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), 2008. / Includes bibliographical references (p. 110-119). / This study presents observations of turbulence dynamics made during the low winds portion of the Coupled Boundary Layers and Air-Sea Transfer experiment (CBLAST-Low). Observations were made of turbulent fluxes, turbulent kinetic energy, and the length scales of flux-carrying and energy-containing eddies in the ocean surface boundary layer. A new technique was developed to separate wave and turbulent motions spectrally, using ideas for turbulence spectra that were developed in the study of the bottom boundary layer of the atmosphere. The observations of turbulent fluxes allowed the closing of heat and momentum budgets across the air-sea interface. The observations also show that flux-carrying eddies are similar in size to those expected in rigid-boundary turbulence, but that energy-containing eddies are smaller than those in rigid-boundary turbulence. This suggests that the relationship between turbulent kinetic energy, depth, and turbulent diffusivity are different in the ocean surface boundary layer than in rigid-boundary turbulence. The observations confirm previous speculation that surface wave breaking provides a surface source of turbulent kinetic energy that is transported to depth where it dissipates. A model that includes the effects of shear production, wave breaking and dissipation is able to reproduce the enhancement of turbulent kinetic energy near the wavy ocean surface. However, because of the different length scale relations in the ocean surface boundary layer, the empirical constants in the energy model are different from the values that are used to model rigid-boundary turbulence. The ocean surface boundary layer is observed to have small but finite temperature gradients that are related to the boundary fluxes of heat and momentum, as assumed by closure models. However, the turbulent diffusivity of heat in the surface boundary layer is larger than predicted by rigid-boundary closure models. Including the combined effects of wave breaking, stress, and buoyancy forcing allows a closure model to predict the turbulent diffusivity for heat in the ocean surface boundary layer. / by Gregory Peter Gerbi. / 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), 2009. / Includes bibliographical references (p. 88-91). / The work presented in this thesis addresses the problem of the detection, classification and localization of seabed objects in shallow water environments using a time reversal approach in a bistatic configuration. The waveguide is insonified at low frequency ('kHz) with an omnidirectional source and the resulting scattered field is sampled by a receiving array towed behind an Autonomous Underwater Vehicle (AUV). The recorded signals are then processed to simulate onboard the AUV, the time reversed transmissions which serve to localize the origin of the scattered field on the seabed and estimate the position of the targets present. The clutter rejection based upon the analysis of the singular values of the Time Reversal operator is investigated with simulated data and field measurements collected off the coast of Palmaria (Italy) in January 2008. / by Alexis J. Dumortier. / S.M.

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 (p. 89-96). / Blainville's beaked whales (Mesoplodon densirostris) use broadband, ultrasonic echolocation signals (27 to 57 kHz) to search for, localize, and approach prey that generally consist of mid-water and deep-water fishes and squid. Although it is well known that the spectral characteristics of broadband echoes from marine organisms are a strong function of size, shape, orientation and anatomical group, little is known as to whether or not these or other toothed whales use spectral cues in discriminating between prey and non-prey. In order to study the prey-classification process, a stereo acoustic tag was mounted on a Blainville's beaked whale so that emitted clicks and corresponding echoes from prey could be recorded. A comparison of echoes from prey selected by the whale and those from randomly chosen scatterers suggests that the whale may have, indeed, discriminated between echoes using spectral features and target strengths. Specifically, the whale appears to have favored prey with one or more deep nulls in the echo spectra as well as ones with higher target strength. A three-dimensional, acoustic scattering model is also developed to simulate broadband scattering from squid, a likely prey of the beaked whale. / (cont.) This model applies the distorted wave Born approximation (DWBA) to a weakly-scattering, inhomogeneous body using a combined ray trace and volume integration approach. Scatterer features are represented with volume elements that are small (less than 1=12th of the wavelength) for the frequency range of interest (0 to 120 kHz). Ranges of validity with respect to material properties and numerical considerations are explored using benchmark computations with simpler geometries such as fluid-filled spherical and cylindrical fluid shells. Modeling predictions are compared with published data from live, freely swimming squid. These results, as well as previously published studies, are used in the analysis of the echo spectra of the whale's ensonified targets. / by Benjamin A. Jones. / S.M.

