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), 2005. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Bibliography: leaves 292-301. / This thesis investigates the application of acoustic measurements in the deep and shallow ocean to infer the sound velocity profile (svp) in the seabed. For the deep water ocean, an exact method based on the Gelfand-Levitan integral equation is evaluated. The input data is the complex plane-wave refection coefficient estimated from measurements of acoustic pressure in water. We apply the method to experimental data and estimate both the refection coefficient and the seabed svp. A rigorous inversion scheme is hence applied in a realistic problem. For the shallow ocean, an inverse eigenvalue technique is developed. The input data are the eigenvalues associated with propagating modes, measured as a function of source receiver range. We investigate the estimation of eigenvalues from acoustic fields measured in laterally varying environments. We also investigate the errors associated with estimating varying modal eigenvalues, analogous to the estimation of time-varying frequencies in multicomponent signals, using time-varying autoregressive (TVAR) methods. We propose and analyze two AR sequential estimators, one for model coefficients, another for the zeros of the AR characteristic polynomial. / (cont.) The decimation of the pressure field defined in a discrete range grid is analyzed as a tool to improve AR estimation. The nonlinear eigenvalue inverse problem of estimating the svp from a sequence of eigenvalues is solved by iterating linearized approximations. The solution to the inverse problem is proposed in the form of a Kalman filter. The resolution and variance of the eigenvalue inverse problem are analyzed in terms of the Cramer-Rao lower bound and the Backus{Gilbert (BG) resolution theory. BG theory is applied to the design of shallow-water experiments. A method is developed to compensate for the Doppler deviation observed in experiments with moving sources. / by Luiz Alberto Lopes de Souza. / Ph.D.

Thesis (Ph. D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references (p. 177-186). / Observations of current velocity, temperature, salinity and pressure from a 2-year moored array deployment and four hydrographic cruises conducted by the United States Southern Ocean GLOBEC program on the western Antarctic Peninsula continental shelf are used to characterize the ocean circulation and its connection to fresh water and heat fluxes on the shelf. Mean velocities on the shelf are of the order of 5 cm/s or less. Tidal motions are dominated by the M2 and S2 semi-diurnal tides and the 01 and K1 diurnal tides, although the tidal velocities are typically less than 2 cm/s. Near-inertial motions are relatively large, with current velocities as high as 26 cm/s. It is shown that Marguerite Trough, a large bathymetric feature connecting the shelf-break to Marguerite Bay, plays a critical role in determining the circulation. The mean flow is strongly steered in the along-slope direction, and the tidal currents also show increasing current polarization at depth in Marguerite Trough. At time-scales of 5 to 20 days, the observations show bottom-intensified motion in Marguerite Trough consistent with bottom-trapped topographic Rossby waves. / (cont.) The subtidal circulation in the trough has a significant wind-driven component in Marguerite Trough, with downwelling-favorable winds forcing cross-shelf flow on the northern side of the trough and along the shore on the outer shelf. Upwelling-favorable winds force roughly the opposite circulation. The cyclonic circulation on the trough helps advect blobs of salty, warm and nutrient-rich water across the shelf. These intrusions are small (;4 km) and frequent (4 events/month). Also, the Antarctic Peninsula Coastal Current (APCC), a coastal buoyant current which is described for the first time here. The APCC is a seasonal current which is only present during the ice-free season and is forced by freshwater fluxes associated with large glacier melt and precipitation rates in the region. / by Carlos F. Moffat Varas. / Ph.D.

Thesis (S.M.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 111-112). / Over the past 20 years, underwater vehicle technology has undergone drastic improvements, and vehicles are quickly gaining popularity as a tool for numerous oceanographic tasks. Systems used on the vehicle to alter buoyancy, or variable buoyancy (VB) systems, have seen only minor improvements during the same time period. Though current VB systems are extremely robust, their lack of performance has become a hinderance to the advancement of vehicle capabilities. This thesis first explores the current status of VB systems, then creates a model of each system to determine performance. Second, in order to quantitatively compare fundamentally different VB systems, two metrics, [beta]m and [beta]vol, are developed and applied to current systems. By determining the ratio of performance to size, these metrics give engineers a tool to aid VB system development. Finally, the fundamental challenges in developing more advanced VB systems are explored, and a couple of technologies are investigated for their potential use in new systems. / by Harold Franklin Jensen III. / 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), 1998. / Includes bibliographical references. / by Youngsook Huh. / 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. / Onshore sediment transport and sandbar migration are important to the morphological evolution of beaches, but are not understood well. Here, a new model that accounts for accelerations of wave-orbital velocities predicts onshore sandbar migration observed on an ocean beach. In both the observations and the model, the location of the maximum acceleration-induced transport moves shoreward with the sandbar, resulting in feedback between waves and morphology that drives the bar shoreward until conditions change. A model that combines the effects of transport by waves and mean currents simulates both onshore and offshore bar migration observed over a 45-day period. A stochastic nonlinear Boussinesq model for the evolution of waves in shallow water is coupled with the wave-acceleration-driven sediment transport model to predict observed onshore sediment transport and sandbar migration given observations of the offshore wave field and initial bathymetry. The Boussinesq-wave model has skill in predicting wave spectra, as well as velocity and acceleration statistics across the surfzone, but it underpredicts acceleration skewness on top of the sandbar. As a result, the coupled wave-sediment transport model underpredicts sediment transport, and thus fails to move the sandbar onshore. Although the coupled wave and sediment model can be tuned to yield skillful predictions of onshore sandbar migration, in general, closer agreement between observed and modeled statistics of the wave field is essential for the successful application of wave models to predict sediment transport. / by Fernanda Gemael Hoefel. / 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. 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 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.