ALBERT

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 1986

Description: The Flying Fish is an autonomous, streamlined, gravity driven underwater vehicle of high speed (15 knots) vertical excursions to depths of 6000 meters. This prototype uses short baseline acoustic interferometry to guide itself to a monochromatic acoustic beacon at the surface. Phase difference measurements made on two orthogonal axes are used to deduce the relative bearing to the beacon. An autopilot uses this information to actuate control surfaces and correct vehicle attitude. This thesis describes the oceanographic context in which the vehicle will be used, translates the scientific mission into a set of coherent engineering specifications, describes a prototype design that meets these specifications, and demonstrates proof-of-concept with a series of sea trials. Some recommendations are made for future refinements.

Description: This research was conducted under NSF contract number OCE-8310168

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2010

Description: Observational and modeling techniques are employed to investigate the thermal and inertial upper ocean response to wind and buoyancy forcing in the North Atlantic Ocean. First, the seasonal kinetic energy variability of near-inertial motions observed with a moored profiler is described. Observed wintertime enhancement and surface intensification of near-inertial kinetic energy support previous work suggesting that near-inertial motions are predominantly driven by surface forcing. The wind energy input into surface ocean near-inertial motions is estimated using the Price-Weller- Pinkel (PWP) one-dimensional mixed layer model. A localized depth-integrated model consisting of a wind forcing term and a dissipation parameterization is developed and shown to have skill capturing the seasonal cycle and order of magnitude of the near-inertial kinetic energy. Focusing in on wintertime storm passage, velocity and density records from drifting profiling floats (EM-APEX) and a meteorological spar buoy/tethered profiler system (ASIS/FILIS) deployed in the Gulf Stream in February 2007 as part of the CLIvar MOde water Dynamics Experiment (CLIMODE) were analyzed. Despite large surface heat loss during cold air outbreaks and the drifting nature of the instruments, changes in the upper ocean heat content were found in a mixed layer heat balance to be controlled primarily by the relative advection of temperature associated with the strong vertical shear of the Gulf Stream. Velocity records from the Gulf Stream exhibited energetic near-inertial oscillations with frequency that was shifted below the local resting inertial frequency. This depression of frequency was linked to the presence of the negative vorticity of the background horizontal current shear, implying the potential for near-inertial wave trapping in the Gulf Stream region through the mechanism described by Kunze and Sanford (1984). Three-dimensional PWP model simulations show evidence of near-inertial wave trapping in the Gulf Stream jet, and are used to quantify the resulting mixing and the effect on the stratification in the Eighteen Degree Water formation region.

Description: This work was supported by National Science Foundation grants OCE-0241354 and OCE-0424865, as well as the Woods Hole Oceanographic Institution's Ocean and Cli- mate Change Institute. Funding to initiate the McLane Moored Pro ler observations at Line W were provided by grants from the G. Unger Vetlesen Foundation and the Comer Charitable Fund to the Woods Hole Oceanographic Institutions Ocean and Climate Change Institute.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution December 1986

Description: The focus of this dissertation is on the description and dynamical interpretation of the tidal band current fluctuations over the continental shelf off northern California. The term "tidal band" is used here to denote fluctuations with periods from about one-half to one day, including all the major diurnal and semidiurnal tidal constituents. The semidiurnal frequency is super-inertial, and the diurnal frequency sub-inertial, at this mid-latitude location. Kinetic and potential energy are strongly peaked at the diurnal and semidiurnal frequencies. Although inertial currents are occasionally observed, particularly during the winter when internal wave energy in general is elevated in this locale, they do not contribute significantly to the current variance. Consequently, the treatment here is divided into discussion of the diurnal and semidiurnal variability. Each chapter emphasizes a process which can cause the tidal currents to deviate from what would be anticipated based solely on observations of sea level. In Chapter II, the diurnal current variability is discussed, and the role played by atmospheric forcing is examined in detail. In Chapter III, the barotropic semidiurnal tidal currents over the shelf are described, and the effect of small-scale bumps in the coastline is evaluated. The baroclinic semi diurnal tidal currents, which are dependent upon the local time-varying hydrographic conditions, are examined in Chapter IV.

Description: Support from the WHOI Education Office, a NASA traineeship, and NSF grants OCE 80-14941 and OCE 84-17769.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution August 1987

Description: This thesis develops a new technique for estimating quasi-homogeneous and quasi-stationary sea surface wave frequency-direction spectra using acoustic tomography. The analysis of acoustic (mode and ray) phase and travel time perturbations due to a rough sea surface is presented. Two canonical waveguides (ideal shallow water and linear squared index of refraction) are used as examples for the mode perturbation. The analysis is used to explain high mode coherence measured in the FRAM N experiment. The forward problem of computing the acoustic phase and travel time perturbation spectra given the surface wave spectrum is solved to first order. An application of the technique to ray phase data taken during the MIZEX '84 experiment is shown. The inverse problems for the homogeneous and quasi-homogel1eous frequency-direction spectrum are introduced. The theory is applied to synthetic data which simulate a fetch-dependent sea. The estimates made agree well with the "actual" (synthetic data) spectrum. The effect of noise in the travel time estimates is studied. The sensitivity of the technique. to the number of rays used in the inversion is investigated and the resolution and variance of the inverse method are addressed.

Description: gratefully acknowledge the financial support of the Office of Naval Research, the General Electric Foundation, and the Ford Foundation.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 1985

Description: The acoustic properties of marine sediments have a direct effect on the propagation of sound in the ocean. In the frequency range of interest (50 - 500 Hz) the sediment can be modelled as a fluid. Assuming horizontal stratification of the ocean bottom, the acoustic parameters of interest are the compressional wave speed, the compressional wave attenuation and density as a function of depth. An inverse method based on a perturbation technique is presented in this thesis for the determination of these parameters. A monochromatic source experiment is proposed because of the desirability of such an experiment for determining the acoustic properties of an anelastic medium. The input information is the plane wave reflection coerricent as a function of the angle of incidence at a fixed frequency. A nonlinear integral equation relating the variations of these acoustic properties from a known reference value to the plane wave reflection coefficient is derived. This is then linearised using the Born approximation. The region of validity of the Born approximation is derived and based on this the optimum angular aperture for the input data is obtained. The linearised integral equation is a Fredholm integral equation of the first kind. An acceptable stable solution of the integral equation is obtained by imposing a priori constraints on the solution. The inversion method is tested using synthetic data and inversions are carried out for various examples of the attenuation coefficient profile and the sound speed profile. The results obtained with noise free data show good agreement between the true profiles and the reconstructed profiles. The resolution obtainable with the data set is studied using the resolving power theory of Backus and Gilbert and the inversion method is shown to provide adequate resolution. The effect of additive noise in data is examined and inversions performed with noisy data yielded stable acceptable results.

Description: I acknowledge the financial support provided by the education office in the Woods Hole Oceanographic Institution and the Office of Naval Research.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2000

Description: This thesis investigates the physical mechanisms of air-water gas transfer through direct measurements of turbulence at the air--water interface. To enable this study, a new approach to the particle image velocimetry (PIV) technique is developed in order to quantify free-surface flows. Two aspects of this work are innovative. First, the use of a three-dimensional laser light cone and optical filtering of the camera allow for the motion of fluorescent flow tracers at the water surface to be isolated and measured. Validation experiments indicate that this measurement reflects the fluid motion within the upper few hundred microns. A key benefit to this approach is the ability to deal with deforming surfaces, provided the amplitudes are not prohibitively large. This feature was used in this thesis to explore the surface flow induced by mechanically generated waves. Second, a new hybrid PIV image processing algorithm was developed that provides high accuracy velocity estimation with improved computational efficiency. This algorithm combines the concepts of dynamic Fourier-domain cross-correlation with a localized direct multiplicative correlation. In order to explore relationships between free-surface hydrodynamics and air-water gas transfer, an oscillating grid-stirred tank was constructed. By its design, this tank can be managed for chemical cleanliness, offers an unobstructed free surface, and is suited for turbulent mixing and air--water gas-exchange studies. A series of acoustic Doppler velocimeter, PIV, and infrared imaging experiments are presented that characterize the flow for the grid forcing conditions studied. Results indicate that the flows are stationary and reasonably repeatable. In addition, the flows exhibit near-isotropic turbulence and are quasi-homogeneous in horizontal planes. Secondary circulations are revealed and investigated. Finally, PIV measurements of free-surface turbulence are performed with concurrent measurements of gas transfer in the grid tank for a range of turbulent mixing and surface conditions. Surface turbulence, vorticity, and divergence are all affected by the presence of a surface film, with significant effects realized for relatively small surface pressures. Results show that while a relationship between surface turbulence and the gas-transfer velocity is an obvious improvement over that found using an estimate of the bulk flow turbulence, this relationship is dependent on the flow regime. This is revealed through additional surface wave studies. However, the data from both the wave experiments and the grid turbulence experiments can be reconciled by a single relationship between the gas-transfer velocity and the 1/2-power of the surface divergence, which agrees with previous conceptual models. These results (1) further our understanding of interfacial transport processes, (2) demonstrate the important role of surface divergence in air-water gas exchange, and (3) relate, in a physically meaningful way, the interactions between surface renewal, surfactants, and gas transfer.

Description: I was supported as an Office of Naval Research Graduate Fellow. This assistance was the impetus for my pursuit of a doctoral degree and is gratefully acknowledged. Very special thanks also to the WHOI Ocean Ventures Fund Program, Mr. F. Thomas Westcott, and the WHOI Education Department for generous financial support over the past several years.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2000

Description: A spectral camera (ALISS - Ambient Light Imaging and Spectral System) was used to image ambient light from high-temperature vents at 9°N East Pacific Rise and the Juan de Fuca Ridge during 1997 and 1998 Alvin dive cruises. ALISS is a low-light digital camera with custom-designed optics. A set of nine lenses, each covered by an individual bandpass filter (50 and 100 nm nominal bandwidths), allows vents to be imaged in nine wavelength bands simultaneously spanning the range of 400-1 000 nm. Thus, both spatial and spectral information are obtained. ALISS was used to image three types of vents: black smokers, flange pools, and beehives. The primary source of light is thermal radiation due to the high temperature of the hydrothermal fluid (-350°C). This light is dominant at wavelengths greater than 700 nm. At flange pools, where the fluid is relatively stable, only thermal radiation is present. Black smokers and beehives, however, are subject to mixing with ambient seawater (2°C) leading to mineral precipitation. Data from these types of vents show the existence of non-thermal, temporally varying light in the 400-700 nm region. This light is probably caused by mechanisms related to mixing and precipitation, such as chemiluminescence, crystalloluminescence and triboluminescence.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2001

Description: This thesis studies interactions between mid-ocean ridges and mantle plumes using geophysics, geochemistry, and geodynamical modeling. Chapter 1 investigates the effects of the Marion and Bouvet hotspots on the ultra-slow spreading, highly-segmented Southwest Indian Ridge (SWIR). Gravity data indicate that both Marion and Bouvet impart high-amplitude mantle Bouguer anomaly lows to the ridge axis, and suggest that long-offset transforms may diminish along-axis plume flow. Building upon this observation, Chapter 2 presents a series of 3D numerical models designed to quantify the sensitivity of along-axis plume-driven mantle flow to transform offset length, spreading rate, and mantle viscosity structure. The calculations illustrate that long-offset transforms in ultra-slow spreading environments may significantly curtail plume dispersion. Chapter 3 investigates helium isotope systematics along the western SWIR as well as near a global array of hotspots. The first part of this study reports uniformly low 3HetHe ratios of 6.3-7.3 RlRa along the SWIR from 9°-24°E, compared to values of 8±1 Ra for normal mid-ocean ridge basalt. The favored explanation for these low values is addition of (U+ Th) into the mantle source by crustal and/or lithospheric recycling. Although high HetHe values have been observed along the SWIR near Bouvet Island to the west, there is no evidence for elevated 3HetHe ratios along this section of the SWIR. The second part of Chapter 3 investigates the relationship between 3HetHe ratios and geophysical indicators of plume robustness for nine hotspots. A close correlation between a plume's flux and maximum 3HetHe ratio suggests a link between plume upwelling strength and origination in the deep, relatively undegassed mantle. Chapter 4 studies 3D mantle flow and temperature patterns beneath oceanic ridge-ridge-ridge triple junctions (TJs). In non-hotspot- affected TJs with geometry similar to the Rodrigues TJ, temperature and upwelling velocity along the slowest-spreading of the three ridges are predicted to increase within a few hundred kilometers of the TJ, to approach those of the fastest-spreading ridge. Along the slowest-spreading branch in hotspot-affected TJs such as the Azores, a strong component of along-axis flow directed away from the TJ is predicted to advect a hotspot thermal anomaly away from its deep-seated source.

Description: Funding was provided by the National Science Foundation through grants OCE- 9811924 and OCE-9907630, and by a National Defense Science and Engineering Graduate Fellowship.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 1986

Description: The dual issues of modal decomposition for tonal sound fields and the temporal coherence of the modal amplitudes are investigated for the case of the central Arctic sound channel at very low frequencies (15-80 Hz). A detailed study of the Arctic modal structure for these frequencies reveals the central role played by the strong Arctic surface duct. The performance of each of four different modal beamforming algorithms when applied to the vertical array deployed during the FRAM IV Arctic Acoustic Experiment is analyzed. A multiple beam (or decoupled beam) least squares processor produces the most acceptable results for Arctic conditions. The modal decomposition is sensitive to vertical array tilt caused by hydrodynamic drag; a technique for its estimation from the acoustie data is developed. Tonal data taken from both the horizontal and vertical arrays deployed during FRAM IV is analyzed. Horizontal array results confirm the modal amplitudes generated from vertical array data. The rough surface scattering from the ice canopy places an upper limit of 40 Hz on efficient surface duct propagation. Attenuation measurements for the first mode show excellent agreement with predictions made for ice scattering using the method of small perturbations and experimental ice statistics. The high levels of coherence observed (O.95 to 0.99) show that tonal signal propagation in the Arctic channel is essentially deterministic for time periods well in excess of one hour. The various modes may then be considered to maintain a constant phase relationship over time.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2000

Description: The thesis develops and demonstrates methods of classifying ocean processes using an underwater moving platform such as an Autonomous Underwater Vehicle (AUV). The "mingled spectrum principle" is established which concisely relates observations from a moving platform to the frequency-wavenumber spectrum of the ocean process. It clearly reveals the role of the AUV speed in mingling temporal and spatial information. For classifying different processes, an AUV is not only able to jointly utilize the time-space information, but also at a tunable proportion by adjusting its cruise speed. In this respect, AUVs are advantageous compared with traditional oceanographic platforms. Based on the mingled spectrum principle, a parametric tool for designing an AUVbased spectral classifier is developed. An AUV's controllable speed tunes the separability between the mingled spectra of different processes. This property is the key to optimizing the classifier's performance. As a case study, AUV-based classification is applied to distinguish ocean convection from internal waves. The mingled spectrum templates are derived from the MIT Ocean Convection Model and the Garrett-Munk internal wave spectrum model. To allow for mismatch between modeled templates and real measurements, the AUVbased classifier is designed to be robust to parameter uncertainties. By simulation tests on the classifier, it is demonstrated that at a higher AUV speed, convection's distinct spatial feature is highlighted to the advantage of classification. Experimental data are used to test the AUV-based classifier. An AUV-borne flow measurement system is designed and built, using an Acoustic Doppler Velocimeter (ADV). The system is calibrated in a high-precision tow tank. In February 1998, the AUV acquired field data of flow velocity in the Labrador Sea Convection Experiment. The Earth-referenced vertical flow velocity is extracted from the raw measurements. The classification test result detects convection's occurrence, a finding supported by more traditional oceanographic analyses and observations. The thesis work provides an important foundation for future work in autonomous detection and sampling of oceanographic processes.

Description: This thesis research has been funded by the Office of Naval Research (ONR) under Grants NOOOl4-95-1-1316, NOO0l4-97-1-0470, and by the MIT Sea Grant College Program under Grant NA46RG0434.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2000

Description: Processes affecting organic carbon distribution and composition can control the speciation of organic contaminants such as polychlorinated biphenyls (PCBs) and ultimately determine their residence time in a particular environment. In marine systems, the microbial loop influences organic carbon dynamics by recycling a significant fraction of dissolved and particulate organic matter. The goal of this thesis was to understand how these recycling processes affect chlorobiphenyl (CB) cycling in marine systems by monitoring CB dynamics among organic carbon pools represented by dissolved organic matter, bacterial prey and phagotrophic protozoan grazers. Initially, I studied the extent to which a protozoan grazer (Uronema sp. - 10μm ciliate) equilibrated with aqueous PCBs within 2-3 hours. Initial calculations predicted rapid equilibration via passive diffusion. Experimentally, no difference in equilibration time was noted between grazing and non-grazing protozoa, indicating that diffusion was the primary uptake pathway for these organisms. The results were extended to determine the transition size of an organism where the rates of diffusive and ingested uptake are equivalent (100-500μm). Disassociation rate constants were estimated for complexes of CB congeners and dissolved organic carbon (DOC). CB-DOC complexes enhanced the diffusive uptake rate constant for Tenax resin and, by inference, protozoan grazers. In the second phase of this work, concentrations of surfactants, organic carbon and cells were monitored over time in protozoan cultures. The effects of bacterial growth substrate and protozoan species were examined. Surfactants increased during protozoan exponential growth while total DOC concentrations decreased. Production of surface-active material in ciliate cultures was significantly higher than in flagellate cultures, and all protozoan cultures were higher than the bacterial control. Common headspace vessels were then used to compare and contrast the affinity of protozoan and bacterial culture filtrates (〈0.2μm) for PCBs relative to a seawater control. Affinities were normalized to bulk DOC and surfactant concentrations to determine underlying relationships among these parameters. Values of equilibrium partition coefficients (Koc) ranged from 1046 in Vineyard Sound seawater to 105.4 and 105.5 in protist cultures, indicating that "grazer-enhanced" DOM was a better sorbent for PCBs than DOM in bacterial controls and Vineyard Sound seawater.

Description: The work described herein was supported by National Science Foundation Contract No. OCE-9253910 and Office of Naval Research AASERT Grant No. NOOO14-96-1-0718.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution December 1999

Description: A new, global inversion is used to estimate the large scale oceanic circulation based on the World Ocean Circulation Experiment and Java Australia Dynamic Experiment hydrographic data. A linear inverse "box" model is used to combine consistently the transoceanic sections. The circulation is geostrophic with an Ekman layer at the surface and oceanic layers defined by neutral surfaces. Near-conservation of mass, salt and top-to-bottom silica is required and, in addition, heat and the phosphate-oxygen combination (170[P04]+[02]) are conserved in layers that are not in contact with the surface. A globally-consistent solution is obtained for a depth-independent adjustment to the thermal wind field, freshwater flux divergenees, the Ekman transport, and the advective and diffusive dianeutral fluxes between layers. A detailed error budget permits calculation of statistical uncertainties, taking into account both the non-resolved part of the solution and the systematic errors due to the temporal oceanic variability. The estimated water mass transports during the WOCE period (1985-1996) are generally similar to previous published estimates. However, important differences are found. In particular, the inflow of bottom waters into the Pacific Ocean is smaller than in most previous estimates. Utilization of property anomaly conservation constraints allows the estimation of significant dianeutral diffusivities in deep layers, with a global average of 3 ± lcm2s- 1 north of 30°S. Dianeutral transfers indicate that about 20 Sv of bottom water is formed in the Southern Ocean. Significant ocean-atmosphere heat fluxes are found, with a global heating of 2.3 ± 0.4PW in the tropical band and a corresponding cooling at high latitudes. The signature of a large-scale average export production is found for nutrients in several temperate regions. Despite the large uncertainties, the production magnitudes are consistent with independent measurements from sediment traps and isotopic data. Net nutrient sources or sinks are found in several regions, suggesting either transport of dissolved organic matter or a seasonal alias. Oxygen indicates large exchanges with the atmosphere, with intake at high latitudes and outgassing/remineralization at low latitudes.

Description: This work was supported in part by the Jet Propulsion Laboratory/CALTECH (contract #958125), and by gifts from Ford, General Motors, and Daimler-Chrysler to MIT's Climate Modelling Initiative.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution August 13, 1987

Description: The inverse problem of obtaining particle size distributions from observations of the angular distribution of near forward scattered light is reexamined. Asymptotic analysis of the forward problem reveals the information content of the observations, and the sources of non-uniqueness and instability in inverting them. A sampling criterion, such that the observations uniquely specify the size distribution is derived, in terms of the largest particle size, and an angle above which the intensity is indistinguishable from an asymptote. The instability of inverting unevenly spaced data is compared to that of super-resolving Fourier spectra. Resolution is shown to be inversely proportional to the angular range of observations. The problem is rephrased so that the size weighted number density is sought from the intensity weighted by the scattering angle cubed. Algorithms which impose positivity and bounds on particle size improve the stability of inversions. The forward problem can be represented by an over-determined matrix equation by choosing a large integration increment in size dependent on the frequency content of the angular intensity, further improving stability. Experimental data obtained using a linear CCD array illustrates the theory, with standard polystyrene spheres as scatterers. The scattering from single and tri-modal distributions is successfully inverted.

Description: I was supported by a NASA Technology Transfer Traineeship grant (NGT-014-800, Supplement 5), and by the Joint Program in Oceanographic Engineering between the Woods Hole Oceanographic Institution and the Massachusetts Institute of Technology. The experimental work was funded by the Coastal Research Laboratory of the Woods Hole Oceanographic Institution, through the generosity of the Mellon Foundation.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution March 1988

Description: Inverse methods are applied to historical hydrographic data to address two aspects of the general circulation of the Atlantic Ocean. The method allows conservation statements for mass and other properties, along with a variety of other constraints, to be combined in a dynamically consistent way to estimate the absolute velocity field and associated property transports. The method is first used to examine the exchange of mass and heat between the South Atlantic and the neighboring ocean basins. The Antarctic Circumpolar Current (ACC) carries a surplus of intermediate water into the South Atlantic through Drake Passage which is compensated by a surplus of deep and bottom water leaving the basin south of Africa. As a result, the ACC loses .25±.18x1015 W of heat in crossing the Atlantic. At 32°S the meridional flux of heat is .25±.19x1015 W equatorward, consistent in sign but smaller in magnitude than other recent estimates. This heat flux is carried primarily by a meridional overturning cell in which the export of 17 Sv of North Atlantic Deep Water (NADW) is balanced by an equatorward return flow equally split between the surface layers, and the intermediate and bottom water. No "leak" of warm Indian Ocean thermocline water is necessary to account for the equatorward heat flux across 32°S; in fact, a large transfer of warm water from the Indian Ocean to the Atlantic is found to be inconsistent with the present data set. Together these results demonstrate that the Atlantic as a whole acts to convert intermediate water to deep and bottom water, and thus that the global thermohaline cell associated with the formation and export of NADW is closed primarily by a "cold water path," in which deep water leaving the Atlantic ultimately returns as intermediate water entering the basin through Drake Passage. The second problem addressed concerns the circulation and property fluxes across 24°and 36°N in the subtropical North Atlantic. Conservation statements are considered for the nutrients as well as mass, and the nutrients are found to contribute significant information independent of temperature and salinity. Silicate is particularly effective in reducing the indeterminacy of circulation estimates based on mass conservation alone. In turn, the results demonstrate that accurate estimates of the chemical fluxes depend on relatively detailed knowledge of the circulation. The zonal-integral of the circulation consists of an overturning cell at both latitudes, with a net export of 19 Sv of NADW. This cell results in a poleward heat flux of 1.3±.2x1015 Wand an equatorward oxygen flux of 2900±180 kmol S-l across each latitude. The net flux of silicate is also equatorward: 138±38 kmol s-1 and 152±56 kmol s -1 across 36°and 24° N, respectively. However, in contrast to heat and oxygen, the overturning cell is not the only important mechanism responsible for the net silicate transport. A horizontal recirculation consisting of northward flow of silica-rich deep water in the eastern basin balanced by southward flow of low silica water in the western basin results in a significant silicate flux to the north. The net equatorward flux is thus smaller than indicated by the overturning cell alone. The net flux of nitrate across 36°N is n9±35 kmol 8- 1 to the north and is indistinguishable from zero at 24°N (-8±39 kmol 8-1 ), leading to a net divergence of nitrate between these two latitudes. Forcing the system to conserve nitrate leads to an unreasonable circulation. The dominant contribution to the nitrate flux at 36°N results from the correlation of strong northward flow and relatively high nitrate concentrations in the sub-surface waters of the Gulf Stream. The observed nitrate divergence between 24°and 36°N, and convergence north of 36°N, can be accounted for by a shallow cell in which the northward flow of inorganic nitrogen (nitrate) in the Gulf Stream is balanced by a southward flux of dissolved organic nitrogen in the recirculation gyre. Oxidation of the dissolved organic matter during its transit of the subtropical gyre supplies the required source of regenerated nitrate to the Gulf Stream and consumes oxygen, consistent with recent observations of oxygen utilization in the Sargasso Sea.

