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 February 2009

Description: Self-localization of an underwater vehicle is particularly challenging due to the absence of Global Positioning System (GPS) reception or features at known positions that could otherwise have been used for position computation. Thus Autonomous Underwater Vehicle (AUV) applications typically require the pre-deployment of a set of beacons. This thesis examines the scenario in which the members of a group of AUVs exchange navigation information with one another so as to improve their individual position estimates. We describe how the underwater environment poses unique challenges to vehicle navigation not encountered in other environments in which robots operate and how cooperation can improve the performance of self-localization. As intra-vehicle communication is crucial to cooperation, we also address the constraints of the communication channel and the effect that these constraints have on the design of cooperation strategies. The classical approaches to underwater self-localization of a single vehicle, as well as more recently developed techniques are presented. We then examine how methods used for cooperating land-vehicles can be transferred to the underwater domain. An algorithm for distributed self-localization, which is designed to take the specific characteristics of the environment into account, is proposed. We also address how correlated position estimates of cooperating vehicles can lead to overconfidence in individual position estimates. Finally, key to any successful cooperative navigation strategy is the incorporation of the relative positioning between vehicles. The performance of localization algorithms with different geometries is analyzed and a distributed algorithm for the dynamic positioning of vehicles, which serve as dedicated navigation beacons for a fleet of AUVs, is proposed.

Description: This work was funded by Office of Naval Research grants N00014-97-1-0202, N00014-05-1-0255, N00014-02-C-0210, N00014-07-1-1102 and the ASAP MURI program led by Naomi Leonard of Princeton University.

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 2009

Description: This research presents a parallel hypothesis method for autonomous underwater vehicle navigation that enables a vehicle to expand the operating envelope of existing long baseline acoustic navigation systems by incorporating information that is not normally used. The parallel hypothesis method allows the in-situ identification of acoustic multipath time-of-flight measurements between a vehicle and an external transponder and uses them in real-time to augment the navigation algorithm during periods when direct-path time-of-flight measurements are not available. A proof of concept was conducted using real-world data obtained by the Woods Hole Oceanographic Institution Deep Submergence Lab's Autonomous Benthic Explorer (ABE) and Sentry autonomous underwater vehicles during operations on the Juan de Fuca Ridge. This algorithm uses a nested architecture to break the navigation solution down into basic building blocks for each type of available external information. The algorithm classifies external information as either line of position or gridded observations. For any line of position observation, the algorithm generates a multi-modal block of parallel position estimate hypotheses. The multimodal hypotheses are input into an arbiter which produces a single unimodal output. If a priori maps of gridded information are available, they are used within the arbiter structure to aid in the elimination of false hypotheses. For the proof of concept, this research uses ranges from a single external acoustic transponder in the hypothesis generation process and grids of low-resolution bathymetric data from a ship-based multibeam sonar in the arbitration process. The major contributions of this research include the in-situ identification of acoustic multipath time-of-flight measurements, the multiscale utilization of a priori low-resolution bathymetric data in a high-resolution navigation algorithm, and the design of a navigation algorithm with a exible architecture. This flexible architecture allows the incorporation of multimodal beliefs without requiring a complex mechanism for real-time hypothesis generation and culling, and it allows the real-time incorporation of multiple types of external information as they become available in situ into the overall navigation solution.

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 2009

Description: The lateral line system on fish has been found to aid in schooling behavior, courtship communication, active and passive hydrodynamic imaging, and prey detection. The most widely used artificial prey stimulus has been the vibrating sphere, which some fish are able to detect even when the signal velocities to its lateral line are orders of magnitude smaller than background current velocities. It is not clear how the fish are able to extract this signal. This thesis uses a series of computational fluid dynamic (CFD) simulations, matched with recent experiments, to quantify the effects of 3D fish body parts on the received dipole signals, and to determine signal detection abilities of the lateral line system in background flow conditions. An approximation is developed for the dipole induced, oscillatory, boundary layer velocity profile over the surface of a fish. An analytic solution is developed for the case when the surface is a wall, and is accurate at points of maximal surface tangential velocity. Results indicate that the flow outside a thin viscous layer remains potential in nature, and that body parts, such as fins, do not significantly affect the received dipole signal in still water conditions. In addition, the canal lateral line system of the sculpin is shown to be over 100 times more sensitive than the superficial lateral line system to high frequency dipole stimuli. Analytical models were developed for the Mottled Sculpin canal and superficial neuromast motions, in response to hydrodynamic signals. When the background flow was laminar, the neuromast motions induced by the stimulus signal at threshold had a spectral peak larger than spectral peaks resulting from the background flow induced motions. When the turbulence level increased, the resulting induced neuromast motions had dominant low frequency oscillations. For fish using the signal encoding mechanisms of phase-locking or spike rate increasing, signal masking should occur.

