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 (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.

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), 2005. / Includes bibliographical references. / The geographic distribution and dynamics of coastal benthic populations are shaped by physical - biological interactions affecting larval dispersal and the demography of juvenile and adult individuals. This thesis focused on nearshore patterns of larval distribution and regional patterns in demography of intertidal barnacles in Southern and Baja California. Horizontal and vertical distributions, and the mortality rates of larvae, were assessed from short term (i.e. days) small- scale observations (0.1-1 km) in nearshore waters. Observations on spatial variability of adult barnacle demography were gathered over 1.5 years at scales of hundreds of kilometers. Stage-specific horizontal distributions and nearshore current measurements suggested that larvae of Balanus g-landula and Chthamalus spp. may experience limited dispersal. High mortality rates could further limit travel distances and the exchange of individuals among disjunct populations. Data on vertical distributions indicated that nauplii and cyprids of Balanus nubilus and Pollicipes polymerus occur at different depths. Nauplii remained near the surface at all times, whereas cyprids occurred in the bottom half of the water column. / (cont.) Such distributions, combined with vertical variability in horizontal flows, might cause the observed horizontal segregation of nauplii and cyprids. Differences in survival, growth rate, size structure, and per capita fertility of adult Balanus glandula were observed between Dana Point (Southern California) and Punta Baja (Baja California), a site located near the species' southern limit of distribution. Effects of spatial differences in demography on population persistence were assessed with a stage-structured matrix model. Model analyses indicated that the Punta Baja population is more susceptible to environmental stochasticity and more prone to local extinction than populations located further north. This thesis emphasizes the importance of characterizing factors that affect the dynamics of benthic populations at multiple spatial-temporal scales, and the usefulness of small scale high- frequency observations of nearshore phenomena, especially in relation with the dispersal of larvae. / by Fabián J. Tapia. / 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), 2006. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Also issued in pages. Barker Engineering Library copy: issued in pages. / Includes bibliographical references (leaves 193-[201]). / The first part of the dissertation investigates the application of the theory of large random matrices to high-dimensional inference problems when the samples are drawn from a multivariate normal distribution. A longstanding problem in sensor array processing is addressed by designing an estimator for the number of signals in white noise that dramatically outperforms that proposed by Wax and Kailath. This methodology is extended to develop new parametric techniques for testing and estimation. Unlike techniques found in the literature, these exhibit robustness to high-dimensionality, sample size constraints and eigenvector misspecification. By interpreting the eigenvalues of the sample covariance matrix as an interacting particle system, the existence of a phase transition phenomenon in the largest ("signal") eigenvalue is derived using heuristic arguments. This exposes a fundamental limit on the identifiability of low-level signals due to sample size constraints when using the sample eigenvalues alone. The analysis is extended to address a problem in sensor array processing, posed by Baggeroer and Cox, on the distribution of the outputs of the Capon-MVDR beamformer when the sample covariance matrix is diagonally loaded. / (cont.) The second part of the dissertation investigates the limiting distribution of the eigenvalues and eigenvectors of a broader class of random matrices. A powerful method is proposed that expands the reach of the theory beyond the special cases of matrices with Gaussian entries; this simultaneously establishes a framework for computational (non-commutative) "free probability" theory. The class of "algebraic" random matrices is defined and the generators of this class are specified. Algebraicity of a random matrix sequence is shown to act as a certificate of the computability of the limiting eigenvalue distribution and, for a subclass, the limiting conditional "eigenvector distribution." The limiting moments of algebraic random matrix sequences, when they exist, are shown to satisfy a finite depth linear recursion so that they may often be efficiently enumerated in closed form. The method is applied to predict the deterioration in the quality of the sample eigenvectors of large algebraic empirical covariance matrices due to sample size constraints. / by Rajesh Rao Nadakuditi. / 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. / Includes bibliographical references. / Trichodesmium spp. are considered the dominant nitrogen (N) fixing cyanobacteria in tropical and subtropical oceans, regimes frequently characterized by low iron (Fe). Limited information exists about what levels of Fe limit Trichodesmium N fixation. I developed a diagnostic for Fe limitation using quantitative reverse transcription PCR (qRT-PCR) of the Fe stress response gene isiB, which encodes for flavodoxin a non-Fe containing substitute for ferredoxin. I determined that high isiB gene expression corresponded to cell-specific reductions in N fixation rates in both phylogenetic clades of Trichodesmium grown on varying levels of Fe. Using these laboratory-determined thresholds, I assessed Fe limitation of Trichodesmium from the Sargasso Sea, equatorial Atlantic Ocean and Western Pacific Warm Pool in conjunction with other analytical measurements (N, phosphorus (P) and dissolved Fe (<0.4[mu]m filtered)). I found widespread Fe limitation in Trichodesmium from the Pacific Ocean and minimal expression in the North Atlantic Ocean. I also found an inverse correlation between isiB expression and dissolved Fe:P ratios in seawater and data suggesting that most dissolved Fe in seawater, including organic ligand-bound Fe, is available to Trichodesmium. These data support and refine previous model predictions and demonstrate, in situ, the importance of Fe to the marine N cycle. / by Phoebe Dreux Chappell. / 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), 2006. / Includes bibliographical references. / Two years of moored oceanographic and automatic weather station data which span the winter ice seasons of 2001-2003 within Marguerite Bay on the western Antarctic Peninsula (wAP) shelf were collected as part of the Southern Ocean Global Ocean Ecosystems Dynamics program. In order to characterize the ice environment in the region, a novel methodology is developed for determining ice coverage, draft and velocity from moored upward-looking acoustic Doppler current profiler data. A linear momentum balance shows the importance of internal ice stresses in the observed motion of the ice pack. Strong inertial, not tidal, motions were observed in both the sea ice and upper ocean. Estimates of upward diapycnal fluxes of heat and salt from the Upper Circumpolar Deep Water to the surface mixed layer indicate almost no contribution from double diffusive convection. A one-dimensional vertical mixed layer model adapted for investigation of mixing beneath an ice-covered ocean indicates that the initial wind event, rather than subsequent inertial shear, causes the majority of the mixing. This work points towards episodic wind-forced shear at the base of the mixed layer coupled with static instability from brine rejection due to ice production as a major factor in mixing on the wAP shelf. / by Jason Hyatt. / Ph.D.

