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), 2019 / Cataloged from PDF of thesis. / Includes bibliographical references (pages 151-174). / This thesis explicates aspects of the basic structure of oceanic lithosphere that are shaped by the processes that form the lithosphere. The strength of lithospheric plates relative to the underlying mantle enables the surface plate motions and plate boundary processes that characterize plate tectonics on Earth. Surprisingly, we have a relatively poor understanding of the physical mechanisms that make the lithosphere strong relative to the asthenosphere, and we lack a reference model for ordinary lithospheric structure that can serve as a baseline for comparing geophysical observations across locations. Chapters 2 and 3 of this thesis investigate the seismic structure of a portion of the Pacific plate where the simple tectonic history of the plate suggests that its structure can be used as a reference model for oceanic lithosphere. We present measurements of shallow azimuthal seismic anisotropy, and of a seismic discontinuity in the upper mantle, that reflect the effects of shear deformation and melting processes involved in the formation of the lithosphere at mid-ocean ridges. Chapter 4 uses numerical models to explore factors controlling fault slip behavior on normal faults that accommodate tectonic extension during plate formation. / by Hannah F. Mark. / Ph. D. / 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)

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), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references. / Antibiotics are naturally occurring chemicals in bacteria that were recently discovered and utilized by humans. Despite a relatively short time of use, anthropogenic use of antibiotics has increased natural levels of antibiotic resistance, which has caused a looming antibiotic resistance crisis, where antibiotics may not work. Understanding resistance patterns is critical to allow for continued therapeutic use of antibiotics. While resistance is often thought of in hospitals, antibiotics and antibiotic resistance genes from human activity are disposed of into nature where they are able to interact with naturally occurring antibiotics and resistance. In this dissertation, I examine the ocean as an understudied region of the environment for antibiotic resistance. The ocean represents an area of human activity with recreation and food consumption and it is an enormous region of the planet that is affected by both land and sea activities. / In Chapter 2, I explore the policies that have contributed to the antibiotic resistance crisis. I offer explanations of market and political failures that contributed to the situation, areas for growth in terms of assessing scientific knowledge, and finally, recommendations for mitigating antibiotic resistance. In Chapters 3 and 4, I collected individual bacterial cultures from Cape Cod, MA beaches to assess the phenotypic response to antibiotic resistance. I show that 73% of Vibrio-like bacteria and 95% of heterotrophic bacteria (both groups operationally defined) are resistant to at least one antibiotic. These results indicate that antibiotic resistance is prevalent and persistent on beaches over both spatial and temporal scales. In Chapter 5, I used metagenomics to assess the abundance and types of resistance genes at coastal impacted Massachusetts sites. I found that, even in sites that seem distinct in terms of anthropogenic impact, prevalence of resistance remained the same. / Finally, in Appendix A, I examined part of the TARA Ocean dataset for prevalence of antibiotic resistance genes across the world's ocean. Here, I found that there are distinctions between different ocean biomes based upon antibiotic, metal, and mobile genetic elements. This dissertation has increased the understanding of temporal and spatial dynamics of antibiotic resistance in the coastal and open ocean. / "This work has be funded by the National Science Foundation Graduate Research Fellowship under Grant No. 1122374 and a Martin Fellows for Sustainability Fellowship (both to MKM). Grants from Woods Hole Oceanographic Institution from the Coastal Ocean Institute, Grassle Family Foundation, Hill Family Foundation, and Biology Department also supported this work"--Page 6 / by Megan Katherine May. / Ph. D. / Ph.D. Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution)

