institution), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 171-181). / Mobile robotic systems operating over long durations require algorithms that are robust and scale efficiently over time as sensor information is continually collected. For mobile robots one of the fundamental problems is navigation; which requires the robot to have a map of its environment, so it can plan its path and execute it. Having the robot use its perception sensors to do simultaneous localization and mapping (SLAM) is beneficial for a fully autonomous system. Extending the time horizon of operations poses problems to current SLAM algorithms, both in terms of robustness and temporal scalability. To address this problem we propose a reduced pose graph model that significantly reduces the complexity of the full pose graph model. Additionally we develop a SLAM system using two different sensor modalities: imaging sonars for underwater navigation and vision based SLAM for terrestrial applications. Underwater navigation is one application domain that benefits from SLAM, where access to a global positioning system (GPS) is not possible. In this thesis we present SLAM systems for two underwater applications. First, we describe our implementation of real-time imaging-sonar aided navigation applied to in-situ autonomous ship hull inspection using the hovering autonomous underwater vehicle (HAUV). In addition we present an architecture that enables the fusion of information from both a sonar and a camera system. The system is evaluated using data collected during experiments on SS Curtiss and USCGC Seneca. Second, we develop a feature-based navigation system supporting multi-session mapping, and provide an algorithm for re-localizing the vehicle between missions. In addition we present a method for managing the complexity of the estimation problem as new information is received. The system is demonstrated using data collected with a REMUS vehicle equipped with a BlueView forward-looking sonar. The model we use for mapping builds on the pose graph representation which has been shown to be an efficient and accurate approach to SLAM. One of the problems with the pose graph formulation is that the state space continuously grows as more information is acquired. To address this problem we propose the reduced pose graph (RPG) model which partitions the space to be mapped and uses the partitions to reduce the number of poses used for estimation. To evaluate our approach, we present results using an online binocular and RGB-Depth visual SLAM system that uses place recognition both for robustness and multi-session operation. Additionally, to enable large-scale indoor mapping, our system automatically detects elevator rides based on accelerometer data. We demonstrate long-term mapping using approximately nine hours of data collected in the MIT Stata Center over the course of six months. Ground truth, derived by aligning laser scans to existing floor plans, is used to evaluate the global accuracy of the system. Our results illustrate the capability of our visual SLAM system to map a large scale environment over an extended period of time. / by Hordur Johannsson. / Ph.D.

Thesis (Ph. D.)--Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), February 2001. / Includes bibliographical references. / Processes that enable marine phytoplankton to acquire trace metals are fundamental to our understanding of primary productivity and global carbon cycling. This thesis explored the biogeochemistry of cobalt using analytical chemistry and physiological experiments with the dominant phytoplankton species, Prochlorococcus. A high sensitivity method for Co speciation was developed using hanging mercury drop cathodic stripping voltammetry. Dissolved Co at the Bermuda Atlantic Time Series station (BATS) in the Sargasso Sea was bound by strong organic complexes with a conditional stability constant of logK=16.3+0.9. A depth profile of Co at BATS revealed a nutrient-like profile. Biweekly time series measurements of total cobalt near Bermuda from the MITESS sampler were 0-47pM throughout 1999, and averaged 20±1 OpM in 1999. A transect of total cobalt from BATS to American coastal waters ranged from 19- 133pM and correlated negatively with salinity (r2=0.93), suggestive of coastal waters as an input source. Prochlorococcus strains MED4-Ax and SS120 showed an absolute requirement for Co, despite replete Zn. 57Co uptake rates and growth rates were enhanced by additions of filtered low Co cultures, suggesting that a ligand is present that facilitates Co uptake. Bottle incubations from a Synechococcus bloom in the Pacific showed production of 425pM strong cobalt ligand. These and other lines of evidence support the hypothesis that a cobalt ligand, or cobalophore, is involved in cobalt uptake. Co-limited Prochlorococcus cultures exhibited an increase in the fraction of cells in G2 relative to other cell cycle stages during exponential growth, and the durations of this stage increased with decreasing cobalt concentrations. This effect was not observed with Fe, N, or P-limited cultures, suggestive of a specific biochemical function of cobalt that would interfere with the late stages of the cell cycle. The ligand Teta was explored as a means to induce cobalt limitation. The CoTeta complex was not bioavailable to the Sargasso Sea microbial assemblage in short-term experiments. Bottle incubations with Teta did not induce cobalt limitation of Prochlorococcus. These results are consistent with the lower conditional stability constant for CoTeta (logK= 11.2+0.1) relative to natural cobalt ligands in seawater, and with culture studies that suggest uptake of cobalt via strong organic ligands. / by Mak A. Saito. / Ph.D.

