Thesis (Ph. D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; 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. / Includes bibliographical references. / The goals of this thesis were to quantify the behavior of gastropod larvae (mud snails Ilyanassa obsoleta) in turbulence, and to investigate how that behavior affects larval supply in a turbulent coastal inlet. Gastropod larvae retract their velums and sink rapidly in strong turbulence. Turbulence-induced sinking would be an adaptive behavior if it resulted in increased larval supply and enhanced settlement in suitable coastal habitats. In laboratory experiments, mud snail larvae were found to have three behavioral modes: swimming, hovering, and sinking. The proportion of sinking larvae increased exponentially with the turbulence dissipation rate over a range comparable to turbulence in a tidal inlet, and the mean larval vertical velocity shifted from upward to downward in turbulence resembling energetic nearshore areas. The larval response to turbulence was incorporated in a vertical advection-diffusion model to characterize the effects of this behavior on larval supply and settlement in a tidal channel. Compared to passive larvae, larvae that sink in turbulence have higher near-bed concentrations throughout flood and ebb tides. / (cont.) This high larval supply enables behaving larvae to settle more successfully than passive larvae in strong currents characteristic of turbulent tidal inlets. A study was conducted at Barnstable Harbor, MA to estimate the responses of larvae to turbulence in the field. Gastropod larvae from different coastal environments had genus-specific responses to turbulence, suggesting that larvae use turbulence for large-scale habitat selection. On ebb tides, mud snail larvae had a similar response to turbulence as in the laboratory, with greater sinking velocities in strong turbulence. Behavior estimates differed for flood and ebb tides, indicating that additional physical cues influence behavior. Turbulence-induced sinking behavior would enhance retention and promote settlement of mud snail larvae in habitats like Barnstable Harbor. / by Heidi L. Fuchs. / Ph.D.

Includes bibliographical references (p. 259-261). / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / 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), 2007. / In this thesis, a numerically effcient three-dimensional propagation and scattering model is developed based on the three-dimensional coupled mode theory for axisymmetric bathymetry. The three-dimensional coupled mode approach applied in this thesis is fundamentally identical to the one applied in earlier models, such as the one presented by Taroudakis [20]. Thus, it is based on a Fourier expansion of the acoustic field around a seamount, with each azimuthal expansion coefficient being represented by a two-way coupled mode formulation. However, earlier formulations were severely limited in terms of frequency, size and geometry of the seamount, the seabed composition, and the distance between the source and the seamount, and are totally inadequate for modeling high-frequency, large-scale seamount problems. By introducing a number of changes in the numerical formulation and using a standard normal mode model (C-SNAP) for determining the fundamental modal solutions and coupling coefficients, orders of magnitude improvement in efficiency and fidelity has been achieved, allowing for realistic propagation and scattering scenarios to be modeled, including effects of seamount roughness and realistic sedimentary structure. / (cont.) Also, by the simple superposition principle, the computational requirements are made independent of the distance between the seamount and the source and receivers, and dependent only on the geometry of the seamount and the frequency of the source. First, this thesis investigates the scattering from a cylindrical island, which is the simplest case of a conical seamount problem. Our model, using the superposition method, can solve the cylindrical problem in Athanassoulis and Prospathopoulos's paper [3] with the same accuracy while saving about 4/5 computational effort. Second, this thesis demonstrates the spectral coupled mode approach, which includes a two-way coupled mode model and a superposition representation of the field. Third, this thesis applies the three-dimensional model to investigate some physics issues of three-dimensional seamount scattering. As a result of the investigation, we learn that the Nx2D model is a poor approximation of the true three-dimensional model when the three-dimensional effects are significant, though it is a good approximation of the three-dimensional model otherwise. The convergence of the model in terms of the seamount discretization is also discussed and demonstrated. / (cont.) Finally, our three-dimensional spectral coupled mode model is tested by the application of the Kermit Seamount problem with realistic ocean environmental data from the 2004 BASSEX experiment. / by Wenyu Luo. / Ph.D.