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 January 1983

Description: A simple model for the bottom boundary layer on the continental shelf is presented. The governing equations are developed for a stratified, turbulent Ekman layer in a combined wave and current flow over a moveable sediment bed. An eddy diffusivity closure scheme that includes the effect of suspended sediment, temperature, and salinity induced stratification on the vertical turbulent diffusion of mass and momentum couples the resulting unsteady conservation equations for fluid momentum, fluid mass, and suspended sediment mass. The wave velocity, current velocity, and suspended sediment concentration profiles predicted by the simultaneous solution of the conservation equations require the physical bottom roughness and a sediment reference concentrati on to be specified as boundary conditions. The physical bottom roughness associated with biologically generated bedforms, wave generated ripples, and near bed sediment transport are calculated as functions of the flow and sediment conditions. Using expressions for the height of sediment transporting layer and the sediment velocity, an expression for the sediment reference concentration is developed by matching laboratory measurements of sediment transport rates in oscillatory flow. The model predicts that the bottom flow field is highly dependent on (1) the nonlinear wave and current interaction, which increases the boundary shear stress and enhances vertical turbulent diffusion, (2) the effect of the boundary shear stress on a moveable sediment bed, which determines the physical bottom roughness and the amount of sediment in suspension, and (3) the effect of stable stratification, which inhibits vertical turbulent transport and couples the flow to the suspended sediment and fluid density profiles. The validity of the theoretical approach is supported by model predictions that are in excellent agreement with high quality data collected during two continental shelf bottom boundary layer experiments for a wide range of flow and bottom conditions.

Description: Funding for the work resulting in this Thesis has been provided by the American Gas Association (Project No. PR-153-126), the National Science Foundation (Grant No. OCE~8014930), and NOAA-Sea Grant (NA-79AA-D-0010l; NA 79AA-D-00102).

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 2002

Description: This thesis addresses the sources and transport of nuclear weapons related contamination in the Ob River region, Siberia. In addition to being one of the largest rivers flowing into the Arctic Ocean, the bulk of the former Soviet Union's nuclear fuel reprocessing and weapons testing facilities (i.e. Mayak, Tomsk-7, and Semipalitinsk) are located within the Ob drainage basin. The atom ratios 240Pu/239Pu, 237Np/239Pu, and 13Cs/240Pu, measured by magnetic-sector ICP-MS, are used to distinguish between contamination derived from global fallout and contamination derived from local sources. Deposition chronologies estimated for sediment cores are used to construct a record of weapons related contamination at the sites sampled. Contaminant records indicate that in addition to debris from atmospheric weapons tests, materials derived from local sources have also played a role in nuclear weapons related contamination of the Ob region. Isotopic data presented in this study clearly demonstrate that non-fallout contamination has been transported the full length of the Tobol, Irysh, and Ob Rivers (i.e. the tributaries draining Mayak, Semipalitinsk, and Tomsk-7, respectively). In several instances, unique isotopic compositions are observed in sediments collected from tributaries draining each of the suspected non-fallout sources. In such cases, these materials and their deposition ages have been used to link contamination in the Ob delta to Mayak, Tomsk-7, or Semipalitinsk. Linear transport rate estimates (km yr-1) indicate that contaminated sediments transit between source tributaries and the Ob delta on time-scales of ≤ l year. These estimates suggest that a catastrophic release of contamination due to dam failure at one of the many reservoirs located at both Mayak and Tomsk-7 that contain high levels of radioactive waste would result in measurable levels of contamination in the delta within as little as 1 year. Isotopic concentrations in sequentially extracted sediments containing weapons related contamination reveal that the majority of plutonium and neptunium (80 to 90 percent) behaves in a similar fashion regardless of the source and is removed by treating the sediments with citrate-dithionite. This indicates that plutonium and neptunium are not truly refractory and likely associate with redox sensitive sedimentary components. Isotopic ratios measured in extracted fractions suggest that only a minor fraction of contamination is associated with acid leachable or acid digestible sedimentary phases.

Description: Funding for this research was provided by the Office of Naval Research under Grants N00014-93-1-1139, and NOOOI4-1-95), and the National Science Foundation under Grant EAR-98-07590.

