Thesis: S.M., Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 123-125). / Underwater acoustic communication is an extremely complex field that faces many challenges due to the time-varying nature of the ocean environment. Vector sensors are a proven technology that when utilizing their directional sensing capabilities allows us to minimize the effect of interfering noise sources. A traditional pressure sensor array has been the standard for years but suffers at degraded signal to noise ratios (SNR) and requires maneuvers or a lengthly array aperture to direction find. This thesis explores the effect of utilizing a vector sensor array to steer to the direction of signal arrival and the effect it has on equalization of the signal at degraded SNRs. It was demonstrated that utilizing a single vector sensor we were able steer to the direction of arrival and improve the ability of an equalizer to determine the transmitted signal. This improvement was most prominent when the SNR was degraded to levels of 0 and 10 dB where the performance of the vector sensor outperformed that of the pressure sensor in nearly 100% of cases. Finally, this performance improvement occurred with a savings in computational expense. / by Matthew Robert Lewis. / 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), 2007. / Includes bibliographical references (p. 60). / An open source, MATLABTM-based propeller design code MPVL was improved to include rapid prototyping capabilities as well as other upgrades as part of this effort. The resulting code, OpenPVL is described in this thesis. In addition, results from the development code BasicPVL are presented. An intermediate code, BasicPVL, was created by the author while OpenPVL was under development, and it provides guidance for initial propeller designs and propeller efficiency analysis. OpenPVL is part of the open source software suite of propeller design codes, OpenProp. OpenPVL is in the form of a Graphical User Interface (GUI) which features both a parametric design technique and a single propeller geometry generator. This code combines a user-friendly interface with a highly modifiable platform for advanced users. This tool offers graphical propeller design feedback while recording propeller input, output, geometry, and performance. OpenPVL features the ability to translate the propeller design geometry into a file readable by a Computer Aided Design (CAD) program and converted into a 3D-printable file. Efficient propellers reduce the overall power requirements for Autonomous Underwater Vehicles (AUVs), and other propulsion-powered vehicles. The focus of this study is based on the need of propeller users to have an open source computer-based engineering tool for the rapid design of propellers suited to a wide range of underwater vehicles. Propeller vortex lattice lifting line (PVL) code in combination with 2D foil theory optimizes propeller design for AUVs. Several case studies demonstrate the functionality of OpenPVL, and serve as guides for future propeller designs. / (cont.) The first study analyzes propeller thruster performance characteristics for an off-the-shelf propeller, while the second study demonstrates the process for propeller optimization-from the initial design to the final file that can be read by a 3D printer. The third study reviews the complete process of the design and production of an AUV propeller. Thus, OpenPVL performs a variety of operations as a propeller lifting line code in streamlining the propeller optimization and prototyping process. / by Kathryn Port D'Epagnier. / 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), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The ultimate goal of early life studies of fish over the past century has been to better understand recruitment variability. Recruitment is the single most important natural event controlling year-class strength and biomass in fish populations. As evident in Georges Bank haddock, Melanogrammus aeglefinus, there is a strong relationship between recruitment success and processes occurring during the planktonic larval stage. Spatially explicit coupled biological-physical individual-based models are ideal for studying the processes of feeding, growth, and predation during the larval stage. This thesis sought new insights into the mechanisms controlling the recruitment process in fish populations by using recent advances in biological-physical modeling methods together with laboratory and field data sets. Interactions between feeding, metabolism and growth, vertical behavior, advection, predation, and the oceanic environment of larval haddock were quantitatively investigated using individual-based models. A mechanistic feeding model illustrated that species-specific behavioral characteristics of copepod prey are critically important in determining food availability to the haddock larvae. Experiments conducted with a one-dimensional vertical behavior model suggested that larval haddock should focus on avoiding visual predation when they are small and vulnerable and food is readily available. Coupled hydrodynamics, concentration-based copepod species, and individual-based larval haddock models demonstrated that