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), 2007. / Includes bibliographical references. / Present-day expeditionary oceanography is beginning to shift from a focus on short-term ship and submersible deployments to an ocean observatory mode where long-term temporally-focused studies are feasible. As a result, a critical need for in situ chemical sensors is evolving. New sensors take a significant amount of time to develop; thus, the evaluation of techniques in the laboratory for use in the ocean environment is becoming increasingly important. Laser-induced breakdown spectroscopy (LIBS) possesses many of the characteristics required for such in situ chemical sensing, and is a promising technique for field measurements in extreme environments. Although many LIBS researchers have focused their work on liquid jets or surfaces, little attention has been paid to bulk liquid analysis, and especially to the effect of oceanic pressures on LIBS signals. In this work, laboratory experiments validate the LIBS technique in a simulated deep ocean environment to pressures up to 2.76 x 10⁷ Pa. A key focus of this work is the validation that select elements important for understanding hydrothermal vent fluid chemistry (Na, Ca, Mn, Mg, K, and Li) are detectable using LIBS. A data processing scheme that accurately deals with the extreme nature of laser-induced plasma formation was developed that allows for statistically accurate comparisons of spectra. The use of both single and double pulse LIBS for high pressure bulk aqueous solutions is explored and the system parameters needed for the detection of the key analytes are optimized. Using both single and double pulse LIBS, the limits of detection were found to be higher than expected as a result of the spectrometer used in this experimentation. However, the results of this validation show that LIBS possesses the characteristics to be a viable chemical sensing method for in situ analyte detection in high pressure environments like the deep ocean. / by Anna Pauline Miranda Michel. / 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. 197-206). / This thesis develops methods for estimating wideband shallow-water acoustic communication channels. The very shallow water wideband channel has three distinct features: large dimension caused by extensive delay spread; limited number of degrees of freedom (DOF) due to resolvable paths and inter-path correlations; and rapid fluctuations induced by scattering from the moving sea surface. Traditional LS estimation techniques often fail to reconcile the rapid fluctuations with the large dimensionality. Subspace based approaches with DOF reduction are confronted with unstable subspace structure subject to significant changes over a short period of time. Based on state-space channel modeling, the first part of this thesis develops algorithms that jointly estimate the channel as well as its dynamics. Algorithms based on the Extended Kalman Filter (EKF) and the Expectation Maximization (EM) approach respectively are developed. / (cont.) Analysis shows conceptual parallels, including an identical second-order innovation form shared by the EKF modification and the suboptimal EM, and the shared issue of parameter identifiability due to channel structure, reflected as parameter unobservability in EKF and insufficient excitation in EM. Modifications of both algorithms, including a two-model based EKF and a subspace EM algorithm which selectively track dominant taps and reduce prediction error, are proposed to overcome the identifiability issue. The second part of the thesis develops algorithms that explicitly find the sparse estimate of the delay-Doppler spread function. The study contributes to a better understanding of the channel physical constraints on algorithm design and potential performance improvement. It may also be generalized to other applications where dimensionality and variability collide. / by Weichang Li. / 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), 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 (p. 173-187). / This thesis describes a vision-based, large-area, simultaneous localization and mapping (SLAM) algorithm that respects the low-overlap imagery constraints typical of autonomous underwater vehicles (AUVs) while exploiting the inertial sensor information that is routinely available on such platforms. We adopt a systems-level approach exploiting the complementary aspects of inertial sensing and visual perception from a calibrated pose-instrumented platform. This systems-level strategy yields a robust solution to underwater imaging that overcomes many of the unique challenges of a marine environment (e.g., unstructured terrain, low-overlap imagery, moving light source). Our large-area SLAM algorithm recursively incorporates relative-pose constraints using a view-based representation that exploits exact sparsity in the Gaussian canonical form. This sparsity allows for efficient O(n) update complexity in the number of images composing the view-based map by utilizing recent multilevel relaxation techniques. We show that our algorithmic formulation is inherently sparse unlike other feature-based canonical SLAM algorithms, which impose sparseness via pruning