Thesis (Ph. D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references. / Surfzone wave height transformation and wave-breaking-driven increases in the mean sea level (setup) are examined on alongshore-uniform beaches with alongshore homogeneous and inhomogeneous wave forcing. While previously derived models predict wave heights adequately (root-mean-square errors typically less than 20%), the models can be improved by tuning a free parameter or by using a new parameterization based on the deep-water wave height. Based on a sensitivity analysis of the cross-shore momentum balance used to predict setup, a one-dimensional (1-D) model is developed that includes wave rollers and bottom stress owing to the mean offshore-directed flow. The model predicts setup accurately at three alongshore homogeneous field sites, as well as at a site where the incident wave field is alongshore non-uniform, suggesting that setup is driven primarily by the cross-shore (1-D) forcing. Furthermore, alongshore gradients of setup can be important to driving alongshore flows in the surfzone, and the 1-D setup model predicts these gradients accurately enough to simulate the observed flows. / by Alex Apotsos. / 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), 2009. / Includes bibliographical references (p. 275-284). / This research presents a parallel hypothesis method for autonomous underwater vehicle navigation that enables a vehicle to expand the operating envelope of existing long baseline acoustic navigation systems by incorporating information that is not normally used. The parallel hypothesis method allows the in-situ identification of acoustic multipath time-of-flight measurements between a vehicle and an external transponder and uses them in real-time to augment the navigation algorithm during periods when direct-path time-of-flight measurements are not available. A proof of concept was conducted using real-world data obtained by the Woods Hole Oceanographic Institution Deep Submergence Lab's Autonomous Benthic Explorer (ABE) and Sentry autonomous underwater vehicles during operations on the Juan de Fuca Ridge. This algorithm uses a nested architecture to break the navigation solution down into basic building blocks for each type of available external information. The algorithm classifies external information as either line of position or gridded observations. For any line of position observation, the algorithm generates a multi-modal block of parallel position estimate hypotheses. The multimodal hypotheses are input into an arbiter which produces a single unimodal output. If a priori maps of gridded information are available, they are used within the arbiter structure to aid in the elimination of false hypotheses. / (cont.) For the proof of concept, this research uses ranges from a single external acoustic transponder in the hypothesis generation process and grids of low-resolution bathymetric data from a ship-based multibeam sonar in the arbitration process. The major contributions of this research include the in-situ identification of acoustic multipath time-of-flight measurements, the multiscale utilization of a priori low resolution bathymetric data in a high-resolution navigation algorithm, and the design of a navigation algorithm with a flexible architecture. This flexible architecture allows the incorporation of multimodal beliefs without requiring a complex mechanism for real-time hypothesis generation and culling, and it allows the real-time incorporation of multiple types of external information as they become available in situ into the overall navigation solution. / by Cara Elizabeth Grupe LaPointe. / 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), 2008. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (p. 79-83). / Oceanographic applications of robotics are as varied as the undersea environment itself. As underwater robotics moves toward the study of dynamic processes with multiple vehicles, there is an increasing need to distill large volumes of data from underwater vehicles and deliver it quickly to human operators. While tethered robots are able to communicate data to surface observers instantly, communicating discoveries is more difficult for untethered vehicles. The ocean imposes severe limitations on wireless communications; light is quickly absorbed by seawater, and tradeoffs between frequency, bitrate and environmental effects result in data rates for acoustic modems that are routinely as low as tens of bits per second. These data rates usually limit telemetry to state and health information, to the exclusion of mission-specific science data. In this thesis, I present a system designed for communicating and presenting science telemetry from untethered underwater vehicles to surface observers. The system's goals are threefold: to aid human operators in understanding oceanographic processes, to enable human operators to play a role in adaptively responding to mission-specific data, and to accelerate mission planning from one vehicle dive to the next. The system uses standard lossy compression techniques to lower required data rates to those supported by commercially available acoustic modems (O(10) - O(100) bits per second). / (cont.) As part of the system, a method for compressing time-series science data based upon the Discrete Wavelet Transform (DWT) is explained, a number of low-bitrate image compression techniques are compared, and a novel user interface for reviewing transmitted telemetry is presented. Each component is motivated by science data from a variety of actual Autonomous Underwater Vehicle (AUV) missions performed in the last year. / by Christopher Alden Murphy. / S.M.

Thesis (S.M. in Oceanographic Engineering)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution); and, (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1998. / Includes bibliographical references (leaves 74-78). / The thesis presents data processing schemes for extracting Earth-referenced current velocity from relative current velocity measurement made by an Acoustic Doppler Current Profiler (ADCP) borne by an Autonomous Underwater Vehicle (AUV). Compared with conventional approaches, current profiling from an AUV platform has advantages including three-dimensional mobility, rapid response, high-level intelligent control, independence from ship motion and weather constraint, and shallow water operation. First, an acausal postprocessing scheme is presented for estimating the AUV's own velocity and removing it from the relative velocity measurement to obtain the true current velocity. Then, a causal scheme for estimating the Earth-referenced current velocity is presented. The causal algorithm is based on an Extended Kalman Filter (EKF) that utilizes the hydrodynamics connecting current velocity to vehicle's motion. In both methods, the raw ADCP measurement is corrected to achieve more accurate current velocity estimate. Field data from the Haro Strait Tidal Front Experiment are processed by both methods. Current velocity estimation results reveal horizontal and vertical velocity structure of the tidal mixing process, and are also consistent with the vehicle's deviated trajectory. The capability of the AUV-borne current profiling system is thus demonstrated. / by Yanwu Zhang. / S.M.in Oceanographic Engineering