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), 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. / Ecological processes at deep-sea hydrothermal vents on fast-spreading mid-ocean ridges are punctuated by frequent physical disturbance. Larval dispersal among disjunct vent sites facilitates the persistence of sessile invertebrate species in these geologically and chemically dynamic habitats despite local extinction events. Regional population extension and rapid recolonization by the siboglinid tubeworm Riftia pachyptila have been well documented along the East Pacific Rise and the Galápagos Rift. To analyze spatial and temporal population genetic patterns and the processes governing them at ephemeral and disjunct habitats, a suite of 12 highly variable microsatellite DNA markers were developed for this species. Eight of these loci were used to assess the regional and within-ridge genetic structure of recent colonists and resident adults collected from nine sites in the eastern Pacific Ocean over period of three to seven years. A significant seafloor eruption during the seven-year sampling period allowed investigation into the role of local extinction in population genetic diversity at the Tica vent site at 9°N EPR, while collections within two and five years of an eruption that created the Rosebud vent field at 86°W GAR provided insights into genetic diversity input over population establishment. For the first time, this thesis demonstrated significant genetic differences between Riftia populations on the East Pacific Rise and Galápagos Rift. Moreover, the separate treatment of colonist and resident subpopulations revealed a high potential for local larval retention at vent sites. This mechanism for recruitment likely sustains disjunct populations and supports the recolonization of locally extinct areas after disturbance events, while episodic long-distance dispersal maintains genetic coherence of the species. / (cont.) Temporal population genetic consideration at the Tica site on the East Pacific Rise suggests that the 2005-2006 seafloor eruption had little to no discernable effect on local population genetic composition. Yet local populations appear to exhibit a small degree of genetic patchiness, with a high degree of relatedness (half-sibs) among subsets of individuals within both colonist and resident cohorts. This thesis broadens the application of recently developed molecular techniques to study the effect of ridge-crest processes and offers new perspectives into marine dispersal, gene flow, and population differentiation. / by Abigail Jean Fusaro. / 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), 2008. / Includes bibliographical references (p. 54-56). / Landmines and mine-like traps are effective weapons that are difficult to detect and discriminate from a safe distance. The ability to detect landmines in their host environment at a distance and to discriminate them from other objects would be valuable for countering the landmine threat. This paper explores a standoff acoustic/laser technique to discriminate landmines from other forms of man-made objects (clutter) in an urban environment. A novel approach currently under investigation by MIT Lincoln Labs, University of Mississippi, and other groups employs a non-contact acoustic/laser technique to detect landmines from a safe standoff range. This technique uses a sound source to excite vibrations in targets with an acoustic wave. These vibrations are in turn measured remotely with a Laser Doppler Vibrometer (LDV). In this thesis, the vibration responses of landmine variants are measured, analyzed, and compared to those of common urban objects likely to be found on a landmine field or roadside. The Fourier Transform of the vibration of the target as measured by the LDV is used to generate a target vibration spectrum. Target vibration spectra in response to a sound source were experimentally measured for 59 trials, 28 of which were of simulated landmine variants and the remaining trials were of urban clutter objects. Using an algorithm adapted from a methodology for mass spectral analysis, parameters of the target signatures are estimated; then individual target signatures are classified using a Support Vector Machine (SVM) with a training set composed of parameters from the remaining members of the total population. The best results obtained from this methodology had a 71% probability of detection and a 3% false alarm rate corresponding to 20 of 28 of the simulated landmine variants correctly identified and a single clutter object misidentified as a landmine variant. / by John Houston Doherty. / S.M.

