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.

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/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 173-186). / This thesis investigates the long-term evolution of rift-bounding normal faults. To first order, the observed diversity of extensional tectonic styles reflects differences in the maximum offset that can be accommodated on individual faults during their life span. My main objective is to develop a theoretical framework that explains these differences in terms of a few key mechanical and geological controls. I start by laying out the energy cost associated with slip on a normal fault, which consists of (1) overcoming the frictional resistance on the fault, (2) bending the faulted layer and (3) sustaining the growth of topography. In Chapter 2, I propose that flexural rotation of the active fault plane enables faults to evolve along a path of minimal energy, thereby enhancing their life span. Flexural rotation occurs more rapidly in thinner faulted layers, and can potentially explain the wide range of normal fault dips documented with focal mechanisms. In Chapter 3, I show that surface processes can enhance the life span of continental normal faults by reducing the energy cost associated with topography buildup. In Chapter 4, I focus on lithospheric bending induced by fault growth, which is well described by elasto-plastic flexure models. I demonstrate that numerical models that treat the lithosphere as a visco-plastic solid can properly predict fault evolution only when the rate-dependent viscous flexural wavelength of the lithosphere is accommodated within the numerical domain. In Chapter 5, I consider the interplay of faulting and crustal emplacement at a slow mid-ocean ridge. I show that a depth-variable rate of magma emplacement can reconcile the formation of long-lived detachment faults, which requires a moderate melt supply, and the exhumation of large volumes of lower crustal material. Finally, in Chapter 6 I investigate the three-dimensional interactions between normal faults in a lithosphere of varying thickness. I suggest that large along-axis gradients in lithospheric thickness can prevent the growth of continuous faults along-axis, and instead decouple the modes of faulting at the segment center and at the segment end. / by Jean-Arthur Louis Olive. / Ph. D.

Thesis (S.M.)--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), 2005. / Includes bibliographical references (leaves 120-121). / This thesis develops and utilizes a method for analyzing data from the North Pacific Acoustic Laboratory's (NPAL) Basin Acoustic Seamount Scattering Experiment (BASSEX). BASSEX was designed to provide data to support the development of analytical techniques and methods which improve the understanding of sound propagation around underwater seamounts. The depth-dependent sound velocity profile of typical ocean waveguides force sound to travel in convergence zones about a minimum sound speed depth. This ducted nature of the ocean makes modeling the acoustic field around seamounts particularly challenging, compared to an isovelocity medium. The conical shape of seamounts also adds to the complexity of the scatter field. It is important to the U.S. Navy to understand how sound is diffracted around this type of topographic feature. Underwater seamounts can be used to conceal submarines by absorbing and scattering the sound they emit. BASSEX measurements have characterized the size and shape of the forward scatter field around the Kermit-Roosevelt Seamount in the Pacific Ocean. Kermit-Roosevelt is a large, conical seamount which shoals close to the minimum sound speed depth, making it ideal for study. Acoustic sources, including M-sequence and linear frequency-modulated sources, were stationed around the seamount at megameter ranges. A hydrophone array was towed around the seamount to locations which allowed measurement of the perturbation zone. Results from the method developed in this thesis show that the size and shape of the perturbation zone measured coincides with theoretical and experimental results derived in previous work. / by Joseph J. Sikora, III. / S.M.