Thesis (S.M. in Oceanographic Engineering)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 1999. / Includes bibliographical references (leaves 85-89). / by Qiang Wang. / S.M.in Oceanographic Engineering

Thesis (S.M.)--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), 2004. / Includes bibliographical references (p. 37-40). / Laterally extensive, well-developed clinoforms have been mapped in Early Cretaceous deposits located in the northeastern 27,000 km2 of the Colville Basin, North Slope of Alaska. Using public domain 2-D seismic data, well logs, core photographs, and grain size data, depositional geometries within the Nanushuk and Torok formations were interpreted in order to constrain the transport conditions associated with progradation of the shoreline and construction of the continental margin out of detritus shed from the ancestral Brooks Range. Using STRATA, a synthetic stratigraphic modeling package, constructional clinoform geometries similar to those preserved in the North Slope clinoform volume (32,400 km3) were simulated. Sediment flux, marine and nonmarine diffusivities, and basin subsidence were systematically varied until a match was found for the foreset and topset slopes, as well as progradation rates over a 6 million year period. The ability of STRATA to match the seismically interpreted geometries allows us to constrain measures of possible water and sediment discharges consistent with the observed development of the Early Cretaceous clinoform suite. Simulations indicate that, in order to reproduce observed geometries and trends using constant input parameters, the subsidence rate must be very small, only a fraction of the most likely rate calculated from the seismic data. Constant sediment transport parameters can successfully describe the evolution of the prograding margin only in the absence of tectonic subsidence. However, further work is needed to constrain the absolute magnitude of these values and determine a unique solution for the NPR-A clinoforms. / by Christina Marie Kaba. / 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), 1999. / Includes bibliographical references (p. 180-184). / During July and August of 1996, a large acoustics/physical oceanography experiment was fielded in the Mid-Atlantic Bight, south of Nantucket Island, MA. Known as the Shelfbreak Front PRIMER Experiment, the study combined acoustic data from a moored array of sources and receivers with very high resolution physical oceanographic measurements. This thesis addresses two of the primary goals of the experiment, explaining the properties of acoustic propagation in the region, and tomographic inversion of the acoustic data. In addition, this thesis develops a new method for predicting acoustic coherence in such regions. Receptions from two 400 Hz tomography sources, transmitting from the continental slope onto the shelf, are analyzed. This data, along with forward propagation modeling utilizing SeaSoar thermohaline measurements, reveal that both the shelfbreak front and tidally-generated soliton packets produce stronger coupling between the acoustic waveguide modes than expected. Arrival time wander and signal spread show variability attributable to the presence of a shelf water meander, changes in frontal configuration, and variability in the soliton field. The highly-coupled nature of the acoustic mode propagation prevents detailed tomographic inversion. Instead, methods based on only the wander of the mode arrivals are used to estimate path-averaged temperatures and internal tide "strength". The modal phase structure function is introduced as a useful proxy for acoustic coherence, and is related via an integral transform to the environmental sound speed correlation function. Advantages of the method are its flexibility and division of the problem into independent contributions, such as from the water column and seabed. / by Brian J. Sperry. / 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), 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Halogenated 1'-methyl-1,2'-bipyrroles (MBPs) are a distinctive class of marine organic compounds. They are naturally produced, they have a unique carbon structure, they are highly halogenated, and they bioaccumulate in upper trophic levels. MBPs share many characteristics with persistent organic pollutants (POPs), and may prove to be useful natural analogues for these anthropogenic compounds. Further, their unique structure suggests that their biosynthetic organism(s) may have new genes to add to current knowledge of biosynthetic chemistry. The objectives of this dissertation were to further clarify the environmental distribution of MBPs, to examine whether MBPs biomagnify, and to investigate possible origins of these compounds through their stable nitrogen isotopic signatures. Results from these investigations have shown that over 40 highly brominated MBP congeners are present in marine mammals, fish, and squid from the Northwestern Atlantic Ocean. The most abundant MBPs do appear to biomagnify through the food web to reach the concentrations observed in marine mammals. This additional evidence affords greater confidence in the use of MBPs as natural analogues for POPs. However, differences in the environmental chemistry of MBPs and anthropogenic compounds are also evident, and may be due to these compounds' different origins, or to the capacity of degradative enzymes to act upon them. / (cont.) Finally, compound-specific nitrogen isotope analyses on MBPs isolated from dolphin blubber show that these compounds are dramatically enriched in 15N relative to other biosynthetic organic compounds. This enrichment is likely a signal imparted during biosynthesis, and may assist in elucidating the organism(s) and mechanism(s) responsible for the biosynthesis of MBPs. / by Kristin C. Pangallo. / Ph.D.