the increased egg hatching rates and lower predation rates on larvae in 1998 contributed to its larger year-class. Additionally, results from these coupled models imply that losses to predation may be responsible for interannual variability in recruitment and larval survival. The findings of this thesis can be used to better manage the haddock population on Georges Bank by providing insights into how changes in the physical and biological environment of haddock affect their survival and recruitment, and more generally about the processes significant for larval fish survival. / by Colleen Mary Petrik. / 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), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references. / To maintain the benefits of group membership, social animals need mechanisms to stay together and reunite if separated. This thesis explores the acoustic signals that dolphins use to overcome this challenge and mediate their complex relationships in a dynamic 3D environment. Bottlenose dolphins are the most extensively studied toothed whale, but research on acoustic behavior has been limited by an inability to identify the vocalizing individual or measure inter-animal distances in the wild. This thesis resolves these problems by simultaneously deploying acoustic tags on closely-associated pairs of known animals. These first reported deployments of acoustic tags on dolphins allowed me to characterize temporal patterns of vocal behavior on an individual level, uncovering large variation in vocal rates and inter-call waiting time between animals. Looking more specifically at signature whistles, a type of call often linked to cohesion, I found that when one animal produced its own signature whistle, its partner was more likely to respond with its own whistle. To better evaluate potential cohesion functions for signature whistles, I then modeled the probability of an animal producing a signature whistle at different times during a temporary separation and reunion from its partner. These data suggest that dolphins use signature whistles to signal a motivation to reunite and to confirm identity prior to rejoining their partner. To examine how cohesion is maintained during separations that do not include whistles, I then investigated whether dolphins could keep track of their partners by passively listening to conspecific echolocation clicks. Using a multi-pronged approach, I demonstrated that the passive detection range of echolocation clicks overlaps with the typical separation ranges of Sarasota mother-calf pairs and that the amount of time since an animal was last able to detect a click from its partner helped explain its probability of producing a signature whistle. Finally, this thesis developed a portable stereo camera system to study cohesion in situations where tagging is not possible. Integrating a GPS receiver, an attitude sensor and 3D stereo photogrammetry, the system rapidly positions multiple animals, grounding behavioral observations in quantitative metrics and characterizing fine-scale changes that might otherwise be missed. / by Nicholas Blair Wootton Macfarlane. / 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. / Although over a dozen elements are needed to support phytoplankton growth, only a few are considered to be growth-limiting. As the central atom in vitamin B12, cobalt is crucial for metabolism, but its status as a limiting nutrient is uncertain. This thesis investigates the geochemical controls on oceanic cobalt scarcity and their biological consequences. Analysis of over 1000 samples collected in the Tropical Pacific Ocean reveals a dissolved cobalt distribution that is strongly coupled to dissolved oxygen, with peak concentrations where oxygen is lowest. Large cobalt plumes within anoxic waters are maintained by three processes: 1) a cobalt supply from organic matter remineralization, 2) an amplified sedimentary source from oxygen-depleted coastlines, and 3) low-oxygen inhibition of manganese oxidation, which scavenges cobalt from the water column. Rates of scavenging are calculated from a global synthesis of recent GEOTRACES data and agree with cobalt accumulation rates in pelagic sediments. Because both sources and sinks are tied to the extent of oxygen minimum zones, oceanic cobalt inventories are likely dynamic on the span of decades. Despite extremely low cobalt in the South Pacific gyre, the cyanobacterium Prochlorococcus thrives. Minimum cobalt and iron requirements of a Prochlorococcus strain isolated from the Equatorial Pacific are quantified. Cobalt quotas are related to demand for ribonucleotide reductase and methionine synthase enzymes, which catalyze critical steps in DNA and protein biosynthesis, respectively. Compared to other cyanobacteria, a streamlined metal physiology makes Prochlorococcus susceptible to competitive inhibition of cobalt uptake by low levels of zinc. Although phytoplankton in the Equatorial Pacific are subject to chronic iron-limitation, widespread cobalt scarcity and vulnerability to zinc inhibition observed in culture imply that wild Prochlorococcus are not far from a cobalt-limitation threshold. / by Nicholas James Hawco. / 