Thesis: Ph. D. in Physical Oceanography, 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), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 121-133). / Global patterns of ocean salinity arise from the exchange of freshwater between the sea surface and the atmosphere. For a quasi-steady state system, these surface fluxes are balanced by compensating transports of salt in the ocean interior. In a warming climate, the atmosphere holds additional water vapor which acts to intensify the global water cycle. Amplified freshwater fluxes are then absorbed at the surface and propagate along ocean circulation pathways. Here, we use coupled model results from the CMIP5 experiment to identify coherent responses in the atmospheric water cycle and in ocean salinity patterns. Some aspects of the response are consistent across models, while other regions show large inter-model spread. In particular, the salinity response in the North Atlantic subpolar gyre, where the mean salinity plays a role in maintaining high surface density for deep-water formation, has low confidence in CMIP5 models. / To understand how differences in ocean circulation may affect this response, we use two techniques to diagnose the role of salt transports in the present-day climate. The first is a salt budget within the surface mixed layer, which identifies major transport processes. The second is a Lagrangian particle tracking tool, used to understand the regional connectivity of water masses. From this analysis, we find that anomalous freshwater signals become well mixed within the ocean gyres, but can be isolated on larger scales. The subpolar Atlantic salinity response generally shows freshening at the surface, but is sensitive to the transport of anomalously salty water from the subtropics, a largely eddy-driven process. As CMIP5 models use a range of eddy parameterizations, this is likely a source of uncertainty in the salinity response. / Finally, we investigate the effect of salinity changes on the deep overturning cells and other circulations, and find a complex influence that also depends on the details of advective pathways. In a warming scenario, water cycle amplification actually works to strengthen the Atlantic meridional overturning circulation due to the influence of enhanced subtropical evaporation. / by Samuel J. Levang. / Ph. D. in Physical Oceanography / Ph.D.inPhysicalOceanography 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 (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2011. / Cataloged from PDF version of thesis. "February 2011." / Includes bibliographical references (leaves 44-48). / Trichodesmium, a genus of diazotrophic cyanobacteria, is an important contributor to the marine nitrogen (N) and carbon (C) cycles. The extent to which Trichodesmium dinitrogen (N2) fixation contributes to the marine N cycle has been modeled based on abundance data and rate estimates from surface populations. However, recent data show that Trichodesmium populations have a broad vertical distribution. The presence of previously unaccounted for subsurface populations suggests that past estimates of the contribution of new N by Trichodesmium to the North Atlantic may be artificially low. Herein, culture and field studies were combined to examine trends in N2 fixation in discrete surface and subsurface Trichodesmium populations in the western North Atlantic. Surface populations were dominated by the raft colony morphology of Trichodesmium and surface N2 fixation rates ranged from (33 to 156 μmol h-1 mol C-1). Subsurface populations were dominated by the puff colony morphology. Subsurface N2 fixation was typically detectable, but consistently lower than surface population rates (9 to 88 μmol h-1 mol C-1). In an analysis of the entire field dataset, N2 fixation rates varied non-linearly as a function of in situ irradiance. This trend in N2 fixation versus in situ irradiance is consistent with field and culture observations in the literature (Bell et al., 2005; Capone et al., 2005), however other models that predict N2 fixation based on light predict higher subsurface N2 fixation than what was detected in this study. In culture, N2 fixation in Trichodesmium was proportional to light level over the range of irradiances tested (10 to 70 μmol quanta m-2 s-1) and over long and short time scales, suggesting subtle changes in the light field could depress subsurface N2 fixation. Since the subsurface samples were dominated by the puff colony morphology, it is unclear if the subsurface N2 fixation rates are the result of the in / by Abigail Heithoff. / S.M.

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), 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 169-174). / Internal tides are internal waves of tidal period generated by tidal currents flowing over submarine topography. Tall ridges that are nominally two-dimensional (2-D) are sites of particularly strong generation. The subsequent dissipation of internal tides contributes to ocean mixing, thereby playing an important role in the circulation of the ocean. Strong internal tides can also evolve into internal wave solitons, which affect acoustic communication, offshore structures and submarine navigation. This thesis addresses the generation of internal tides by tall submarine ridges using a combined analytical and experimental approach. The first part of the thesis is an experimental investigation of a pre-existing Green function formulation for internal tide generation by a tall symmetric ridge in a uniform density stratification. A modal decomposition technique was developed to characterize the structure of the experimental wave fields generated by 2D model topographies in a specially configured wave tank. The theory accurately predicts the low mode structure of internal tides, and reasonably predicts the conversion rate of internal tides in finite tidal excursion regimes, for which the emergence of non-linearities was notable in the laboratory. In the second part of the thesis, the Green function method is advanced for asymmetric and multiple ridges in weakly non-uniform stratifications akin to realistic ocean situations. / (cont.) A preliminary investigation in uniform stratification with canonical asymmetric and double ridges reveals asymmetry in the internal tide that can be very sensitive to the geometric configuration. This approach is then used with realistic topography and stratification data to predict the internal tide generated by the ridges at Hawaii and at the Luzon Strait. Despite the assumption of two-dimensionality, there is remarkably good agreement between field data, simulations and the new theory for the magnitude, asymmetry and modal content of the internal tide at these sites. The final part of the thesis investigates the possibility of internal wave attractors in the valley of double-ridge configurations. A one-dimensional map is developed to identify the existence and stability of attractors as a function of the ridge geometry. The Green function method is further advanced to include a viscous correction to balance energy focusing and dissipation along an attracting orbit of internal wave rays, and very good agreement is obtained between experiment and theory, even in the presence of an attractor. / by Paula Echeverri Mondragón. / Ph.D.