Description: This research was supported by NASA under contract NAG5-534 and NSF under contract OCE-8521685.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1997

Description: In order to constrain the processes controlling the cycles of biogeochemically important gases such as 02 and C02, and thereby infer rates of biological activity in the upper ocean or the uptake of radiatively important "greenhouse" gases, the noble gases are used to characterize and quantify the physical processes affecting the dissolved gases in aquatic environments. The processes of vertical mixing, gas exchange, air injection, and radiative heating are investigated using a 2 year time-series of the noble gases, temperature, and meteorological data from Station S near Bermuda, coupled with a 1- dimensional upper ocean mixing model to simulate the physical processes in the upper ocean. The rate of vertical mixing that best simulates the thermal cycle is 1.1±0.1 x104 m The gas exchange rate required to simulate the data is consistent with the formulation of Wanninkhof (1992) to ± 40%, while the formulation of Liss and Merlivat 1986 must be increased by a factor of 1.7± 0.6. The air injection rate is consistent with the formulation of Monahan and Torgersen (1991) using an air entrainment velocity of 3±1 cm s1. Gas flux from bubbles is dominated on yearly time-scales by larger bubbles that do not dissolve completely, while the bubble flux is dominated by complete dissolution of bubbles in the winter at Bermuda. In order to obtain a high-frequency time-series of the noble gases to better parameterize the gas flux from bubbles, a moorable, sequential noble gas sampler was developed. Preliminary results indicate that the sampler is capable of obtaining the necessary data. Dissolved gas concentrations can be significantly modified by ice formation and melting, and due to the solubility of He and Ne in ice, the noble gases are shown to be unique tracers of these interactions. A three-phase equilibrium partitioning model was constructed to quantify these interactions in perennially ice-covered Lake Fryxell, and this work was extended to oceanic environments. Preliminary surveys indicate that the noble gases may provide useful and unique information about interactions between water and ice.

Description: This work has been supported by the National Science Foundation - OCE 9302812 and DPP 9118363, the Ocean Ventures Fund Ditty Bag Fund and Westcott Fund and the WHOI Education Office.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 1998

Description: A freshwater plume often forms when a river or an estuary discharges water onto the continental shelf. Freshwater plumes are ubiquitous features of the coastal ocean and usually leave a striking signature in the coastal hydrography. The present study combines both hydrographic data and idealized numerical simulations to examine how ambient currents and winds influence the transport and mixing of plume waters. The first portion of the thesis considers the alongshore transport of freshwater using idealized numerical simulations. In the absence of any ambient current, the downstream coastal current only carries a fraction of the discharged fresh water; the remaining fraction recirculates in a continually growing "bulge" of fresh water in the vicinity of the river mouth. The fraction of fresh water transported in the coastal current is dependent on the source conditions at the river mouth. The presence of an ambient current augments the transport in the plume so that its freshwater transport matches the freshwater source. For any ambient current in the same direction as the geostrophic coastal current, the plume will evolve to a steady-state width. A key result is that an external forcing agent is required in order for the entire freshwater volume discharged by a river to be transported as a coastal current. The next section of the thesis addresses the wind-induced advection of a river plume, using hydrographic data collected in the western Gulf of Maine. The observations suggest that the plume's cross-shore structure varies markedly as a function of fluctuations in alongshore wind forcing. Consistent with Ekman dynamics, upwelling favorable winds spread the plume offshore, at times widening it to over 50 km in offshore extent, while downwelling favorable winds narrow the plume width to a few Rossby radii. Near-surface current meters show significant correlations between cross-shore currents and alongshore wind stress, consistent with Ekman theory. Estimates of the terms in the alongshore momentum equation calculated from moored current meter arrays also indicate an approximate Ekman balance within the plume. A significant correlation between alongshore currents and alongshore wind stress suggests that interfacial drag may be important. The final section of the thesis is an investigation of the advection and mixing of a surface-trapped river plume in the presence of an upwelling favorable wind stress, using a three-dimensional model in a simple, rectangular domain. Model simulations demonstrate that the plume thins and is advected offshore by the crossshore Ekman transport. The thinned plume is susceptible to significant mixing due to the vertically sheared horizontal currents. The first order plume response is explained by Ekman dynamics and a Richardson number mixing criterion. Under a sustained wind event, the plume evolves to a quasi-steady, uniform thickness. The rate of mixing slowly decreases for longer times as the stratification in the plume weakens, but mixing persists under a sustained upwelling wind until the plume is destroyed. Mixing is most intense at the seaward plume front due to an Ekman straining mechanism in which the advection of cross-shore salinity gradients balances vertical mixing. The mean mixing rate observed in the plume is consistent with the mixing power law suggested by previous studies of I-D mixing, in spite of the two-dimensional dynamics driving the mixing in the plume.

Description: This research was funded by a National Science Foundation graduate fellowship, and Gulf of Maine Regional Marine Research Program grants UM-S227 and UM-S276.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 1998

Description: In this thesis, I investigated the how the life history characteristics of the clam Mya arenaria determine the population response to chronic contaminant exposure. To predict the potential responses of a broadcast-spawning life history such as that of M. arenaria, I surveyed the literature on a variety of bivalve species. By incorporating information on growth, survival, and reproduction into matrix population models I could evaluate the relative contributions of these factors to fitness. For broadcast-spawners, long life is an important factor enabling them to gamble on rare, large recruitment events. Another important aspect of the broadcast spawning strategy is the possibility of high variation in larval settlement from year to year. I evaluated the role that this variability plays using a stochastic matrix model, and showed that it tends to increase population growth because of the larger size of rarer, successful recruitment events. With an understanding of how the life history traits of M. arenaria might control its responses to change in the environment, I analyzed the vital rates of clams at clean and contaminated sites. The effects of contaminants measured in the lab do not necessarily predict population condition in the field. Since surviving with a long life span contributes the most to fitness in broadcast-spawning bivalves, effects on reproductive output and juvenile survival, which are strong in many lab studies, may not necessarily playa large role in field populations. The life history of this clam, with natural variation in recruitment from year to year, further reduces the population dependence on high reproductive output and larval survival. The combination of little population-level relevance of the strongest contaminant effects, and potential contaminant effects on very important clam predators, could explain why populations at contaminated sites are observed to be growing the fastest. The interaction of contaminant exposure and normal ecological processes determines the overall impact on the population.

Description: This research was supported by a Massachusetts Bay Programs grant to Judith McDowell and Damian Shea, NSF grant # DEB-9211945 to Hal Caswell, a National Defense Science and Engineering Graduate Fellowship to Bonnie Ripley, a Pew Fellowship in Conservation and the Environment to Judith McDowell, Sea Grant grant # NA46RG0470 (project # RIP-54), and by the M.I.T./W.H.O.I. Joint Program Education Office.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2011

Description: Corals are increasingly threatened by warming sea surface temperatures and other anthropogenic changes. The delicate symbiosis between corals and their algal endosymbionts (zooxanthellae) is easily disrupted by thermal stress, leading to bleaching and eventual mortality. The use of lipid ratios as biomarkers of environmental conditions is well established. Coral biomass contains abundant lipids, and the potential of lipid parameters to diagnose thermal tolerance in zooxanthellae has been previously suggested. In this thesis, I explore the response of specific fatty acids, sterols, and thylakoid membrane lipids to thermal and disease stress in zooxanthellae grown in culture, as well as those isolated from living corals. I present the discovery of a bioactive thylakoid lipid within zooxanthellae cells, and show how this compound is selectively mobilized in thermally stressed cells. I present a plausible mechanism for the breakdown of this compound into products that may cause apoptosis and disrupt the coral-­‐algal symbiosis, eventually causing bleaching. I present two new lipid biomarkers of thermal stress in zooxanthellae, the C18 fatty acid unsaturation ratio, and the fatty acid to sterol ratio. I calibrate the decline of these two parameters to levels of thermal stress comparable to those needed to cause bleaching. I further show that these parameters are sensitive to pathogen stress as well. In several case studies of diseased and thermally stressed corals, I demonstrate that these lipid biomarkers of coral stress may be applied to zooxanthellae isolated from environmental samples. I show that these same compounds are preserved within coral aragonite, which opens up the potential to retrieve lipid-­‐based historical records of coral health from annual layers of coral skeleton. This work demonstrates the value of using lipid biomarkers to assess coral health and better understand the biochemical mechanisms of coral bleaching.

Description: This work was supported by a grant from the Summit Foundation, Award No. USA 00002/KSA 00011 made by King Abdullah University of Science and Technology (KAUST), and funding from the Woods Hole Oceanographic Institution.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution April 1999

Description: The goal of this thesis was to use high resolution analytical techniques coupled with molecular level analyses to chemically characterize high molecular weight (〉 1 k Da (HMW)) dissolved organic matter (DOM) isolated from seawater in an attempt to provide new insights in to the cycling of DOM in the ocean. While a variety of sites spanning different environments (fluvial, coastal and oceanic) and ocean basins were examined, the chemical structure of the isolated HMW DOM varied little at both the polymer and monomer levels. All samples show similar ratios of carbohydrate: acetate: lipid carbon (80±4: 10±2:9±4) indicating that these biochemicals are present within a family of related polymers. The carbohydrate fraction shows a characteristic distribution of seven major neutral monosaccharides: rhamnose, fucose, arabinose, xylose, mannose, glucose and galactose; and additionally contains Nacetylated amino sugars as seen by Nuclear Magnetic Resonance Spectroscopy (NMR). This family of compounds, consisting of a specifically linked polysaccharide backbone that is acylated at several positions, has been termed acylated polysaccharides (APS) by our laboratory. APS accounts for 50% of the carbon in HMW DOM isolated from the surface ocean and 20% of the carbon in HMW DOM isolated from the deep ocean. In order to identify a possible source for APS three species of phytoplankton, Thalassiossira weissflogii, Emiliania huxleyi and Phaeocystis, were cultured in seawater and their HMW DOM exudates examined by variety of analytical techniques. Both the T. weissflogii and E. huxleyi exudates contain compounds that resemble APS indicating that phytoplankton are indeed a source of APS to the marine environment. Furthermore, the degradation of the T. weissflogii exudate by a natural assemblage of microorganisms indicates that the component resembling APS is more resistant to microbial degradation compared to other polysaccharides present in the culture. Molecular level analyses show the distribution of monosaccharides to be conservative in surface and deep waters suggesting that APS is present throughout the water column. In order to determine the mechanism by which APS is delivered to the deep ocean the Δ14C value of APS in the deep ocean was compared to the Δ14C value of the dissolved inorganic carbon (DIC) at the same depth. If the formation of deep water is the dominant mode of transport then both the DIC and APS will have similar Δ14C values. However, if APS is injected into the deep ocean from particles or marine snow then the Δ14C value of APS will be higher than the DIC at the same depth. Our results indicate that APS in the deep Pacific Ocean carries a modem Δ14C value and is substantially enriched in 14C relative to the total HMW DOM and the DIC at that depth. Thus, particle dissolution appears to be the most important pathway for the delivery of APS to the deep ocean.

Description: This thesis was funded by a grant from the US Department of Energy, Ocean Margins Program.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1999

Description: Odontocetes are assumed to use echolocation for navigation and foraging, but neither of these uses of biosonar has been conclusively demonstrated in free-ranging animals. Many bats are known to use echolocation throughout foraging sequences, changing the structure and timing of clicks as they progress towards prey capture. For odontocetes, however, we do not know enough about their foraging behavior to describe such sequences. To conduct detailed behavioral observations of any subject animal, the observer must be able to maintain continuous visual contact with the subject for a period commensurate with the duration of the behavior(s) of interest. Behavioral studies of cetaceans, which spend approximately 95% of their time below the water's surface, have been limited to sampling surface behavior except in special circumstances, e.g. clear-water environments, or with the use of technological tools. I addressed this limitation through development of an observation platform consisting of a remote controlled video camera suspended from a tethered airship with boat-based monitoring, adjustment, and recording of video. The system was used successfully to conduct continuous behavioral observations of bottlenose dolphins in the Sarasota Bay, FL area. This system allowed me to describe previously unreported foraging behaviors and elucidate functions for behaviors already defined but poorly understood. Dolphin foraging was modeled as a stage-structured sequence of behaviors, with the goal-directed feeding event occurring at the end of a series of search, encounter, and pursuit behaviors. The behaviors preceding a feeding event do not occur in a deterministic sequence, but are adaptive and plastic. A single-step transition analysis beginning with prey capture and receding in time has identified significant links between observed behaviors and demonstrated the stage-structured nature of dolphin foraging. Factors affecting the occurrence of specific behaviors and behavioral transitions include mesoscale habitat variation and individual preferences. The role of sound in foraging, especially echolocation, is less well understood than the behavioral component. Recent studies have explored the use of echolocation in captive odontocete foraging and presumed feeding in wild animals, but simultaneous, detailed behavioral and acoustic observations have eluded researchers. The current study used two methods to obtain acoustic data. The overhead video system includes two towed hydrophones used to record 'ambient' sounds of dolphin foraging. The recordings are of the 'ambient' sounds because the source of the sounds, i.e. animal, could not be localized. Many focal follows, however, were conducted with single animals, and from these records the timing of echolocation and other sounds relative to the foraging sequence could be examined. The 'ambient' recordings revealed that single animals are much more vocal than animals in groups, both overall and during foraging. When not foraging, single animals vocalized at a rate similar to the per animal rate in groups of ≥2 animals. For single foraging animals, the use of different sound types varies significantly by the habitat in which the animal is foraging. These patterns of use coupled with the characteristics of the different sound types suggest specific functions for each. The presence of multiple animals in a foraging group apparently reduces the need to vocalize, and potential reasons for this pattern are discussed. In addition, the increased vocal activity of single foraging animals lends support to specific hypotheses of sound use in bottlenose dolphins and odontocetes in general. The second acoustic data collection method records sounds known to be from a specific animal. An acoustic recording tag was developed that records all sounds produced by an animal including every echolocation click. The tag also includes an acoustic sampling interval controller and a sensor suite that measures pitch, roll, heading, and surfacing events. While no foraging events occurred while an animal was wearing an acoustic data logger, the rates of echolocation and whistling during different activities, e.g. traveling, were measured.

Description: This work was supported by the Education Office of the Woods Hole Oceanographic Institution, two grants from the Rinehart Coastal Research Center, the Ocean Ventures Fund; WHOI Sea Grant, ONR Grant #N00014-94-1-0692 to P. Tyack, and a Graduate Fellowship from the Office of Naval Research.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2011

Description: Eastern oceanic boundary currents are subject to hydrodynamic instability, generate small scale features that are visible in satellite images and may radiate westward into the interior, where they can be modified by the large-scale circulations. This thesis studies the stability of an eastern boundary current with and without the large-scale flow influence in an idealized framework represented by barotropic quasi-geostrophic dynamics. The linear stability analysis of a meridional current with a continuous velocity profile shows that meridional eastern and western boundary currents support a limited number of radiating modes with long meridional and zonal wavelengths and small growth rates. However, the linearly stable, long radiating modes of an eastern boundary current can become nonlinearly unstable by resonating with short trapped unstable modes. This phenomenon is clearly demonstrated in the weakly nonlinear simulations. Results suggest that linearly stable longwave modes deserve more attention when the radiating instability of a meridional boundary current is considered. A large-scale flow affects the short trapped unstable mode and long radiating mode through different mechanisms. The large-scale flow modifies the structure of the boundary current to stabilize or destabilize the unstable modes, leading to a meridionally localized maximum in the perturbation kinetic energy field. The shortwave mode is accelerated or decelerated by the meridional velocity adjustment of the large-scale flow to have an elongated or a squeezed meridional structure, which is confirmed both in a linear WKB analysis and in nonlinear simulations. The squeezed or elongated unstable mode detunes the nonlinear resonance with the longwave modes, which then become less energetic. These two modes show different meridional structures in kinetic energy field because of the different mechanisms. In spite of the model simplicity, these results can potentially explain the formation of the zonal jets observed in altimeter data, and indicate the influence of the large-scale wind-driven circulation on eastern boundary upwelling systems in the real ocean. Studies with more realistic configurations remain future challenges.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2011

Description: The colonization dynamics and life histories of pioneer species are vital components in understanding the early succession of nascent hydrothermal vents. The reproductive ecology of pioneer species at deep-sea hydrothermal vents may provide insight into their dispersal, population connectivity, and ability to colonize after disturbance. An opportunity to study the reproductive traits of two pioneer gastropod species, Ctenopelta porifera and Lepetodrilus tevnianus, presented itself in 2006 after an eruption on the East Pacific Rise (EPR) eliminated vent communities near 9°50ʹ′N. Standard histological techniques were used to determine whether reproductive characteristics, such as timing of gamete release, fecundity, or time to maturation, differed from other vent gastropods in ways that might explain arrival of these two species as early colonizers. Both species exhibited two-component oocyte size frequency distributions that indicated they were quasi-continuous reproducers with high fecundity. In C. porifera, the oocyte size distributions differed slightly between two collection dates, suggesting that environmental cues may introduce some variability in gamete release. In samples collected within one year of the estimated eruption date, individuals in populations of both C. porifera and L. tevnianus were reproductively mature. The smallest reproducing C. porifera were 4.2 mm (males) and 5.4 mm (females) in shell length, whereas reproductive L. tevnianus were smaller (2.3 and 2.4 mm in males and females respectively). Most C porifera in the population were large (〉 6.0 mm) compared to their settlement size and reproductively mature. In contrast, most L tevnianus were small (〈 1.0 mm) and immature. Reproductive traits of the two species are consistent with opportunistic colonization, but are also similar to those of other Lepetodrilus species and peltospirids at vents, and do not explain why these particular two species were the dominant pioneers. It is likely that their larvae were in high supply immediately after the eruption due to oceanographic transport processes from remote source populations.

Description: This work was supported by National Science Foundation grant OCE- 0424953 to Mullineaux and by funds provided through the WHOI Summer Student Fellowship program and the Brown University Ecology and Evolutionary Biology Department to Bayer.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 1999

Description: This study is a geochemical investigation ofthe evolution of the Kerguelen plume, on the basis of upper mantle and lower crustal xenoliths. Ultramafic xenoliths include harzburgites predominant, a lherzolite, dunites and pyroxenites, whereas lower crustal xenoliths are cumulate gabbros recrystallized under granulite facies conditions. On the basis of the whole rock major element characteristics and trace element abundance patterns in clinopyroxenes, the harzburgites were found to be residues of extensive melting at high pressures within the Kerguelen plume. These were then recrystallized at low pressures and metasomatized by plume generated melts. Details of the metasomatic process were determined from trace element variations in clinopyroxene in connection to texture. This demonstrated that meltrock reaction and the precipitation of new clinopyroxenes occurred by metasomatic carbonatitic melts. It was also found that some of the harzburgites had distinctly unradiogenic Os isotopic compositions and were identified as originating from the sub-Gondwanaland lithosphere. On the basis of major and trace element compositions, the granulite xenoliths were found to be originally gabbroic cumulates formed from plume-derived basaltic melts emplaced at the base of the crust by underplating and subsequently recrystallized isobarically under granulite conditions. The Sr, Nd and Os isotopic compositions of the peridotite and granulite xenoliths demonstrate that the Kerguelen plume is isotopically heterogeneous and displays a temporal progression toward more enriched Sr and Nd isotopic compositions from the Ninetyeast Ridge to granulite xenoliths to Kerguelen basalts and Heard Island basalts.

Description: This research was supported by the National Geographic Society 4629-9 1, the National Science Foundation EAR-9219158 and OPP-9417806, and William Van Alan Clark Senior Scientist Chair to Nobu Shimizu. I was also supported by a Cecil and Ida Green Fellowship and a Education Graduate Research Fellowship.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 1999

Description: The objective of this thesis is to develop the methods necessary for evaluating the role of learning in the natural whistle development of bottlenose dolphins. Bottlenose dolphins provide a unique opportunity to study social influences on vocal learning in a highly social non-human mammal. Vocal learning is critical for the development of human language but plays a much smaller role in the vocal development of most non-human terrestrial mammals. Preliminary evidence has indicated that the signature whistles of dolphin calves are modeled on the whistles in the calves' early environments and that the calves' social interactions influence the choice of model. The methods currently used to study the acoustic and social behavior of dolphins are insufficient to evaluate the role of learning in whistle development and the social influences on that development. The techniques necessary to perform such a study have therefore been developed and tested in this thesis. The methods used to study vocal learning in various species were reviewed and a study of vocal learning appropriate to dolphins was designed. A strategy for sampling the dolphins' social and acoustic behavior was developed. To test the sampling strategy, and to provide data for the development of analysis techniques, a pilot study was performed on dolphin calves born in captivity. Focal samples of the social interactions of dolphin mothers and calves were taken over several months before and after the births of four calves, with simultaneous acoustic recordings during all focal sessions. A test of sampling times determined that five focal samples spaced throughout the day adequately represented the dolphins' behavior for the entire day. The interactions recorded during the focal samples were analyzed with loglinear analysis, multidimensional scaling, and hierarchical cluster analysis to determine the types of social relationships that occurred between the dolphins. For both calves and adults, three types of relationships were found. An analysis of a prolonged alloparenting incident demonstrated that the social relationship between mothers and calves was a care-giving relationship independent of their genetic relationship. Measures other than the total association were found to be necessary to the evaluation of the subtle relationships between the dolphins. Methods for the quantitative analysis of the whistles produced by the dolphins were needed. Therefore, programs were developed to automatically detect and extract the whistles from the recordings in an unbiased manner. Several methods for categorizing whistles were compared and hierarchical cluster analysis of dynamic time warping of extracted contours was shown to perform well for comparing both stereotyped and un-stereotyped whistles. These techniques were then used to compare the early acoustic environments of the calves born in the pilot study. The early environments of the four calves were found to be distinctive. In particular, the putative signature whistle of each calf s mother made up a substantial proportion of the whistles in that calf's early environment. The combination techniques developed in this thesis for the analysis of the social and acoustic behavior of dolphins will allow a study of vocal learning in dolphin whistle development to be performed in a quantitative, unbiased manner.

Description: The first five years of my thesis work were funded by a pre-doctoral fellowship from the Howard Hughes Medical Institute. The WHOI Education office funded the following year and a half. My fieldwork was funded by two grants, from the Rinehart Coastal Research Center and the Ocean Ventures Fund.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 1999

Description: This thesis studies the problems of generation and maintenance of recirculations by Gulf Stream instabilities. Observations show that the horizontal structure of the jet and its recirculations suffer significant changes in time. Here, the role of internal dynamics of the jet is isolated as one of the possible sources of such variability, and the differences between barotropic and baroclinic instabilities are investigated. The problem of recirculation development is considered in a framework of a free spin down of the 2-layer and the 1-layer, zonally symmetric, quasi-geostrophic jets. Linear stability analysis shows that in strongly baroclinic basic flows, eddies are capable of driving recirculations in the lower layer through the residual meridional circulation. In strongly barotropic jets, the linearly most unstable wave simply diffuses the jet. Nonlinear stability analysis indicates that recirculations are robust features of the 2-layer model. The strength of recirculations is a function of the model’s parameters. It increases with a decrease in the value of the nondimensional /3 due to potential vorticity homogenization constrained by enstrophy conservation. The recirculation strength is a non-monotonic function of the baroclinic velocity parameter; it is the strongest for strongly baroclinic basic flows, weakest for flows with intermediate baroclinic structure and of medium strength for strongly barotropic basic flows. Such non-monotonic behavior is the result of two different processes responsible for the recirculation development: linear eddy-mean flow interactions for strongly baroclinic basic flows and strongly nonlinear eddy-eddy and eddy-mean flow interaction for strongly barotropic flows. In the case of the reduced-gravity model, recirculations develop only for infinite deformation raduis. Basic flows with finite deformation radius are only weakly supercritical and therefore produced negligible recirculations after equilibration. The problem of maintenance of the recirculations is coupled to the questions of existence of low frequency variability and of multiple dynamical regimes of a system consisting of a quasi-geostrophic jet and its recirculations. The problem is studied in a framework of a 2-layer or a reduced-gravity colliding jets model which has no windforcing. Instead, it is forced by inflows and outflows through the open boundaries. Oniy the western boundary of the domain is closed, and a free slip boundary condition is used there. The results of the numerical experiments show that when oniy the mechanism of barotropic instability is present, the model has two energy states for a wide range of interfacial friction coefficients. The high energy state is characterized by well-developed recirculations and displays strong variability associated with either large recirculating gyres and a weak eddy field or small recirculations and a strong eddy field. The iow energy state is characterized by large meridional excursions in the separation point and large amplitude, westward propagating meanders that produce strong rings after interacting with the western wall. For physically relevant bottom friction values, the presence of baroclinic in stability in the recirculation regions of the 2-layer model allows for a unique dynamical regime characterized by well-developed recirculations in both layers. The low-frequency variability associated with the regime is weak and is related to meridional shifts in the position of the jet, to wrapping of the recirculations around each other, and to pulsations in their zonal extent. For strong bottom friction, the 2-layer model has only the mechanism of barotropic instability which reduces it to a 1 1/2-layer configuration; the model displays two dynamical regimes and strong low frequency variability in the upper layer, while the lower layer is strongly frictional.

