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 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.

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. / In the ocean, chromium (Cr) is a redox-sensitive trace metal. The reduction of Cr(VI) to Cr(III) occurs in oxygen deficient zones (ODZs), and Cr reduction in general has been identified as a significant Cr isotope fractionation mechanism. This thesis presents the first Cr isotope variations (653 Cr) in ODZs of the ocean and adds to the sparse Cr isotope data published for modern seawater. I developed a precise and accurate Cr isotope method for seawater samples. Seawater acidification converts total Cr to Cr(III) which is preconcentrated by Mg(OH) 2 coprecipitation. A three-column anion exchange chromatography scheme separates Cr from isobaric and polyatomic interferences present in the seawater and reagent matrixes. Isotope analysis is performed on a MC-ICP-MS IsoProbe. The addition of a 50Cr-54Cr double spike allows for accurate correction of procedural and instrumental Cr mass fractionations. The first Cr isotope ratio data for a full water column profile in the Pacific Ocean is presented. This station serves as a fully oxic counterpart to stations located within the ODZ of the Eastern Tropical North Pacific. At one station, Cr concentrations are lower and [delta]53Cr values are heavier within the ODZ. This is consistent with Cr reduction resulting in isotopically lighter, particle-reactive Cr(III), which is scavenged and exported from the water column. A strong correlation of [delta]53Cr and [delta]15 NNo3- at this station suggests that Cr reduction may be microbially mediated instead of simply being a product of thermodynamic equilibrium. Alternatively, Cr may be reduced by Fe(II). In the anoxic bottom waters of the Santa Barbara Basin a strong Cr reduction signal (lower [Cr], heavier [delta]53Cr) is observed, which may result from the same aforementioned Cr reduction mechanisms. A shift to the heaviest seawater Cr isotope signatures yet observed was detected in the oxic bottom waters of the shallow Arctic Chukchi shelf, while Cr concentrations decreased. This extreme isotope signal may result from Cr reduction by a reduced species (e.g. Fe(II)), which was released from the underlying anoxic shelf sediments. Cr in the Atlantic layer and in the bottom water of a central Arctic station appears to be shaped by a novel, unidentified process. / by Simone Beatrice Moos. / 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), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Microorganisms play a central role mediating biogeochemical cycles in the ocean. Marine dissolved organic matter (DOM) - a reservoir of organic solutes and colloids derived from plankton is a major source of carbon, nutrients, and energy to microbial communities. The biological transformation and remineralization of DOM sustains marine productivity by linking the microbial food web to higher trophic levels (the microbial loop) and exerts important controls over the cycles of carbon and bioessential elements, such as nitrogen and phosphorus, in the sea. Yet insight into the underlying metabolism and reactions driving the degradation of DOM is limited partly because its exact molecular composition is difficult to constrain and appropriate microbial model systems known to decompose marine DOM are lacking. This thesis identifies marine microorganisms that can serve as model systems to study the metabolic pathways and biochemical reactions that control an important ecosystem function, DOM turnover. To accomplish this goal, bacterial isolates were obtained by enriching seawater in dilution-to-extinction culturing experiments with a natural source of DOM, specifically, the high molecular weight (HMW) fraction (>1 kDa nominal molecular weight) obtained by ultrafiltration. Because it is relatively easy to concentrate and it is fairly uniform in its chemical composition across the global ocean and other aquatic environments, HMW DOM has the potential to serve as a model growth substrate to study the biological breakdown of DOM. The phylogeny, genomes, and growth characteristics of the organisms identified through this work indicate that HMW DOM contains bioavailable substrates that may support widespread microbial populations in coastal and open-ocean environments. The availability of ecologically relevant isolates in culture can now serve to test hypothesis emerging from cultivation-independent studies pertaining the potential role of microbial groups in the decomposition of organic matter in the sea. Detailed studies of the biochemical changes exerted on DOM by selected bacterial strains will provide new insight into the processes driving the aerobic microbial food chain in the upper ocean. / by Oscar Abraham Sosa. / 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. / Holes and channels were excavated in the surf zone on an ocean beach near Duck, NC, and observations of the subsequent evolution of waves, currents, and the modified seafloor were used to