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 February 2002

Description: The linear and nonlinear Rossby wave solutions are examined in homogeneous square basins on the ß-plane both with and without a thin meridional barrier In the presence of the meridional barrier the basin is almost partitioned into two; only two small gaps of equal width, d, to the north and south of the barrier allow communication between the eastern.and western sub-basins. Solutions are forced by a steady periodic wind forcing applied over a meridional strip near the eastern side. Bottom friction is present to allow the solutions to reach equilibrium. The linear solution for the basin containing the barrier is determined analytically and the nonlinear solutions for both basins are found numerically. In the linear solution with the barrier present, particular attention was paid to the resonant solutions. We examined the effects of varying the symmetry of the forcing about the mid-latitude, the frequency of the periodic forcing and the strength of the bottom friction. For each solution we focus on how the no net circulation condition, which is central to any solution in a barrier basin, is satisfied. The nonlinear solutions were studied for both basin configurations. In each case the transition from the weakly nonlinear solution to the turbulent solution was examined, as the forcing frequency and forcing strength were varied. Only integer multiples of the forcing frequency are present in the weakly nonlinear solutions. The turbulent solutions were accompanied by the appearance of many other frequencies whose exact origins are unknown, but are probably the result of instabilities. A hysteresis was found for the turbulent solutions of both the barrier-free and barrier basins. In the weakly nonlinear solutions of the barrier basin it was predicted and confirmed that there is never a steady net flow from sub-basin to sub-basin. It was also shown that with a symmetric forcing all modes oscillating with an odd multiple of the forcing frequency are symmetric and all modes oscillating with even multiples of the forcing frequency are antisymmetric.

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 1982

Description: Zooplankton samples were collected with the MOCNESS (Multiple Opening/ Closing Net and Environmental Sensing System) on six cruises in the western North Atlantic Ocean during the period from August 1975 to November 1977 as part of the study of the biology, physics, and chemistry of Gulf Stream cold core rings. The physical, chemical and biological properties of the Slope Water to the North of the Gulf Stream differ substantially from the properties of the Northern Sargasso Sea to the south. The purpose of this thesis was to identify the horizontal, vertical and seasonal abundance patterns of chaetognaths in this region and to relate these patterns to environmental conditions. Twenty one chaetognath species were identified, of which eighteen were abundant enough for analysis of the spatial and temporal abundance patterns. The most important sources of sampling error in this study were mesh selection and avoidance, which bias the abundance estimates, and patchiness and subsampling, which add variability to the abundance estimates. The 0.333 mm mesh of the MOCNESS does not appear to sample individuals of any of the species less than 6 mm in length very well. Avoidance appears to be a problem only for the larger individuals (〉20 mm) of the larger species. Variability due to small scale patchiness was less for this study than for many previous studies, and this may have been due either to the location of the tows in presumably less variable open ocean regions or to the increased volume of water filtered relative to previous studies. Subsampling with the Folsom plankton sample splitter introduced more variability than predicted by the binomial distribution, and for some species the subsampling variability was greater than that due to patchiness. In spite of these sources of variability, significant spatial and temporal abundance patterns were detectable for most of the species in this region. Vertical distributions of chaetognaths in this region were similar to those reported for these species from other regions. Nine species were classified as epipelagic, four were classified as mesopelagic, and five species were classified as bathypelagic. Diel vertical migrations were not detected for any of the species, but due to the depth intervals sampled, migrations of less than 100 m were not detectable. Ontogenetic migrations were detected for the seven meso- and bathypelagic species for which these migrations were examined. The epi- and bathypelagic species were shallower in the Slope Water than in the Northern Sargasso Sea, suggesting that they were orienting their vertical distributions to temperature. The mesopelagic species showed little difference in vertical distribution between the two hydrographic regions. For Sagitta lyra, the only species for which size frequency data was collected from all the tows, the vertical distribution as measured by median population depth was found to be significantly correlated with average individual size. This suggests that observed differences in vertical distribution for the meso- and bathypelagic species at different times and places in the oceans may be due to changes in the size structure of the population coupled with ontogenetic migrations rather than to responses to differing environmental conditions. It may be possible to correlate the vertical distributions of size or sexual maturity classes with environmental variables such as temperature and light. The differences in hydrography between the Slope Water and the Northern Sargasso Sea were also reflected in the species abundances. Seven species were significantly more abundant in the Slope Water, nine were significantly more abundant in the Northern Sargasso Sea, and two species showed no significant differences between the two regions. Recurrent group analysis did not delineate these groupings, and it is suggested that quantitative methods employing abundance estimates be used to detect associations among species. Ordination analysis (e.g. factor analysis and correspondence analysis) was found to delineate the species groupings adequately. The hydrographic differences in abundance for these chaetognaths were most likely related to differences in food abundance and temperature structure of the water column between the Slope Water and Northern Sargasso Sea. Seasonal abundance differences were not detected for the seven Slope Water species, yet seasonal abundance differences are expected in such temperate regions. Most of the Northern Sargasso Sea species were most abundant in the spring, and this was presumably related to the late winter-early spring peak in primary productivity and zooplankton biomass in this region. The spatial and temporal abundance patterns of chaetognaths in Gulf Stream cold core rings were also studied. The patterns were similar to predictions made on the basis of their abundance differences between the Slope Water and Northern Sargasso Sea, but a few species showed anamolous patterns. Further studies of the chaetognath fauna of both warm and cold Core rings should provide invaluable insight into the processes regulating the spatial and temporal abundance patterns of these organisms.

