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. 101-107). / Marine mammal whistle calls present an attractive medium for covert underwater communications. High quality models of the whistle calls are needed in order to synthesize natural-sounding whistles with embedded information. Since the whistle calls are composed of frequency modulated harmonic tones, they are best modeled as a weighted superposition of harmonically related sinusoids. Previous research with bottlenose dolphin whistle calls has produced synthetic whistles that sound too "clean" for use in a covert communications system. Due to the sensitivity of the human auditory system, watermarking schemes that slightly modify the fundamental frequency contour have good potential for producing natural-sounding whistles embedded with retrievable watermarks. Structured total least squares is used with linear prediction analysis to track the time-varying fundamental frequency and harmonic amplitude contours throughout a whistle call. Simulation and experimental results demonstrate the capability to accurately model bottlenose dolphin whistle calls and retrieve embedded information from watermarked synthetic whistle calls. Different fundamental frequency watermarking schemes are proposed based on their ability to produce natural sounding synthetic whistles and yield suitable watermark detection and retrieval. / by Jared Severson. / S.M.

Includes bibliographical references (leaves 189-191). / Thesis (S.M. in Oceanographic Engineering)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2006. / (cont.) To that end, the space-time correlations of the error, turbulence, and wave processes are developed and then utilized to find the extent to which the environmental and internal processing parameters contribute to this error. It is found that the wave-induced velocities, even when filtered, introduce error variances which are of similar magnitude to that of the Reynolds stresses. / The challenge of estimating the Reynolds stress in an energetic ocean environment derives from the turbulence process overlapping in frequency, or in wavenumber, with the wave process. It was surmised that they would not overlap in the combined wavenumber-frequency spectrum, due to each process having a different dispersion relationship. The turbulence process is thought to obey a linear dispersion relationship, as the turbulent flow is advected with the mean current (Taylor's frozen turbulence approximation). However, the Acoustic Doppler Current Profiler (ADCP) looks at radial wavenumbers and frequencies, and finds overlap. Another approach is to exploit the physical differences of each process, namely that the wave induced velocities are correlated over much larger distances than the turbulence induced velocities. This method was explored for current meters by Shaw and Trowbridge. Upon adapting the method for the ADCP, it is found that the resulting Reynolds stress estimates are of the correct order of magnitude, but somewhat noisy. The work of this thesis is to uncover the source of that noise, and to quantify the performance limits of estimating the Reynolds Stress when using ADCP measurements that are contaminated with strong wave-induced velocities. / by Mark Rapo. / S.M.in Oceanographic Engineering

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), 2013. / In title on title page, "[delta]" appears as lower case Greek letters. Cataloged from PDF version of thesis. / Includes bibliographical references. / The stable isotopes, [delta]¹⁵N and [delta]¹⁸O, of nitrite and nitrate can be powerful tools used to interpret nitrogen cycling in the ocean. They are particularly useful in regions of the ocean where there are multiple sources and sinks of nitrogenous nutrients, which concentration profiles alone cannot distinguish. Examples of such regions are "oxygen deficient zones" (ODZ). They are of particular interest because they are also important hot spots of fixed N loss and production of N₂O, a potent greenhouse gas. In order to interpret these isotope profiles, the isotope systematics of each process involved must be known so that we can distinguish the isotopic signature of each process. One of the important processes to consider here is nitrification, the process by which ammonium is oxidized nitrite and then to nitrate. This thesis describes numerous experiments using both cultures of nitrifying organisms as well as natural seawater samples to determine the oxygen isotope systematics of nitrification. These experimental incubations show that the accumulation of nitrite has a large effect on the resulting [delta]¹⁸ONO3. In experiments where nitrite does not accumulate, [delta]¹⁸ONO3 produced from nitrification is between -1 to l%o. These values will be applicable for the majority of the ocean, but the nitrite isotopic exchange will be important in the regions of the ocean where nitrite accumulates, such as the base of the euphotic zone and oxygen deficient zones. [delta]¹⁸ONO2 was developed as a unique tracer in this thesis because it undergoes abiotic equilibration with water [delta]¹⁸O at a predictable rate based on pH, temperature and salinity. This rate, its dependencies, and how the [delta]¹⁸ONO2 values can be used as not only biological source indicators but also indicators of age are described. This method was applied to samples from the primary nitrite maximum in the Arabian Sea, revealing that the dominant source and sinks of nitrite are ammonia oxidation and nitrite oxidation with an average age of 37 days. Finally, using the isotope systematics of nitrification as well as the properties of nitrite oxygen isotope exchange described in this thesis, the final chapter interprets multiisotope nitrate and nitrite profiles in the Costa Rica Upwelling Dome using a simple ID model. The nitrite isotopes showed that there were multiple sources of nitrite in the primary nitrite maximum including (1) decoupling of ammonia oxidation and nitrite oxidation, (2) nitrate reduction during assimilation and leakage of nitrite by phytoplankton. In the oxygen deficient zone and secondary nitrite maximum, there were equal contributions of nitrite removal from nitrite oxidation and nitrite reduction. This recycling of nitrite to nitrate through oxidation indicates that the percentage of reduced nitrate fully consumed to N2 gas is actually smaller than previous estimates. Overall, this thesis describes new nitrogen and oxygen isotopic tracers and uses them to elucidate the complicated nitrogen biogeochemistry in oxygen deficient zones. / by Carolyn Buchwald. / 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. 