investigate nearshore dynamics. In one set of seafloor perturbation experiments, deep holes with steeply sloping sides were excavated in the inner surfzone seafloor. Observations of the infilling holes were used to make the first field estimates of the surfzone morphological diffusivity, which describes the rate of seafloor smoothing by downslope sediment transport. To improve the temporal resolution of bathymetric estimates, a mapping method was developed to combine infrequent, spatially dense watercraft surveys with continuous, spatially sparse in situ altimeter estimates of the seafloor location. In another set of seafloor perturbation experiments, channels were dredged across the surf zone with the propellers of a landing craft. Alongshore variations in wave breaking caused by the perturbed bathymetry resulted in strong rip currents in the channels under some conditions, whereas alongshore currents bypassed the channels under other conditions. The dynamics of the circulation response for changing wave forcing, bathymetry, and tidal elevation are investigated using the observations, a numerical model, and a parameter based on wave properties and bathymetry. / by Melissa Moulton. / 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), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / To understand how waves and sea level shape sandy shoreline profiles, I use existing energetics-based equations of cross-shore sediment flux to describe shoreface evolution and equilibrium profiles, utilizing linear Airy wave theory instead of shallow-water wave assumptions. By calculating a depth-dependent characteristic diffusivity timescale, I develop a morphodynamic depth of shoreface closure for a given time envelope, with depth increasing as temporal scale increases. To assess which wave events are most important in shaping the shoreface in terms of occurrence and severity, I calculate the characteristic effective wave conditions for both cross-shore and alongshore shoreline evolution. Extreme events are formative in the cross-shore shoreface evolution, while alongshore shoreline evolution scales linearly with the mean wave climate. Bimodal distributions of weighted wave heights are indicative of a site impacted more frequently by tropical storms rather than extra-tropical storms. To understand how offshore wave climate and underlying geometry of a carbonate reef platform shapes evolution of atolls, I simulate the hydrodynamics of a simplified reef flat, using XBeach, a two-dimensional model of infragravity wave propagation. The reef flat self-organizes to a specific width and water depth depending on the offshore wave climate and characteristics of the available sediment. Formation of a sub-aerial landmass, like a motu, can be initiated by a change in offshore wave climate (like a storm), which can create a nucleation site from mobilization and deposition of coarse sediment on the reef flat. Once a motu is present, the shoreline should prograde until reaching a critical reef-flat width. Our conceptual model of reef-flat evolution and motu formation is governed by understanding the hydrodynamics of the system and subsequent response of sediment transport. / by Alejandra C. Ortiz. / Ph. D.

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), 2016. / 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 209-225). / Identifying and tracking an unknown linear system from observations of its inputs and outputs is a problem at the heart of many different applications. Due to the complexity and rapid variability of modern systems, there is extensive interest in solving the problem with as little data and computation as possible. This thesis introduces the novel approach of reducing problem dimension by exploiting statistical structure on the input. By modeling the input to the system of interest as a graph-structured random process, it is shown that a large parameter identification problem can be reduced into several smaller pieces, making the overall problem considerably simpler. Algorithms that can leverage this property in order to either improve the performance or reduce the computational complexity of the estimation problem are developed. The first of these, termed the graphical expectation-maximization least squares (GEM-LS) algorithm, can utilize the reduced dimensional problems induced by the structure to improve the accuracy of the system identification problem in the low sample regime over conventional methods for linear learning with limited data, including regularized least squares methods. Next, a relaxation of the GEM-LS algorithm termed the relaxed approximate graph structured least squares (RAGS-LS) algorithm is obtained that exploits structure to perform highly efficient estimation. The RAGS-LS algorithm is then recast into a recursive framework termed the relaxed approximate graph structured recursive least squares (RAGS-RLS) algorithm, which can be used to track time-varying linear systems with low complexity while achieving tracking performance comparable to much more computationally