approximations. In particular, we investigate the sparsication methodology employed by sparse extended information filters (SEIFs) and offer new insight as to why, and how, its approximation can lead to inconsistencies in the estimated state errors. Lastly, we present a novel algorithm for efficiently extracting consistent marginal covariances useful for data association from the information matrix. / (cont.) In summary, this thesis advances the current state-of-the-art in underwater visual navigation by demonstrating end-to-end automatic processing of the largest visually navigated dataset to date using data collected from a survey of the RMS Titanic (path length over 3 km and 3100 m² of mapped area). This accomplishment embodies the summed contributions of this thesis to several current SLAM research issues including scalability, 6 degree of freedom motion, unstructured environments, and visual perception. / by Ryan M. Eustice. / 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), 2007. / Includes bibliographical references. / This thesis employs compound-specific stable carbon and radiocarbon isotopic analysis of organic biomarkers to (a) resolve petrogenic from pre-aged vascular plant organic carbon (OC) in continental margin sediments, (b) investigate the underlying mechanisms controlling the anomalously old ages that are often observed for the terrestrial component of sedimentary OC, and (c) address the associated consequences for biomarker-based climate reconstructions. In Chapters 2 and 3, coupled molecular isotope mass balances demonstrate that the amount of petrogenic OC residing on the Beaufort Shelf (Arctic Ocean) and the Eel River Margin (coastal California) has been previously overestimated due to the presence of significantly 'pre-aged' terrestrial OC. However, even though the contribution of organic matter emanating from sedimentary rocks may be smaller, these results reinforce the emerging notion that it is not completely oxidized during weathering and subsequent seaward transport. In Chapter 4, comparison of the down-core radiocarbon profiles for certain vascular plant biomarkers extracted from Cariaco Basin (Caribbean Sea) and Saanich Inlet (coastal British Columbia) sediments with the radiocarbon evolution of atmospheric carbon dioxide reveals that the vast majority of the terrestrial OC experiences multi-millennial residence times on land prior to entering the sea. Most of the remaining inventory is deposited in sediments within one or two decades, providing direct evidence that very little terrestrial organic matter is rapidly transferred to the marine environment. / (cont.) With this in mind, the striking modulation in the signal amplitude of a biomarker-based tropical paleoaridity record presented in Chapter 5 was instead used to evaluate the role of low versus high latitude forcing in abrupt paleoclimate oscillations during the last full glacial cycle. Seasonal variations in the position of the Intertropical Convergence Zone were interpreted to be a response to both high latitude adjustments in meridional overturning circulation and precessionally-driven modifications in local insolation. Finally, Chapter 6 addresses the broader implications of multi-millennial terrestrial residence times for paleoclimate records based on vascular plant biomarkers. / by Nicholas J. Drenzek. / Ph.D.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2008. / Includes bibliographical references (leaves 52-56). / Functional screening of environmental genomic libraries permits the identification of clones expressing activities of interest without requiring prior knowledge of the genes responsible. In this study, protocols were optimized for the construction of mid-size DNA insert, inducible expression environmental genomic plasmid libraries for this purpose. A library with a mean insert size of 5.2 kilobases was constructed with environmental DNA isolated from surface ocean water collected at Hawaii Ocean Time-series station ALOHA in plasmid cloning vector pMCL200 under the inducible control of the PLAC promoter. To begin to evaluate the utility of such libraries for gene expression-based screens, this library was screened phenotypically for clones expressing genes that confer fluorescence or distinctive coloration on colonies of host Escherichia coli cells, and results were compared to those for a fosmid library constructed from the same marine microbial DNA sample. Ecologically relevant sequences were identified in both libraries, and each was observed to offer both advantages and disadvantages. Results of this study suggest that mid-size insert plasmid libraries under the control of inducible promoters can provide a useful and complementary approach for both functional screening and shotgun sequencing of environmental genomic libraries. / by Jennifer C. Braff. / 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 (p. 59-65). / Estimates of natural climate variability during the past millennium provide a frame of reference in which to assess the significance of recent changes. This thesis investigates new methods of reconstructing low-latitude sea surface temperature (SST) and hydrography, and combines these methods with traditional techniques to