Thesis: Ph. D., Joint Program in 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 153-156). / One of the long term goals of Autonomous Underwater Vehicle (AUV) minehunting is to have multiple inexpensive AUVs in a harbor autonomously classify hazards. Existing acoustic methods for target classification using AUV-based sensing, such as sidescan and synthetic aperture sonar, require an expensive payload on each outfitted vehicle and expert image interpretation. This thesis proposes a vehicle payload and machine learning classification methodology using bistatic angle dependence of target scattering amplitudes between a fixed acoustic source and target for lower cost-per-vehicle sensing and onboard, fully autonomous classification. The contributions of this thesis include the collection of novel high-quality bistatic data sets around spherical and cylindrical targets in situ during the BayEx'14 and Massachusetts Bay 2014 scattering experiments and the development of a machine learning methodology for classifying target shape and estimating orientation using bistatic amplitude data collected by an AUV. To achieve the high quality, densely sampled 3D bistatic scattering data required by this research, vehicle broadside sampling behaviors and an acoustic payload with precision timed data acquisition were developed. Classification was successfully demonstrated for spherical versus cylindrical targets using bistatic scattered field data collected by the AUV Unicorn as a part of the BayEx'14 scattering experiment and compared to simulated scattering models. The same machine learning methodology was applied to the estimation of orientation of aspect-dependent targets, and was demonstrated by training a model on data from simulation then successfully estimating the orientations of a steel pipe in the Massachusetts Bay 2014 experiment. The final models produced from real and simulated data sets were used for classification and parameter estimation of simulated targets in real time in the LAMSS MOOS-IvP simulation environment. / by Erin Marie Fischell. / Ph. D.

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), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 335-357). / This thesis presents a sum-product inference algorithm for in-situ, nonparametric platform navigation called Multi-modal iSAM (incremental smoothing and mapping), for problems of thousands of variables. Our method tracks dominant modes in the marginal posteriors of all variables with minimal approximation error, while suppressing almost all low likelihood modes (in a non-permanent manner) to save computation. The joint probability is described by a non-Gaussian factor graph model. Existing inference algorithms in simultaneous localization and mapping assume Gaussian measurement uncertainty, resulting in complex front-end processes that attempt to deal with non-Gaussian measurements. Existing robustness approaches work to remove "outlier" measurements, resulting heuristics and the loss of valuable information. Track different hypotheses in the system has prohibitive computational cost and and low likelihood hypotheses are permanently pruned. Our approach relaxes the Gaussian only restriction allowing the frontend to defer ambiguities (such as data association) until inference. Probabilistic consensus ensures dominant modes across all measurement information. Our approach propagates continuous beliefs on the Bayes (Junction) tree, which is an efficient symbolic refactorization of the nonparametric factor graph, and approximates the underlying Chapman-Kolmogorov equations. Like the predecessor iSAM2 max-product algorithm [Kaess et al., IJRR 2012], we retain the Bayes tree incremental update property, which allows for tractable recycling of previous computations. Several non-Gaussian measurement likelihood models are introduced, such as ambiguous data association or highly non-Gaussian measurement modalities. In addition, keeping with existing inertial navigation for dynamic platforms, we present a novel continuous-time inertial odometry residual function. Inertial odometry uses preintegration to seamlessly incorporate pure inertial sensor measurements into a factor graph, while supporting retroactive (dynamic) calibration of sensor biases. By centralizing our approach around a factor graph, with the aid of modern starved graph database techniques, concerns from different elements of the navigation ecosystem can be separated. We illustrate with practical examples how various sensing modalities can be combined into a common factor graph framework, such as: ambiguous loop closures; raw beam-formed acoustic measurements; inertial odometry; or conventional Gaussian-only likelihoods (parametric) to infer multi-modal marginal posterior belief estimates of system variables. / by Dehann Fourie. / 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), 2005. / Includes bibliographical references (leaves 96-98). / The changing state of warfare has driven the US Navy's area of operations closer to shore into littoral coastal waters. Mine Warfare has been proven as an extremely effective means of battlespace control in these waters. Mines can be inexpensively mass produced and rapidly deployed over large areas. The most common type of mine in use is the bottom placed mine, an object with simple geometry that sits on the seafloor. These mines often exhibit scour induced burial below the seafloor, making detection through traditional mine hunting methods difficult or impossible, while the mines themselves remain lethal. The Office of Naval Research (ONR) has developed a computer model that predicts the extent of mine burial to aid mine hunting and mine clearing operations. Investigations under ONR's Mine Burial Program are presently being conducted to calibrate and validate this model. This thesis uses data from the deployment of an acoustically instrumented model mine near the Martha's Vineyard Coastal Observatory in part of a larger, 16 total object investigation. A 2-axis pencil beam sonar was deployed concurrently with the mine to obtain microbathymetric measurements of the scour pit development and the progression of mine burial. Data correction techniques to correct for beam pattern induced bathymetry errors and a transformed coordinate system are detailed within. / (cont.) An analysis of scour pit dimensions includes scour depth, area, and volume as well as a look into percent burial by depth as a characteristic measurement important for operational mine hunting. The progression of mine burial is related to the wave climate, unsteady flow hydrodynamic forcing, and bed-load transport. The analysis examines the relative roles of these mechanisms in the scour-infill-bury process. / by Brendan Reed Gotowka. / S.M.