Description: Financial support for this research was provided by NSF grant number OCE 9617848.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2011

Description: Sampling the vast volumes of the ocean requires tools capable of observing from a distance while retaining detail necessary for biology and ecology, ideal for optical methods. Algorithms that work with existing SeaBED AUV imagery are developed, including habitat classi fication with bag-of-words models and multi-stage boosting for rock sh detection. Methods for extracting images of sh from videos of longline operations are demonstrated. A prototype digital holographic imaging device is designed and tested for quantitative in situ microscale imaging. Theory to support the device is developed, including particle noise and the effects of motion. A Wigner-domain model provides optimal settings and optical limits for spherical and planar holographic references. Algorithms to extract the information from real-world digital holograms are created. Focus metrics are discussed, including a novel focus detector using local Zernike moments. Two methods for estimating lateral positions of objects in holograms without reconstruction are presented by extending a summation kernel to spherical references and using a local frequency signature from a Riesz transform. A new metric for quickly estimating object depths without reconstruction is proposed and tested. An example application, quantifying oil droplet size distributions in an underwater plume, demonstrates the efficacy of the prototype and algorithms.

Description: Funding was provided by NOAA Grant #5710002014, NOAA NMFS Grant #NA17RJ1223, NSF Grant #OCE-0925284, and NOAA Grant #NA10OAR4170086

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution January 1999

Description: Today, deep waters produced in the North Atlantic are exported through the western South Atlantic. Antarctic intermediate water AAJW also enters the Atlantic in this region. Circumpolar deep water (CDW) fills the depths below AAIW and above and below northern source waters. A depth transect of cores from 1567-3909 m water depth in the western South Atlantic are ideally located to monitor inter-ocean exchange of deep water, and variations in the relative strength of northern versus southern source water production. Last glacial maximum (LGM) Cd/Ca and δ13C data indicate a nutrient-depleted intermediate-depth water mass. In the mid-depth western South Atlantic, a simple conversion of LGM δ13C data suggests significantly less nutrient enrichment than LGM Cd/Ca ratios, but Cd/Ca and δ13C data can be reconciled when plotted in CdW/δ13C space. Paired LGM Cd/Ca and δ13C data from mid-depth cores suggest increasingly nutrient rich waters below 2000 m, but do not require an increase in Southern Ocean water contribution relative to today. Cd/Ca data suggest no glacial-interglacial change in the hydrography of the deepest waters ofthe region. To maintain relatively low Cd/Ca ratios low nutrients in the deepest western South Atlantic waters, and in CDW in general, during the LGM requires an increased supply ofnutrient-depleted glacial North Atlantic intermediate water (GNA1W) and/or nutrient-depleted glacial Subantarctic surface waters to CDW to balance reduced NADW contribution to CDW. LGM Cd/Ca and δ13C data suggest strong GNA1W influence in the western South Atlantic which in turn implies export of GNAIW from the Atlantic, and entrainment of GNA1W into the Antarctic Circumpolar current.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 1999

Description: Changes in morphology of the Marquesas Fracture Zone are correlated with small changes in Pacific-Farallon relative motion. The simple flexural signal of a locked fracture zone may be obscured by tectonic effects, and there is no evidence for the release of shear stress on the fracture zone by vertical slip after leaving the active transform. One such small change in plate motion is documented in the South ern Austral Island region of the South Pacific. A twelve degree clock wise change in Pacific-Farallon relative motion occurred around fifty million years ago. This Eocene change in spreading direction and rate is locally constrained with observations of magnetic anomalies and spreading fabric orientation. At the southeastern end of the Cook-Austral Island chain, multiple episodes of volcanism have left a diverse population of seamounts. Volume estimates from geophysical data and modeling show that one-half to two-thirds of the volcanic material is over thirty million years old, while the remainder is less than five million years old. Seismic and bathymetric data imply the presence of abyssal basalt flows in the flexural moat of the Austral Islands, probably associated with Austral Islands volcanism, which may contribute a significant amount of material to the archipelagic apron.

Description: The research presented in Chapter 2 was supported by National Science Founda tion grants OCE-9012949 and OCE-9012529. Chapters 3, 4 and 5 were supported by National Science Foundation grant OCE-9415930. A National Science Foundation graduate fellowship supported my first three years of graduate study.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 1999

Description: This thesis focuses on improving the productivity of autonomous and telemanipulation systems consisting of a manipulator arm mounted to a free flying underwater vehicle. Part I minimizes system sensitivity to misalignment by developing a gripper and a suite of handles that passively self align when grasped. After presenting a gripper guaranteed to passively align cylinders we present several other self aligning handles. The mix of handle alignment and load resisting properties enables handles to be matched to the needs of each task. Part I concludes with a discussion of successful field use of the system on the Jason Remotely Operated Undersea Vehicle operated by the Woods Hole Oceanographic Institution. To enable the exploitation of contact with the environment to help stabilize the vehicle, Part II develops a technique which identifies the contact state of a planar vehicle interacting with a fixed environment. Knowing the vehicle geometry and velocity we identify kinematically feasible contact points, from which we construct the set of feasible contact models. The measured vehicle data violates each model’s constraints; we use the associated violation power and work to select the best overall model. Part II concludes with experimental confirmation of the contact identification techniques efficacy.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 1999

Description: During July and August of 1996, a large acoustics/physical oceanography experiment was fielded in the Mid-Atlantic Bight, south of Nantucket Island, MA. Known as the Shelfbreak Front PRIMER Experiment, the study combined acoustic data from a moored array of sources and receivers with very high resolution physical oceanographic measurements. This thesis addresses two of the primary goals of the experiment, explaining the properties of acoustic propagation in the region, and tomographic inversion of the acoustic data. In addition, this thesis develops a new method for predicting acoustic coherence in such regions. Receptions from two 400 Hz tomography sources, transmitting from the continental slope onto the shelf, are analyzed. This data, along with forward propagation modeling utilizing SeaSoar thermohaline measurements, reveal that both the shelfbreak front and tidally-generated soliton packets produce stronger coupling between the acoustic waveguide modes than expected. Arrival time wander and signal spread show variability attributable to the presence of a shelf water meander, changes in frontal configuration, and variability in the soliton field. The highly-coupled nature of the acoustic mode propagation prevents detailed tomographic inversion. Instead, methods based on only the wander of the mode arrivals are used to estimate path-averaged temperatures and internal tide "strength". The modal phase structure function is introduced as a useful proxy for acoustic coherence, and is related via an integral transform to the environmental sound speed correlation function. Advantages of the method are its flexibility and division of the problem into independent contributions, such as from the water column and seabed.

Description: Office of Naval Research for providing funding for this thesis through AASERT Grant N00014-96-1-0918, and through ONR Grant N00014-98-1-0059.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 1999

Description: In this thesis the analysis of natural ice events is carried out based on direct measurements of ice-borne seismo-acoustic waves generated by ice fracturing processes. A major reason for studying this phenomenon is that this acoustic emission is a significant contributor to Arctic ocean ambient noise. Also the Arctic contains rich mineral and oil resources and in order to design mining facilities able to withstand the harsh environmental conditions, we need to have a better understanding of the processes of sea ice mechanics. The data analyzed in this thesis were collected during the Sea Ice Mechanics Initiative SIMI’94 experiment which was carried out in the spring of 1994 in the Central Arctic. One of the contributions of this thesis was the determination of the polarization characteristics of elastic waves using multicomponent geophone data. Polarization methods are well known in seismology, but they have never been used for ice event data processing. In this work one of the polarization methods so called Motion Product Detector method has been successfully applied for localization of ice events and determination of polarization characteristics of elastic waves generated by fracturing events. This application demonstrates the feasibility of the polarization method for ice event data processing because it allows one to identify areas of high stress concentration and "hot spots" in ridge building process. The identification of source mechanisms is based on the radiation patterns of the events. This identification was carried out through the analysis of the seismo-acoustic emission of natural ice events in the ice sheet. Previous work on natural ice event identification was done indirectly by analyzing the acoustic energy radiated into the water through coupling from elastic energy in the ice sheet. After identification of the events, the estimation of the parameters of fault processes in Arctic ice is carried out. Stress drop, seismic moment and the type of ice fracture are determined using direct near-field measurements of seismo-acoustic signals generated by ice events. Estimated values of fracture parameters were in good agreement with previous work for marginal ice zone. During data processing the new phenomenon was discovered: "edge waves", which are waves propagating back and forth along a newly opened ice lead. These waves exhibit a quasi-periodic behavior suggesting some kind of stick-slip generation mechanism somewhere along the length of the lead. The propagation characteristics of these waves were determined using seismic wavenumber estimation techniques. In the low frequency limit the dispersion can be modeled approximately by an interaction at the lead edges of the lowest order, antisymmetric modes of the infinite plate.

Description: Support for this thesis was provided by Office of Naval Research.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 1999

Description: In the marine bacterium Vibrio fischeri two intercellular homoserine-Iactone signal molecules (luxI-dependent 30C6-HSL and the ainS-dependent C8-HSL) and the transcriptional activator LuxR regulate the luminescence system in a cell-density dependent manner by a process termed quorum sensing. In this study, five additional proteins whose production is regulated by quorum sensing are described, and the genes encoding four of the five proteins, denoted as QsrP, RibB, QsrV, and AcfA, are analyzed. Each protein is positively regulated by 30C6-HSL and LuxR and negatively regulated at low population density by C8-HSL. Probable LuxR/autoinducer binding sites are found in the promoter region of each. QsrP and RibB are encoded monocistronically, whereas AcfA and QsrV appear to be encoded by a two-gene operon. On the basis of sequence similarity to proteins of known function from other organisms, RibB is believed to be an enzyme that catalyzes the transformation of ribulose 5-phosphate to 3,4-dihydroxy-2- butanone 4-phosphate, a precursor for the xylene ring of riboflavin; AcfA is believed to be a pilus subunit; and the functions of QsrP and QsrV are unknown at this time. A qsrP mutant was reduced in its ability to colonize its symbiotic partner, Euprymna scolopes when placed in competition with the parent strain. On the other hand, a mutant strain of V. fischeri containing an insertion in acfA, which is believed to be polar with respect to qsrV, displayed enhanced colonization competence in a competition assay. A ribB mutant grew well on media not supplemented with additional riboflavin and displayed normal induction of luminescence. Both phenotypes suggest that the lack of a functional ribB gene is complemented by another gene of similar function in the mutant. Oriented divergently from acfA are open reading frames that code for two putative proteins that are similar in sequence to members of the LysR family of transcriptional regulators. Organization of the two divergent sets of genes and the shared promoter region suggests that transcription of acfA and qsrV may be regulated by one or both of these divergently transcribed proteins. This work defines a quorum-sensing regulon in V. fischeri. A model describing its regulation is presented.

Description: Woods Hole Oceanographic Institution, including The J. Seward Johnson Fund, for contributing financially

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology [and the Woods Hole Oceanographic Institution] June 1975

Description: Many species of prosobranch gastropod deposit their eggs in tough capsules affixed to hard substrates. Generally, there is a small opening near the top of such capsules, occluded by a firm plug (operculum) which must be removed before the veligers can escape. Although the removal of the operculum is generally attributed to embryonic secretion of enzymes, there is little experimental support for this sugsestion. In the limited experiments which have been reported, all dealing with species that emerge as juvenile snails, no attempt was made to determine the properties of the hatching substance, or the timing of its production. My research has dealt with the escape of veligers from the egg capsules of two related species, Nassarius obsoletus and N. trivittatus. Their egg capsules are quite similar in size, number of eggs contained, general morphology, and the thickness of the material plugging the opening at the top. Both hatch as swimming veligers, after about one week of encapsulated. development. By adding fresh plug material to small volumes of sea-water containing veligers obtained prior to, or at known times after their normal hatching, I have demonstrated conclusively the essentially chemical nature of operculum removal for these two species. In addition, the hatching substance was found to be produced in a short pulse, to be functionally short-lived, and to be species-specific in its action for the two species considered. There is no evidence that the secretion of the hatching substance is stimulated by short pulses of light or increased temperature; the capsules of N. obsoletus contain many more embryos than are needed to successfully remove the plug, so that complete synchrony of hatching substance production by all individuals within a capsule is probably not necessary. Lastly, the observed rates at which N. obsoletus veligers leave their egg capsules were compared with those predicted from an equation assuming random movement of individuals. A close agreement was found, the capsules losing 98% of their residents within 45 to 55 minutes of the first escape. Thus, the location of the exit by an individual is probably by chance.

Description: This work was supported by a graduate fellowship from the Woods Hole Oceanographic Institution.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2011

Description: The ocean depths provide an ever changing and complex imaging environment. As scientists and researches strive to document and study more remote and optically challenging areas, specifically scatter-limited environments. There is a requirement for new illumination systems that improve both image quality and increase imaging distance. One of the most constraining optical properties to underwater image quality are scattering caused by ocean chemistry and entrained organic material. By reducing the size of the scatter interaction volume, one can immediately improve both the focus (forward scatter limited) and contrast (backscatter limited) of underwater images. This thesis describes a relatively simple, cost-effective and field-deployable low-power dynamic lighting system that minimizes the scatter interaction volume with both subjective and quantifiable improvements in imaging performance.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2011

Description: Melting and crystallization processes on the Earth and Moon are explored in this thesis, and the topics of melt generation, transport, and crystallization are discussed in three distinct geologic environments: the Moon's mantle, the Greenland ice sheet, and the Earth's crust. Experiments have been conducted to determine the conditions of origin for two high-titanium magmas from the Moon. The lunar experiments (Chapter 2) were designed to explore the e ects of variable oxygen fugacity (fO2) on the high pressure and high temperature crystallization of olivine and orthopyroxene in high-Ti magmas. The results of these experiments showed that the source regions for the high-Ti lunar magmas are distributed both laterally and vertically within the lunar mantle, and that it is critical to estimate the pre-eruptive oxygen fugacity in order to determine true depth of origin for these magmas within the lunar mantle. Chapter 3 models the behavior of water ow through the Greenland ice sheet driven by hydrofracture of water through ice. The results show that melt water in the ablation zone of Greenland has almost immediate access to the base of the ice sheet in areas with up two kilometers of ice. Chapter 4 is an experimental study of two hydrous high-silica mantle melts from the Mt. Shasta, CA region. Crystallization is simulated at H2O saturated conditions at all crustal depths, and a new geobarometerhygrometer based on amphibole magnesium number is calibrated. In Chapter 5 I use the new barometer to study a suite of ma c enclaves from the Mt. Shasta region, and apply it to amphiboles in these enclaves. Evidence for pre-eruptive H2O contents of up to 14 wt% is presented, and bulk chemical analyses of the inclusions are used to show that extensive magma mixing has occurred at all crustal depths up to 35km beneath Mt. Shasta.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2011

Description: Remote sensing and in situ observations are used to investigate the ocean response to the Tokar Wind Jet in the Red Sea. The wind jet blows down the pressure gradient through the Tokar Gap on the Sudanese coast, at about 18°N, during the summer monsoon season. It disturbs the prevailing along-sea (southeastward) winds with strong cross-sea (northeastward) winds that can last from days to weeks and reach amplitudes of 20-25 m/s. By comparing scatterometer winds with along-track and gridded sea level anomaly observations, it is shown that an intense dipolar eddy spins up in less than seven days in response to the wind jet. The eddy pair has a horizontal scale of 140 km. Maximum ocean surface velocities can reach 1 m/s and eddy currents extend at least 200 m into the water column. The eddy currents appear to cover the width of the sea, providing a pathway for rapid transport of marine organisms and other drifting material from one coast to the other. Interannual variability in the strength of the dipole is closely matched with variability in the strength of the wind jet. The dipole is observed to be quasi-stationary, although there is some evidence for slow eastward propagation—simulation of the dipole in an idealized high-resolution numerical model suggests that this is the result of self-advection. These and other recent in situ observations in the Red Sea show that the upper ocean currents are dominated by mesoscale eddies rather than by a slow overturning circulation.

Description: This work is supported by Award Nos. USA 00002, KSA 00011 and KSA 00011/02 made by King Abdullah University of Science and Technology (KAUST).

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1983

Description: Novel methods were developed for the determination of 12 of the 14 Rare Earth Elements (REE) in seawater. Initial extractions of the REE by chelating ion exchange chromatography is followed by cation exchange for removal of co-extracted U and remaining traces of major ions. Finally traces of U are removed by anion exchange before irradiation for 8 hours at a flux of 5 x 1013 neutrons.cm-2.sec-l. After post-irradiation separation of 24 Na, the gamma spectra are recorded over four different time intervals with a Ge(Li) detector. An internal standard (144Ce) is carried all along the procedure for improved precision by avoidance of counting geometry errors. Vertical profiles are reported for three stations in respectively the Northwest Atlantic Ocean, the Eastern Equatorial Pacific Ocean and the Cariaco Trench, an anoxic basin. This data set represents the first detailed profiles of Pr, Tb, Ho, Tm and Lu in seawater, together with profiles of La, Ce, Nd, Sm, Eu, Gd and Yb. The first observations of positive Ce anomalies in seawater are ascribed to regeneration of Ce under reducing conditions. The first reported positive Gd anomalies are ascribed to the unique chemical properties of the Gd(III)-cation, which has an exactly half-filled 4f electron shell. Concentrations of the REE range from 0.3 pmol.kg-l (Lu) to 86 pmol.kg-l (Ce) and are among the lowest reported so far for trace elements in seawater. The REE as a group typically exhibit a quasi-linear increase with depth. In the deep water there appears to be some degree of correlation with silicate. Concentration levels in the deep Pacific Ocean are 2-4 times those in deep Atlantic waters. Ce has an opposite behaviour, with very strong depletions in deep Pacific waters. In the Cariaco Trench all REE, but especially Ce, are strongly affected by the chemical changes across the oxic/anoxic interface. The REE distributions normalized versus shales (crustal abundance) exhibit four major features: i) a gradual enrichment of the heavy REE, most strongly developed in the deep Pacific Ocean. This is compatible with the stabilization of heavy REE by stronger inorganic complexation in seawater as predicted by the TURNER- WHITFIELD-DICKSON speciation model. ii) the first description of positive Gd anomalies, in agreement with the anomalously strong complexation of the Gd(III)-cation predicted by the same speciation model. iii) most commonly negative, but sometimes positive, Ce anomalies. iv) a linear Eu/Sm relation for all samples. Distributions of the dissolved REE in ocean waters seem to be dominated by their internal cycling within the ocean basins. With a few notable exceptions, the ultimate external sources (riverine, aeolian, hydrothermal) and sinks (authigenic minerals) appear to have little impact on the spatial distribution of the REE in oceanic water masses. Analogies with distributions of other properties within the oceans suggest that the REE as a group are controlled by two simultaneous processes: A) cycling like or identical to opal and calcium-carbonate, with circumstantial evidence in support of the latter as a possible carrier. B) adsorptive scavenging, possibly by manganese-oxide phases on settling particles. The latter mechanism is strongly supported by the parallels between REE(III) speciation in seawater and the 'typical 1 seawater REE pattern. This general correspondence is highlighted by the very distinct excursions of Gd in both Gd(III) speciation and the observed seawater REE patterns. Combination of both apparent mechanisms, for instance scavenging of REE by adsorptive coatings (Mn oxides) on settling skeletal material, is very well conceivable. Upon dissolution of the shells at or near the seafloor the adsorbed REE fraction would be released into the bottom waters. The observations of positive Ce anomalies in Northwest Atlantic surface waters, enhanced Ce anomalies and Mn levels in the OZ-minimum zone of the Eastern Equatorial Pacific Ocean, and enhanced Ce concentrations in anoxic waters all support the contention that a vigorous cycling driven by oxidation and reduction reactions dominates both Ce and Mn in the ocean basins. Under conditions of thermodynamic equilibrium, Ce tends to become depleted in well-oxygenated open ocean waters, and normal or enriched in waters below a pOZ threshold of about 0.001-0.010 atm partial pressure. The latter threshold level generally lies below the sediment/water interface. However, the kinetics of oxidation (and reduction) of Ce appears to be slow relative to various transport processes. This leads to disequilibria, i.e. a major uncoupling of the pOZ threshold level and the Ce anomaly distribution. The REE are definitely non-conservative in seawater and in general the REE pattern or 143Nd/144Nd isotopic ratio cannot be treated as ideal water mass tracers. The continuous redistribution of Ce within the modern ocean, combined with the likelihood of active diagenesis, precludes the use of Ce anomalies as indicators of oxic versus anoxic conditions in ancient oceans. On the other hand, the Eu/Sm ratio, possibly combined with 143Nd/144Nd , would have potential as a tracer for understanding modern and ancient processes of hydrothermal circulation.

Description: This research was supported by Department of Energy contract DE-AS02-76EV03566 and Office of Naval Research Contract NOOOl 4-82-C-00l 9 NR 083-004.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution August 1998

Description: Two cytochrome P4501A-dependent mechanisms of aryl hydrocarbon receptor (AhR) agonist toxicity were examined in the marine teleost scup (Stenotomus chrysops), alteration of arachidonic acid (AA) metabolism and production of reactive oxygen species (ROS). In scup hepatic microsomes, cytochrome P450s including CYP1A and CYP2B-like proteins catalyzed regioselective metabolism of AA to eicosatrienoic and hydroxyeicosatetraenoic acids. Benzo[a]pyrene (BP) treatment induced liver microsomal AA metabolism, but that effect varied with season. Endogenous AA epoxides were recovered from scup liver, heart, and kidney, and their composition in the liver was altered by treatment with BP or 2,3,7,8-tetrachlorodibenzo-p-dioxin. In scup and mammals, the formation of ROS was stimulated by binding of 3,3',4,4-tetrachlorobiphenyl (TCB) to CYP1A, apparently CYP1Al. Attack of that ROS inactivated scup CYP1A. ROS release and inactivation of CYP1A were stimulated only by substrates of CYP1A that are slowly metabolized. In vivo, 3,3',4,4',5- pentachlorobiphenyl (PeCB) potently induced CYP1A mRNA, protein and catalytic activity at low doses (0.01-0.1 mg/kg), suppressed induction of CYP1A protein and catalytic activity at a high dose (1 mg/kg) and transiently induced oxidative stress in scup liver. The suppression of CYP1A induction was organ-dependent, with hepatic CYP1A being most susceptible to inactivation. The results suggest that ROS could be involved in the in vivo suppression of scup liver CYP1A by planar halogenated aromatic hydrocarbons. The reactive oxygen sensitive transcription factor, nuclear factor-KB (NF-KB), was characterized in scup. An NF-KB consensus binding sequence bound specifically to 3 proteins in scup liver, heart and kidney. One protein was recognized by an antibody to mammalian p50. Injection alone appeared to activate NF-KB. BP did not increase the activation ofNF-KB, and PeCB activated NF-KB in only 1 of 2 experiments. Last, CYP1A induction in endothelial cells of the American eel (Anguilla rostrata), a site which may be particularly susceptible to alterations in AA metabolism and ROS production, was described. Eel liver CYP1A responded to BP, 13-naphthoflavone and TCB in a dose-dependent fashion, and induction was correlated with hepatic inducer concentration. Endothelial CYP1A was inducible in a number of organs and was metabolically active. In the rete mirabile, penetration of endothelial CYP1A induction increased with increasing dose of AhR agonists, corresponding with an increase in inducer concentration. A transition from endothelial to epithelial staining occurred in the gill, heart and kidney at high inducer doses.