improve the present understanding of western North Atlantic climate variability. A new strontium/calcium (Sr/Ca) - SST calibration is derived for Atlantic Montastrea corals. This calibration shows that Montastrea Sr/Ca is a promising SST proxy if the effect of coral growth is considered. Further analyses of coral growth using Computed Axial Tomography (CAT) imaging indicate growth in Siderastrea corals varies inversely with SST on interannual timescales. A 440-year reconstruction of low-latitude western North Atlantic SST based on this relationship suggests the largest cooling of the last few centuries occurred from -1650-1730 A.D., and was -I°C cooler than today. Sporadic multidecadal variability in this record is inconsistent with evidence for a persistent 65-80 year North Atlantic SST oscillation. Volcanic and anthropogenic radiative forcing are identified as important sources of externally-forced SST variability, with the latter accounting for most of the 20th century warming trend. An 1800-year reconstruction of SST and hydrography near the Gulf Stream also suggests SSTs remained within about I°C of modern values. This cooling is small relative to other regional proxy records and may reflect the influence of internal oceanic and atmospheric circulation. / (cont.) Simulations with an atmospheric general circulation model (AGCM) indicate that the magnitude of cooling estimated by proxy records is consistent with tropical hydrologic proxy records. / by Casey Pearce Saenger. / 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), 2007. / 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. 257-267). / The water circulation and evolution of water temperature over the inner continental shelf are investigated using observations of water velocity, temperature, density, and bottom pressure; surface gravity waves; wind stress; and heat flux between the ocean and atmosphere during 2001-2007. When waves are small, cross-shelf wind stress is the dominant mechanism driving cross-shelf circulation. The along-shelf wind stress does not drive a substantial cross-shelf circulation. The response to a given wind stress is stronger in summer than winter. The cross-shelf transport in the surface layer during winter agrees with a two-dimensional, unstratified model. During large waves and onshore winds the crossshelf velocity is nearly vertically uniform, because the wind- and wave-driven shears cancel. During large waves and offshore winds the velocity is strongly vertically sheared because the wind- and wave-driven shears have the same sign. The subtidal, depth-average cross-shelf momentum balance is a combination of geostrophic balance and a coastal set-up and set-down balance driven by the cross-shelf wind stress. The estimated wave radiation stress gradient is also large. The dominant along-shelf momentum balance is between the wind stress and pressure gradient, but the bottom stress, acceleration, Coriolis, Hasselmann wave stress, and nonlinear advection are not negligible. The fluctuating along-shelf pressure gradient is a local sea level response to wind forcing, not a remotely generated pressure gradient. In summer, the water is persistently cooled due to a mean upwelling circulation. The cross-shelf heat flux nearly balances the strong surface heating throughout mid-summer, so the water temperature is almost constant. The along-shelf heat flux divergence is apparently small. In winter, the change in water temperature is closer to that expected due to the surface cooling. Heat transport due to surface gravity waves is substantial. / by Melanie Rinn Fewings. / 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), 2008. / Includes bibliographical references (p. 155-161). / The subtidal circulation of the southeast Greenland shelf is described using a set of high resolution hydrographic and velocity transects occupied in summer 2004. The main feature present is the East Greenland Coastal Current (EGCC), a low-salinity, high velocity jet with a wedge-shaped hydrographic structure characteristic of other surface buoyancy-driven currents. The EGCC was observed along the entire Greenland shelf south of Denmark Strait, while the transect north of the strait showed only a weak shelf flow. This observation, combined with evidence from chemical tracer measurements that imply the EGCC contains a significant Pacific Water signal, suggests that the EGCC is an inner branch of the polar-origin East Greenland Current (EGC). A set of idealized laboratory experiments on the interaction of a buoyant current with a submarine canyon also supported this hypothesis, showing that for the observed range of oceanic parameters, a buoyant current such as the EGC could exhibit both flow across the canyon mouth or into the canyon itself, setting the stage for EGCC formation. Repeat sections occupied at Cape Farewell between 1997 and 2004 show that the along shelf wind stress can also have a strong influence on the structure and strength of the EGCC and EGC on timescales of 2-3 days. Accounting for the wind-induced effects, the volume transport of the combined EGC/EGCC system is found to be roughly constant (-2 Sv) over the study domain, from 68*N to Cape Farewell near 60°N. The corresponding freshwater