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), 2008. / Includes bibliographical references (p. 159-170). / This thesis formulates an estimation framework for Simultaneous Localization and Mapping (SLAM) that addresses the problem of scalability in large environments. We describe an estimation-theoretic algorithm that achieves significant gains in computational efficiency while maintaining consistent estimates for the vehicle pose and the map of the environment.We specifically address the feature-based SLAM problem in which the robot represents the environment as a collection of landmarks. The thesis takes a Bayesian approach whereby we maintain a joint posterior over the vehicle pose and feature states, conditioned upon measurement data. We model the distribution as Gaussian and parametrize the posterior in the canonical form, in terms of the information (inverse covariance) matrix. When sparse, this representation is amenable to computationally efficient Bayesian SLAM filtering. However, while a large majority of the elements within the normalized information matrix are very small in magnitude, it is fully populated nonetheless. Recent feature-based SLAM filters achieve the scalability benefits of a sparse parametrization by explicitly pruning these weak links in an effort to enforce sparsity. We analyze one such algorithm, the Sparse Extended Information Filter (SEIF), which has laid much of the groundwork concerning the computational benefits of the sparse canonical form. The thesis performs a detailed analysis of the process by which the SEIF approximates the sparsity of the information matrix and reveals key insights into the consequences of different sparsification strategies. We demonstrate that the SEIF yields a sparse approximation to the posterior that is inconsistent, suffering from exaggerated confidence estimates. / (cont) This overconfidence has detrimental effects on important aspects of the SLAM process and affects the higher level goal of producing accurate maps for subsequent localization and path planning. This thesis proposes an alternative scalable filter that maintains sparsity while preserving the consistency of the distribution. We leverage insights into the natural structure of the feature-based canonical parametrization and derive a method that actively maintains an exactly sparse posterior. Our algorithm exploits the structure of the parametrization to achieve gains in efficiency, with a computational cost that scales linearly with the size of the map. Unlike similar techniques that sacrifice consistency for improved scalability, our algorithm performs inference over a posterior that is conservative relative to the nominal Gaussian distribution. Consequently, we preserve the consistency of the pose and map estimates and avoid the effects of an overconfident posterior. We demonstrate our filter alongside the SEIF and the standard EKEF both in simulation as well as on two real-world datasets. While we maintain the computational advantages of an exactly sparse representation, the results show convincingly that our method yields conservative estimates for the robot pose and map that are nearly identical to those of the original Gaussian distribution as produced by the EKF, but at much less computational expense. The thesis concludes with an extension of our SLAM filter to a complex underwater environment. We describe a systems-level framework for localization and mapping relative to a ship hull with an Autonomous Underwater Vehicle (AUV) equipped with a forward-looking sonar. The approach utilizes our filter to fuse measurements of vehicle attitude and motion from onboard sensors with data from sonar images of the hull. We employ the system to perform three-dimensional, 6-DOF SLAM on a ship hull. / by Matthew R. Walter. / S.M.

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), 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. / The benthic habitat is the terminal destination for marine animals in terms of their reproductive lifecycle. Recruitment dynamics relating to seasonal changes in the benthic habitat may be the best source of information for predicting recruit abundance and for marine resources management. The transition from the pelagic to the benthic phases is the last stage in the connectivity between benthic populations. The transition to the benthos may be a process that dominates recruitment dynamics to the exclusion of other characteristics of larvae such as their quality and their density. Recruitment of benthic marine animals is influenced by two seasonally varying factors of the benthic habitat. First, the availability of suitable habitat for recruitment can in large part determine the survival probability for settlers, a trend that is most pronounced for low or no survival when the settlement substrate is saturated by conspecifics from a recruitment cohort. Preemption is caused by the presence of current occupants from a recruit cohort, and it influences the settlement rate or the survival probability of conspecifics. Descriptive statistics (Chapter 2) and a field experiment (Chapter 4) highlight the role of preemption on barnacle recruitment. The second factor results from seasonal changes in environmental conditions that settlers experience in the benthic habitat, which could affect the physiology and survival probability of barnacle settlers. Highly unpredictable features of recruitment dynamics also play a role, such as wind that enhances wave action in the rocky intertidal that has been linked to the rate of settlement. Day to day variability in wind may cause patterns of settlement to be highly unpredictable. Predator induced mortality is spatially aggregated, and the random pattern of mortality in space is highly unpredictable. In contrast to these high frequency sources of recruitment variability, seasonal factors that vary at lower frequencies and that often change monotonically lend great predictive ability for recruitment dynamics. It appears that barnacles have evolved to compete for suitable habitat and have mechanisms to cope with seasonally varying environmental conditions in the benthic habitat, which may be the basis for why these features dominate the barnacle recruitment dynamic. / by Jonathan N. Blythe. / Ph.D.

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.