Description: My research was supported in part by the Lyons Fellowship, the MIT!WHOI Joint program, the Rinehart Coastal Research Center, NIH grant P42-ES07381, EPA grant R823890 and the Air Force Office of Scientific Research grant F40620-94-1039.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2012

Description: The distribution and magnitude of marine primary production helps determine the ocean's role in global carbon cycling. Constraining factors that impact this productivity and elucidating selective pressures that drive the composition of marine microbial communities are thus essential aspects of marine biogeochemistry. Vitamin B12, also known as cobalamin, is a cobalt containing organometallic micronutrient produced by some bacteria and archaea and required by many eukaryotic phytoplankton for methionine biosynthesis and regeneration. Although the potential for vitamin B12 availability to impact primary production and phytoplankton species composition has long been recognized, the lack of molecular-level tools for studying B12 production, use and acquisition has limited inquiry into the role of the vitamin in marine biogeochemical processes. This thesis describes the development of such tools and implements them for the study of B12 dynamics in an Antarctic shelf ecosystem. Nucleic acid probes for B12 biosynthesis genes were designed and used to identify a potentially dominant group of B12 producers in the Ross Sea. The activity of this group was then verified by mass spectrometry-based peptide measurements. Then, possible interconnections between iron and B12 dynamics in this region were identified using field-based bottle incubation experiments and vitamin uptake measurements, showing that iron availability may impact both B12 production and consumption. Changes in diatom proteomes induced by low B12 and low iron availability were then examined and used to identify a novel B12 acquisition protein, CBA 1, in diatoms. This represents the first identification of a B12 acquisition protein in eukaryotic phytoplankton. Transcripts encoding CBAl were detected in natural phytoplankton communities, confirming that B12 acquisition is an important part of phytoplankton molecular physiology. Selected reaction monitoring mass spectrometry was used to measure the abundance of CBA 1 and methionine synthase proteins in diatoms cultures, revealing distinct protein abundance patterns as a function ofB12 availability. These peptide measurements were implemented to quantify methionine synthase proteins in McMurdo Sound, revealing that there is both B12 utilization and starvation in natural diatom communities and that these peptide measurements hold promise for revealing the metabolic status of marine ecosystems with respect to vitamin B12.

Description: The work described in this thesis was supported by a National Science Foundation (NSF) Graduate Research Fellowship (2007037200) and an Environmental Protection Agency STAR Fellowship (F6E20324), the WHOI Ocean Life Institute, the WHOI Ocean Ventures Fund, the MIT Houghton Fund, NSF awards ANT 0732665, OCE 0752291, OPP 0440840, OCE 0327225, OCE 0452883, OCE 0723667, OCE 1031271, and OCE 0928414, the Center for Environmental Bioinorganic Chemistry at Princeton, the Center for Microbial Oceanography: Research and Education (CMORE), the Australian Research Council and the Gordon and Betty Moore Foundation.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2012

Description: This thesis presents a system for automatically building 3-D optical and bathymetric maps of underwater terrain using autonomous robots. The maps that are built improve the state of the art in resolution by an order of magnitude, while fusing bathymetric information from acoustic ranging sensors with visual texture captured by cameras. As part of the mapping process, several internal relationships between sensors are automatically calibrated, including the roll and pitch offsets of the velocity sensor, the attitude offset of the multibeam acoustic ranging sensor, and the full six-degree of freedom offset of the camera. The system uses pose graph optimization to simultaneously solve for the robot’s trajectory, the map, and the camera location in the robot’s frame, and takes into account the case where the terrain being mapped is drifting and rotating by estimating the orientation of the terrain at each time step in the robot’s trajectory. Relative pose constraints are introduced into the pose graph based on multibeam submap matching using depth image correlation, while landmark-based constraints are used in the graph where visual features are available. The two types of constraints work in concert in a single optimization, fusing information from both types of mapping sensors and yielding a texture-mapped 3-D mesh for visualization. The optimization framework also allows for the straightforward introduction of constraints provided by the particular suite of sensors available, so that the navigation and mapping system presented works under a variety of deployment scenarios, including the potential incorporation of external localization systems such as long-baseline acoustic networks. Results of using the system to map the draft of rotating Antarctic ice floes are presented, as are results fusing optical and range data of a coral reef.

Description: My first year was funded through an MIT Presidential Fellowship. Since then, I’ve been covered first by the National Science Foundation Censsis ERC under grant number EEC-9986821, and then by the National Oceanic and Atmospheric Administration under grant number NA090AR4320129.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2012

Description: As analysis of imagery and environmental data plays a greater role in mission construction and execution, there is an increasing need for autonomous marine vehicles to transmit this data to the surface. Without access to the data acquired by a vehicle, surface operators cannot fully understand the state of the mission. Communicating imagery and high-resolution sensor readings to surface observers remains a significant challenge – as a result, current telemetry from free-roaming autonomous marine vehicles remains limited to ‘heartbeat’ status messages, with minimal scientific data available until after recovery. Increasing the challenge, longdistance communication may require relaying data across multiple acoustic hops between vehicles, yet fixed infrastructure is not always appropriate or possible. In this thesis I present an analysis of the unique considerations facing telemetry systems for free-roaming Autonomous Underwater Vehicles (AUVs) used in exploration. These considerations include high-cost vehicle nodes with persistent storage and significant computation capabilities, combined with human surface operators monitoring each node. I then propose mechanisms for interactive, progressive communication of data across multiple acoustic hops. These mechanisms include wavelet-based embedded coding methods, and a novel image compression scheme based on texture classification and synthesis. The specific characteristics of underwater communication channels, including high latency, intermittent communication, the lack of instantaneous end-to-end connectivity, and a broadcast medium, inform these proposals. Human feedback is incorporated by allowing operators to identify segments of data thatwarrant higher quality refinement, ensuring efficient use of limited throughput. I then analyze the performance of these mechanisms relative to current practices. Finally, I present CAPTURE, a telemetry architecture that builds on this analysis. CAPTURE draws on advances in compression and delay tolerant networking to enable progressive transmission of scientific data, including imagery, across multiple acoustic hops. In concert with a physical layer, CAPTURE provides an endto- end networking solution for communicating science data from autonomous marine vehicles. Automatically selected imagery, sonar, and time-series sensor data are progressively transmitted across multiple hops to surface operators. Human operators can request arbitrarily high-quality refinement of any resource, up to an error-free reconstruction. The components of this system are then demonstrated through three field trials in diverse environments on SeaBED, OceanServer and Bluefin AUVs, each in different software architectures.

Description: Thanks to the National Science Foundation, and the National Oceanic and Atmospheric Administration for their funding of my education and this work.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2012

Description: The focus of this thesis is the design and development of a system for rapid extraction of dissolved inorganic carbon from seawater and groundwater samples for radiocarbon dating. The Rapid Extraction of Dissolved Inorganic Carbon System (REDICS) consists of two subsystems – one for sample introduction, acidification, and carbon dioxide extraction, and one for carbon dioxide quantification and storing. The first subsystem efficiently extracts the dissolved inorganic carbon from the water sample in the form of carbon dioxide by utilizing a gas-permeable polymer membrane contractor. The second subsystem traps, quantifies and stores the extracted gas using cryogenics. The extracted carbon dioxide is further processed for stable and radiocarbon isotope analysis at the National Ocean Sciences Accelerator Mass Spectrometer Facility at the Woods Hole Oceanographic Institution. The REDICS system was tested using seawater standards collected at 470m and 4000m depth in the Atlantic Ocean and analyzing the extracted CO2. The results were compared to the results for the same standards processed on the current NOSAMS water stripping line. The results demonstrate that the system successfully extracts more than 99% of the dissolved inorganic carbon in less than 20 minutes. Stable isotope and radiocarbon isotope analyses demonstrated system precision of 0.02‰ and 3.5‰ respectively.

Description: Funded by the National Science Foundation as well as the MIT WHOI Joint Program

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2012

Description: Observations from a three-year field program on the inner shelf south of Martha's Vineyard, MA and a numerical model are used to describe the effect of stratification on inner shelf circulation, transport, and sediment resuspension height. Thermal stratification above the bottom mixed layer is shown to cap the height to which sediment is resuspended. Stratification increases the transport driven by cross-shelf wind stresses, and this effect is larger in the response to offshore winds than onshore winds. However, a one-dimensional view of the dynamics is not sufficient to explain the relationship between circulation and stratification. An idealized, cross-shelf transect in a numerical model (ROMS) is used to isolate the effects of stratification, wind stress magnitude, surface heat flux, cross-shelf density gradient, and wind direction on the inner shelf response to the cross-shelf component of the wind stress. In well mixed and weakly stratified conditions, the cross-shelf density gradient can be used to predict the transport efficiency of the cross-shelf wind stress. In stratified conditions, the presence of an along-shelf wind stress component makes the inner shelf response to cross-shelf wind stress strongly asymmetric.

Description: This work was supported through National Science Foundation grant no. OCE-0548961, the WHOI Academic Programs Office, and the WHOI Coastal Ocean Institute.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2012

Description: Adaptive equalization is an important aspect of communication systems in various environments. It is particularly important in underwater acoustic communication systems, as the channel has a long delay spread and is subject to the effects of time- varying multipath fading and Doppler spreading. The design of the adaptation algorithm has a profound influence on the performance of the system. In this thesis, we explore this aspect of the system. The emphasis of the work presented is on applying concepts from inference and decision theory and information theory to provide an approach to deriving and analyzing adaptation algorithms. Limited work has been done so far on rigorously devising adaptation algorithms to suit a particular situation, and the aim of this thesis is to concretize such efforts and possibly to provide a mathematical basis for expanding it to other applications. We derive an algorithm for the adaptation of the coefficients of an equalizer when the receiver has limited or no information about the transmitted symbols, which we term the Soft-Decision Directed Recursive Least Squares algorithm. We will demonstrate connections between the Expectation-Maximization (EM) algorithm and the Recursive Least Squares algorithm, and show how to derive a computationally efficient, purely recursive algorithm from the optimal EM algorithm. Then, we use our understanding of Markov processes to analyze the performance of the RLS algorithm in hard-decision directed mode, as well as of the Soft-Decision Directed RLS algorithm. We demonstrate scenarios in which the adaptation procedures fail catastrophically, and discuss why this happens. The lessons from the analysis guide us on the choice of models for the adaptation procedure. We then demonstrate how to use the algorithm derived in a practical system for underwater communication using turbo equalization. As the algorithm naturally incorporates soft information into the adaptation process, it becomes easy to fit it into a turbo equalization framework. We thus provide an instance of how to use the information of a turbo equalizer in an adaptation procedure, which has not been very well explored in the past. Experimental data is used to prove the value of the algorithm in a practical context.

Description: Support from the agencies that funded this research- the Academic Programs Office at WHOI and the Office of Naval Research (through ONR Grant #N00014-07-10738 and #N00014-10-10259).

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 1998

Description: Work on the forward problem in zooplankton bioacoustics has resulted in the identification of three categories of acoustic scatterers: elastic-shelled (e.g. pteropods), fluid-like (e.g. euphausiids), and gas-bearing (e.g. siphonophores). The relationship between backscattered energy and animal biomass has been shown to vary by a factor of —19,000 across these categories, so that to make accurate estimates of zooplankton biomass from acoustic backscatter measurements of the ocean, the acoustic characteristics of the species of interest must be well-understood. This thesis describes the development of both feature based and model based classification techniques to invert broadband acoustic echoes from individual zooplankton for scatterer type, as well as for particular parameters such as animal orientation. The feature based Empirical Orthogonal Function Classifier (EOFC) discriminates scatterer types by identifying characteristic modes of variability in the echo spectra, exploiting only the inherent characteristic structure of the acoustic signatures. The model based Model Parameterisation Classifier (MPC) classifies based on correlation of observed echo spectra with simplified parameterisations of theoretical scattering models for the three classes. The Covariance Mean Variance Classifiers (CMVC) are a set of advanced model based techniques which exploit the full complexity of the theoretical models by searching the entire physical model parameter space without employing simplifying parameterisations. Three different CMVC algorithms were developed: the Integrated Score Classifier (ISC), the Pairwise Score Classifier (PSC) and the Bayesian Probability Classifier (BPC); these classifiers assign observations to a class based on similarities in covariance, mean, and variance, while accounting for model ambiguity and validity. These feature based and model based inversion techniques were successfully applied to several thousand echoes acquired from broadband (-350 kHz - 750 kHz) insonifications of live zooplankton collected on Georges Bank and the Gulf of Maine to determine scatterer class. CMVC techniques were also applied to echoes from fluid-like zooplankton (Antarctic krill) to invert for angle of orientation using generic and animal-specific theoretical and empirical models. Application of these inversion techniques in situ will allow correct apportionment of backscattered energy to animal biomass, significantly improving estimates of zooplankton biomass based on acoustic surveys.

Description: Thanks to the WHOI/MIT Joint Program Education Office for partial funding. Other sources of funding for my thesis work include the Ocean Acoustics, Oceanic Biology and URIP programs of the Office of Naval Research grant numbers N00014-89- J-1729, N00014-95-1-0287 and N00014-924-1527, and the Biological Oceanography program of the National Science Foundation grant number OCE-9201264.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2012

Description: Estuarine density stratification may be controlled primarily by cross-shore processes (analogous to longitudinal control in narrow estuaries), or by both cross- and alongshore processes (typical of coastal plumes). Here field observations and numerical modeling are used to investigate stratification on the low-sloped, periodically inundated Skagit Bay tidal flats. Advection of stratification by the depth-averaged velocity, straining of the horizontal density gradient by velocity shear, and turbulent mixing are shown to be the dominant processes. On the south-central flats (near the south fork river mouth) velocities are roughly rectilinear, and the largest terms are in the major velocity direction (roughly cross-shore). However, on the north flats (near the north fork river mouth), velocity ellipses are nearly circular owing to strong alongshore tidal flows and alongshore stratification processes are important. Stratification was largest in areas where velocities and density gradients were aligned. The maximum stratification occurred during the prolonged high water of nearly diurnal tides when advection and straining with relatively weak flows increased stratification with little mixing. Simulations suggest that the dominance of straining (increasing stratification) or mixing (decreasing stratification) on ebb tides depends on the instantaneous Simpson number being above or below unity.

Description: Support for the work was provided by the Office of Naval Research, contracts N00014-10-10220, N00014-08-10050, N00014- 07-10461, N00014-0710755, N00014-0810787, N00014-0910933, the National Science foundation, grant OCE-0622844 the PADI Foundation, grant 74, an MIT Linden Earth Systems Fellowship, 2006-2007, and Academic Programs Office funds.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution December 1988

Description: In a field study of blue shark swimming behavior, acoustic telemetry was used to record depth, swimming speed and tailbeat frequency from free-ranging blue sharks (Prionace glauca) in northwestern Atlantic slope waters. Records obtained from five sharks show a consistent pattern of vertical migration between the surface and depths as great as 450 meters, with the deepest dives occurring during the daytime and shallower dives at night. Mean swimming speed was 44.5 ± 1.6 (X±S.E.) cm.s-1 (0.179 ± 0.014 lengths.s-1) for three sharks, with short bursts up to 180 cm.s-1. Mean tailbeat frequency was 0.335 ± 0.021 beats.s-1. Measurement of swimming speed and rate of vertical movement during dives permits calculation of angles of ascent and descent. For 84 dives deeper than 50 m, the descent angle averaged 8.0 ± 0.7 degrees from the horizontal while the ascent angle was 6.4 ± 0.5 degrees. Tailbeat records indicate that blue sharks actively swam downward during most of the descent, with brief periods of gliding which appear to be associated with the most rapid descent rates. The observed diving behavior does not match that predicted by theory to be energetically optimal for migration, and may instead represent a strategy for encountering and capturing prey. Heart rate, metabolic rate and activity were simultaneously recorded in the laboratory from lemon sharks (Negaprion brevirostris) during rest and spontaneous exercise, and from leopard sharks (Triakis semifasciata) during steady swimming at controlled speeds to evaluate the usefulness of heart rate as a measure of field metabolic rate. Heart rate was monitored by acoustic telemetry using a frequency modulated ECG transmitter, and metabolic rate was measured as oxygen consumption rate. For seven lemon sharks at 25°C, mean resting values for heart rate and oxygen consumption rate were 52.0 + 0.4 (S.E.) beats.min-1 and 162.0 ± 2.0 (S.E.) mg02.kg-1hr-1, respectively. Both parameters increased significantly (p〈.001) during swimming, to means of 55.9 ± 0.2 beats.min-1 and 233.6 + 2.3 mg Oz.kg-1hr-1, at a mean swimming speed of 0.400 ± 0.003 body heart rate and oxygen consumption rate were 36.6 + 1.8 beats.min-1 and 105.3 ± 35.6 mg Oz.kg-1.hr-1. While swimming-at the maximum sustained speed (0.84 ± 0.03 lengths.s-1) for 30-60 minutes, these rates were 46.9 + 0.9 beats.min- and 229.3 + 13.2 mg Oz.kg-1.hr-1. The observed elevations in heart rate from rest to exercise account for 20% of the increase in oxygen uptake in the lemon shark and 32% in the leopard shark, leaving the remainder to be brought about by increases in stroke volume and/or arteriovenous oxygen difference. Significant linear regressions of oxygen consumption rate on heart rate were obtained for both lemon sharks and leopard sharks; separate regressions were obtained for individual lemon sharks . Heart rate was approximately as closely correlated to oxygen consumption rate as was swimming speed.

Description: Financial support throughout this project was from several sources: the WHO! education office, a grant from the Coastal Research Center to the author, and NSF grants OCE-8311512 to FGC, OCE-8743949 to SHG, and DCB-8416852 to JBG.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution August 1989

Description: The dynamics of deeply-towed cable/vehicle systems are governed by nonlinear partial differential equations and as a result, trajectory control is generally difficult using the available techniques. This work examines the possibility of utilizing parametric dynamic models in differential equation form, to present a far more tractable controls problem. A learning-model method for generating accurate approximations of this type is used, and the identification process is unique in that an analytically-based model provides the primary data sets, allowing for a priori characterization of system responses without using any real data. The performances of the parametric forms are then verified through comparison of model output against actual sea data obtained during recent cruises in the Caribbean and Mediterranean Seas. The respective merits and limitations of several different model structures are discussed, with respect to both pure performance and identification efficiency.

Description: The Office of Naval Research is gratefully acknowledged for its financial support of my graduate education, under Contract N00014-85-G-0084; in addition, this work has been sponsored in part by the National Science Foundation under Contract OCE-8511431. Finally, the International Business Machines Corporation is acknowledged for graciously providing the computing facilities that were critical to this thesis.

Description: Submitted in partial fulfillment of the requirements for the degree of Ocean Engineer at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution August 1989

Description: When ocean waves in deep water interact with a current, the direction of propagation and characteristics of the waves such as height and length are affected. Swell in the open ocean can undergo significant refraction as it passes through major current systems like the Gulf Stream or Antarctic Circumpolar Current. Remote sensing techniques such as synthetic aperture radars (SAR) have the potential to detect wave systems over a wide geographical area. Combining a model for wave refraction in the presence of currents with SAR measurements, the inverse problem of using the measured wave data can be solved to determine the direction and magnitude of the intervening currents. In this study the behavior of swell measured by SAR on a satellite pass over the Gulf Stream is examined. The refraction predicted by a numerical model under conditions of varying current profiles and velocities is compared to SAR generated wave spectra. By matching the current profile which results in the best correlation of wave refraction to the SAR data, the tomographic problem of measuring the Gulf Stream current is solved. The best correlation between the model and SAR data is obtained when a current is modeled by a top hat velocity profile with a direction of 75° and a current speed of 2 m/s. The direction agrees with that visually observed from the SAR images, and the direction and speeds are close to the Coast Guard estimates for the Gulf Stream at the time of the SEASAT,pass. The current profiles used did not take into account a possible widening of the Gulf Stream at the position of the satellite overpass. There is a great deal of scatter in the SAR data, both before and in the Gulf Stream, so it is difficult to correlate every point with specific current behavior, but the increase in wave length and change in wave angle in the center of the Gulf Stream seem to indicate that there may be a non-uniform feature such as the formation of an eddy or other lateral variability near the current's edge.

Description: I was supported by the U. S. Navy.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1990

Description: An acoustic tomography experiment consisting of a source near Hawaii and seven receivers along the west coast of North America was conducted from November 1987 to May 1988 and from February 1989 to July 1989. In this thesis, the acoustic ray travel times are analyzed in order to investigate inter-annual basin-scale thermal variability. These thermal fluctuations may help detect any greenhouse warming and greater understanding of them will increase knowledge of ocean-atmosphere interactions which affect weather and climate. A discussion of the program for finding the travel times is included along with a comparison of two methods of measuring travel times.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1990

Description: Travel-times of acoustic signals were measured between a bottom-mounted source near Oahu and four bottom-mounted receivers located near Washington, Oregon, and California in 1988 and 1989. This paper discusses the observed tidal signals. At three out of four receivers, observed travel times at M2 and S2 periods agree with predictions from barotropic tide models to within ±30° in phase and a factor of 1.6 in amplitude. The discrepancy at the fourth receiver can be removed by including predicted effects of phase-locked baroclinic tides generated by seamounts. Our estimates of barotropic M2 tidal dissipation by seamounts vary between 2 x 1016 and 1 X 1018 erg·s-1. The variation by two orders of magnitude is due to uncertainties in the numbers and sizes of seamounts. The larger dissipation (1 x 1018 erg·s-1) is the same order as previous estimates and amounts to 4% of the total dissipation at M2.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 1990

Description: A recently developed technique for determining past sea surface temperatures (SST), based on an analysis of the unsaturation ratio of long chain C37 methyl alkenones (Uk37) produced by Prymnesiophyceae phytoplankton, has been applied to late Quaternary sediment cores. Previous studies have shown that the Uk37 ratio of these alkenones is linearly proportional to the sea-water temperature in which the plankton grow, both in culture and water column samples. Furthermore, a reasonable correlation has been found between open ocean paleo-SST estimates based on Uk37 values and those derived from δ180, for the period spanning approximately the last 100,000 years (Brassell, 1986b). These results indicate this technique has potential for determining paleo-SST from analysis of alkenones extracted from marine sediments. In order to apply the Uk37 method quantitatively, it is necessary to calibrate the method for sediment samples, and to assess how well the alkenones maintain their temperature signal under some common conditions of sediment deposition and sample handling. It is also necessary to determine the method's usefulness downcore, that is, back in time, by comparing it to established methods. This study examined the effect on Uk37 of conditions that cause dissolution of carbonates in the sediment, and methods of storage and 'sample handling. These are two problems that must be resolved before the method can be applied rigorously and quantitatively to sediments for paleotemperature estimations. A comparison of duplicate samples collected and stored frozen versus those stored at room temperature for up to four years showed no resolvable differences in Uk37. Laboratory experiments of carbonate dissolution indicated there is no effect on Uk37 values under the acidic conditions that dissolve carbonates. Initial field results support this, but indicate more studies are necessary. The Uk37 "thermometer" was calibrated by analyzing Uk37 in coretops from widely varying open ocean sites. Sediment values of Uk37 reflected overlying SST for the appropriate season of the phytoplankton bloom, which for this study was assumed to be summer in high latitudes. These results fall on the same regression line for culture and water column samples derived by Prahl and Wakeham (1987), indicating that their equation (Uk37 = 0.033 T + 0.043) is suitable for use in converting Uk37 values in sediments to overlying SST for the season of coccolith bloom. Using this calibration for sediments, the Uk37 paleotemperature method can be quantitatively applied down core to open ocean sediments. In the Equatorial Atlantic, Uk37 temperature estimates were compared to those obtained from δ18O of the planktonic foraminifer Globigerinoides sacculifer, and planktonic foraminiferal assemblages for the last glacial cycle. The alkenone method showed ~1.56°C cooling at the last glacial maximum. This is about half the decrease shown by both the isotopic method ( ~3.40°C) and foraminiferal assemblages (~3.75°C), implying that, if Uk37 estimates are correct, SST in the equatorial Atlantic was only reduced slightly in the last glaciation. In the Northeast Atlantic, Uk37 temperature estimates show a profile downcore which is similar to the estimates from foram assemblages but with a constant offset toward warmer values throughout the core. Uk37 SST estimates are substantially warmer than foraminiferal estimates at all times, which may indicate inaccuracy in Uk37 temperatures at this site. Uk37 indicates a SST of 12°C for the late glacial and 18°C for the Recent, whereas assemblages give estimates of 9°C and 13°C, respectively. At 12,700 yrs BP, the Uk37 and foram assemblage methods indicate a 2°C warming. A temperature change of 2°C can account for only 0.44°/oo of the observed 1.2°/oo δ18O signal, indicating that the additional 0.8°/oo change in δ18O must result from changes in surface salinity most likely due to a meltwater lid. Uk37 estimates show the major temperature shift from glacial to interglacial temperatures occured at about 9,000 yrs BP disagreeing with assemblage data which shows the shift to Holocene values at about 12,700 yrs BP. If Uk37 temperature estimates are accurate, this disagreement may reflect differing habitats of flora and fauna under the unusual sea surface conditions in this area during the deglaciation.