Description: Financial support was provided by the Education Office at WHOI and from NSF Grants OCE-7709l32 and OCE-80l7248 to Peter Wiebe.

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 2003

Description: Oceanic observations indicate that abyssal mixing is localized in regions of rough topography. How locally mixed fluid interacts with the ambient fluid is an open question. Laboratory experiments explore the interaction of mechanically induced boundary mixing and an interior body of linearly stratified rotating fluid. A single oscillating bar produces a small region of turbulence along the wall at middepth. Mixed fluid quickly reaches a steady state height set by a turbulent-buoyant balance, independent of rotation. Initially, the bar is exposed on three sides. Mixed fluid intrudes directly into the interior rather than forming a boundary current. The circulation patterns suggest a model of unmixed fluid being laterally entrained into the turbulent zone. In accord with the model, observed outflux is constant, independent of stratification and restricted by rotation. Later the bar is laterally confines between two walls, which form a channel opening into the basin. A small percentage of mixed fluid enters a boundary current, which exits the channel. The bulk forms a cyclonic circulation in front of the bar, which blocks the channel and restricts horizontal entrainment. In the confined case, the volume flux of mixed fluid decays with time.

Description: This work was supported by the Ocean Ventures Fund, the Westcott Fund and the WHOI Education Office. Financial support was also provided by the National Science Foundation through grant OCE-9616949.

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 February 2002

Description: One of the major problems in wireless communications is compensating for the time-varying intersymbol interference (ISI) due to multipath. Underwater acoustic communications is one such type of wireless communications in which the channel is highly dynamic and the amount of ISI due to multipath is relatively large. In the underwater acoustic channel, associated with each of the deterministic propagation paths are macro-multipath fluctuations which depend on large scale environmental features and geometry, and micro-multipath fluctuations which are dependent on small scale environmental inhomogeneities. For arrivals which are unsaturated or partially saturated, the fluctuations in ISI are dominated by the macro-multipath fluctuations resulting in correlated fluctuations between different taps of the sampled channel impulse response. Traditional recursive least squares (RLS) algorithms used for adapting channel equalizers do not exploit this structure. A channel subspace post-filtering algorithm that treats the least squares channel estimate as a noisy time series and exploits the channel correlation structure to reduce the channel estimation error is presented. The improvement in performance of the algorithm with respect to traditional least squares algorithms is predicted theoretically, and demonstrated using both simulation and experimental data. An adaptive equalizer structure that explicitly uses this improved estimate of the channel impulse response is discussed. The improvement in performance of such an equalizer due to the use of the post-filtered estimate is also predicted theoretically, and demonstrated using both simulation and experimental data.

Description: This research was supported by an ONR Graduate Traineeship Award Grant #N00014-00-10049.

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: Geometrically compliant mooring systems that change their shape to accommodate deformations are common in oceanographic and offshore energy production applications. Because of the inherent geometric nonlinearities, analyses of such systems typically require the use of a sophisticated numerical model. This thesis describes one such model and uses that model along with experimental results to develop simpler forms for understanding the dynamic response of geometrically compliant moorings. The numerical program combines the box method spatial discretization with the generalized- a method for temporal integration. Compared to other schemes commonly employed for the temporal integration of the cable dynamics equations, including box method, trapezoidal rule, backward differences, and Newmark’s method, the generalized-a algorithm has the advantages of second-order accuracy, controllable numerical dissipation, and improved stability when applied to the nonlinear problem. The numerical program is validated using results from laboratory and field experiments. Field experiment and numerical results are used to develop a simple model for dynamic tension response to vertical motion in geometrically compliant moorings. As part of that development, the role of inertia, drag, and stiffness in the tension response are explored. For most moorings, the response is dominated by inertial and drag effects. The simple model uses just two terms to accurately capture these effects, including the coupling between inertia and drag. The separability of the responses to vertical and horizontal motions is demonstrated and a preliminary model for the response to horizontal motions is presented. The interaction of the mooring line with the sea floor in catenary moorings is considered. Using video and tension data from laboratory experiments, the tension shock condition at the touchdown point and its implications are observed for the first time. The lateral motion of line along the bottom associated with a shock during unloading may be a significant cause of chain wear in the touchdown region. Results from the laboratory experiments are also used to demonstrate the suitability of the elastic foundation approach to modeling sea floor interaction in numerical programs.

