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 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 (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 Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2006. / Includes bibliographical references (p. 155-169). / Hurricanes, powerful storms with wind speeds that can exceed 80 m/s, are one of the most destructive natural disasters known to man. While current satellite technology has made it possible to effectively detect and track hurricanes, expensive 'hurricane-hunting' aircraft are required to accurately classify their destructive power. Here we show that passive undersea acoustic techniques may provide a promising tool for accurately quantifying the destructive power of a hurricane and so may provide a safe and inexpensive alternative to aircraft-based techniques. It is well known that the crashing of wind-driven waves generates underwater noise in the 10 Hz to 10 kHz range. Theoretical and empirical evidence are combined to show that underwater acoustic sensing techniques may be valuable for measuring the wind speed and determining the destructive power of a hurricane. This is done by first developing a model for the acoustic intensity and mutual intensity in an ocean waveguide due to a hurricane and then determining the relationship between local wind speed and underwater acoustic intensity. / (cont.) Acoustic measurements of the underwater noise generated by hurricane Gert are correlated with meteorological data from reconnaissance aircraft and satellites to show that underwater noise intensity between 10 and 50 Hz is approximately proportional to the cube of the local wind speed. From this it is shown that it should be feasible to accurately measure the local wind speed and quantify the destructive power of a hurricane if its eye wall passes directly over a single underwater acoustic sensor. The potential advantages and disadvantages of the proposed acoustic method are weighed against those of currently employed techniques. It has also long been known that hurricanes generate microseisms in the 0.1 to 0.6 Hz frequency range through the non-linear interaction of ocean surface waves. Here we model microseisms generated by the spatially inhomogeneous waves of a hurricane with the non-linear wave equation where a second-order acoustic field is created by first-order ocean surface wave motion. We account for the propagation of microseismic noise through range-dependent waveguide environments from the deep ocean to a receiver on land. We compare estimates based on the ocean surface wave field measured in hurricane Bonnie with seismic measurements from Florida. / by Joshua David Wilson. / Ph.D.

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), 2006. / Includes bibliographical references (leaves 155-173). / A fundamental problem in limnology and oceanography is the inability to quickly identify and map distributions of plankton. This thesis addresses the problem by applying statistical machine learning to video images collected by an optical sampler, the Video Plankton Recorder (VPR). The research is focused on development of a real-time automatic plankton recognition system to estimate plankton abundance. The system includes four major components: pattern representation/feature measurement, feature extraction/selection, classification, and abundance estimation. After an extensive study on a traditional learning vector quantization (LVQ) neural network (NN) classifier built on shape-based features and different pattern representation methods, I developed a classification system combined multi-scale cooccurrence matrices feature with support vector machine classifier. This new method outperforms the traditional shape-based-NN classifier method by 12% in classification accuracy. Subsequent plankton abundance estimates are improved in the regions of low relative abundance by more than 50%. Both the NN and SVM classifiers have no rejection metrics. In this thesis, two rejection metrics were developed. / (cont.) One was based on the Euclidean distance in the feature space for NN classifier. The other used dual classifier (NN and SVM) voting as output. Using the dual-classification method alone yields almost as good abundance estimation as human labeling on a test-bed of real world data. However, the distance rejection metric for NN classifier might be more useful when the training samples are not "good" ie, representative of the field data. In summary, this thesis advances the current state-of-the-art plankton recognition system by demonstrating multi-scale texture-based features are more suitable for classifying field-collected images. The system was verified on a very large real-world dataset in systematic way for the first time. The accomplishments include developing a multi-scale occurrence matrices and support vector machine system, a dual-classification system, automatic correction in abundance estimation, and ability to get accurate abundance estimation from real-time automatic classification. The methods developed are generic and are likely to work on range of other image classification applications. / by Qiao Hu. / 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), 2007. / Includes bibliographical references (p. 73-76). / In order to overcome the challenges that an anisotropic noise field poses for underwater target tracking, we conduct an onboard estimation of the horizontal noise directionality in the real-time processing suite of an autonomous underwater vehicle (AUV) towing a horizontal line array. The estimation of the noise directionality is a precursor to another adaptive behavior: optimizing tracking capability of a towed array by choosing a particular heading that minimizes the detection level in the target's direction. In each distinct simulated anisotropic noise field, the AUV successfully calculates the optimal towed array headings based on the real-time estimation of the horizontal noise directionality. The findings reveal a clear advantage over the conventional broadside beam tracking method, with some limitations due predominantly to the noise field itself. / by Maria Alejandra Parra-Orlandoni. / S.M.

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), 2003. / Includes bibliographical references. / The presence of aqueous organic compounds derived from sedimentary organic matter has the potential to influence a range of chemical processes in hydrothermal vent environments. For example, hydrothermal alteration experiments indicate that alteration of organic-rich sediments leads to up to an order of magnitude more metals in solution than alteration of organic-poor basalt. This result is in contrast to traditional models for the evolution of vent fluids at sediment-covered mid-ocean ridge axis environments, and indicates the fundamental importance of including the effects of organic compounds in models of crustal alteration processes. However, in order to rigorously constrain their role in crustal alteration processes, quantitative information on the abundances and distributions of organic compounds in hydrothermal vent fluids is required. This thesis was undertaken to provide quantitative information on the distributions and stable carbon isotopic compositions of several low-molecular weight organic compounds (C1-C4 alkanes, C2-C3 alkenes, benzene and toluene) in fluids collected in July, 2000, at three sites on the northern Juan de Fuca Ridge: the Dead Dog and ODP Mound fields, which are located at Middle Valley, and the Main Endeavour Field, located on the Endeavour segment. At Middle Valley, the ridge axis is covered by up to 1.5 km of hemipelagic sediment containing up to 0.5 wt. % organic carbon. The Main Endeavour Field (MEF) is located approximately 70 km south of Middle Valley in a sediment-free ridge-crest environment, but previously measured high concentrations of NH3 and isotopically light CH4 relative to other bare-rock sites suggest that the chemical composition of these fluids is affected by sub-seafloor alteration of sedimentary material (LILLEY et al., 1993). / (cont.) Differences in the absolute and relative concentrations of NH3 and organic compounds and the stable carbon isotopic compositions of the C1-C3 organic compounds suggest that the three fields represent a continuum in terms of the extent of secondary alteration of the aqueous organic compounds, with the Dead Dog fluids the least altered, the MEF fluids the most altered and ODP Mound fluids in an intermediate state. At the two Middle Valley sites, the greater extent of alteration in the ODP Mound fluids as compared to the Dead Dog fluids is due either to higher temperatures in the subsurface reaction zone, or a greater residence time of the fluids at high temperatures. Higher reaction zone temperatures at the ODP Mound field than at the Dead Dog field are consistent with differences in endmember Cl concentrations between the two fields. The greater extent of alteration in the MEF fluids is caused by relatively oxidizing conditions in the subsurface reaction zone that promote faster reaction kinetics. Temperatures in the subsurface reaction zones calculated by assuming equilibrium among aqueous alkanes, alkenes and hydrogen are ... / by Anna M. Cruse. / Ph.D.