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), 2005. / Includes bibliographical references (leaves 124-125). / A detailed study was conducted to prove the concept of an iterative approach to single transponder navigation for REMUS Autonomous Underwater Vehicles (AUVs). Although the concept of navigation with one acoustic beacon is not new, the objective was to develop a computer algorithm that could eventually be integrated into the REMUS architecture. This approach uses a least squares fit routine coupled with restrictive geometry and simulated annealing vice Kalman filtering and state vectors. In addition, to provide maximum flexibility, the single transponder was located on a GPS equipped surface ship that was free to move instead of the more common single bottom mounted beacon. Using only a series of spread spectrum ranges logged with time stamp, REMUS standard vehicle data, and reasonable initial conditions, the position at a later time was derived with a figure of merit fit score. Initial investigation was conducted using a noise model developed to simulate the errors suspected with the REMUS sensor suite. Results of this effort were applied to a small at sea test in 3,300 meters with the REMUS 6000 deep water AUV. A more detailed test was executed in Buzzard's Bay, Massachusetts, in 20 meters of water with a REMUS 100 AUV focusing on navigation in a typical search box. / (cont.) While deep water data was too sparse to reveal conclusive results, the Buzzard's Bay work strongly supports the premise that an iterative algorithm can reliably integrate REMUS logged data and an accurate time sequence of ranges to provide position fixes through simple least squares fitting. Ten navigational legs up to 1500 meters in length showed that over 90% of the radial position error can be removed from an AUV's position estimate using the STRONG algorithm vice dead reckon navigation with a magnetic compass and Doppler Velocity Log alone (DVL). / by J. Carl Hartsfield, Jr. / S.M.

Thesis (Ph. D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2005. / Bibliography: p. 119-129. / Obtaining accurate and repeatable navigation for robotic vehicles in the deep ocean is difficult and consequently a limiting factor when constructing vehicle-based bathymetric maps. This thesis presents a methodology to produce self-consistent maps and simultaneously improve vehicle position estimation by exploiting accurate local navigation and utilizing terrain relative Measurements. It is common for errors in the vehicle position estimate to far exceed the errors associated with the acoustic range sensor. This disparity creates inconsistency when an area is imaged multiple times and causes artifacts that distort map integrity. Our technique utilizes small terrain "sub-maps" that can be pairwise registered and used to additionally constrain the vehicle position estimates in accordance with actual bottom topography. A delayed state Kalman filter is used to incorporate these sub-map registrations as relative position measurements between previously visited vehicle locations. The archiving of previous positions in a filter state vector allows for continual adjustment of the sub-map locations. The terrain registration is accomplished using a two dimensional correlation and a six degree of freedom point cloud alignment method tailored for bathymetric data. / (cont.) The complete bathymetric map is then created from the union of all sub-maps that have been aligned in a consistent manner. Experimental results from the fully automated processing of a multibeamn survey over the TAG hydrothermal structure at the Mid-Atlantic ridge are presented to validate the proposed method. / by Christopher N. Roman. / Ph.D.