Description: During my initial three years of study I was supported by an Office of Naval Research Graduate Fellowship. More recently, including the time spent on the research described in this thesis, I have been supported by the Office of Naval Research under grant numbers N00014-92-J-1269 and N00014-97-1-0583.

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 2009

Description: Observations and inverse models suggest that small-scale turbulent mixing is enhanced in the Southern Ocean in regions above rough topography. The enhancement extends 1 km above the topography suggesting that mixing is supported by breaking of gravity waves radiated from the ocean bottom. In other regions, gravity wave radiation by bottom topography has been primarily associated with the barotropic tide. In this study, we explore the alternative hypothesis that the enhanced mixing in the Southern Ocean is sustained by internal waves generated by geostrophic motions flowing over bottom topography. Weakly-nonlinear theory is used to describe the internal wave generation and the feedback of the waves on the zonally averaged flow. A major finding is that the waves generated at the ocean bottom at finite inverse Froude numbers drive vigorous inertial oscillations. The wave radiation and dissipation at equilibrium is therefore the result of both geostrophic flow and inertial oscillations and differs substantially from the classical lee wave problem. The theoretical predictions are tested versus two-dimensional and three-dimensional high resolution numerical simulations with parameters representative of the Drake Passage region. Theory and fully nonlinear numerical simulations are used to estimate internal wave radiation from LADCP, CTD and topography data from two regions in the Southern Ocean: Drake Passage and the Southeast Pacific. The results show that radiation and dissipation of internal waves generated by geostrophic motions reproduce the magnitude and distribution of dissipation measured in the 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 September 2009

Description: A confluence of several coastal oceanographic features creates an acoustically interesting region with high variability along the New England Shelfbreak. Determining the effect of the variability on acoustic propagation is critical for sonar systems. In the Nantucket Shoals area of the Middle Atlantic Bight, two experiments, the New England Shelfbreak Tests (NEST), were conducted in May and June, 2007 and 2008, to study this variability. A comprehensive climatology of the region along with the experimental data provided detailed information about the variability of the water column, particularly the temperature and sound speed fields. Empirical orthogonal function (EOF) analysis of the ocean sound speed field defined a set of perturbations to the background sound speed field for each of the NEST Scanfish surveys. Attenuation due to bottom sediments is the major contributor of transmission loss in the ocean. In shallow water, available propagation paths most often include bottom interaction. Perturbations in the ocean sound speed field can cause changes in the angle of incidence of sound rays with the bottom, which can result in changes to the amount of sound energy lost to the bottom. In lieu of complex transmission loss models, the loss/bounce model provides a simpler way to predict transmission loss changes due to perturbations in the background sound speed field in the ocean. Using an acoustic wavenumber perturbation method, sound speed perturbations, defined by the ocean EOF modes, are translated into a change in the horizontal wavenumber, which in turn changes the modal angle of incidence. The loss/bounce model calculates the loss of sound energy (dB) per bottom bounce over a given distance based on the change in angle of incidence. Evaluated using experimental data from NEST, the loss/bounce model provided accurate predictions of changes to transmission loss due to perturbations of the background sound speed field.

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 2001

Description: The interaction between the eddy field and the mean flow near the Gulf Stream is studied here using satellite altimeter measurements and an eddy resolving numerical modeL. The eddy vorticity flux in the quasigeostrophic framework is obtained from the stream function standard deviation and spatial correlation function assuming the correlation function is homogeneous. An analytical expression is found for the stream function correlation using the altimetric and numerical data. Cases when the correlation function is anisotropic are compared to the isotropic case previously studied by Hogg (1993), who found that the eddy vorticity flux drives two counter rotating gyres on either side of the stream. The anisotropy can be important in the eddy vorticity flux, even when its departure from the isotropic case is smalL. Meridional or zonal anisotropies can drive recirculation gyres similar in strength and position to the ones driven by the isotropic case. The results when including anisotropy in the diagonal direction suggest that the homogenoeus assumption may not be valid.

Description: This work was founded in part by a Fulbright/CONACyT fellowship and a J. Seward Johnson Fellowship through the Education Offce in WHOI.