313-325). / This thesis presents a stochastic mapping framework for autonomous robotic chemical plume source localization in environments with multiple sources. Potential applications for robotic chemical plume source localization include pollution and environmental monitoring, chemical plant safety, search and rescue, anti-terrorism, narcotics control, explosive ordinance removal, and hydrothermal vent prospecting. Turbulent flows make the spatial relationship between the detectable manifestation of a chemical plume source, the plume itself, and the location of its source inherently uncertain. Search domains with multiple sources compound this uncertainty because the number of sources as well as their locations is unknown a priori. Our framework for stochastic mapping is an adaptation of occupancy grid mapping where the binary state of map nodes is redefined to denote either the presence (occupancy) or absence of an active plume source. A key characteristic of the chemical plume source localization problem is that only a few sources are expected in the search domain. The occupancy grid framework allows for both plume detections and non-detections to inform the estimated state of grid nodes in the map, thereby explicitly representing explored but empty portions of the domain as well as probable source locations. / (cont.) However, sparsity in the expected number of occupied grid nodes strongly violates a critical conditional independence assumption required by the standard Bayesian recursive map update rule. While that assumption makes for a computationally attractive algorithm, in our application it results in occupancy grid maps that are grossly inconsistent with the assumption of a small number of occupied cells. To overcome this limitation, several alternative occupancy grid update algorithms are presented, including an exact solution that is computationally tractable for small numbers of detections and an approximate recursive algorithm with improved performance relative to the standard algorithm but equivalent computational cost. Application to hydrothermal plume data collected by the autonomous underwater vehicle ABE during vent prospecting operations in both the Pacific and Atlantic oceans verifies the utility of the approach. The resulting maps enable nested surveys for homing-in on seafloor vent sites to be carried out autonomously. This eliminates inter-dive processing, recharging of batteries, and time spent deploying and recovering the vehicle that would otherwise be necessary with survey design directed by human operators. / by Michael V. Jakuba. / 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), 2006. / Includes bibliographical references. / South American climate has undergone dramatic changes since the last glacial period, as evidenced from Cariaco Basin (Venezuelan coast) and Peru Margin marine sediment biomarker records. Compounds derived from vascular plant leaf waxes and delivered to the marine sedimentary environment, including long-chain (C24-C32) n-alkanoic acids, were used as proxies for terrestrial vegetation type, aridity, and atmospheric circulation. Marine biomarkers, such as sterols and phytol, were used to reconstruct productivity in the Peru Margin upwelling zone, where sedimentary conditions are not conducive to the preservation of foraminifera. Through the use of organic molecular isotopic techniques and multi-molecular stratigraphy, a great deal can be learned about communities of marine organisms and terrestrial plants that existed in the past and the environments in which they lived. Vascular plant leaf wax carbon and hydrogen isotopic records were generated from n-alkanoic acids preserved in Cariaco Basin marine sediments. These records were compared to previously established pollen and climate records and were found to parallel local millennial-scale climate changes between the late Glacial and Preboreal periods, which were characterized by migrations of the inter-tropical convergence zone. / (cont.) Differences in 6D between C,6-C18 and C24-C30 n-alkanoic acids suggest a marine source for the shorter chain lengths and a terrestrial source for the longer chains. Stacked 6D and 613C records both exhibited isotopic enrichment during the late Glacial and Younger Dryas periods and depletion during the B011ing-Aller0d and Preboreal periods. If interpreted as an aridity proxy, the 6D record is in agreement with Cariaco Basin sediment grey scale records, suggesting that the late Glacial and Younger Dryas were more arid than the B011ing-Aller0d and Preboreal periods. n-Alkanoic acid 613C, which is a proxy for C3 versus C4 plant type, indicates that C3 plants predominated in this area of the tropics during warm and wet periods, such as the Bolling-Aller0d and the Holocene, and C4 plants proliferated during cooler and more arid periods, such as the Glacial and Younger Dryas. The biomarker 613C record agrees with pollen data previously developed from Cariaco Basin sediments, confirming that leaf wax compounds preserved in marine sediments can accurately record terrestrial vegetation changes. Analytical methods utilizing stir bar sorptive extraction (SBSE) and thermal desorption were developed and applied to investigate lipid organic matter in a suite of alpine ice cores. / (cont.) These methods permit use