Thesis (Ph.D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences and the Woods Hole Oceanographic Institution), 2000. / Vita. / Includes bibliographical references (leaves 179-187). / A spectral camera (ALISS - Ambient Light Imaging and Spectral System) was used to image ambient light from high-temperature vents at 9°N East Pacific Rise and the Juan de Fuca Ridge during 1997 and 1998 Alvin dive cruises. ALISS is a low-light digital camera with custom-designed optics. A set of nine lenses, each covered by an individual bandpass filter (50 and 100 nm nominal bandwidths), allows vents to be imaged in nine wavelength bands simultaneously spanning the range of 400-1000 nm. Thus, both spatial and spectral information are obtained. ALISS was used to image three types of vents: black smokers, flange pools, and beehives. The primary source of light is thermal radiation due to the high temperature of the hydrothermal fluid (~350°C). This light is dominant at wavelengths greater than 700 nm. At flange pools, where the fluid is relatively stable, only thermal radiation is present. Black smokers and beehives, however, are subject to mixing with ambient seawater (2°C) leading to mineral precipitation. Data from these types of vents show the existence of non-thermal, temporally varying light in the 400-700 nm region. This light is probably caused by mechanisms related to mixing and precipitation, such as chemiluminescence, crystalloluminescence and triboluminescence. / by Sheri N. White. / Ph.D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Males and females may differ in stage-specific survival, maturation, fertility, or mating availability. These demographic differences, in turn, affect population growth rates, equilibrium structure, and evolutionary trajectories. Models considering only a single sex cannot capture these effects, motivating the use of demographic two-sex models for sexually reproducing populations. I developed a new two-sex modeling framework that incorporates population structure and multiple life cycle processes through transition rate matrices. These models can be applied to a variety of life histories to address both ecological and evolutionary questions. Here, I apply the model to the effects of sex-biased harvest on populations with various mating systems. Demographic considerations also affect evolutionary projections. I derived matrix calculus expressions for key evolutionary quantities in my two-sex models, including the invasion fitness, selection gradient, and second derivatives of growth rates (which have many applications, including the classification of evolutionary singular strategies). I used these quantities to analyze the evolution of the primary sex ratio, under various sex- and stage-specific offspring costs and maternal conditions. Demographic two-sex models lend insight into complex, and sometimes counterintuitive, results that are not captured by models lacking population structure. These findings highlight the importance of demographic structure in ecology and evolution. / by Esther Shyu. / 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), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 165-172). / Glacial fjords form conduits between glaciers of the Greenland Ice Sheet and the North Atlantic. They are the gateways for importing oceanic heat to melt ice and for exporting meltwater into the ocean. Submarine melting in fjords has been implicated as a driver of recent glacier acceleration; however, there are no direct measurements of this melting, and little is known about the fjord processes that modulate melt rates. Combining observations, theory, and modeling, this thesis investigates the circulation, heat transport, and meltwater export in glacial fjords. While most recent studies focus on glacial buoyancy forcing, there are other drivers - e.g. tides, local wind, shelf variability - that can be important for fjord circulation. Using moored records from two major Greenlandic fjords, shelf forcing (from shelf density fluctuations) is found to dominate the fjord circulation, driving rapid exchange with the shelf and large heat content variability near the glacier. Contrary to the conventional paradigm, these flows mask any glacier-driven circulation in the non-summer months. During the summer, when shelf forcing is reduced and freshwater forcing peaks, a mean exchange flow transports warm Atlantic-origin water towards the glacier and exports glacial meltwater. Many recent studies have inferred submarine melt rates from oceanic heat transport, but the fjord budgets that underlie this method have been overlooked. Building on estuarine studies of salt fluxes, this thesis presents a new framework for assessing glacial fjord budgets and revised equations for inferring meltwater fluxes. Two different seasonal regimes are found in the heat/salt budgets for Sermilik Fjord, and the results provide the first time-series of submarine meltwater and subglacial discharge fluxes into a glacial fjord. Finally, building on the observations, ROMS numerical simulations and two analytical models are used to investigate the dynamics of shelf-driven flows and their importance relative to local wind forcing across the parameter space of Greenland's fjords. The fjord response is found to vary primarily with the width relative to the deformation radius and the fjord adjustment timescale relative to the forcing timescale. Understanding these modes of circulation is a step towards accurate modeling of ocean-glacier interactions. / by Rebecca H. Jackson. / Ph. D.