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 February 2001

Description: Megamullions in slow-spreading oceanic crust are characterized by smooth "turtle-back" morphology and are interpreted to be rotated footwalls of long-lived detachment faults. Megamullions have been analyzed in preliminary studies, but many questions remain about structural and tectonic details of their formation, in particular how the hanging wall develops in conjugate crust on the opposing side of the rift axis. This study compares the structure of an off-axis megamullion complex and its conjugate hanging wall crust on the Mid-Atlantic Ridge near 27°N. Two megamullion complexes, an older (Ml) and younger (M2), formed successively on the west side of the rift axis in approximately the same location within one spreading segment. Megamullion M1 formed while the spreading segment had only one inside comer on the west flank, and megamullion M2 formed after the segment developed double inside comers west of the axis and double outside comers east of the axis. The older megamullion formed between ~22.3 and ~20.4 Ma, and the younger megamullion formed between ~20.6 and ~18.3 Ma; they are presently ~200-300 km off-axis. Reconstruction poles of plate rotation were derived and plate reconstructions were made for periods prior to initiation of the megamullion complex (anomaly 6Ar, ~22.6 Ma), after the termination of mega mullion M1 and during the development of megamullion M2 (anomaly 5E, ~19 9 Ma), and shortly following the termination of megamullion M2 (anomaly 5C, ~17.6 Ma). These reconstructions were used to compare morphological and geophysical features of both flanks at each stage of the megamullions' development. Megamullion M1's breakaway occurred at ~22.3 Ma and slip along this detachment fault continued and propagated northward at ~20.6 Ma to form the northern portion ofM2. The exhumed footwall of mega mullion M1 has weak spreading-parallel lineations interpreted as mullion structures on its surface, and it forms an elevated plateau between the enclosing segment boundaries (non-transform discontinuities). There was an expansion southward of the detachment fault forming megamullion M2 at ~ 20.1 Ma. It either cut a new detachment fault through megamullion M1, stranding a piece of megamullion M1 on the conjugate side (east flank), or it linked into the active detachment fault that was forming megamullion M1 or propagated into its hanging wall. The expanded detachment of mega mullion M2 and the termination of mega mullion M1 occurred during a time when the enclosing spreading segment roughly doubled in length and formed two inside comers. Megamullion M2 developed prominent, high-amplitude (~600 m) mullion structures that parallel the spreading direction for more than 20 km at each inside comer. Its detachment fault was abandoned ~ 18.6 Ma in the south and ~ 18.3 Ma in the north. The gravity of this area demonstrates a consistent pattern of higher gravity corresponding to inside comers with thinner crust, apparently caused by fault exhumation of deep lithosphere, and lower gravity values corresponding to outside comers, indicating thicker crust, most likely a result of volcanic accretion. The gravity pattern of the area also helps with interpreting evolution of the megamullion complex. The southern section of megamullion M1 exhibits a series of inside-comer highs and elevated gravity values while the northern section has lower gravity values until megamullion M2 began to form. This change coincides with the change of the northern segment edge from an outside comer to an inside comer. During the formation of megamullion M2, a gravity high developed over the center of the megamullion. After the termination of megamullion M2, the gravity values of both the northern and southern sections of the spreading segment decrease. This pattern suggests exhumation of higher-density lithosphere during formation of M1 and M2, and a return to more normal ridge-axis conditions following termination of the megamullion complex. The gravity of conjugate crust is consistently more negative, slightly decreasing in value during the formation of megamullion M2. This suggests that crust on the east flank is significantly thicker than that on the west flank, and that rift-axis magmatism may have slightly increased at the time that megamullion M2 formed. We modeled gravity of an idealized structural cross-section of megamullion M2 to investigate possible structure and composition of the megamullion. Models with different detachment-fault angles and degrees of serpentinization of exhumed mantle that may be present in the megamullion were compared to Residual Mantle Bouguer Anomaly (RMBA) profiles. All models show gravity peaks slightly skewed towards the termination because higher-density rock is exposed closer to the termination than to the breakaway. Four models that varied the detachment fault angle show small variations that are unresolvable in the actual gravity data. Thus, the gravity profile of a megamullion is not diagnostic of its detachment fault angle from 30° to 60°/90°. Models that varied the degree of serpentinization of a lithospheric wedge beneath the megamullion show that slight variations in density give rise to large changes in the modeled gravity profiles. Comparison of model results against gravity profiles taken across megamullion M2 indicate that the magnitude of the gravity high associated with the megamullion is best explained by densities between 2800 kg/m3 and 3000 kg/m3 in the main body of the megamullion. This corresponds to peridotite serpentinized approximately 50%, or to gabbro (~2800 kg/m3).