of small volume (10-30 ml) samples, as would be required for high-resolution down-core analyses. SBSE involves using a polymer coated stir bar to extract organic matter from aqueous samples, after which it is loaded directly into a thermal desorption unit and the organic matter transferred in its entirety to a gas chromatograph inlet. To test these methods and the organic content of tropical ice, post-industrial samples from two South American, two Asian, and one African ice core were analyzed. Compounds identified in the modem ice core samples included natural and anthropogenic biomarkers such as n-alkanes, n-alkanoic acids, n-alkyl amides and nitriles, polycyclic aromatic hydrocarbons (PAHs), and diterpenoids. Variability in the distributions of these compounds between different cores demonstrated that the lipid organic fraction in each core was representative of mostly local inputs. To further investigate natural inputs, several pre-industrial samples were analyzed from the Sajama ice core in the Andes and The Puruogangri core on the Tibetan Plateau. Inputs of terrestrial vegetation combustion biomarkers such as PAHs, diterpenoids, and alkyl amides were consistent with periods of enhanced aridity in each core. / (cont.) The results of this investigation demonstrate the utility of the methodology, which could now be applied to generate very high-resolution biomarker records from tropical ice cores. Gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS) was used to generate a high-resolution, multi-molecular organic biomarker record from Peru Margin sediments (-110S, 252 m water depth) for the last 15 ka. Because of their position beneath the oxygen minimum zone of a productive upwelling region, these sediments contain a wealth of compounds that can be exploited as paleoclimate indicators. TOF-MS and fast GC techniques allowed me to generate this record in a short amount of time and without employing the traditional suite of purification techniques. Before about 9 ka, organic carbon and biomarker concentration records exhibited similar variability, implying a forcing mechanism that affected input and/or preservation of both marine and terrestrial organic matter, such as large-scale climate change. ... / by Matthew C. Makou. / 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), 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Oceanic transform faults that accommodate strain at mid-ocean ridge offsets represent a unique environment for studying fault mechanics. Here, I use seismic observations and models to explore how fault structure affects mechanisms of slip at oceanic transforms. Using teleseismic data, I find that seismic swarms on East Pacific Rise (EPR) transforms exhibit characteristics consistent with the rupture propagation velocity of shallow aseismic creep transients. I also develop new thermal models for the ridge-transform fault environment to estimate the spatial distribution of earthquakes at transforms. Assuming a temperature-dependent rheology, thermal models indicated that a significant amount of slip within the predicted temperature-dependent seismogenic area occurs without producing large-magnitude earthquakes. Using a set of local seismic observations, I consider how along-fault variation in the mechanical behavior may be linked to material properties and fault structure. I use wide-angle refraction data from the Gofar and Quebrada faults on the equatorial EPR to determine the seismic velocity structure, and image wide low-velocity zones at both faults. Evidence for fractured fault zone rocks throughout the crust suggests that unique friction characteristics may influence earthquake behavior. Together, earthquake observations and fault structure provide new information about the controls on fault slip at oceanic transform faults. / by Emily Carlson Roland. / 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), 2009. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (leaves 264-277). / The lateral line system on fish has been found to aid in schooling behavior, courtship communication, active and passive hydrodynamic imaging, and prey detection. The most widely used artificial prey stimulus has been the vibrating sphere, which some fish are able to detect even when the signal velocities to its lateral line are orders of magnitude smaller than background current velocities. It is not clear how the fish are able to extract this signal. This thesis uses a series of computational fluid dynamic (CFD) simulations, matched with recent experiments, to quantify the effects of 3D fish body parts on the received dipole signals, and to determine signal detection abilities of the lateral line system in background flow conditions. An approximation is developed for the dipole induced, oscillatory, boundary layer velocity profile over the surface of a fish. An analytic solution is developed for the case when the surface is a wall, and is accurate at points of maximal surface tangential velocity. Results indicate that the flow outside a thin viscous layer remains potential in nature, and that body parts, such as fins, do not significantly affect the received dipole signal in still water conditions. In addition, the canal lateral line system of the sculpin is shown to be over 100 times more sensitive than the superficial lateral line system to high frequency dipole stimuli. Analytical models were developed for the Mottled Sculpin canal and superficial neuromast motions, in response to hydrodynamic signals. When the background flow was laminar, the neuromast motions induced by the stimulus signal at threshold had a spectral peak larger than spectral peaks resulting from the background flow induced motions. / (cont.) When the turbulence level increased, the resulting induced neuromast motions had dominant low frequency oscillations. For fish using the signal encoding mechanisms of phase-locking or spike rate increasing, signal masking should occur. / by Mark Andrew Rapo. / Ph.D.

