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, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references. / Paralytic shellfish poisoning (PSP) is a human intoxication associated with the consumption of shellfish contaminated with a family of neurotoxins called saxitoxins. Many species in the dinoflagellate genus Alexandrium have been shown to produce these toxins. Here I report the first case of a culture of Alexandrium that has completely lost the ability to produce saxitoxins. The loss of toxicity was accompanied by a reduction in growth capability. A subculture of this isolate maintains the ability to produce toxins and to grow at rates and to cell abundances that were characteristic of the original Alexandrium culture. The growth and toxicity differences in the two isolates were demonstrated to be a property of the dinoflagellate itself and were not dependent on the different bacterial symbionts associated with each culture. The pair of subcultures is a novel experimental system to study gene expression related to toxin production and growth in dinoflagellates. The products of gene expression were analyzed in the two subcultures of Alexandrium grown under the same conditions, but where toxicity and growth differ. At the metabolome level, compounds were identified that were unique to the non-toxic isolate; their emergence may be correlated to a disruption of the biosynthetic pathway for PSP toxins. / (cont.) These compounds share some characteristics and potential structural similarities with saxitoxins, though they are not any of the known toxin derivatives. Difference gel electrophoresis (DIGE) identified proteins differentially expressed between the two subcultures. Identification of some of these proteins was possible by searching the expressed sequence tag (EST) database for dinoflagellates. Proteins shown to be down-regulated in the non-toxic, slower growing subculture are all enzymes from the Calvin cycle, which may explain the limited growth of the non-toxic isolate. Other unknown, differentially expressed proteins may relate to the loss of toxicity, but their identity and function remain unresolved. / by Claudia A. Martins. / 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 (v. 2, leaves 211-215). / In recent years the focus of passive detection and localization of submarines has moved from the deep ocean into the littoral regions. the problem of passive detection in these regions is complicated by strong multipath propagation with high transmission loss. Large aperture planar arrays have the potential to improve detection performance due to their high resolution and high gain, but are suceptible to two main performance degradation mechanisms: limited spatial coherence of signals and nonstationarity of high bearing rate interference sources common in littoral regions of strategic importance. This thesis presents subarray processing as a method of improving passive detection performance using such large arrays. This thesis develops statistical models for the detection of performance of three adaptive, sample-covariance-based subarray processing algorithms which incorporate the effects of limited spatial coherence as well as finite snapshot support. The performance of the optimum processor conditioned on known data coveriances is derived as well for comparison. These models are then used to compare subarray algorithms and partitioning schemes in a variety of interference environments using plane wave and matched-field propagation models. / (cont.) The analysis shows a tradeoff between the required adaptive degrees of freedom, snapshot support, and adaptive resolution. This thesis shows that for both plane-wave and matched-field processing, the Conventional-Then-Adaptive (CTA) algorithm optimizes this tradeoff most efficiently. Finally, a comparison of the CTA algorithm to beam-space adaptive processing shows that for moderate beam coverage, the subarray algorithm performs as well as or superior to the adaptive beamspace algorighm. / by Jennifer Anne Watson. / 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 (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), 2006. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (leaf 75). / This thesis explores the feasibility of making wind speed profile measurements from an oceanographic buoy using a Doppler sodar. In the fall of 2005, we deployed a Scintec SFAS sodar on an ASIS buoy. Roughly one week of buoy motion data and one day of sodar observations were collected. Data from both this deployment, and the Martha's Vineyard Coastal Observatory, were used in conjunction with models to predict sodar performance. Results are compared for an ASIS and a 3-meter discus buoy. We also predict the yearly average probability of sodar data availability in the presence of buoy motion. We show that buoy tilting in response to wave forcing is the main factor affecting sodar performance. Our results strongly suggest that ASIS is a suitable platform for sodar measurements at sea. / by Allison M. Berg. / S.M.