Description: This study was supported by ONR grant N00014-90-J-1621 and by NSF grant OCE-9503561

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 2001

Description: Processes that enable marine phytoplankton to acquire trace metals are fundamental to our understanding of primary productivity and global carbon cycling. This thesis explored the biogeochemistry of cobalt using analytical chemistry and physiological experiments with the dominant phytoplankton species, Prochlorococcus. A high sensitivity method for Co speciation was developed using hanging mercury drop cathodic stripping voltammetry. Dissolved Co at the Bermuda Atlantic Time Series station (BATS) in the Sargasso Sea was bound by strong organic complexes with a conditional stability constant of logK=16.3l0.9. A depth profile of Co at BATS revealed a nutrient-like profile. Biweekly time series measurements of total cobalt near Bermuda from the MITESS sampler were 0-47pM throughout 1999, and averaged 20±10pM in 1999. A transect of total cobalt from BATS to American coastal waters ranged from 19- 133pM and correlated negatively with salinity (r2=0.93), suggestive of coastal waters as an input source. Prochlorococcus strains MED4-Ax and SS120 showed an absolute requirement for Co, despite replete Zn. 57Co uptake rates and growth rates were enhanced by additions of filtered low Co cultures, suggesting that a ligand is present that facilitates Co uptake. Bottle incubations from a Synechococcus bloom in the Pacific showed production of 425pM strong cobalt ligand. These and other lines of evidence support the hypothesis that a cobalt ligand, or cobalophore, is involved in cobalt uptake. Co-limited Prochlorococcus cultures exhibited an increase in the fraction of cells in G2 relative to other cell cycle stages during exponential growth, and the durations of this stage increased with decreasing cobalt concentrations. This effect was not observed with Fe, N, or P-limited cultures, suggestive of a specific biochemical function of cobalt that would interfere with the late stages of the cell cycle. The ligand Teta was explored as a means to induce cobalt limitation. The CoTeta complex was not bioavailable to the Sargasso Sea microbial assemblage in short-term experiments. Bottle incubations with Teta did not induce cobalt limitation of Prochlorococcus. These results are consistent with the lower conditional stability constant for CoTeta (logK=11.2l0.1) relative to natural cobalt ligands in seawater, and with culture studies that suggest uptake of cobalt via strong organic ligands.

Description: The work in this thesis was supported by a grant from the National Science Foundation (#OCE-9618729) for cyanobacteria metal interactions in the Sargasso Sea. I have been funded through WHOI on an NSF coastal traineeship (#DGE-9454129) for my first year, followed by an EP A STAR Graduate Fellowship for the subsequent years. Additional funding was supplied by the WHOI Educational Endowment Funds and by the WHOI Ditty Bag fund for part of the DNA/cell cycle 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 August 2001

Description: Pinniped (seal and sea lion) auditory systems operate in two acoustically distinct environments, air and water. Piniped species differ in how much time they typically spend in water. They therefore offer an exceptional opportunity to investigate aquatic versus terrestrial hearing mechanisms. The Otariidae (sea lions and fur seals) generally divide their time evenly between land and water and have several adaptations; e.g. external pinnae, related to this lifestyle. Phocidae (true seals) spend the majority of their time in water; they lack external pinnae and have well developed ear canal valves. Differences in hearing ranges and sensitivities have been reported recently for members of both of these familes (Kastak, D., Schusterman, RJ., 1998. Low frequency amphibious hearing in pinnipeds. J. Acoust. Soc. Am. 1303,2216- 2228.; Moore, P.W.B., Schusterman, RJ., 1987. Audiometric assessment of northern fur seals, Callorhinus ursinus. Mar. Mamm. Sci. 3,31-53.). In this project, the ear anatomy of three species of pinnipeds: an otariid, the California sea lion (Zalophus californianus), and two phocids, the northern elephant seal (Mirounga angustirostris) and the harbor seal (Phoca vitulina), was examined using computerized tomography (CT scans) and gross dissection. Thee-dimensional reconstructions of the heads and ears from CT data were used to determine interaural dimensions and ossicular chain morphometrics. Ossicular weights and densities were measured conventionally. Results strongly support a canalcentric system for pinniped sound reception and localization. Further, true seals show adaptations for aquatic high frequency specialization.

Description: I was supported by an NDSEG fellowship from ONR.