Description: Primary financial support for this research came from the Ocean Ventures Fund (grant 25/ 85.08), without which this project would not have been possible. Funding supporting the labs of John Farrington (OCE 88-11409) and Lloyd Keigwin (OCE 83-08893 and ATM 84-14335) in which I worked also provided funding for part for this research.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 1990

Description: Estimates of the heat output of hydrothermal vents, identified along the Endeavor and Southern Segments of the Juan de Fuca Ridge, are used to evaluate the total heat flux associated with hydrothermal circulation for the ridge segment. An array carried by D/V ALVIN sampled the temperature and velocity structure of hydrothermal plumes from individual vents . The maximum heat flux calculated for a single vent is 50 MW, but the average vent output is only 13 MW per vent for 31 vents. The estimates for any given vent may vary over an order of magnitude. This uncertainty is due mainly to the difficulty of locating the centerline of the plume relative to the point of measurement, although the uncertainty in determining the constants from the appropriate equations based on laboratory experiments contributes a significant share to the net error. For the Endeavor Segment, the minimum total geothermal heat flux due to hydrothermal circulation exceeds 70 MW. The minimum estimate for the Southern Segment is 16 MW. The maximum estimate is probably closer to the total heat flux (236 MW and 66 MW respectively) . The estimated heat flux density is 3300 W/m2 for the Endeavor vent field and 39 W/m2 for the Southern vent field. Focused hydrothermal venting accounts for only a small fraction of the heat available according to steady-state predictions of conductive heat flux; however, other hydrothermal phenomena (e.g., diffuse flow) account for the greater share of the total hydrothermal heat flux.

Description: This project was supported by NSF grant #OCE87-14511 and by the WHOI Education Office.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 1990

Description: The variation in the depth and width of the median valley along the Mid-Atlantic Ridge (MAR) suggests that the formation of ocean crust at slow spreading centers is not a simple two-dimensional process in which crustal accretion occurs uniformly both along the ridge axis and with time. Rather, it has been proposed that the ridge axis can be divided into a number of distinct segments or spreading cells. This thesis investigates the segmentation model by studying the variability in the structure and tectonics within spreading cells at 23°N and 26°N along the MAR. The results support the segmentation model in which accretion varies along the ridge, evolving as independent spreading cells or segments, with different portions of the ridge system being in different stages of volcanic and tectonic evolution. Chapter 2 presents an overview of morphologic and tectonic variations along a 100- km-length of the MAR south of the Kane Fracture Zone (MARK area). Sea MARC.I side scan sonar data and multi-beam Sea Beam bathymetry are used to document the distribution of crustal magmatism and extensional tectonism near 23°N. The data indicate a complex median valley composed by two distinct en echelon spreading cells which overlap in a discordant zone that lacks a well-developed rift valley or neovolcanic zone. The northern cell, immediately south of the fracture zone, is dominated by a large constructional volcanic ridge and is associated with active high-temperature hydrothermal activity. In contrast, the southern cell is characterized by a NNE-trending band of small fissured and faulted volcanos that are built upon relatively old, fissured and sediment-covered lavas; this cell is inferred to be in a predominantly extensional phase with only small, isolated volcanic eruptions. Despite the complexity of the MARK area, volcanic and tectonic activity appears to be confined to the 10-17 km wide inner rift valley. Small-offset normal faulting along near-vertical planes begins within a few kilometers of the ridge axis and appears to be largely completed by the time the crust moves out of the median valley. Mass-wasting and gullying of scarp faces, and sedimentation which buries low-relief seafloor features, are the major geological processes occurring outside the rift valley. In Chapters 3 and 4, the microearthquake characteristics and P wave velocity structure beneath the median valley of the Mid-Atlantic Ridge near 26°N are studied; this ridge segment is characterized by a large high-temperature hydrothermal field situated within the inner floor at the along-axis high. Chapter 3 explores the tectonic variations within the crust as evidenced from the distribution and source mechanisms of microearthquakes observed by a network of seven ocean bottom hydrophones and two ocean bottom seismometers over a three week period in 1985. Hypocenters were determined for 189 earthquakes, with good resolution of focal depth obtained for 105 events. Almost all events occurred at depths between 3 and 7 km beneath the seafloor, with earthquakes occurring at shallower depths beneath the along-axis high (〈4 km). The distribution of hypocenters and the diversity of faulting associated with earthquakes beneath the inner floor and walls suggests a spatially variable tectonic state for the ridge segment at 26°N. These variations are presumably a signature of lateral heterogeneity in the depth region over which brittle failure occurs, and are a consequence of along-axis changes in the thermal structure and state of stress. We suggest that at present the hydrothermal activity and deposition of massive sulfides is being sustained by heat generated by a recent magmatic intrusion. A consequence of this scenario is that thermal stresses play a dominant role in controlling the distribution of earthquakes and nature of faulting. Such a hypothesis is consistent with an apparent lack of seismicity beneath the hydrothermal field, the location of hypocenters around the low velocity zone (Chapter 4), attenuation of P wave energy to instruments atop the high (Chapter 4), the higher b-values associated with the along-axis high region, and the occurrence of high-angle (or very low angle) normal faulting and reverse faulting, as well as the variability in nodal plane orientations, associated with inner floor events beneath the along-axis high and the volcano. In Chapter 4, we report results from the explosive refraction line and from the tomographic inversion of P wave travel time residuals for seismic velocity structure in the vicinity of the hydrothermal field. The twcrdimensional along-axis P wave structure beneath the inner floor indicates that young oceanic crust cannot be adequately characterized by a simple, laterally homogeneous velocity structure, but that one-dimensional StruGtures are at least locally valid (at 5-10 km length scales). The shallowmost crust (upper 1-2 km) beneath an axial volcano and the along-axis high is characterized by significantly higher velocities (by more than 1 km/s) than are associated with the upper crust in the deepest portions of the median valley. The variation is inferred to be a consequence of more recent magmatic and volcanic activity in the along-axis high region, as compared with the alongaxis deep where tectonic fissuring has created a highly porous crust characterized by lower seafloor velocities. The crust beneath the along-axis deep appears to be typical of normal young oceanic crust, with a mantle velocity of 8.25 krn/s observed at 5 k:m depth. A low velocity zone centered beneath the along-axis high and extending under an axial volcano is imaged from 3 to 5 km depth (7.2 km/s to 6.0 km/s); the velocity decrease is required to satisfy the travel time residual data and to explain the severe attenuation in compressional wave energy to instruments atop the along-axis high. The presence of an active high-temperature hydrothermal field atop the along-axis high, together with the observations of lower P wave velocities, the absence of microearthquake activity greater than 4 km in depth, and the propagation of S waves through the crust beneath the volcano and along-axis high (Chapter 3), suggest that the volume corresponds to a region of hot rock with no seismically-resolvable pockets of partial melt. The shallow velocity gradients describing the low velocity volume(〈0.6 s-l) appear to be a corrunon characteristic of inferred zones of magmatic intrusion on the MAR. Comparison of the depth to the velocity inversion with the depths determined in other seismic studies at locally high regions along the MAR, the Juan de Fuca Ridge, and the East Pacific Rise reveals a correlation between lid thickness and spreading rate, suggesting that the amount of magma available at each location is spatially variable, or that the differences in lid thickness are describing the temporal evolution of magmatic intrusions beneath mid-ocean ridges. In Chapter 5, the first direct measurement of upper mantle P- and S-wave delay times beneath an oceanic spreading center is presented. Two independent estimates of the epicenters and origin times are made for each of two earthquakes in a 1985 earthquake swarm near 25°50'N on the Mid-Atlantic Ridge using local and teleseismic arrival time data. Comparison indicates a 14-20 km northward bias in the epicenters teleseismically located using a Herrin [1968] Earth model. The bias is due to departures of the actual velocity structure from that implicit in the travel time tables used for the locations, combined with unbalanced station distribution. The comparison of origin times for the best-located event, after correction for the epicentral bias and for an oceanic crustal thickness, shows there to be only slightly lower velocities than a Herrin [1968] upper mantle; the P-wave delay is +0.3 ± 0.9 s (+0.2 ± 0.9 sand -2.4 ± 0.9 s relative to the isotropic Preliminary Earth Reference Model (PREM) and the Jeffreys-Bullen [1940] (JB) travel time tables, respectively). The lack of a resolvable P-wave delay suggests that the Herrin [1968] model is a good approximation to the average upper mantle velocity beneath this segment of the MAR. Measurement of the S-wave delay for the same MAR swarm event shows there to be a positive delay (+3.1 ± 2.0 s), or larger travel times and slower velocities compared to the JB S-wave tables (+ 3.9 ± 2.0 s relative to the isotropic PREM S-wave model). In contrast to the larger P-wave delays found in other MAR studies, the lack of a significant seismic anomaly near 26°N indicates that sizeable regions of low velocity material do not presently exist in the upper few hundred kilometers of mantle beneath this section of the ridge. This evidence argues for substantial along-axis variations in the active upwel~ng of mantle material along the slowly-spreading Mid-Atlantic Ridge. In order to explain the observation of a smaller than expected P wave delay in a region where the S delay suggests significant temperature anomalies (low velocities), we propose a model for mantle upwelling in which the decrease in travel time is due to an anisotropic P wave structure (fast direction vertical); the anisotropy results from the reorientation of olivine crystals parallel to the ascending flow and balances the travel time delay due to a region of low velocities.

Description: This thesis was funded in part by grants EAR-8407798, EAR-8407745, and EAR- 8817173 from the National Science Foundation.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 1990

Description: Numerous studies have shown dinoflagellate blooms to be closely related to density discontinuities and fronts in the ocean. The spatial and temporal patterns of the dinoflagellate population depend on the predominant mode of physical forcing, and its scales of variability. The present study combined field sampling of hydrographic and biological variables to examine the relationship of dinoflagellate population distributions to physical factors along the southwestern cost of the Gulf of Maine. A bloom of Ceratium longipes occurred along this coast during the month of June, 1987. A simple model which coupled along-isopycnal diffusion with the logistic growth equation suggested that the cells had a growth rate of about 0.1 d-1 , and had reached a steady horizontal across-shelf distribution within about 10 d. Fur~her variations in population density appeared to be related to fluctuations of light with periods of -10 d. To our knowledge, this was the first use of this simple diffusion model as a diagnostic tool for quantifying parameters describing the growth and movement of a specific phytoplankton population. Blooms of the toxic dinoflagellate, Alexandrium tamarense have been nearly annual features along the coasts of southern Maine, New Hampshire and Massachusetts since 1972; however the mechanisms controlling the distribution of cells and concomitant shellfish toxicity are relatively poorly understood. Analysis of field data gathered from April to September, 1987-1989, showed that in two years when toxicity was detected in the southern part of this region, A. tamarense cells were apparently transported into the study area between Portsmouth and Cape Ann, Massachusetts, in a coastally trapped buoyant plume. This plume appears to have been formed off Maine by the outflow from the Androscoggin and Kennebec Rivers. Flow rates of these rivers, hydrographic sections, and satellite images suggest that the plume had a duration of about a month, and extended alongshore for several hundred kilometers. The distribution of cells followed the position of the plume as it was influenced by wind and topography. Thus when winds were downwelling-favourable, cells were moved alongshore to the south, and were held to the coast; when winds were upwelling-favourable, the plume sometimes separated from the coast, advecting the cells offshore. The alongshore advection of toxic cells within a coastally trapped buoyant plume can explain the temporal and spatial patterns of shellfish toxicity along the coast. The general observation of a north-to-south temporal trend of toxicity is consistent with the southward advection of the plume. In 1987 when no plume was present, Alexandrium tamarense cells were scarce, and no toxicity was recorded at the southern stations. A hypothesis was formulated explaining the development and spread of toxic dinoflagellate blooms in this region. This plume-advection hypothesis included: source A. tamarense populations in the north, possibly associated with the Androscoggin and Kennebec estuaries; a relationship between toxicity patterns and river flow volume and timing of flow peaks; and a relationship between wind stresses and the distribution of low salinity water and cells. Predictions of the plume-advection hypothesis were tested with historical records of shellfish toxicity, wind speed and direction, and river flow. The predictions tested included the north-south progression of toxic outbreaks, the occurrence of a peak in river flow prior to the PSP events, the relationship of transit time of PSP toxicity along the coast with river flow volume, and the influence of surface wind stress on the timing and location of shellfish toxicity. All the predictions tested were supported by the historical records. In addition it was found that the plume-advection hypothesis explains many details of the timing and spread of shellfish toxicity, including the sporadic nature of toxic outbreaks south of Massachusetts Bay, and the apparently rare occurrence of toxicity well offshore on Nantucket Shoals and Georges Bank.

Description: This research was supported by ONR contract N00014-87-K-0007 and ONR grant N00014-89-J-111 to Donald M. Anderson, and NOAA Office of Sea Grant contract NA86AA-D-SG090.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 1993

Description: Breaking waves charge the surface layer of the ocean with small air bubbles which play an important role in air-sea gas transfer and in underwater acoustics near the ocean surface. This work reports on a series of laboratory and field experiments on the measurement on air entrainment by breaking waves. The first part of this thesis addresses the measurement of high volumetric concentrations of air (0.3% to 100% void-fraction) found immediately beneath breaking waves. Instrumentation based on the change of electrical impedance of the bubbly mixture with change in void-fraction is developed. Laboratory measurements are conducted in a wave channel and in a large three-dimensional wave basin. Maps of the evolution of the void-fraction distribution in bubble plumes generated by various size breaking waves are presented. Moments of the void-fraction field are shown to scale with the initially enclosed air volume at breaking and the energy dissipated by breaking. A significant fraction (30 to 50%) of the energy dissipated by breaking is found to be expanded in entraining bubbles against their buoyancy. The results reveal that the bubble plumes experience rapid transformations within the first wave period after the onset of breaking. In particular, the plumes loose 95% of the initially entrained air volume during the fust wave period. Predictions of the low-frequency resonant oscillations of the bubble plumes from measurements of the void-fraction compare well with acoustic measurements. Measurements near the ocean surface show high void-fractions up to 24% immediately beneath breaking waves. These are several orders of magnitude greater than previously reported time-averaged measurements. The second part addresses the measurement of very low void-fractions. Instrumentation based on the propagation velocity of low-frequency acoustic pulses is developed. Simultaneous measurements of the sound-speed (and thus the void-fraction) at several depths are conducted during two field experiments. Time-series of sound-speed and attenuation show dramatic fluctuations over time periods on the order of minutes or less. These are attributed to the formation of bubble plumes or passage of bubble clouds. Frequent occurences of sound-speed anomalies greater than 1 OOrnls and attenuation greater than 30dB/m are observed for moderate wind conditions (8m/s). The signals at various depths are highly correlated and mostly coherent at frequencies below 0.05Hz. The time-averaged (20min) sound-speed profile is found to be significantly more pronounced and shallower than previously reported. Simultaneous measurements at several acoustic frequencies show that the sound-speed is non-dispersive below 20kHz for moderate wind conditions. Bubble size distributions are inferred from the soundspeed and attenuation measurements.

Description: This research was funded by the Office of Naval Research (Ocean Acoustics and Oceanography) and the National Science Foundation.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution August 1993

Description: We begin with the linearized irrotational theory describing the diffraction of an incoming plane wave by a vertical cylinder. From the free-surface motion, we describe the boundary-layer flow field U0i near that cylinder. The flow field is then used to calculate the modified convective velocities Ui and symmetric dispersivities Dij. Through our calculations we have demonstrated convective flow reversal for both large and very small cylinders. In addition we have characterized four regions of waves and transport about the large cylinder relating to the different characteristics of each region: reflected region, scattered region, plane wave region, and sharp-edged shadow region. Our understanding of the transport velocities and dispersivities allows us to speculate qualitatively on the transport of fine particles near a round island in a diffracted wave field.

Description: National Science Foundation's Creativity Award for Graduate Study in Engineering for funding the author's fellowship; the Office of Naval Research (Contract N00014-89 J 3128) for partial research assistantship

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1992

Description: The family Labridae, or wrasses, is one of the most speciose fish families and is exceptional in its wide range of morphological and behavioral diversities. The cunner Tautogolabrus adspersus is one of two temperate-dwelling Western North Atlantic representatives of this family, and they are one of the few fishes that remain in New England waters throughout the year. In the winter, the cunner enters a state of "torpor" which has previously been described based solely on behavioral observations. The present study showed that cunner undergo physiological torpor, or hibernation, based on low oxygen consumption rates in winter, contributing to a large Q10 value of 8.5. It is thus established as one of the few marine species that is known to hibernate. Cunner withstood four months of starvation at 4°C. Glycogen, lipid, and protein in the liver decreased during this period, as did the liver/body ratio, but these components did not decrease significantly in the whole-body samples. Since liver components were not exhausted, and body components were not significantly affected, cunner can withstand long periods without eating. Regression analysis predicts that they can live at least 6 months given the rate of decrease of glycogen and lipid reserves, and 9 months based on their protein reserves. Oxygen consumption rates were monitored continuously over several days to determine diel variations in metabolic rate. The values obtained at night were significantly lower than the daytime values. Cunner did not maintain a diel cycle throughout the year; the length of this cycle varied from approximately 24 hours during warm temperatures to approximately 48 hours at temperatures generally below 8°C. Metabolic rates were more variable at warmer temperatures, which is in agreement with the expected increase in spontaneous activity. Two tropicallabroids, the wrasse Thalassoma bifasciatwn and the parrotfish Scarus iserti, also had significantly higher oxygen consumption rates during the day than at night. Both hibernation and sleep are thought to be energy conserving mechanisms in fishes. The ability of labrids to sleep may have predisposed them to becoming established in temperate waters by surviving cold temperatures through hibernation.

Description: Funding for this research came from the Ocean Ventures Fund (OVF), and from private funding from the Mobil Co. administered by the Coastal Research Center (CRC) at WHO!. This research was also partially the result of research sponsored by NOAA National Sea Grant College Program Office, Dept. of Commerce, under Grant No. NA86- AA-D-SG090, WHOI Sea Grant Project Nos. R/A-26-PD and R/B-106-PD.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution August 1993

Description: Control systems for underwater vehicles have reached the level of sophistication where they are limited by the dynamic performance of the thrust actuators. Standard fixed-pitch propellers have been shown to have very poor dynamic characteristics, particularly at low thrust levels The dynamic response of a fixed-pitch propeller is dependent upon highly non-linear transients encountered while the shaft speed approaches its steady-state value. This thesis proposes the use of a controllable pitch propeller system to address this problem. A controllable pitch propeller varies the amount of thrust produced by varying the pitch angle of the blades at a constant shaft speed. The bandwidth of this type of thrust actuator would be dependent primarily on the speed at which the pitch angle of the blades are changed. A variable pitch propeller system suitable for retrofit into an ROV is designed and built. The system is designed for maximal pitch angle bandwidth with low actuator power consumption.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution December 1993

Description: Mechanical transmission mechanisms enable a designer to match the abilities (e .g. velocity, torque capacity) of an actuator to the needs of an application. Unfortunately the mechanical limitations of the transmission (e.g. stiffness, backlash, friction, etc.) often become the source of new problems. Therefore identifying the best transmission option for a particular application requires the designer to be familiar with the inherent characteristics of each type of transmission mechanism. In this thesis we model load/deflection behavior of one particular transmission option; closed circuit cable/pulley transmissions. Cable drives are well suited to force and position control applications because of their unique combination of zero backlash motion, high stiffness and low friction. We begin the modelling process by determining the equilibrium elongation of a cable wrapped around a nonrotating pulley during loading and unloading. These results enable us to model the load/deflection behavior of the open circuit cable drive. Using the open circuit results we model the more useful closed circuit cable drive. We present experimental results which confirm the validity of both cable drive models and then extend these models to multistage drives. We end by discussing the use of these models in the design of force and position control mechanisms and comment on the limitations of these models.

Description: Submitted in partial fulfillment of the requirements for the degree of Ocean Engineer at the Massachusetts Institute of Technology and Woods Hole Oceanographic Institution January 1994

Description: In 1991 the Heard Island Feasibility Test demonstrated that it is possible to transmit coded acoustic signals nearly half way around the world. One of the key issues in the feasibility test was to determine the spatial structure of the received transmissions. In this thesis, data from the Canadian Defense Research Establishment Pacific horizontal line array is used to form an estimate of the directional power spectrum. This spectrum determines if any horizontal multipath is detectable. The preliminary signal conditioning, including frequency spectrum estimation and demodulation required before beamforming is described. Conventional and adaptive beamforming methods are examined with synthetic data to demonstrate the limitations on the directional spectrum results. The principle result of this work is that no stable horizontal multipath is evident. The mean arrival angle for the five hours of data analyzed is 212° ± 1.5°.

Description: The Office of Naval Research provided funding for the author under the ONR fellowship program.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2012

Description: Interactions between the ocean circulation in sub-ice shelf cavities and the overlying ice shelf have received considerable attention in the context of observed changes in flow speeds of marine ice sheets around Antarctica. Modeling these interactions requires parameterizing the turbulent boundary layer processes to infer melt rates from the oceanic state at the ice-ocean interface. Here we explore two such parameterizations in the context of the MIT ocean general circulation model coupled to the z-coordinates ice shelf cavity model of Losch (2008). We investigate both idealized ice shelf cavity geometries as well as a realistic cavity under Pine Island Ice Shelf (PIIS), West Antarctica. Our starting point is a three-equation melt rate parameterization implemented by Losch (2008), which is based on the work of Hellmer and Olbers (1989). In this form, the transfer coefficients for calculating heat and freshwater fluxes are independent of frictional turbulence induced by the proximity of the moving ocean to the fixed ice interface. More recently, Holland and Jenkins (1999) have proposed a parameterization in which the transfer coefficients do depend on the ocean-induced turbulence and are directly coupled to the speed of currents in the ocean mixed layer underneath the ice shelf through a quadratic drag formulation and a bulk drag coefficient. The melt rate parameterization in the MITgcm is augmented to account for this velocity dependence. First, the effect of the augmented formulation is investigated in terms of its impact on melt rates as well as on its feedback on the wider sub-ice shelf circulation. We find that, over a wide range of drag coefficients, velocity-dependent melt rates are more strongly constrained by the distribution of mixed layer currents than by the temperature gradient between the shelf base and underlying ocean, as opposed to velocity-independent melt rates. This leads to large differences in melt rate patterns under PIIS when including versus not including the velocity dependence. In a second time, the modulating effects of tidal currents on melting at the base of PIIS are examined. We find that the temporal variability of velocity-dependent melt rates under tidal forcing is greater than that of velocity-independent melt rates. Our experiments suggest that because tidal currents under PIIS are weak and buoyancy fluxes are strong, tidal mixing is negligible and tidal rectification is restricted to very steep bathymetric features, such as the ice shelf front. Nonetheless, strong tidally-rectified currents at the ice shelf front significantly increase ablation rates there when the formulation of the transfer coefficients includes the velocity dependence. The enhanced melting then feedbacks positively on the rectified currents, which are susceptible to insulate the cavity interior from changes in open ocean conditions.

Description: National Science and Engineering Research Council of Canada

Description: Submitted in partial fulfillment of the requirements for the degree of Ocean Engineer at the Massachusetts Institute of Technology and Woods Hole Oceanographic Institution September 1994

Description: Closed loop control of an unmanned underwater vehicle (UUV) in the dynamically difficult environment of shallow water requires explicit consideration of the highly coupled nature of the governing non-linear equations of motion. This coupling between an UUV's six degrees of freedom (6 DOF) is particularly important when attempting complex maneuvers such as coordinated turns (e.g. simultaneous dive and heading change) or vehicle hovering in such an environment. Given the parameter and modelling uncertainties endemic to these equations of motion, then a robust 6 DOF sliding controller employing six-element vector sliding surfaces provides a framework in which satisfactory UUV control can be achieved in shallow water. The vehicle equations of motion are developed and cast in a form that is amenable to non-linear sliding control design. A complete 6 DOF sliding controller with vector sliding surfaces is then formulated via a Lyapunov-like analysis. The sliding controller is then modified via a weighted least-squares approach to work with a particular UUV which has only 4 DOF control authority available. The modified controller is shown to work well for a variety of commanded UUV maneuvers in the presence of significant environmental disturbances and vehicle hydrodynamic parameter uncertainties via numerical simulation. Use of the signals generated by the controller are shown to be of utility in vehicle buoyancy control.