intensive methods. The performance of the algorithms developed in the thesis in applications such as channel identification, echo cancellation and adaptive equalization demonstrate that the gains admitted by the graph framework are realizable in practice. The methods have wide applicability, and in particular show promise as the estimation and adaptation algorithms for a new breed of fast, accurate underwater acoustic modems. The contributions of the thesis illustrate the power of graphical model structure in simplifying difficult learning problems, even when the target system is not directly structured. / by Atulya Yellepeddi. / 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 (p. 191-202). / Melting and crystallization processes on the Earth and Moon are explored in this thesis, and the topics of melt generation, transport, and crystallization are discussed in three distinct geologic environments: the Moon's mantle, the Greenland ice sheet, and the Earth's crust. Experiments have been conducted to determine the conditions of origin for two high-titanium magmas from the Moon. The lunar experiments (Chapter 2) were designed to explore the effects of variable oxygen fugacity (fo₂) on the high pressure and high temperature crystallization of olivine and orthopyroxene in high-Ti magmas. The results of these experiments showed that the source regions for the high-Ti lunar magmas are distributed both laterally and vertically within the lunar mantle, and that it is critical to estimate the pre-eruptive oxygen fugacity in order to determine true depth of origin for these magmas within the lunar mantle. Chapter 3 models the behavior of water flow through the Greenland ice sheet driven by hydrofracture of water through ice. The results show that melt water in the ablation zone of Greenland has almost immediate access to the base of the ice sheet in areas with up two kilometers of ice. Chapter 4 is an experimental study of two hydrous high-silica mantle melts from the Mt. Shasta, CA region. Crystallization is simulated at H₂O saturated conditions at all crustal depths, and a new geobarometer-hygrometer based on amphibole magnesium number is calibrated. In Chapter 5 I use the new barometer to study a suite of mafic enclaves from the Mt. Shasta region, and apply it to amphiboles in these enclaves. Evidence for pre-eruptive H₂O contents of up to 14 wt% is presented, and bulk chemical analyses of the inclusions are used to show that extensive magma mixing has occurred at all crustal depths up to 35 km beneath Mt. Shasta. / by Michael James Krawczynski. / Ph.D.

Thesis: Ph. D., Joint Program in Oceanography (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2014. / 122 / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 149-158). / Understanding the fate of primary production in the ocean is a challenging task because once produced, organic material is oxidized over timescales which range from minutes, to millions of years. This timescale diversity is matched by an equal heterogeneity in both the local physical and chemical environment. In this thesis we explore the relationship between the distinct reservoirs of organic carbon in the ocean and their underlying complexity. First, we show how the heterogeneity of portions of the carbon cycle can be packaged in terms of age structured models and their accompanying age and rate distributions. We further relate the moments of the rate distributions to bulk reservoir properties like average age and flux. Explicit relationships are then derived for the specific case of a single turnover time and a lognormal distribution. We apply these ideas to the problem of dissolved organic carbon (DOC) cycling in the ocean. Current models of bulk concentration and isotope data suggest a microbially sourced DOC reservoir consisting of two components. A nearly homogeneous background component with a long turnover time (> 6000 years) is joined by a component of fast turnover time (~ 1 year) and equal concentration in the surface ocean. We confirm the presence of isotopically enriched, modern DOC co-cycling with an isotopically depleted older fraction in the upper ocean. However, our results show that up to 30% of the deep DOC reservoir is modern and supported by a 1 Pg per year carbon flux, ten times higher than inferred from bulk isotope measurements. Isotopically depleted material turns over at an apparent time scale of 30, 000 years, far slower than indicated by bulk isotope measurements. These results are consistent with global DOC measurements and explain both the fluctuations in deep DOC concentration and the anomalous radiocarbon values of DOC in the Southern Ocean. Finally, the thesis explores methods for determining the validity of diffusion limitation as the mechanism behind the power-law slowdown in organic remineralization in sediment. We find that diffusion limitation connects the decay behavior of organic material to the correlations found between mineral surface area and organic matter content in sediments. / by Christopher L. Follett. / Ph. D.