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2006. / Includes bibliographical references (leaves 209-213). / In this thesis, an innovative architecture for real-time adaptive and cooperative control of autonomous sensor platforms in a marine sensor network is described in the context of the autonomous oceanographic network scenario. This architecture has three major components, an intelligent, logical sensor that provides high-level environmental state information to a behavior-based autonomous vehicle control system, a new approach to behavior-based control of autonomous vehicles using multiple objective functions that allows reactive control in complex environments with multiple constraints, and an approach to cooperative robotics that is a hybrid between the swarm cooperation and intentional cooperation approaches. The mobility of the sensor platforms is a key advantage of this strategy, allowing dynamic optimization of the sensor locations with respect to the classification or localization of a process of interest including processes which can be time varying, not spatially isotropic and for which action is required in real-time. Experimental results are presented for a 2-D target tracking application in which fully autonomous surface craft using simulated bearing sensors acquire and track a moving target in open water. / (cont.) In the first example, a single sensor vehicle adaptively tracks a target while simultaneously relaying the estimated track to a second vehicle acting as a classification platform. In the second example, two spatially distributed sensor vehicles adaptively track a moving target by fusing their sensor information to form a single target track estimate. In both cases the goal is to adapt the platform motion to minimize the uncertainty of the target track parameter estimates. The link between the sensor platform motion and the target track estimate uncertainty is fully derived and this information is used to develop the behaviors for the sensor platform control system. The experimental results clearly illustrate the significant processing gain that spatially distributed sensors can achieve over a single sensor when observing a dynamic phenomenon as well as the viability of behavior-based control for dealing with uncertainty in complex situations in marine sensor networks. / by Donald Patrick Eickstedt. / 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), 2004. / Includes bibliographical references. / This study is a geochemical investigation into the accretion of lower oceanic crust and processes of shallow melt-rock reaction at mid-ocean ridges. Major-, trace-elements, and isotopes from whole-rocks and minerals from the Lyngen Gabbro, a 480-My old dismembered ophiolite from the Scandinavian Caledonides, indicate that this igneous complex was produced from hydrous supra-subduction zone magmas, a remnant of an incipient ocean-arc. Such ophiolites are better models for the structural evolution than the geochemical evolution of the lower oceanic crust at mid-ocean ridges. Minerals in gabbros from Atlantis Bank, Southwest Indian Ridge, a modern, in-situ example of lower ocean-crust, were analyzed for major and trace-elements. The MELTS algorithm indicates that these gabbros formed by near-fractional crystallization at mid-crustal pressures. The gabbroic crust is more evolved than the lavas and represents melts fractionated 50-95% relative to a mantle-derived melt-composition, supported by trace-element models. This argues against the often-cited gabbro-glacier accretion model, where mantle-derived melts are transported to a shallow melt-lens and fractionates there before eruption. There remain >770-m of additional primitive cumulates below 1500-m deep Hole 735B or within the underlying mantle. Thus, the seismic Moho, beneath Hole 735B, could be the crust-mantle boundary, rather than an alteration front as suggested elsewhere. The Atlantis Bank gabbros have augites that are more primitive than plagioclases and olivines with which they coexist. Melt-rock interaction, where ascending melts dissolve the pre-existing gabbroic rocks and create hybrid magma may have caused this. Dissolution-experiments for plagioclase-olivine and plagioclase-augite mineral pairs / (cont.) were performed at 1180⁰-1330⁰C and 20-min - 24hrs. Dissolution occurs rapidly and out of equilibrium, with the dissolution rates dependent on the [delta]T above the solidus. Rocks with small grain-boundary areas (coarse grained or nearly mono-mineralic) heat internally when enclosed in hot magma, causing xenoliths or wall-rock to melt and disaggregate. The dissolution-derived magma crystallizes minerals more refractory-looking than the melts that precipitated the original gabbroic rocks. Assimilation of gabbroic rocks increases the Na content and decreases the Fe content of the melt that digests it, thus basaltic glasses formed after this hybridization will falsely reflect a lower degree and pressure of mantle melting. / by Astri Jæger Sweetman Kvassnes. / Ph.D.