Description: The financial support of the Office of Naval Research under Contract No. N00014-90-J-1912 is gratefully acknowledged.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and Woods Hole Oceanographic Institution September 1994

Description: Normal mode theory provides an efficient description of signals which propagate axially in the SOFAR channel and are detectable at long ranges. Mode amplitudes and their second order statistics are useful in studies of long-range acoustic propagation and for applications such as Matched Mode Processing (MMP) and Matched Field Tomography (MFT). The purpose of this research is to investigate techniques for estimating the average power in the modes of a signal given pressure measurements from a vertical line array. This thesis develops the problem of mode estimation within a general array processing framework which includes both deterministic and stochastic characterizations of the modal structure. A review of conventional modal beamforming indicates that these methods provide poor resolution in low signal-to-noise ratio environments. This is not surprising since standard estimation techniques rely on minimizing a squared error criterion without regard to the ambient noise. The primary contribution of this thesis is an adaptive estimator for coherent modes that is based on a method suggested by Ferrara and Parks for array processing using diversely-polarized antennas. Two formulations of the adaptive method are investigated using a combination of analytical techniques and numerical simulations. The performance evaluation considers the following issues: (i) power level of the noise, (ii) orthogonality of the sampled modeshapes, (iii) number of data snapshots, and (iv) coherence of the signal. The new approach is fundamentally different from other modal estimators such as those used in MMP because it is data-adaptive and maximizes the received power instead of minimizing the squared error. As a result, the new methods perform significantly better than least squares in high noise environments. Specifically, the Ferrara/Parks formulations are able to maintain nulls in the modal spectrum since they do not suffer the bias error that significantly affects the least squares processor. A second contribution of the thesis is an extension of the coherent estimator to facilitate estimation of phase-randomized modes. Although the results of this work are preliminary, the extended formulation appears to offer several advantages over least squares in certain cases.

Description: Funding for this work was provided by a Clare Boothe Luce Fellowship (1991-1992) and the University of California-Scripps ATOC Agreement, P0# 10037359.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and Woods Hole Oceanographic Institution February 1995

Description: Laboratory and numerical experiments are carried out in a parameter regime relevant to open-ocean deep convection. We consider the case of convection in a rotating stratified ocean of finite depth. Convection is induced from the surface by extracting buoyancy over a circular area. The external parameters are buoyancy forcing of strength Bo applied over a circular area of radius Rs, the rotation rate is measured by f, ambient stratification N and finite depth H. Theoretical scaling predictions are derived to describe the length and velocity scales of the convective chimney as it adjusts under gravity and rotation, and breaks up through baroclinic instability. The scales of interest include the number (M), size (leddy) and strength (Urim) of the baroclinic eddies formed. Also of interest are the final depth of penetration of the convective mixed layer (dfinal) and the final volume of convectively produced water (Vfinal). These scales are tested against the laboratory and numerical experiments and found to be appropriate. We show that for this idealized problem dfinal depends only on the size and strength of the forcing and t he ambient stratification encountered by the convection event; it does not depend explicitly on rotation. The volume of convectively modified water produced continues to increase as long as forcing continues, but the rate of production depends again only on the size and strength of the forcing and on the ambient stratification. The implications of the work to deep water formation in the Labrador Sea and elsewhere are discussed. Finally, the study has relevance to the role and representation of baroclinic eddies in large-scale circulation of the ocean.

Description: This research was funded by John Marshall on Office of Naval Research (ONR) contract N00014-92-J-1567.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution January 18, 1988

Description: We have contrived a regional model Φ(K, ω, η, φ, λ) for the distribution of low frequency variability energy in horizontal wavenumber, frequency, vertical mode and geography. We assume horizontal isotropy, Φ(K, ω, η, φ, λ) = 2πKψ(k, l, ω, η, φ, λ), with K designating the amplitude of total horizontal wavenumber. The parameters of Φ(K, ω, η, φ, λ) can be derived from observations: (i) satellite altimetry measurements yield the surface eddy kinetic energy wavenumber and frequency spectra and the geographic distribution of surface eddy kinetic energy magnitude, (ii) XBT measurements yield the temperature wavenumber spectra, (iii) current meter and thermistor measurements yield the frequency spectra of kinetic energy and temperature, (iv) tomographic measurements yield the frequency spectra of range— and depth—averaged temperature, and (v) the combination of satellite altimetry and current meter measurements yields the vertical partitioning of kinetic energy among dynamical modes. We assume the form of the geography—independent part of our model Φ(K, ω, η) ∝Kpωq. The observed kinetic energy and temperature wavenumber spectra suggest p = 3/2 at K 〈 K0 and p = —2 at K 〉 K0 for the barotropic mode, and p = —1/2 at K 〈 K0 and p = —3 at K 〉 K0 for the baroclinic mods, where K0 is the transitional wavenumber of the wavenumber spectra. The observed frequency spectra of temperature and kinetic energy suggest that q = —1/2 for ω 〈 ω0 and q = —2 for ω 〉 ω0, where ω0 is the transitional frequency of the frequency spectra. The combination of satellite altimetry and current meter measurements suggests the vertical structure of the low frequency variability is governed by the first few modes. The geography—dependent part of our model is the energy magnitude. Although we have shown analytically that the tomographic measurements behave as a low—pass filter, it is impossible to identify this filtering effect in the real data due to the strong geographic variability of the energy magnitude and the vertical gradient of the mean temperature. The model wavenumber spectrum is appropriate only where the statistical properties are relatively homogeneous in space.

Description: My first year in the Joint Program was supported by the National Science Foundation under grant OCE 92-16628, then were supported by the National Science Foundation under grant OCE 95-29545.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 1994

Description: This thesis presents a series of investigations on the specialized cell covering of a dormant stage (the resting cyst) in the life cycle of the marine dinoflagellate Lingulodinium polyedra. These cell walls, along with those of resting cysts formed by many other dinoflagellate species, are resistant to degradation and persist in the depositional environment. Selective preservation of these materials has created a rich dinoflagellate fossil record (extending back ~225 million years) which has shown great utility in biostratigraphic applications. By elucidating the nature of resting cyst walls and directly observing their development in laboratory cultures, the research presented here addresses several long-standing questions regarding both the paleontology and biology of dinoflagellates. Although resting cyst formation has been reported in other extant species, this thesis documents for the first time the morphological development of resting cysts having "fossilizable", morphologically complex cell walls. In laboratory cultures of L. polyedra, resting cyst formation is an extremely rapid phenomenon; the transition from thecate, actively swimming planozygote to spine-bearing, morphologically mature hypnozygote occurs within 10-20 minutes. The basic mechanism consists of dramatic cell expansion resulting from the widening of an interstice between the planozygotic cytoplasm and a balloon-like membrane external to the theca. Key morphological events in the development of the distinctive L. polyedra resting cyst cell covering occur within this interstice. These include early dissociation and outward migration of the theca, formation of the resistant endophragm, and growth of spines from globules on the surface of the cytoplasm. The level of morphological maturity attained by the encysting cell depends primarily on how much development occurs before rupture of the expanding outer membrane. H rupture is premature, a wide variation of resting cyst morphology may occur, particularly with respect to the size, number, and distribution of processes. The direct observation of these developmental events has shed much light on several issues regarding resting cyst morphogenesis. First, growth of L. polyedra resting cyst spines is clearly centrifugal (i.e. growing radially outward). Although not necessarily representative of spine growth in all species, this mode of formation provides a useful preliminary framework for interpreting some of the "histrichosphaerid" morphologies present in the fossil record. Second, in this species at least, the theca plays no direct role in influencing the morphology of spines. Finally, considerable variation in spine morphology is possible within one biologically-defined species. This last point has considerable significance for cyst-based taxonomy, and strongly suggests that several of the fossil morphotypes traditionally designated as separate species of Lingulodinium are, in fact, synonymous. Ultrastructural examination of L. polyedra resting cysts formed in laboratory culture has shown, for the first time, the fine structure of the cell walls enclosing a living, paleontologically-signillcant resting cyst. Unfortunately, difficulties associated with fixation and infiltration of these thick-walled structures precluded an in-depth investigation of the ultrastructural dynamics underlying the morphological development described above. Preliminary results, however, confirm earlier speculation that only the outermost wall of the L. polyedra resting cyst is normally preserved in the fossil record. This outer wall (including spines) appears constructed of closely appressed structural units, an ultrastructural style apparently widespread among species related to L. polyedra. The resistant cell walls of L. polyedra resting cysts were isolated from laboratory cultures and chemically characterized by an extensive array of analytical techniques. Both thermal (pyrolysis) and chemical (CuO oxidation) dissociation of this material yielded suites of products consistent with a macromolecular substance composed signillcantly of aromatic components. In addition, the relative abundance of carboxylated phenols among resting cyst CuO oxidation products indicated that aromatic structural units in the dinoflagellate material may be largely carbon-carbon linked, probably directly through aromatic nuclei. Such a "condensed" arrangement may be, in part, responsible for the remarkable resistance of the dinoflagellate resting cyst wall biopolymer. Overall, the aromatic signature of L. polyedra resting cyst wall material can be clearly distinguished from that of both pollen wall "sporopollenin" and classical lignin. Although some short chain carboxylic acids are generated during CuO oxidation, there is little evidence obtained by dissociation techniques to suggest the significant presence of extended polymethylenic elements in this macromolecular substance. As a result, the dinoflagellate material appears fundamentally different from the highly aliphatic "algaenans" recently identified in the cell wall of several chlorophyte species. Interestingly, pyrolysis (Py-GC/MS) of resting cyst wall material produced an abundance ofprist-1-ene, strongly suggesting the presence of bound tocopherols which may play an important structural role in the resistant cell wall biopolymer. Lipid analysis of L. polyedra culture extract revealed a series of even carbon numbered fatty acids (C14 - C24), as well as sterols (including dinosterol and cholesterol), and a full suite of tocopherols. These compounds are present during construction of the resistant outer wall of the resting cyst, and could function as precursors to the resting cyst wall biopolymer. Another possibility, given the strong aromaticity predicted by the results of pyrolysis and CuO oxidation, is some contribution by aromatic amino acids in an analogous fashion to lignin biosynthesis. The extensive chemical characterization of the outermost cell wall of L. polyedra resting cysts reported in this thesis provides the first rigorous analysis of "fossilizable" biopolymer(s) produced by an extant dinoflagellate. Furthermore, these analyses represent an unprecedented level of chemical characterization of a resistant algal cell wall biopolymer, and clearly demonstrate the unique nature of the L. polyedra resting cyst wall. As a result, this work provides the first chemical data to justify the term "dinosporin", previously proposed to distinguish the highly resistant material comprising dinoflagellate resting cyst walls from other resistant cell wall biopolymers.

Description: Primary financial support for this work was provided by a WHOI graduate research fellowship funded through the Amoco Foundation, Inc. Supplies and instrument time for the chemical investigations were supported by National Science Foundation grants OCE- 9201189 (T. I. Eglinton) and OCE-9300890 (T. I. Eglinton and M.A. Gofii). Additional funding came through the Ocean Ventures Fund, a Phycological Society of America Grant-in-Aid of Research, NSF grant OCE-8911226 (D. M. Anderson), and WHOI Education.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Woods Hole Oceanographic Institution and the Massachusetts Institute of Technology June 1995

Description: In marine ecology, the variability of the physical environment is often considered a main determinant of biological pattern. A common approach to identifying key environmental forcings is to match scales of variability: fluctuations of a biological variable at a particular frequency are attributed to forcing by the physical environment at a similar frequency. In nonlinear systems, however, different scales of variability interact and forcing at one frequency can produce variability at a different frequency. The general theme of this dissertation regards the interplay of scales in nonlinear ecological systems, with an emphasis on the mismatch of scales between biological variables and environmental forcings in the plankton. The approach is theoretical: I use simple models to identify conditions leading to such a mismatch. The models are motivated by planktonic systems and focus on one ubiquitous nonlinear ecological interaction, that between a consumer and a resource. This work is organized in three main parts as follows. In the first part, I consider the interaction between a phytoplankton population and a limiting nutrient resource. Most models for this interaction consider all cells as equal and group them under a single variable, the total biomass or cell density. They do not take into account any population heterogeneity resulting from the life histories of individual cells. However, single cells do have life histories: each cell progresses through a determinate sequence of events preceding cell division and the population is distributed in stages of the cell cycle. I incorporate this distribution (i.e. population structure) , as well as observations on resource control of cell cycle progression, into chemostat models for the phytoplankton-nutrient interaction. Simulation results demonstrate that the· population structure can generate oscillatory dynamics under a constant nutrient supply, and that such oscillations are important to population dynamics under a variable nutrient supply. Specifically, for a periodic resource supply, the population displays an aperiodic response with frequencies different from that of the forcing. I then show that a chemostat model without population structure (the Droop equations) does not exhibit this transfer of variability: a periodic nutrient supply produces a periodic population response of exactly the same frequency. In the second part, I consider a predator and a prey that interact and diffuse along an environmental gradient. The model is a reaction-diffusion equation, a type of model used in biological oceanography for planktonic interactions in turbulent flows. I demonstrate that weak diffusion along a spatial gradient may drive an otherwise periodic system into complex temporal dynamics that include chaotic behavior. I provide evidence for a quasiperiodic route to chaos as the diffusion rate decreases. Then, I focus on the spatial properties of the gradient and their consequences for the spatia-temporal dynamics of the system. In particular, I ask: how do the spatial patterns of the populations compare to the underlying environmental gradient in the different dynamic regimes (periodicity, quasiperiodicity, and chaos)? I show that the spatial patterns of predator and prey can differ strongly from the environmental gradient. In the route to chaos, as diffusion becomes weaker, this difference is magnified and the populations display smaller spatial scales. In the work summarized so far, nonlinearity leads to variability in biological variables at scales not present in the environmental forcings. In the third part of this work, I consider another consequence of the transfer of variability in nonlinear systems: the lack of a dominant scale. Patterns that lack a dominant scale but exhibit scale similarity are known as fractals. The characterization of numerical quantities that vary intermittently has motivated a generalization of fractals known as multifractals. Here, I give a first application of multifractals to biological oceanography. I analyze an acoustic data set on zooplankton biomass to describe the distribution in time of the total variability in the data. This distribution is highly intermittent: extreme localized contributions account for a large proportion of total variability. I show that multifractals provide a good characterization of such variability.

Description: The Education Office partially supported this work through the Ocean Ventures Fund. The Office of Naval Research and the National Science Foundation generously supported this work through the following grants to Hal Caswell: ONR-URIP Grant N00014-92-J-1527 and NSF Grant OCE-8900231.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Woods Hole Oceanographic Institution and the Massachusetts Institute of Technology February 1995

Description: Periodic structures which are slightly disordered undergo dramatic changes in mode shapes such that the responses go from being spatially extended to spatially localized. This phenomenon called mode localization, offers an excellent option for passive vibration isolation. In the first part of the thesis, we provide analytical prediction of modes exhibiting moderate localization using a newly developed Jordan Block Perturbation Method. We estimate and compare convergence zones of our newly developed method with perturbation techniques used to describe localized modes. In the second part of the thesis, we provide numerical evidence that complex branch points, which occur for complex disorder values in the mode-disorder relation, are responsible for modal sensitivity. We investigate the effects of the strength of the branch point and their location in the complex plane. In the third part of the thesis we perform an optimization study involving the selection of parameters which ensure a minimum level of localization of all modes. Optimal solutions were found to lie at maximum distances from the branch points, and the convergence basin of each optimum was demarcated by the branch point surface. The number of local optima were found to grow exponentially with the number of pendula. A statistical analysis showed that sampling of 10% provided an estimate that was within 2% of the global optimum, thereby reducing the computational effort for small to moderate systems of pendula. For larger systems of pendula, the problem of obtaining the global optimum in reasonable time still remains an open problem. In the fourth part of the thesis we propose an application for mode localization in vibration isolation. An oceanographic mooring with regularly spaced buoys is investigated for localization of inline elastic oscillations. Localization is found to be useful for confining the harmonics in deep water moorings of 1000 - 4000m.

Description: I wish to gratefully acknowledge educational support of the Office of Naval Research contract numbers N00014-89-C-0179 and N00014-90-C-0098. Computational time was supported by Office of Naval Research under grant number N00014-92-J-1269.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2012

Description: Despite widespread concerns about the effects of anthropogenic noise on baleen whales (suborder Mysticeti), we lack basic information about their auditory physiology for comprehensive risk assessments. Hearing ranges and sensitivities could be measured if customized equipment and methods were developed based on how baleen whales receive sound. However, sound reception pathways in baleen whales are currently unknown. This thesis presents an integrative approach to understanding hearing in baleen whales through dissections, biomedical imaging, biochemical analyses, and modeling sound propagation through a whale head using the Finite Element Method (FEM). We focused on the minke whale (Balaenoptera acutorostrata) because it is one of the smallest and most abundant mysticete species, reducing logistical difficulties for dissections and experiments. We discovered a large, well-formed fat body extending from the blubber region to the ears and contacting the ossicles. Although odontocetes, or toothed whales, are thought to use specialized “acoustic fats” for sound reception, no such tissues had been described for mysticetes to date. Our study indicates that the basic morphology and biochemical composition of the minke whale “ear fats” are very different from those of odontocete acoustic fats. However, the odontocete and mysticete fatty tissues share some characteristics, such as being conserved even during starvation, containing fewer dietary signals compared to blubber, and having well-defined attachments to the tympano-periotic complex, which houses the middle and inner ears. FE models of the whale head indicated that the ear fats caused a slight increase in the total pressure magnitude by the ears, and this focusing effect could be attributed to the low density and low sound speed of the ear fats in the models. Fatty tissues are known to have lower densities and sound speeds than other types of soft tissues, which may explain why they are an important component of the auditory system of odontocetes, and perhaps mysticete cetaceans as well. In an aquatic habitat where the pinna and air-filled ear canal are no longer effective at collecting and focusing sound towards the ears, we propose that both odontocete and mysticete cetaceans have incorporated fatty tissues into their auditory systems for underwater sound reception.

Description: This study was funded by the National Science Foundation Graduate Research Fellowship Program, WHOI Academic Programs Office, WHOI Ocean Life Institute Fellowship, Ocean Ventures Fund, WHOI Coastal Ocean Institute Award, WHOI Summer Student Fellowship, WHOI Minority Fellowship, the MIT Student Assistance Fund, the Joint Industry Program, the Marine Mammal Program of the Office of Naval Research, and the Naval Operations Energy and Environmental Readiness Division.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1997

Description: Saltwater marshes and wetlands are important buffers at the land-sea interface. Among the most biologically active ecosystems on Earth, natural and man-made wetlands are important interceptors of pollutants and nutrients bound for the coastal ocean. The transport, dilution, and deposition processes occurring within the marsh are key factors in determining this interception, and these are in turn determined largely by tidally driven flows as influenced by marsh vegetation and other physical characteristics. Vegetation type and density are of primary importance in these processes, both for pollutant/nutrient uptake concerns and in determining hydrodynamic characteristics of the marsh. This study examines the effect of vegetation density and ambient flow on diffusivity within a tidal marsh canopy, specifically Spartina alterniflora. Vegetation densities from 0-1.4% stem coverage and flows from 2-12 cm/sec were investigated using Rhodamine WT tracer, with resultant measured diffusivities ranging from approximately 0.5-3.0 cm2/sec. Diffusivity was found to be a strong function of ambient current, but a much weaker function of vegetation density. Presence of vegetation caused transverse and vertical diffusivities to be essentially isotropic over all vegetation densities, as opposed to the order of magnitude difference found in earlier non-vegetated studies. Only slight vegetation coverage was found to be necessary to produce this isotropy, with little additional change as stem density increased.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1997

Description: A review of the Odyssey IIB autonomous underwater vehicle shows that energy costs associated with vehicle controls can be reduced and operational flexibility improved with relatively simple, low cost improvements. Because the operating speed that minimizes forward drag is not necessarily the same as that required for optimum sensor performance, a variable speed capability extending to the bottom of the vehicle speed range is sought. Optimizing Odyssey IIB AUV performance for slower speed operations and extended duration missions necessitates a multi-disciplinary review including control system design, hydrodynamic performance and sensor selection and utilization. Reducing the vehicle controls-fixed directional instability by adding vertical fixed fins, implementing an actuation filter, and designing a model based adaptive sliding controller improves the variable speed performance and reduces the control actuation necessary to provide the desired performance level with energy savings.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1996

Description: Description of the shelfbreak front in the Middle Atlantic Bight is hampered by the extreme variability of the front. In order to gain more insight into the mean frontal structure and associated baroclinic jet, historical data is used to produce two dimensional climatological fields of temperature and salinity for the region south of Nantucket shoals. Associated cross-shelf fields of density, geostrophic velocity, relative vorticity, and shallow water potential vorticity have also been computed. Historical data from a quality-controlled database (HydroBase) in the region 69-72°W, 39.5-41°N is included. Cross-shelf sections are obtained by averaging the data in nine depth bins with an average cross-shelf spacing of 10 km but an increased resolution of 4 km near the shelfbreak. The vertical averaging interval was 10 m over the shelf and upper slope waters, increasing to 50 m in the deep slope waters. The data were averaged in bimonthly periods to study seasonal trends. For inter-regional comparison, similar analyses were performed for the south flank of Georges Bank and the shelf off New Jersey. The climatological temperature and salinity are consistent with previous descriptions of the frontal hydrography (e.g. Wright [1976], Beardsley and Flagg [1976], and Flagg [1987]). Most importantly, features such as the "cold pool", the upper slope pycnostad, and the frontal boundary are well resolved when compared with synoptic sections. The temperature contrast across the front varies seasonally between 2-6°C near the surface and at depths of 45-65 m. The salinity contrast is 1.5-2 PSS, with little seasonal variation. The resulting cross-frontal near surface density gradients are strongest during the winter and weakest during the summer, when the seasonal thermocline is established. The crossfrontal density gradients are stronger near the bottom outcrop of the front, consistent with previous modeling studies [Gawarkiewicz and Chapman, 1992]. Despite the inherent smearing of frontal gradients incurred by averaging over large temporal and spatial scales, the geostrophic velocity field shows a strong (20-30 cm s-1) baroclinic jet associated with the cross-frontal density gradients. The core of the jet, having a width of 15-20 km, is located between the 100-120 m isobaths. The core of the jet is well shoreward of the surface expression of the front, resulting from strong density gradients at the foot of the front. The horizontal velocity shear on the cyclonic, offshore edge of the front is roughly 0.2-0.4 * 10-4 s-1, with shears on the anticyclonic, offshore edge of the jet being half as large. The potential vorticity structure is drastically affected by the seasonal pycnocline during the summer but remains relatively uniform during the winter months. Comparisons of the mean fields from Georges Bank, Nantucket Shoals, and New Jersey show that the foot of the front shoals as the flow progresses to the southwest. The seasonal migration of the frontal boundary experiences a phase shift consistent with an alongshelf propagation of minimum salinities to the southwest. Finally, transport calculations for the flow over the outer shelf and slope give values in the range of 0.1-0.6 Sv to the west. This is comparable to the estimated transport shoreward of the 100 m isobath of 0.38 Sv [Beardsley et al., 1985], which suggests that the shelfbreak frontal jet may be an extremely important element in the alongshelf transport of fresh water in this region.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution January 1997

Description: This thesis investigates the petrology and geochemistry of an abyssal peridotite dredged from the Atlantis II Fracture Zone in the southwestern Indian Ocean Ridge. Texturally, this sample is a serpentinized peridotite with a crosscutting coarse-grained clinopyroxenite vein. One of the alteration veinlets contains rutile and ilmenite in association with plagioclase and amphibole. This veinlet is not related to the pyroxenite vein. In tenns of mineralogy, the composition of the major silicate minerals indicates that this plagioclase llierzolite represents the depleted residue after mantle melting, similar to other abyssal peridotites from this region. In addition to the presence of the unique pyroxenite vein, this sample was earlier shown to be a carrier of 'orphan Sr-87'. Unfortunately, I was unable to find such high Sr isotopic ratios in the magnetic separations of different fractions of the sample. The sulfide mineralogy, together with the whole rock chemistry, suggests that sea water alteration occurs mainly as a result of serpentinization at temperatures higher than 200°C. Since the sample is less than l Ma old, and the low temperature weathering occurred only after the sample was exposed at the sea floor, it is possible that the weathering process was restricted to major alteration veins. This suggests that the alteration process is highly fracture controlled and time dependent Trace element data from clinopyroxene grains in the peridotite shows large variations from grain to grain. The (Ce/Yb )n ranges from 0.17 to 0.54 in the pyroxenite vein, and from 0.75 to 2.35 away from the vein. The tendency for LREE enrichment with the increase of distance from the vein suggests the presence of highly reacted melts. An assimilation-fractional crystallization (AFC) model was derived which supports the idea that the source of the clinopyroxenite vein reacts with the depleted peridotite to form a central reaction zone. Some of the highly reacted melt, after melt-rock reaction, migrates out of the reaction zone, and precipitates some late magmatic phases while being trapped in the country rocks. Since the sulfide is a major Os reservoir in the abyssal peridotites, as shown in leaching experiments, and the melt is saturated in sulfur as a consequence of the reaction process, it is possible to model the heterogeneous distribution of the Os isotopic data by mixing the residual peridotite with 0.2 to 0.5 wt% of sulfides precipitated from the melt. This mixing process can explain most of the heterogeneity from 1.034 to 1.148 for 187Os/186Os. The impact on the peridotite from the melt-rock reaction and impregnation of the late melt is obvious. As evident in Hess Deep gabbroic rocks, conductive heat loss in the transform fault fulfils the physical requirement to create and to preserve such geochemical signature.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1996

Description: This thesis addresses the question of how a highly energetic eddy field could be generated in the interior of the ocean away from the swift boundary currents. The energy radiation due to the temporal growth of non-trapped (radiating) disturbances in such a boundary current is thought to be one of the main sources for the described variability. The problem of stability of an energetic current, such as the Gulf Stream, is formulated. The study then focuses on the ability of the current to support radiating instabilities capable of significant penetration into the far-field and their development with time. The conventional model of the Gulf Stream as a zonal current is extended to allow the jet axis to make an angle to a latitude circle. The linear stability of such a nonzonal flow, uniform in the along-jet direction on a beta-plane, is first studied. The stability computations are performed for piece-wise constant and continuous velocity profiles. New stability properties of nonzonal jets are discussed. In particular, the destabilizing effect of the meridional tilt of the jet axis is demonstrated. The radiating properties of nonzonal currents are found to be very different from those of zonal currents. In particular, purely zonal flows do not support radiating instabilities, whereas flows with a meridional component are capable of radiating long and slowly growing waves. The nonlinear terms are then included in the consideration and the effects of the nonlinear interactions on the radiating properties of the solution are studied in detail. For these purposes, the efficient numerical code for solving equation for the QG potential vorticity with open boundary conditions of Orlanski's type is constructed. The results show that even fast growing linear solutions, which are trapped during the linear stage of developement, can radiate energy in the nonlinear regime if the basic current is nonzonal. The radiation starts as soon as the initial fast exponential growth significantly slows. The initial trapping of those solutions is caused by their fast temporal growth. The new mechanism for radiation is related to the nonzonality of a current.