transport increases by roughly 60% over this distance (59 to 96 mSv, referenced to a salinity of 34.8). This trend is explained by constructing a simple freshwater budget of the EGCC/EGC system that accounts for melt water runoff, melting sea-ice and icebergs, and net precipitation minus evaporation. / (cont.) Variability on inter annual timescales is examined by calculating the Pacific Water content in the EGC/EGCC from 1984-2004 in the vicinity of Denmark Strait. The PW content is found to correlate significantly with the Arctic Oscillation index, lagged by 9 years, suggesting that the Arctic Ocean circulation patterns bring varying amounts of Pacific Water to the North Atlantic via the EGC/EGCC. / by David A. Sutherland. / 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. / The North Atlantic right whale, Eubalaena glacialis, one of the most critically endangered whales in the world, is subject to high anthropogenic mortality. Vessel-whale collisions and entanglement in fishing gear were indicated in 27 (67.5%) of the 40 right whales necropsied between 1970 and December 2006. Of those, at least 9 deaths (22.5%) resulted from blunt contact with a vessel. To reduce the likelihood of fatal collisions, speed restrictions are being considered for vessels traversing critical habitat, although the effects of speed on collision outcomes have not been specifically evaluated from a biomechanics perspective. The ultimate goal of a larger collaborative project is to evaluate the efficacy of speed restrictions for reducing blunt collision mortality using a multi-scale finite element model. Complete, transverse fracture of the right whale mandible, an injury seen only in right whales killed by vessels, is used as a proxy for mortality in the model. Vital for that model are the material properties and biomechanical behavior of the right whale mandible. Here, the internal structure and physical properties of right whale jawbone tissue are reported. The average apparent densities, 0.4258 g/cc ±0.0970 and 1.2370 g/cc ±0.0535 for trabecular and cortical bone respectively, indicate that the bone is of relatively low density. Average ash content for trabecular bone (64.38% ±1.1330) is comparable with values from other species, indicating that low density results from a reduction of bone mass, not mineralization. Mechanical properties of right whale bone (Young's modulus of elasticity and Poisson's ratio) were determined via uniaxial compression testing. / (cont.) These data are incorporated into the finite element model simulating different loading conditions (e.g. vessel speeds) that likely lead to mandibular failure and thereby mortality from blunt vessel collisions. Model results (e.g. risk of fracture) are used to determine the effect of speed restrictions on collision outcomes. / by Regina Campbell-Malone. / 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), 2007. / Includes bibliographical references (p. 183-191). / This thesis covers a comprehensive analysis of long-range, deep-ocean, low-frequency, sound propagation experimental results obtained from the North Pacific Ocean. The statistics of acoustic fields after propagation through internal-wave-induced sound-speed fluctuations are explored experimentally and theoretically. The thesis starts with the investigation of the North Pacific Acoustic Laboratory 98-99 data by exploring the space-time scales of ocean sound speed variability and the contributions from different frequency bands. The validity of the Garret & Munk internal-wave model is checked in the upper ocean of the eastern North Pacific. All these results impose hard bounds on the strength and characteristic scales of sound speed fluctuations one might expect in this region of the North Pacific for both internal-wave band fluctuations and mesoscale band fluctuations. The thesis then presents a detailed analysis of the low frequency, broadband sound arrivals obtained in the North Pacific Ocean. The observed acoustic variability is compared with acoustic predictions based on the weak fluctuation theory of Rytov, and direct parabolic equation Monte Carlo simulations. The comparisons show that a resonance condition exists between the local acoustic ray and the internal wave field such that only the internal-waves whose crests are parallel to the local ray path will contribute to acoustic scattering: This effect leads to an important filtering of the acoustic spectra relative to the internal-wave spectra. We believe that this is the first observational evidence for the acoustic ray and internal wave resonance. Finally, the thesis examined the evolution with distance, of the acoustic arrival pattern of the off-axis sound source transmissions in the Long-range Ocean Acoustic Propagation EXperiment. / (cont.) The observations of mean intensity time-fronts are compared to the deterministic ray, parabolic equation (with/without internal waves) and (one-way coupled) normal mode calculations. It is found the diffraction effect is dominant in the shorter-range transmission. In the longer range, the (internal wave) scattering effect smears the energy in both the spatial and temporal scales and thus has a dominant role in the finale region. / by Jinshan Xu. / Ph.D.