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), 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The mechanisms involved in the formation of coral skeletons are examined using a laboratory model for coral calcification and the growth of living corals under different environmental conditions. Abiogenic aragonite was precipitated from seawater over a range of saturation states (Chapter 1). Abiogenic aragonite formed at high saturation state ([Omega]>~20) had a granular appearance and was enriched in trace elements, similar to the crystals found within the centers of calcification and dark bands in coral skeletons. Abiogenic aragonite formed fibrous crystals at lower saturation states, similar to the crystals which radiate out from the centers of calcification. These similarities suggest that the internal calcifying environment of the coral experiences a wide range of saturation states. To estimate when periods of high or low saturation state occur within the coral, corals were stained to mark the skeleton deposited during specific time intervals (Chapter 2). Dark bands are shown to form between dusk and dawn. A conceptual model is proposed in which daytime saturation state is limited by the availability of CO₂ due to the uptake of CO₂ by photosynthesis. To test the potential for photosynthesis to limit CO₂ availability to calcification, corals were grown under experimentally manipulated CO₂ and nutrient levels. Elevated CO₂ levels were found to decrease calcification in zooxanthellate colonies of the coral Astrangia poculata, however the addition of inorganic nutrients reduced the negative impact of CO₂ (Chapter 3), while reduced calcification rates were associated with elevated nutrients at ambient CO₂ levels. Together these results suggest that nutrient availability may limit photosynthesis under elevated pCO₂ conditions, while at ambient conditions additional stimulation of photosynthesis may limit the CO₂ supply to calcification. To further test the interaction of photosynthesis with calcification, the effects of nutrients, CO₂, and temperature were tested on both zooxanthellate and azooxanthellate coral colonies (Chapter 4). No clear pattern of nutrient enhancement of photosynthesis or calcification was found. However, a pronounced gender difference was found in the effect of CO₂ on calcification in spawning corals, with female corals being more sensitive to elevated CO₂. / (cont.) Coral calcification is examined using a laboratory model and living corals. In the laboratory model, abiogenic aragonite formed at high saturation state ([Omega]>~20) had a granular appearance and was enriched in trace elements, similar to centers of calcification and dark bands in corals. Abiogenic aragonite formed fibrous crystals at lower saturation states, similar to crystals which radiate out from centers of calcification. These similarities suggest the calcifying environment of the coral experiences a range of saturation states. To estimate when high or low saturation states occur within the coral, living corals were stained, staining patterns suggest dark bands form between dusk and dawn. A model is proposed in which daytime saturation state is limited by the availability of CO₂. To test the potential for photosynthesis to limit CO₂ availability to calcification, corals were grown under altered CO₂ and nutrient levels. Elevated CO₂ levels decreased calcification in zooxanthellate corals, however addition of nutrients reduced the negative impact of CO₂. This suggests nutrient availability may limit photosynthesis under elevated pCO₂2 conditions. The effects of nutrients, CO₂, and temperature were further tested on both zooxanthellate and azooxanthellate coral colonies. Unexpectedly, a gender difference was found in the effect of CO₂ on calcification. / by Michael Holcomb. / 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 / 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 (pages 183-193). / This thesis is motivated by a series of biological experiments that display the harbor seal's extraordinary ability to track the wake of an object several seconds after it has swum by. They do so despite having auditory and visual cues blocked, pointing to use of their whiskers as sensors of minute water movements. In this work, I elucidate the basic uid mechanisms that seals may employ to accomplish this detection. Key are the unique ow-induced vibration properties resulting from the geometry of the harbor seal whisker, which is undulatory and elliptical in cross-section. First, the vortex-induced vibration (VIV) characteristics of the whisker geometry are tested. Direct force measurements and ow visualizations on a rigid whisker model undergoing a range of 1-D imposed oscillations show that the geometry passively reduces VIV (factor of > 10), despite contributions from eective added mass and damping. Next, a biomimetic whisker sensor is designed and fabricated. The rigid whisker model is mounted on a four-armed flexure, allowing it to freely vibrate in both in-line and crossflow directions. Strain gauges on the flexure measure deflections at the base. Finally, this device is tested in a simplified version of the sh wake { seal whisker interaction scenario. The