Description: This work was supported by NSF Grant OCE 9301845.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1997

Description: Expression and regulation of the ferredoxin and flavodoxin proteins in marine phytoplankton were investigated to assess their utility as biomarkers of iron limitation. A phylogenetic survey of seventeen microalgal species showed flavodoxin induction, with accompanying ferredoxin repression, to be a common response to iron stress. A minority of organisms examined never expressed flavodoxin, a condition associated with, but not characteristic of, neritic habitats. Antibodies raised against ferredoxin and flavodoxin from Thalassiosira weissflogii proved to be mono- and diatom-specific, respectively. Flavodoxin induction responded specifically to iron limitation and not to nitrogen, phosphorus, silicate, zinc or light deficiency. In iron-limited T. weissflogii, relative cellular ferredoxin and flavodoxin content (Fd index) varied with growth rates above ~50%μmax and was not affected by growth on either nitrate or ammonium as a sole nitrogen source. Below ~50%μmax, ferredoxin was absent. This variation with severity of stress and specificity to iron limitation make the Fd index an excellent choice as an indicator of iron limitation. HPLC measurement of ferredoxin and flavodoxin during the IronExII mesoscale enrichment experiment detected a strong flavodoxin signal but no significant ferredoxin synthesis, despite increases in chlorophyll and photosynthetic efficiency (Fv/Fm) observed by others. The absence of ferredoxin and the persistence of flavodoxin suggested that iron addition released the phytoplankton from iron starvation but was insufficient to completely relieve physiological iron limitation. Laboratory experiments demonstrated that a pennate diatom clone isolated from the IronExII bloom expressed both flavodoxin and ferredoxin and could alter its protein expression in about one day, further supporting the conclusion of continued iron limitation during IronExII. During IronExII, Fd index was uniformly zero while Fv/Fm increased from 0.26 to 0.56. In contrast, a laboratory iron addition experiment showed little change in Fv/Fm when the Fd index increased from 0.5-0.9. A conceptual model of the covariation of Fv/Fm and Fd index describes a complementary relationship between the two measures. Model results suggest that photochemical systems are affected by iron limitation only after cellular adaptive capacity, in the form of ferredoxin, is exhausted.

Description: This work was supported in part by a Department of Energy Graduate Fellowship for Global Change to D. Erdner and an Exploratory Research Agreement No. RP8021-05 from the Electric Power Research Institute to D.M. Anderson.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution December 1996

Description: Two-thirds of the surface of the Earth is created at mid-ocean ridges where magmas rise from the mantle and cool to form the oceanic crust. The objective of this Thesis is to examine the influence of magma supply and eruptive processes on axial morphology, crustal construction, and the properties of crustal magma chambers at intermediate and fast spreading ridges. Variations in magma supply on time scales of ~100 Kyr generate along-axis changes in crustal thickness and temperature. Magma sill properties and hydrothermal activity are closely linked to spreading events which occur on much shorter time scales (ca. 10-100 yr) than the longer-term variations in magma supply reflected in along-axis changes in ridge morphology. The seismically constrained depths of ridge crest magma sills (〉1-2 km) are considerably deeper than the level of neutral buoyancy (100-400 m). The apparent inverse relationship between magma sill depth and spreading rate suggests that a thermally controlled permeability boundary, such as the solidus horizon, controls the depth at which magma ponds beneath mid-ocean ridges. Recent thermo-mechanical models predict that, at intermediate spreading rates, rift valley and magma sill formation are sensitive to small changes in crustal thickness and mantle temperature. Analysis of gravity at an intermediate spreading ridge shows that small differences in crustal thickness (300-700 m) and mantle temperature (10-15°C) are indeed sufficient to produce major changes in lithospheric strength and axial morphology. A stochastic model for the emplacement of dikes and lava flows with a bimodal distribution of lava flows is required to satisfy geological and geophysical constraints on the construction of the extrusive section. Most dikes are intruded within a narrow zone at the ridge axis. Short flows build up approximately half the extrusive volume. Occasional flows that pond at a considerable distance off-axis build up the remainder of the extrusive section. This Thesis underlines the importance of eruption dynamics in the emplacement of the uppermost volcanic layer of the crust and of the crustal thermal structure in controlling local variations in magma sill depth and ridge morphology.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution January 1996

Description: Acoustic propagation in the ocean can be strongly affected by small random variations in ocean properties, including rough surfaces and volume fluctuations in the ocean or seabed. Such inhomogeneities scatter part of the incident acoustic field, stripping energy from the coherent part of the field. This scattered energy, or reverberation, propagates further in the modes of the ocean waveguide. The distribution of energy among modes is changed and the coherence of the acoustic field is reduced. This thesis introduces several models which describe scattering of low-frequency sound. First, the rough surface scattering theory of Kuperman and Schmidt is reformulated in terms of normal modes. Scattering from rough fluid-fluid interfaces and rough elastic halfspaces is modeled, and statistics of the acoustic field are calculated. Numerical results show the modal formulation agrees well with Kuperman and Schmidt's model, while reducing computation times by several orders of magnitude for the scenarios considered. Next, a perturbation theory describing scattering from sound speed and density fluctuations in acoustic media is developed. The theory is used to find the scattered field generated by volume fluctuations in sediment bottoms. Modal attenuations due to sediment volume scattering are calculated, and agreement is demonstrated with previous work. The surface and volume scattering theories are implemented in a unified modal reverberation code and used to study bottom scattering in shallow water. Numerical examples are used to demonstrate the relationship between volume and surface scattering. Energy distribution among scattered field modes is found to be a complicated function of the scattering mechanism, the scatterer statistics, and the acoustic environment. In particular, the bottom properties strongly influence the coherence of the acoustic field. Examples show that excitation of fluid-elastic interface waves is a potentially important scattering path. Cross-modal coherences are calculated and used to study the loss of signal coherence with range. Finally, earlier work on scattering from the Arctic ice sheet is extended. Simulations of long-range transmissions are compared with data from the April 1994 trans-Arctic propagation test. The results show modal attenuations and group speeds can be predicted reasonably well, indicating that acoustic monitoring of Arctic climate is feasible.

Description: I am extremely grateful for the financial support of the Office of Naval Research, under contracts N00014-92-J -1282 and N00014-95-1-0307.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution May 1997

Description: Navigation is a key technology for autonomous underwater vehicles (AUVs), and currently, it limits potential and existing vehicle capabilities and applications. This thesis presents a terrain-relative navigation system for AUVs that does not require the deployment of acoustic beacons or other navigational aids, but instead depends on a supplied digital bathymetric map and the ability of the vehicle to image the seafloor. At each time step, a bathymetric profile is measured and compared to a local region of the supplied map using a mean absolute difference criterion. The region size is determined by the current navigation uncertainty. For large regions, a coarse-to-fine algorithm with a modified beam search is used to intelligently search for good matches while reducing the computational requirements. A validation gate is defined around the position estimate using the navigation uncertainty, which is explicitly represented through a covariance matrix. A probabilistic data association filter with amplitude information (PDAFAI), grounded in the Kalman Filter framework, probabilistically weights each good match that lies within the validation gate. Weights are a function of both the match quality and the size of the innovation. Navigation updates are then a function of the predicted position, the gate size, all matches within the gate, and the uncertainties on both the prediction and the matches. The system was tested in simulation on several terrain types using a deep-ocean bathymetry map of the western flank of the Mid-Atlantic Ridge between the Kane and Atlantis Transforms. Results show more accurate navigation in the areas with greater bathymetric variability and less accurate navigation in flatter areas with more gentle terrain contours. In most places, the uncertainties assigned to the navigation positions reflect the ability of the system to follow the true track. In no case did the navigation diverge from the true track beyond the point of recovery.

Description: Funding was provided by Office of Naval Research Grants N00014-96-1-5028, N00014-94-1- 0466 and N00017-92-J-1714; Naval Research Underwater Warfare Center Grant N0014-90-D- 1979, and Naval Research Laboratory N00014-92-C-6028.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2013

Description: In this thesis we present results from inversion of data using dense arrays of collocated seismic and magnetotelluric stations located in the Cascadia subduction zone region of central Washington. In the migrated seismic section, we clearly image the top of the slab and oceanic Moho, as well as a velocity increase corresponding to the eclogitization of the hydrated upper crust. A deeper velocity increase is interpreted as the eclogitization of metastable gabbros, assisted by fluids released from the dehydration of upper mantle chlorite. A low velocity feature interpreted as a fluid/melt phase is present above this transition. The serpentinized wedge and continental Moho are also imaged. The magnetotelluric image further constrains the fluid/melt features, showing a rising conductive feature that forms a column up to a conductor indicative of a magma chamber feeding Mt. Rainier. This feature also explains the disruption of the continental Moho found in the migrated image. Exploration of the assumption of smoothness implicit in the standard MT inversion provides tools that enable us to generate a more accurate MT model. This final MT model clearly demonstrates the link between slab derived fluids/melting and the Mt. Rainier magma chamber.

Description: Funding for this work was made possible by the American Society for Engineering education through a National Defense Science and Engineering Fellowship, and by the National Science Foundation through two grants for the CAFE and CAFE MT projects.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2013

Description: Studying oceanic eddies is important for understanding and predicting ocean circulation and climate variability. The central focus of this dissertation is the energy exchange between eddies and mean flow and banded structures in the low-frequency component of the eddy field. A combination of a realistic eddy-permitting ocean state estimate and simplified theoretical models is used to address the following specific questions. (1) What are the major spatial characteristics of eddy-mean flow interaction from an energy perspective? Is eddy-mean flow interaction a local process in most ocean regions? (2) The banded structures in the low-frequency eddy field are termed striations. How much oceanic variability is associated with striations? How does the time-mean circulation, for example a subtropical gyre or constant mean flow, influence the origin and characteristics of striations? How much do striations contribute to the energy budget and tracer mixing?

Description: This research was supported by the National Aeronautics and Space Administration contracts NNX09AI87G and NNX08AR33G.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2013

Description: Quantifying uncertainty and error bounds is a key outstanding challenge in ocean state estimation and climate research. It is particularly difficult due to the large dimensionality of this nonlinear estimation problem and the number of uncertain variables involved. The “Estimating the Circulation and Climate of the Oceans” (ECCO) consortium has developed a scalable system for dynamically consistent estimation of global time-evolving ocean state by optimal combination of ocean general circulation model (GCM) with diverse ocean observations. The estimation system is based on the "adjoint method" solution of an unconstrained least-squares optimization problem formulated with the method of Lagrange multipliers for fitting the dynamical ocean model to observations. The dynamical consistency requirement of ocean state estimation necessitates this approach over sequential data assimilation and reanalysis smoothing techniques. In addition, it is computationally advantageous because calculation and storage of large covariance matrices is not required. However, this is also a drawback of the adjoint method, which lacks a native formalism for error propagation and quantification of assimilated uncertainty. The objective of this dissertation is to resolve that limitation by developing a feasible computational methodology for uncertainty analysis in dynamically consistent state estimation, applicable to the large dimensionality of global ocean models. Hessian (second derivative-based) methodology is developed for Uncertainty Quantification (UQ) in large-scale ocean state estimation, extending the gradient-based adjoint method to employ the second order geometry information of the model-data misfit function in a high-dimensional control space. Large error covariance matrices are evaluated by inverting the Hessian matrix with the developed scalable matrix-free numerical linear algebra algorithms. Hessian-vector product and Jacobian derivative codes of the MIT general circulation model (MITgcm) are generated by means of algorithmic differentiation (AD). Computational complexity of the Hessian code is reduced by tangent linear differentiation of the adjoint code, which preserves the speedup of adjoint checkpointing schemes in the second derivative calculation. A Lanczos algorithm is applied for extracting the leading rank eigenvectors and eigenvalues of the Hessian matrix. The eigenvectors represent the constrained uncertainty patterns. The inverse eigenvalues are the corresponding uncertainties. The dimensionality of UQ calculations is reduced by eliminating the uncertainty null-space unconstrained by the supplied observations. Inverse and forward uncertainty propagation schemes are designed for assimilating observation and control variable uncertainties, and for projecting these uncertainties onto oceanographic target quantities. Two versions of these schemes are developed: one evaluates reduction of prior uncertainties, while another does not require prior assumptions. The analysis of uncertainty propagation in the ocean model is time-resolving. It captures the dynamics of uncertainty evolution and reveals transient and stationary uncertainty regimes. The system is applied to quantifying uncertainties of Antarctic Circumpolar Current (ACC) transport in a global barotropic configuration of the MITgcm. The model is constrained by synthetic observations of sea surface height and velocities. The control space consists of two-dimensional maps of initial and boundary conditions and model parameters. The size of the Hessian matrix is O(1010) elements, which would require O(60GB) of uncompressed storage. It is demonstrated how the choice of observations and their geographic coverage determines the reduction in uncertainties of the estimated transport. The system also yields information on how well the control fields are constrained by the observations. The effects of controls uncertainty reduction due to decrease of diagonal covariance terms are compared to dynamical coupling of controls through off-diagonal covariance terms. The correlations of controls introduced by observation uncertainty assimilation are found to dominate the reduction of uncertainty of transport. An idealized analytical model of ACC guides a detailed time-resolving understanding of uncertainty dynamics.

Description: This thesis was supported in part by the National Science Foundation (NSF) Collaboration in Mathematical Geosciences (CMG) grant ARC-0934404, and the Department of Energy (DOE) ISICLES initiative under LANL sub-contract 139843-1. Partial funding was provided by the department of Mechanical Engineering at MIT and by the Academic Programs Office at WHOI. My participation in the IMA "Large-scale Inverse Problems and Quantification of Uncertainty" workshop was partially funded by IMA NSF grants.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2013

Description: The interpretation of echoes collected by active remote-sensing systems, such as sonar and radar, is often ambiguous due to the complexities in the scattering processes involving the scatterers, the environment, and the sensing system. This thesis addresses this challenge using a combination of laboratory and fi eld experiments, theoretical modeling, and numerical simulations in the context of acoustic scattering by marine organisms. The unifying themes of the thesis are 1) quantitative characterization of the spectral, temporal, and statistical features derived from echoes collected using both broadband and narrowband signals, and 2) the interpretation of echoes by establishing explicit links between echo features and the sources of scattering through physics principles. This physics-based approach is distinct from the subjective descriptions and empirical methods employed in most conventional fisheries acoustic studies. The fi rst part focuses on understanding the dominant backscattering mechanisms of live squid as a function of orientation. The study provides the first broadband backscattering laboratory data set from live squid at all angles of orientation, and conclusively con firms the fluidlike, weakly-scattering material properties of squid through a series of detailed comparisons between data and predictions given by models derived based on the distorted-wave Born approximation. In the second part, an exact analytical narrowband model and a numerical broadband model are developed based on physics principles to describe the probability density function of the amplitudes of echo envelopes (echo pdf) of arbitrary aggregations of scatterers. The narrowband echo pdf model signi cantly outperforms the conventional mixture models in analyzing simulated mixed assemblages. When applied to analyze fish echoes collected in the ocean, the numerical density of sh estimated using the broadband echo pdf model is comparable to the density estimated using echo integration methods. These results demonstrate the power of the physics-based approach and give a rst-order assessment of the performance of echo statistics methods in echo interpretation. The new data, models, and approaches provided here are important for advancing the eld of active acoustic observation of the ocean.

Description: Taiwan Merit Scholarship (NSC-095-SAF-I-564-021-TMS), Office of Naval Research (ONR; grants N00014-10-1-0127, N00014-08-1-1162, N00014-07-1-1034), National Science Foundation (NSF; grant OCE-0928801), Naval Oceanographic Offi ce (grant N62306007-D9002), WHOI Ocean Life Institute, and the WHOI Academic Programs O ffice funds.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 1993

Description: There is a growing consensus that the sound generated by breaking waves is responsible for much of the ambient noise level in the ocean. While numerous field measurements have shown a strong correlation between the ambient noise spectrum level (N) in the range 100Hz to 25kHz and wind speed in the ocean, very little has been done to establish a comparable correlation between the ambient noise spectrum level and surface wave field parameters. The difficulty in establishing this relationship is remarkable given that the frequency and intensity of wave breaking are dependent on the characteristics of the wave field. In Fall 1991, an experiment was conducted from the research platform Flip 130 kilometers off the coast of Oregon, where the ambient noise between 2.5 and 25 kHz, the wind speed, and the sea surface elevation using wire wave gauges were measured. The correlation between N and the root mean square wave amplitude a was found to be poor but could be improved if the swell was filtered out from the wave elevation time series. The influence of swell on the value of a was disproportionate to the level of ambient noise since its characteristics were not directly due to the local wind-wave conditions. Observations of the dependence of the high frequency wind waves and the directional wave spectrum under turning winds suggested that the high frequency wave components responded more quickly to changes in the wind speed and wind direction than the energy-containing frequencies. The ambient noise level also correlated well with the root mean square wave slopes. This is consistent with previous laboratory measurements which showed that the steepness of a packet of waves correlates with the strength of wave breaking and with characteristics of breaking waves such as loss of momentum flux, dissipation, initial volume of air entrained, mixing, and sound generation. Comparisons of surface wave dissipation estimates using field measurements and models developed by Phillips (1985) and Hasselmann (1974) show that although the two models have very different forms, they give values that are comparable in magnitude. The relationship between the ambient noise level and log of dissipation give correlation coefficients (0.93-0.95) that are comparable to those between ambient noise and wind speed. The mean square acoustic pressure was shown to vary with the dissipation, with p2 ∝ D0.6-0.8. The results suggest that measurements of ambient sound may prove to be useful in inferring surface wave dissipation.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1997

Description: Acoustic propagation in the ocean inevitably encounters inhomogeneities of various types, which give rise to scattering. Acoustic scattering from rough water /bottom interfaces comprised of exposed rocks and sea mountains gives way to volumetric scattering in areas with fiat interfaces and thick sediment cover. The data analysis of the ARSRP backscattering experiment revealed that random inhomogeneities in two irregular layers beneath the seafloor were the primary contributors to oblique backscattering in a sediment pond on the western flank of the Mid-Atlantic Ridge. In this thesis, an attempt has been made to model monostatic backscattering from 3-D volume inhomogeneities in the sediment and to compare the results with the ARSRP backscattering data. A scattering process cannot be modeled correctly without a proper account of the incident field . Several approximate propagation models have been evaluated against the exact solution, while the appropriateness of using the equivalent surface scattering strength in volume scattering characterizations is studied. This study concludes that precautions need to be taken in modeling both the propagation effects and the scattering mechanisms associated with the bottom volume scattering process. A volume scattering model based on perturbation theory and the Born approximation is developed incorporating contributions from both sound speed and density fluctuations. With the propagation part handled accurately by OASES and random fluctuations generated effectively by a new scheme modified from the spectral method, the model is capable of simulating the monostatic backscattered field and time series due to 3-D volumetric sediment inhomogeneities. Both the characteristic length scale and power spectrum descriptions of the random inhomogeneities are shown to have great impact on the backscattered field by parameter studies in a free-space scenario. The important roles played by horizontal anisotropy and the vertical correlation of the random field have been demonstrated. Density fluctuations are further confirmed to be the dominant force in backscattering. The model matches the ARSRP backscattering data very well, with the fluctuations of sound speed and density in the two irregular layers described by a power law type of power spectrum.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 1997

Description: Surface swell over the continental shelf generates a sheet of oscillatory shear flow at the base of the water column, the continental shelf wave bottom boundary layer. The short periods of surface swell sharply limit the thickness of the wave boundary layer, confining it to a thin region below an oscillatory, but essentially irrotational, core. For a wide range of shelf conditions, the vertical extent of the wave boundary layer does not exceed 2.5 cm and is commonly less. The extreme narrowness of this boundary layer is responsible for high levels of bottom stress and turbulent dissipation. Even in relatively mild sea states, the wave induced bottom shear stress can be sufficient to initiate sediment motion. The wave bottom boundary layer plays an important role in the processes of sediment entrainment and transport on the continental margins. This thesis documents the development, testing, and field use of a new instrument, the BASS Rake, designed to measure velocity profiles in the wave boundary layer. The mechanical design supports multiple measurement levels with millimeter vertical spacing. The mechanical design is integrated with an electronic interface designed to permit flexible acquisition of a suite of horizontal and vertical velocity measurements without sacrificing the electronic characteristics necessary for high measurement accuracy. The effects of velocity averaging over the sample volume are calculated with a model of acoustic propagation in a scattering medium appropriate to the scales of a single differential travel time axis. A simpler parametric model of the averaging process is then developed and used to specify the transducer characteristics necessary to image the wave boundary layer on the continental shelf. A flow distortion model for the sensor head is developed and the empirical determinations of the Reynolds number, Keulegan-Carpenter number, and angular dependencies of the sensor response for the laboratory and field prototypes is presented. The calibrated sensor response of the laboratory prototype is tested against concurrent LDV measurements over a natural sand bed in a flume. The single measurement accuracy of the BASS Rake is higher than that of the LDV and the multiple sample volumes confer other advantages. For example, the ability of the BASS Rake to image vertically coherent turbulent instabilities, invisible to the LDV, is demonstrated. Selected data from a twenty-four day field deployment outside the surf zone of a local beach are presented and analyzed. The data reveal regular reworking of the sand bed, the generation and modification of sand ripples, and strong tidal modulation of the current and wave velocities on semi-diurnal, diurnal, and spring/neap time scales. The data set is unique in containing concurrent velocity time series, of several weeks duration, with coverage from 1 cm to 20 cm above the bottom.

Description: ONR has contributed substantial financial support to this research and to my graduate education through AASERT funding under ONR Grant N00014-93-1-1140. NSF supported the purchase of hardware and services under NSF Grant OCE-9314357.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2013

Description: The stable isotopes, δ15N and δ18O, of nitrite and nitrate can be powerful tools used to interpret nitrogen cycling in the ocean. In order to interpret isotope profiles, the isotope systematics of each process involved must be known. 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 experiments show that the accumulation of nitrite has a large effect on the resulting δ18ONO3. Also, the δ18ONO2 was developed as a unique tracer because it undergoes abiotic equilibration with water δ18O at a predictable rate based on pH, temperature and salinity. This rate, its dependencies, and how the δ18ONO2 values can be used as not only biological source indicators but also indicators of age are described. 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 multi-isotope nitrate and nitrite profiles in the Costa Rica Upwelling Dome using a simple 1D model. Overall, this thesis describes new nitrogen and oxygen isotopic tracers and uses them to elucidate the complicated nitrogen biogeochemistry in oxygen deficient zones.