Thesis: S.M., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 93-99). / In terms of national security, the advancement of unmanned underwater vehicle (UUV) technology has transformed UUVs from tools for intelligence, surveillance, and reconnaissance and mine countermeasures to autonomous platforms that can perform complex tasks like tracking submarines, jamming, and smart mining. Today, they play a major role in asymmetric warfare, as UUVs have attributes that are desirable for less-established navies. They are covert, easy to deploy, low-cost, and low-risk to personnel. The concern of protecting against UUVs of malicious intent is that existing defense systems fall short in detecting, tracking, and preventing the vehicles from causing harm. Addressing this gap in technology, this thesis is the first to demonstrate passively detecting and tracking UUVs in realistic environments strictly from the vehicle's self-generated noise. This work contributes the first power spectral density estimate of an underway micro-UUV, field experiments in a pond and river detecting a UUV with energy thresholding and spectral filters, and field experiments in a pond and river tracking a UUV using conventional and adaptive beamforming. The spectral filters resulted in a probability of detection of 96 % and false alarms of 18 % at a distance of 100 m, with boat traffic in a river environment. Tracking the vehicle with adaptive beamforming resulted in a 6.2 ± 5.7° absolute difference in bearing. The principal achievement of this work is to quantify how well a UUV can be covertly tracked with knowledge of its spectral features. This work can be implemented into existing passive acoustic surveillance systems and be applied to larger classes of UUVs, which potentially have louder identifying acoustic signatures. / by Kristen Elizabeth Railey. / S.M.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science; and the Woods Hole Oceanographic Institution), 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 85-87). / Mode filtering is most commonly implemented using the sampled mode shape or pseudoinverse algorithms. Buck et al [1] placed these techniques in the context of a broader maximum a posteriori (MAP) framework. However, the MAP algorithm requires that the signal and noise statistics be known a priori. Adaptive array processing algorithms are candidates for improving performance without the need for a priori signal and noise statistics. A variant of the physically constrained, maximum likelihood (PCML) algorithm [2] is developed for mode filtering that achieves the same performance as the MAP mode filter yet does not need a priori knowledge of the signal and noise statistics. The central innovation of this adaptive mode filter is that the received signal's sample covariance matrix, as estimated by the algorithm, is constrained to be that which can be physically realized given a modal propagation model and an appropriate noise model. The first simulation presented in this thesis models the acoustic pressure field as a complex Gaussian random vector and compares the performance of the pseudoinverse, reduced rank pseudoinverse, sampled mode shape, PCML minimum power distortionless response (MPDR), PCML-MAP, and MAP mode filters. The PCML-MAP filter performs as well as the MAP filter without the need for a priori data statistics. The PCML-MPDR filter performs nearly as well as the MAP filter as well, and avoids a sawtooth pattern that occurs with the reduced rank pseudoinverse filter. The second simulation presented models the underwater environment and broadband communication setup of the Shallow Water 2006 (SW06) experiment. / (cont.) Data processing results are presented from the Shallow Water 2006 experiment, showing the reduced sensitivity of the PCML-MPDR filter to white noise compared with the reduced rank pseudoinverse filter. Lastly, a linear, decision-directed, RLS equalizer is used to combine the response of several modes and its performance is compared with an equalizer applied directly to the data received on each hydrophone. / by Joseph C. Papp. / 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. 145-149). / Benthic shells can contribute greatly to the scattering variability of the ocean bottom, particularly at low grazing angles. Among the effects of shell aggregates are increased scattering strength and potential subcritical angle penetration of the seafloor. Sand dollars (Dendraster excentricus) occur commonly in the ocean and have been shown to be significant scatters of sound. In order to understand more fully the scattering mechanisms of these organisms, the scattering from individual sand dollars was studied using several methods. Using an approximation to the Helmholtz-Kirchhoff integral, the Kirchhoff method gives an analytic integral expression to the backscattering from an object. This integral was first solved analytically for a disk and a spherical cap, two high aspect ratio oblate shapes which simplify the shape of an individual sand dollar. A method for solving the Kirchhoff integral numerically was then developed. An exact three dimensional model of a sand dollar test was created from computed tomography scans. The Kirchhoff integral was then solved numerically for this model of the sand dollar. The finite element method, a numerical technique for approximating the solutions to partial differential equations and integral equations, was used to model the scattering from an individual sand dollar as well. COMSOL Multiphysics was used for the implementation of the finite element method. Modeling results were compared with published laboratory experimental data from the free field scattering of both an aluminum disk and a sand dollar. Insight on the scattering mechanisms of individual sand dollar, including elastic behavior and diffraction effects, was gained from these comparisons. / by Gregory C. Dietzen. / S.M.