whisker is towed behind an upstream cylinder with larger diameter. Whereas in open water the whisker exhibits very low vibration when its long axis is aligned with the incoming ow, once it enters the wake it oscillates with large amplitude and its frequency coincides with the Strouhal frequency of the upstream cylinder. This makes the detection of an upstream wake as well as an estimation of the size of the wake-generating body possible. A slaloming motion among the wake vortices causes the whisker to oscillate in this manner. The same mechanism has been previously observed in energy-extracting foils and trout actively swimming behind bluff cylinders in a stream. / by Heather Rachel Beem. / 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), 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references. / This thesis investigates the timing and source(s) of water and volatile elements to the inner solar system by studying the basaltic meteorites angrites and eucrites. In chapters 2 and 3, I present the results from angrite meteorites. Chapter 2 examines the water and volatile element content of the angrite parent body and I suggest that some water and other volatile elements accreted to inner solar system bodies by ~2 Myr after the start of the solar system. Chapter 3 examines the D/H of this water and I suggest it is derived from carbonaceous chondrites. Chapter 4, 5, 6, and 7 addresses eucrite meteorites. Chapter 4 expands on existing models to explain geochemical trends observed in eucrites. In Chapter 5, I examine the water and F content of the eucrite parent body, 4 Vesta. In chapter 6, I determine the source of water for 4 Vesta and determine that carbonaceous chondrites delivered water to this body. Chapter 7 discusses degassing on 4 Vesta while it was forming. / by Adam Robert Sarafian. / Ph. D.

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), 2004. / Includes bibliographical references (p. 177-190). / Our ability to image extended underwater scenes is severely limited by attenuation and backscatter. Generating a composite view from multiple overlapping images is usually the most practical and flexible way around this limitation. In this thesis we look at the general constraints associated with imaging from underwater vehicles for scientific applications - low overlap, non-uniform lighting and unstructured motion - and present a methodology for dealing with these constraints toward a solution of the problem of large area 3D reconstruction. Our approach assumes navigation data is available to constrain the structure from motion problem. We take a hierarchical approach where the temporal image sequence is broken into subsequences that are processed into 3D reconstructions independently. These submaps are then registered to infer their overall layout in a global frame. From this point a bundle adjustment refines camera and structure estimates. We demonstrate the utility of our techniques using real data obtained during a SeaBED AUV coral reef survey. Test tank results with ground truth are also presented to validate the methodology. / by Oscar Pizarro. / 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), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Corals are increasingly threatened by warming sea surface temperatures and other anthropogenic changes. The delicate symbiosis between corals and their algal endosymbionts (zooxanthellae) is easily disrupted by thermal stress, leading to bleaching and eventual mortality. The use of lipid ratios as biomarkers of environmental conditions is well established. Coral biomass contains abundant lipids, and the potential of lipid parameters to diagnose thermal tolerance in zooxanthellae has been previously suggested. In this thesis, I explore the response of specific fatty acids, sterols, and thylakoid membrane lipids to thermal and disease stress in zooxanthellae grown in culture, as well as those isolated from living corals. I present the discovery of a bioactive thylakoid lipid within zooxanthellae cells, and show how this compound is selectively mobilized in thermally stressed cells. I present a plausible mechanism for the breakdown of this compound into products that may cause apoptosis and disrupt the coral-algal symbiosis, eventually causing bleaching. I present two new lipid biomarkers of thermal stress in zooxanthellae, the C18 fatty acid unsaturation ratio, and the fatty acid to sterol ratio. I calibrate the decline of these two parameters to levels of thermal stress comparable to those needed to cause bleaching. I further show that these parameters are sensitive to pathogen stress as well. In several case studies of diseased and thermally stressed corals, I demonstrate that these lipid biomarkers of coral stress may be applied to zooxanthellae isolated from environmental samples. I show that these same compounds are preserved within coral aragonite, which opens up the potential to retrieve lipid-based historical records of coral health from annual layers of coral skeleton. This work demonstrates the value of using lipid biomarkers to assess coral health and better understand the biochemical mechanisms of coral bleaching. / by Jessie Mary Kneeland. / Ph.D.