Description: The work described in this thesis was funded by the National Science Foundation grants OCE 05-26277 and OCE 09-610998 to KLC, the MIT Presidential Fellowship, the WHOI Coastal Ocean Institute, the WHOI Academic Programs Office, and the MIT Houghton fund.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2013

Description: Marine phytoplankton are the principal producers of oceanic dissolved organic matter (DOM), the organic substrate responsible for secondary production by heterotrophic microbes in the sea. Despite the importance of DOM in marine food webs, details regarding how marine microbes cycle DOM are limited, and few definitive connections have been made between specific producers and consumers. Consumption is thought to depend on the source of the DOM as well as the identity of the consumer; however, it remains unclear how phytoplankton diversity and DOM composition are related, and the metabolic pathways involved in the turnover of DOM by different microbial taxa are largely unknown. The motivation for this thesis is to examine the role of microbial diversity in determining the composition, lability, and physiological consumption of marine DOM. The chemical composition of DOM produced by marine phytoplankton was investigated at the molecular level using mass spectrometry. Results demonstrate that individual phytoplankton strains release a unique suite of organic compounds. Connections between DOM composition and the phylogenetic identity of the producing organism were identified on multiple levels, revealing a direct relationship between phytoplankton diversity and DOM composition. Phytoplankton-derived DOM was also employed in growth assays with oligotrophic bacterioplankton strains to examine effects on heterotrophic growth dynamics. Reproducible responses ranged from suppressed to enhanced growth rates and cell yields, and depended both on the identity of the heterotroph and the source of the DOM. Novel relationships between specific bacterioplankton types and DOM from known biological sources were found, and targets for additional studies on reactive DOM components were identified. The physiology of DOM consumption by a marine Oceanospirillales strain was studied using a combined transcriptomic and untargeted metabolomic approach. The transcriptional response of this bacterium to Prochlorococcus-derived DOM revealed an increase in anabolic processes related to metabolism of carboxylic acids and glucosides, increased gene expression related to proteorhodopsin-based phototrophy, and decreased gene expression related to motility. Putative identification of compounds present in Prochlorococcus-derived DOM supported these responses. Collectively, these findings highlight the potential for linking detailed chemical analyses of labile DOM from a known biological source with bacterioplankton diversity and physiology.

Description: Financial support for this work was provided by the National Science Foundation Center for Microbial Oceanography: Research and Education (award #EF0424599 and #DBI0424599) including generous contributions from the EDventures program, the Gordon and Betty Moore Foundation (grant #1711), and a student research grant from the Coastal Ocean Institute at the Woods Hole Oceanographic Institution.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2013

Description: Nitrogen and trace metal biogeochemical effects on phytoplankton productivity were compared through whole water bottle incubations and proteomic evaluation of in situ harvested particulate matter from two distinct oceanographic regions: the Equatorial Pacific Upwelling and the South Pacific Gyre. Phytoplankton growth in both regions was stimulated by nitrogen additions with equivalent response from nitrate and urea. In the gyre, trace metal additions did not yield a chlorophyll response, however nickel treatments showed evidence of nickel-limited nitrogen fixation. In contrast, cell growth at the upwelling site was primarily iron-limited and iron plus urea or nitrate additions further enhanced the chlorophyll response, indicative of secondary nitrogen limitation. Nitrogen stress proteins and urea transporters from cyanobacteria in these field sites showed similar trends, with both increasing in waters containing lower dissolved inorganic nitrogen. Together with bottle incubations, the abundant urea transporters and nitrogen stress proteins indicate the importance of urea in these field sites. Representative cyanobacteria cultures (Synechococcus strain WH8020, and Prochlorococcus strain MED4) were evaluated to constrain urea uptake rates and explore the potential for compound specific uptake rates. Together, results from this study indicate that urea may represent an under-recognized component of the marine microbial nitrogen cycle.

Description: Funding of our lab by The Gordon and Betty Moore Foundation, the Center for Microbial Oceanography: Research and Education (C-MORE), “Metzyme” (KM1128) by NSF Division of Ocean Sciences (OCE-1031271) and “BiG RAPA” (MV1015) by NSF (DBI-0424599).

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2013

Description: Between 2002 and 2011 a single mooring was maintained in the core of the Pacific Water boundary current in the Alaskan Beaufort Sea near 152° W. Using velocity and hydrographic data from six year-long deployments during this time period, we examine the interannual variability of the current. It is found that the volume, heat, and freshwater transport have all decreased drastically over the decade, by more than 80%. The most striking changes have occurred during the summer months. Using a combination of weather station data, atmospheric reanalysis fields, and concurrent shipboard and mooring data from the Chukchi Sea, we investigate the physical drivers responsible for these changes. It is demonstrated that an increase in summertime easterly winds along the Beaufort slope is the primary reason for the drop in transport. The intensification of the local winds has in turn been driven by a strengthening of the summer Beaufort High in conjunction with a deepening of the summer Aleutian Low. Since the fluxes of mass, heat, and freshwater through Bering Strait have increased over the same time period, this raises the question as to the fate of the Pacific water during recent years and its impacts. We present evidence that more heat has been fluxed directly into the interior basin from Barrow Canyon rather than entering the Beaufort shelfbreak jet, and this is responsible for a significant portion of the increased ice melt in the Pacific sector of the Arctic Ocean.

Description: The majority of the data for this project was funded by grant # ARC-0856244 from the O ce of Polar Programs of the National Science Foundation. My time at WHOI was funded by the United States Navy, the National Science Foundation Graduate Research Fellowship Program and the WHOI Academic Programs O ffice.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2014

Description: Marine particles include living and non-living solid components of seawater, representing a dynamic and chemically diverse mixture of phases. Through a combination of method development, basin-scale particulate collection and analyses, modeling, and field experiments, this thesis examines both the distributions of marine particulate trace metals and the underlying processes—inputs, scavenging, vertical and horizontal transport, and biotic uptake—in which marine particles participate. I first present the results of an intercalibration exercise among several US laboratories. We use inter-lab and intra-lab total elemental recoveries of these particles to determine our state of our intercalibration and to identify means of future improvement. We present a new chemical method for dissolution of polyethersulfone filters and compare it to other total particle digestion procedures. I then present the marine particulate distributions of the lithogenic elements Al, Fe, and Ti in the North Atlantic GEOTRACES section. A one-dimensional multi-box model that describes lithogenic particle distributions is also proposed and its parameter sensitivities and potential implications are discussed. I conclude with presentation of results from a series of bottle incubations in iron-limited waters using isotopically labeled Fe-minerals. We demonstrate solubilization of minerals ferrihydrite and fayalite via transfer of isotopic label into suspended particles.

Description: Funding was provided by the Williams College Tyng Fellowship, the MIT/WHOI Academic Programs Office, the International and US GEOTRACES Offices, and U.S. National Science Foundation (NSF) #0960880 and #0963026 and PLR #0838921 to P.J. Lam.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2014

Description: Methylation of mercury (Hg) in the marine water column has been hypothesized to serve as the primary source of the bioaccumulating chemical species monomethylmercury (MMHg) to marine food webs. Despite decades of research describing mercury methylation in anoxic sediments by anaerobic bacteria, mechanistic studies of water column methylation are severely limited. These essential studies have faced analytical challenges associated with quantifying femtomolar concentrations of the methylated Hg species dimethylmercury (DMHg) and MMHg in marine systems. In addition, the complex biogeochemical cycling of Hg in natural systems require consideration of gaseous, dissolved, and particulate species of Hg in order to probe potential controls on its ultimate transfer into marine food webs. The presented work provides a comprehensive study of Hg chemical speciation and transformations in Tropical Pacific waters. We developed an analytical method for MMHg determination from seawater that has the potential to ease measurements of MMHg distributions, as well as mechanistic studies of Hg species transformations. We used this method, in addition to previously established methods, to measure dissolved and particulate Hg species distributions and fluxes along a transect of the Pacific Ocean. Over significant gradients in oxygen utilization and primary productivity, we observed a region of methylated Hg species focused in the Equatorial Pacific that appeared spatially separated from higher concentrations in North Pacific Intermediate Waters. From the first full water column depth profiles of this region, we also observed the intrusion of elevated Hg into deep waters of the Equatorial and South Pacific Ocean. In addition we observed substantial potential rates of mercury methylation in subsurface and low oxygen waters along the Pacific transect as well as the Sargasso Sea using Hg isotope tracers. We observed dynamic production and decomposition of methylated Hg in low productivity waters, despite low ambient methylated Hg concentrations. From the addition of bulk organic matter as well as individual compounds important for methylation in anaerobic bacteria, we observe no simple limitation of Hg methylation in marine waters but highly dynamic conversion of Hg between methylated and inorganic species.

Description: OCE-1031271 87626900

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2013

Description: Steroidal estrogens are potent endocrine disrupting chemicals that are naturally excreted by vertebrates (e.g., humans and fish) and can enter natural waters through the discharge of treated and raw sewage. Because estrogens are detrimental to aquatic organisms at picomolar concentrations, many studies have measured so-called “free” estrogen concentrations in wastewater effluents, rivers, and lakes. Yet, to our knowledge, no studies have characterized the broader range of estrogens that includes free, conjugated, and halogenated forms. Conjugated estrogens are important because they can be easily converted to potent free forms by bacteria in wastewater treatment plants and receiving waters. And halogenated estrogens, produced during wastewater disinfection, are only slightly less potent than free estrogens but much more likely to bioaccumulate. We have developed a tandem mass spectrometry method that is capable of simultaneously quantifying free, conjugated, and halogenated estrogens at picomolar levels in wastewater effluent and coastal seawater. The method was validated using treated effluent from the greater Boston metropolitan area, where we found that halogenated estrogens represented over 50% of the total estrogen discharge flux. A kinetic model of estrogen halogenation was used to predict the distribution of free and halogenated forms in wastewater effluent and suggested that chlorinated estrogens may be formed en route to the wastewater treatment plant. In the receiving waters of Massachusetts Bay, we detected a range of conjugated, free, and halogenated forms at concentrations that were well-predicted by dilution near the sewage outfall. Farther downstream, we found significantly higher estrone concentrations which points to large inputs of estrogens from sources other than sewage. Finally, we have used compound-specific measurements of 13C and 14C in commercial and pharmaceutical estrogen preparations to evaluate the potential for using carbon isotopes to distinguish between synthetic and endogenous steroids in wastewater and other environmental matrices. Our results show that synthetic estrogens and progestogens exhibit significantly depleted δ13C values (~ -30‰) compared to endogenous steroids (-16‰ to -26‰). This isotopic difference should make it possible to apportion synthetic and endogenous hormone sources in complex environments.

Description: This research was supported by a U.S. Environmental Protection Agency STAR graduate fellowship (FP-91713401), NSF grants to T. Eglinton (OCE-0851350 and OCE-0402533) and W. Martin (OCE-0526389), the Ocean Ventures Fund and Coastal Ocean Institute at the Woods Hole Oceanographic Institution, the Martin Family Society of Fellows for Sustainability (MIT), and MIT Sea Grant (NA10OAR4170086).

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2014

Description: This thesis explores the buoyancy-driven circulation in the Red Sea, using a combination of observations, as well as numerical modeling and analytical method. The first part of the thesis investigates the formation mechanism and spreading of Red Sea Overflow Water (RSOW) in the Red Sea. The preconditions required for open-ocean convection, which is suggested to be the formation mechanism of RSOW, are examined. The RSOW is identified and tracked as a layer with minimum potential vorticity and maximum chlorofluorocarbon-12. The pathway of the RSOW is also explored using numerical simulation. If diffusivity is not considered, the production rate of the RSOW is estimated to be 0.63 Sv using Walin’s method. By comparing this 0.63 Sv to the actual RSOW transport at the Strait of Bab el Mandeb, it is implied that the vertical diffusivity is about 3.4 x 10-5m2 s-1 . The second part of the thesis studies buoyancy-forced circulation in an idealized Red Sea. Buoyancy-loss driven circulation in marginal seas is usually dominated by cyclonic boundary currents on f-plane, as suggested by previous observations and numerical modeling. This thesis suggests that by including β-effect and buoyancy loss that increases linearly with latitude, the resultant mean Red Sea circulation consists of an anticyclonic gyre in the south and a cyclonic gyre in the north. In mid-basin, the northward surface flow crosses from the western boundary to the eastern boundary. The observational support is also reviewed. The mechanism that controls the crossover of boundary currents is further explored using an ad hoc analytical model based on PV dynamics. This ad hoc analytical model successfully predicts the crossover latitude of boundary currents. It suggests that the competition between advection of planetary vorticity and buoyancy-loss related term determines the crossover latitude. The third part of the thesis investigates three mechanisms that might account for eddy generation in the Red Sea, by conducting a series of numerical experiments. The three mechanisms are: i) baroclinic instability; ii) meridional structure of surface buoyancy losses; iii) cross-basin wind fields.

Description: This work is supported by Award Nos. USA 00002, KSA 00011 and KSA 00011/02 made by King Abdullah University of Science and Technology (KAUST) , National Science Foundation OCE0927017, and WHOI Academic Program Office.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2014

Description: Synechococcus is a ubiquitous marine primary producer. Our understanding of the factors that determine its abundance has been limited by available observational tools, which have not been able to resolve population dynamics at timescales that match response times of cells (hours-days). Development of an automated flow cytometer (FlowCytobot) has enabled hourly observation of Synechococcus at the Martha’s Vineyard Coastal Observatory (MVCO) since 2003. In order to ascribe changes in cell abundances to either growth or loss processes, information on division rate is needed. I refined a matrix population model that relates diel changes in the distribution of cell volume to division rate and demonstrated that it provides accurate estimates of daily division rate for both cultured and natural populations. Application of the model to the 11-year MVCO time series reveals that division rate is temperature limited during winter and spring, but light limited during fall. Inferred loss rates closely follow division rate in magnitude over the entire seasonal cycle, suggesting that losses are mainly generated by biological processes. While Synechococcus cell abundance, division rate, and loss rate demonstrate striking seasonal patterns, there are also significant shorter timescale variations and important multi-year trends that may be linked to climate. Interpretation of population dynamic patterns is complicated by the diversity found within marine Synechococcus, which is partitioned into 20 genetically distinct clades. Each clade may represent an ecotype, with a distinct ecological niche. To understand how diversity may affect population dynamics, I assessed the diversity at MVCO over annual cycles with culture-independent and dependent approaches. The population at MVCO is diverse, but dominated by clade I representatives throughout the year. Other clades were only found during summer and fall. High through-put sequencing of a diversity marker allowed a more quantitative investigation into these patterns. Five main Synechococcus oligotypes that comprise the population showed seasonal abundance patterns: peaking either during the spring bloom or during late summer and fall. This pattern strongly suggests that features of seasonal abundance are affected by the underlying diversity structure. Synechococcus abundance patterns result from a complex interplay among seasonal environmental changes, diversity, and biological losses.

Description: This work was supported by a Department of Defense National Defense Science and Engineering Graduate Fellowship, National Science Foundation Grants (OCE- 0530830 to M.G. Neubert, H.M. Sosik, R.J. Olson, and A.R. Solow, OCE-1031256 to H.M. Sosik, DEB-1257545 to M.N. Neubert, and OCE-1155566 to A.F. Post), Gordon and Betty Moore Foundation Grant 934 to H.M. Sosik, NASA Ocean Biology and Biogeochemistry Program Grants NNX11AF07G and NNX13AC98G to H.M. Sosik, student awards from the WHOI Ocean Ventures Fund and WHOI Coastal Ocean Institute, and private donation.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2014

Description: The great geologic and climatic diversity of the Fraser River basin in southwestern Canada render it an excellent location for understanding biogeochemical cycling of sediments and terrigenous organic carbon in a relatively pristine, large, temperate watershed. Sediments delivered by all tributaries have the potential to reach the ocean due to a lack of main stem lakes or impoundments, a unique feature for a river of its size. This study documents the concentrations of a suite of dissolved and particulate organic and inorganic constituents, which elucidate spatial and temporal variations in chemical weathering (including carbonate weathering in certain areas) as well as organic carbon mobilization, export, and biogeochemical transformation. Radiogenic strontium isotopes are employed as a tracer of sediment provenance based on the wide variation in bedrock age and lithology in the Fraser basin. The influence of sediments derived from the headwaters is detectable at the river mouth, however more downstream sediment sources predominate, particularly during high discharge conditions. Bulk radiocarbon analyses are used to quantify terrestrial storage timescales of organic carbon and distinguish between petrogenic and biospheric organic carbon, which is critical to assessing the role of rivers in long-term atmospheric CO2 consumption. The estimated terrestrial residence time of biospheric organic carbon in the Fraser basin is 650 years, which is relatively short compared to other larger rivers (Amazon, Ganges-Brahmaputra) in which this assessment has been performed, and is likely related to the limited floodplain storage capacity and non-steady-state post-glacial erosion state of the Fraser River. A large portion of the dissolved inorganic carbon load of the Fraser River (〉80%) is estimated to derive from remineralization of dissolved organic carbon, particularly during the annual spring freshet when organic carbon concentrations increase rapidly. This thesis establishes a baseline for carbon cycling in a largely unperturbed modern mid-latitude river system and establishes a framework for future process studies on the mechanisms of organic carbon turnover and organic matter-mineral associations in river systems.

Description: Principle funding for this thesis was provided by grants from the National Science Foundation (OCE-0851015, OCE-0851101, and EAR-1226818). Financial support for field and analytical work was also provided by the WHOI Ocean Ventures Fund, James and Jane Orr, the WHOI Deep Ocean Exploration Institute for supporting the 2011 Geodynamics Program study tour, the MIT Student Assistance Fund, NSF grant OCE-0928582, the LightHawk organization, the WHOI Coastal Ocean Institute, the MIT PAOC Houghton Fund, the Friends of Switzerland Stratton Fellowship, and the WHOI Academic Programs Office.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2015

Description: Global climate models project a 21st century strengthening of the Pacific Equatorial Undercurrent (EUC). The consequent increase in topographic upwelling of cool waters onto equatorial coral reef islands would mitigate warming locally and modulate the intensity of coral bleaching. However, EUC water is potentially more acidic and richer in dissolved inorganic nutrients (DIN), both widely considered detrimental to coral reef health. My analysis of the Simple Ocean Data Assimilation product indicates that the EUC has indeed strengthened over the past 130 years. This result provides an historical baseline and dynamical reference for future intensification. Additionally, I reared corals in laboratory experiments, co-manipulating food, light and CO2 (acidity) to test the role of nutrition in coral response to elevate CO2 conditions: Heterotrophy yields larger corals but CO2 sensitivity is independent of feeding. Conversely, factors that enhance zooxanthellate photosynthesis (light and DIN) reduce CO2 sensitivity. Corals under higher light also store more lipid but these reserves are not utilized to maintain calcification under elevated CO2. My results suggest that while mitigation of CO2 effects on calcification is not linked to energetic reserve, EUC fueled increases in DIN and productivity could reduce effects of elevated CO2 on coral calcification.

Description: NSF grants OCE-1220529, OCE-1041106, OCE-1031971, OCE-1233282, and OCE-1041052; the MIT Bermuda Biological Research Station Fund, the WHOI Oceans Venture Fund, and the EAPS Student Research Fund.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2015

Description: The capabilities of autonomous underwater vehicles (AUVs) and their ability to perform tasks both autonomously and adaptively are rapidly improving, and the desire to quickly and efficiently sample the ocean environment as Earth's climate changes and natural disasters occur has increased significantly in the last decade. As such, this thesis proposes to develop a method for single and multiple AUVs to collaborate autonomously underwater while autonomously adapting their motion to changes in their local environments, allowing them to sample and track various features of interest with greater efficiency and synopticity than previously possible with preplanned AUV or ship-based surveys. This concept is demonstrated to work in field testing on multiple occasions: with a single AUV autonomously and adaptively tracking the depth range of a thermocline or acousticline, and with two AUVs coordinating their motion to collect a data set in which internal waves could be detected. This research is then taken to the next level by exploring the problem of adaptively and autonomously tracking spatiotemporally dynamic underwater fronts and plumes using individual and autonomously collaborating AUVs.

Description: Government support under and awarded by DoD, Air Force Office of Scientific Research, NDSEG Fellowship, 32 CFR 168a, U.S. Office of Naval Research (ONR) GOATS ’11 (N00014-11-1-0097) and GOATS ’14 (N00014-14-1-0214) projects, ONR TechSolutions Program Office (Lightweight NSW UUV program)—Technical Support, Naval Undersea Warfare Center (NUWC) Division, Newport (Code 25)—Technical Support and Logistics

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2015

Description: Fifty-six million years ago Earth experienced rapid global warming (~6°C) that was caused by the release of large amounts of carbon into the ocean-atmosphere system. This Paleocene-Eocene Thermal Maximum (PETM) is often cited as an analogue of anthropogenic climate change. Many trigger mechanisms for the carbon release at the PETM have been proposed. Common to all scenarios is rapid release of isotopically light carbon (〈13C/12C values) from methane hydrates, terrestrial or marine organic matter, as indicated by a pronounced excursion to light carbon isotope values across the PETM. I test the hypothesis that the PETM warming and isotope excursion were caused by the intrusion of a magmatic sill complex into organic-rich sediments in the North Atlantic. The intrusion of magma into sedimentary rocks will cause heating and metamorphic reactions in a thermal aureole around the intrusion. If these sediments are rich in organic matter, large volumes of isotopically light carbon are rapidly released. I examine geochemical evidence from lead, osmium, and organic carbon to place constraints on the extent the carbon isotope excursion during the PETM may have been caused by contact metamorphism of organic-rich sediments. Potential terrestrial and submarine analogs are examined to determine the behavior of these elements during thermal alteration. Furthermore, geochemical evidence from sediment cores at the PETM provides additional information about what might have caused the carbon isotope excursion. I find that lead is not a suitable proxy for carbon mobilization to the overlying seawater during contact metamorphism. Osmium, however, is mobilized together with carbon. Making reasonable assumptions for the 187Os/188Os of the sediments from the North Atlantic Magmatic Province (NAMP), constrained by the 187Re/188Os of organic-rich sediments and the depositional age of the sediment, the entire marine osmium isotope anomaly at the PETM could be explained without the need to invoke enhanced continental weathering. Based on estimates of the extent of mobilization of organic carbon relative to osmium, approximately 47% to 60% of the carbon released at the PETM may have been derived from thermal alteration of organic-rich sediments in the NAMP.

Description: This research was funded by a grant from the Ocean and Climate Change Institute at the Woods Hole Oceanographic Institution. The work was also partially funded by the United States Environmental Protection Agency through an EPA STAR fellowship, and by the WHOI Academic Programs Office. Partial funding for the sampling trip to Texas A&M was provided by the MIT Student Assistance Fund.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2015

Description: The copepod Calanus glacialis is one of the most important zooplankton taxa in the Arctic shelf seas where it serves as a key grazer, predator, and food source. Its summer distribution and abundance have direct effects on much of the food web, from blooming phytoplankton to migrating bowhead whales. The Chukchi Sea represents a highly advective regime dominated by a barotropicly driven northward flow modulated by wind driven currents that reach the bottom boundary layer of this shallow environment. In addition, a general northward gradient of decreasing temperature and food concentration leads to geographically divergent copepod growth and development rates. The physics of this system establish the connection potential between specific regions. Unless biological factors are uniform and ideal the true connections will be an uneven subset of this physically derived connection potential. In August 2012 and 2013, C. glacialis distributions were observed over Hanna Shoal in the northeast Chukchi Sea. Here we used the Finite Volume Community Ocean Model i-State Configuration Model to advect these distributions forward and back in time to determine the source and sink regions of the transient Hanna Shoal C. glacialis population. We found that Hanna Shoal supplies diapause competent C. glacialis to both the Beaufort Slope and the Chukchi Cap, mainly receives juveniles from the broad slope between Hanna Shoal and Herald Canyon and receives second year adults from as far as the Anadyr Gulf and as close as the broad slope between Hanna Shoal and Herald Canyon. These connection potentials were not sensitive to precise times and locations of release, but were quite sensitive to depth of release. Deeper particles often traveled further than shallow particles due to strong vertical shear in the shallow Chukchi. The 2013 sink region was shifted west relative to the 2012 region and the 2013 adult source region was shifted north relative to the 2012 region.

Description: The U.S. Department of Interior, Bureau of Ocean Energy and Management (BOEM), Alaska Outer Continental Shelf Region, Anchorage, Alaska provided funding for the fieldwork and plankton sample enumeration as part of the Chukchi Sea Offshore Monitoring in Drilling Area (COMIDA) Project and the BOEM Alaska Environmental Studies Program under contract Number M11AC00007 to the University of Texas and a subcontract to the Woods Hole Oceanographic Institution.