Thesis (S.M.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (leaves 70-72). / The uncertainty in the determination of the momentum and scalar fluxes remains one of the main obstacles to accurate numerical forecasts in low to moderate wind conditions. For example, latent heat fluxes computed from data using direct covariance and bulk aerodynamic methods show that there is good agreement in unstable conditions when the latent heat flux values are generally positive. However, the agreement is relatively poor in stable conditions, particularly when the moisture flux is directed downward. If the direct covariance measurements are indeed accurate, then they clearly indicate that the bulk aerodynamic formula overestimate the downward moisture flux in stable conditions. As a result, comparisons of the Dalton number for unstable and stable conditions indicate a marked difference in value between the two stability regimes. Investigations done for this thesis used data taken primarily at the Air-Sea Interaction Tower (ASIT) during the Coupled Boundary Layers and Air-Sea Transfer (CBLAST) Experiment 2003 from the 20-27 August 2003. Other data from the shore based Martha's Vineyard Coastal Observatory (MVCO) and moored buoys in the vicinity of the ASIT were also incorporated. / (cont.) During this eight day period, the boundary layer was often characterized by light winds, a stably stratified surface layer and a swell dominated wave field. Additionally, the advection of warm moist air over cooler water resulted in fog formation and a downward flux of moisture on at least three occasions. Therefore, a primary objective of this thesis is to present a case study to investigate the cause of this shortcoming in the bulk formula under these conditions by examining the physical processes that are unique to these boundary layers. Particular attention will be paid to the behavior of the Dalton number in a stable marine atmospheric boundary layer under foggy conditions using insights derived from the study of fog formation and current flux parameterization methods. / by Robert Farrington Crofoot. / S.M.

Thesis (S.M.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (p. 63-65). / Hydrothermal vents discharge superheated, mineral rich water into our oceans, thereby providing a habitat for exotic chemosynthetic biological communities. Hydrothermal fluids are convected upwards until they cool and reach density equilibrium, at which point they advect laterally with the current. The neutrally buoyant plume layer can have length scales on the order of several kilometers, and it therefore provides the best means to detect the presence of vent fields on the seafloor, which typically have length scales on the order of a few meters. This thesis uses field measurements of the velocity, temperature and particulate anomalies associated with the TAG hydrothermal plume to demonstrate that tidal currents exert a strong impact on the plume shape, and to provide new constraints on the thermal power of the TAG hydrothermal system. The results show that the power output of the TAG system is on the order of 6000 MW, which is up to two orders of magnitude greater than previous estimates, and that there is considerably more entrainment than had previously been assumed. / by Sacha Wichers. / 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), 2006. / Includes bibliographical references (p. 297-311). / The physical and biological forces that drive zooplankton distribution and patchiness in an antarctic continental shelf region were examined, with particular emphasis on the Antarctic krill, Euphausia superba. This was accomplished by the application of acoustic, video, and environmental sensors during surveys of the region in and around Marguerite Bay, west of the Antarctic Peninsula, in the falls and winters of 2001 and 2002. An important component of the research involved the development and verification of methods for extracting estimates of ecologically-meaningful quantities from measurements of scattered sound. The distribution of acoustic volume backscattering at the single frequency of 120 kHz was first examined as an index of the overall biomass of zooplankton. Distinct spatial and seasonal patterns were observed that coincided with advective features. Improved parameterization was then achieved for a theoretical model of Antarctic krill target strength, the quantity necessary in scaling measurements of scattered sound to estimates of abundance, through direct measurement of all necessary model parameters for krill sampled in the study region and survey period. / (cont.) Methods were developed for identifying and delineating krill aggregations, allowing the distribution of krill to be distinguished from that of the overall zooplankton community. Additional methods were developed and verified for estimating the length, abundance, and biomass of krill in each acoustically-identified aggregation. These methods were applied to multi-frequency acoustic survey data, demonstrating strong seasonal, inter-annual, and spatial variability in the distribution of krill biomass. Highest biomass was consistently associated with regions close to land where temperatures at depth were cool. Finally, the morphology, internal structure, and vertical position of individual krill aggregations were examined. The observed patterns of variability in aggregation characteristics between day and night, regions of high versus low food availability, and in the presence or absence of predators, together reinforced the conclusion that aggregation and diel vertical migration represent strategies to avoid visual predators, while also allowing the krill access to shallowly-distributed food resources. The various findings of this work have important implications to the fields of zooplankton acoustics and Antarctic krill ecology, especially in relation to the interactions of the krill with its predators. / by Gareth L. Lawson. / Ph.D.