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: Half of the ocean crust is formed at spreading centers with total opening rates less than 40 km/Myr. The objective of this Thesis is to investigate temporal variations in active ridge processes and crustal aging at slow-spreading centers by comparing axial crustal structure with that on conjugate flanks of the slow-spreading Mid-Atlantic Ridge (MAR) (full rate, 20 km/Myr) and the ultra-slow spreading Southwest Indian Ridge (SWIR) (full rate, 14 km/Myr). Seismic refraction data collected along the rift valley and flanking rift mountains of the OH-l segment (35°N) at the MAR show that the entire crustal section is constructed within a zone that is less than 5 km wide. Shallow-level hydrothermal circulation within the axial valley is suggested by the rift mountain seismic profiles, which show that the upper crust is 20% thinner and 16% faster along strike than zero-age crust. These effects probably result from fissure sealing within the extrusive crust. Deeper crustal velocities remain relatively constant at the segment midpoint within the first 2 Myr, but are reduced near the segment offsets presumably by faulting and fracturing associated with uplift out of the rift valley. A temporal variation in axial melt supply is suggested by a 15% difference in along-strike crustal thickness between the rift valley and rift mountains, with relatively less melt supplied today than 2 Ma. Crustal accretion at the SWIR appears to occur in a similar manner as at the MAR, although gravity and seismic data indicate that the average crustal thickness is 2-4 km less at the ultra-slow spreading SWIR. A 25 Myr record on both flanks of the ridge shows that seafloor spreading has been highly asymmetric through time, with 35% faster crustal accretion on the Antarctic (south) plate. A small-offset non-transform discontinuity between two ridge segments is just as stable as two neighboring transform discontinuities, although a single mantle Bouguer gravity anomaly centered over the non-transform offset indicates that this boundary does not significantly perturb underlying mantle flow. Off-axis magnetic anomalies are recorded with high fidelity despite the very low spreading rates and the absence of a basaltic upper crust in one area. The lower crust may be the dominant off-axis carrier of the magnetic signal, contrary to traditional models of crustal magnetic structure. Morphological and gravity data show evidence of asymmetric crustal accretion across the SWIR ridge axis, with slightly warmer mantle temperatures beneath the slower-spreading African (north) plate.

Description: Funding was provided by the National Science Foundation through Contract No. OCE-9300450 and by the Joint Oceanographic Institutions through Subcontract No. JSC1-00.

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 2009

Description: Over the past 20 years, underwater vehicle technology has undergone drastic improvements, and vehicles are quickly gaining popularity as a tool for numerous oceanographic tasks. Systems used on the vehicle to alter buoyancy, or variable buoyancy (VB) systems, have seen only minor improvements during the same time period. Though current VB systems are extremely robust, their lack of performance has become a hinderance to the advancement of vehicle capabilities. This thesis first explores the current status of VB systems, then creates a model of each system to determine performance. Second, in order to quantitatively compare fundamentally different VB systems, two metrics, βm and βvol, are developed and applied to current systems. By determining the ratio of performance to size, these metrics give engineers a tool to aid VB system development. Finally, the fundamental challenges in developing more advanced VB systems are explored, and a couple of technologies are investigated for their potential use in new systems.

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 March 2001

Description: Numerical solutions of the unstable, growing modes are found for the two-layer inviscid quasigeostrophic equations in a meridional channel. A steady mean flow in the N-S direction is imposed in the upper layer, and it is assumed that changes in planetary vorticity following this mean flow are balanced by the input of vorticity from an imposed wind stress curl. Thus in the two-layer system, the vertical shear, in thermal wind balance, is associated with an interface slope which provides a gradient of potential vorticity (PV) in the x-direction, of equal magnitude and opposite sign in the two layers. In the y-direction the PV gradient has the value of planetary beta, β in both layers. The unstable modes of this system exhibit a boundary-layer structure across the channel. They are intensified in the west. The growth rates of the unstable modes are of the same order as the zonal case, however the range of wavenumber and shear for which instability is possible is larger. Established cutoff criteria for the equal-layer zonal case are not applicable, and no analogous criteria has yet been found. Growing modes are found even for very weakly sheared flows, and this suggests that baroclinic instability may represent a more significant source of mid-ocean eddy energy than previously believed.

Description: This research was supported by the National Science Foundation under grant 9901654.

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: In recent years, the use of clay minerals has emerged as one of the most promising strategies for directly controlling harmful algal blooms (HABs). Its principle is based on the mutual aggregation of algal cells and mineral particles, leading to the formation of large flocs that rapidly settle to the ocean floor. This work investigated the effectiveness of various domestic clays against a number of bloom-forming species from the United States. Twenty-five clays were tested against the dinoflagellate, Karenia brevis (formerly Gymnodinium breve), and the chrysophyte, Aureococcus anophagefferens. In general, the highest removal efficiencies (RE 〉 90% at 0.25 g rl of clay) against K. brevis were found using montmorillonite, bentonite and phosphatic clays (i.e. a product of phosphate mining containing large amounts of montmorillonite). The RE of phosphatic clays remained high (〉 80%) even at 0.03 g rl. Kaolinite and zeolite were mostly ineffective against K. brevis. Removal with clay exceeded those for alum, polyaluminum chloride (PAC) and several other polymeric flocculants by a factor of two. However, the combination of phosphatic clay and PAC (at 5 mg rl) decreased the amount of clay needed to maintain 80% RE by one order of magnitude. Cell viability and recovery remained high when clay loading stayed below 0.03 g rl with or without resuspension of the sediment. However, cell mortality approached 100% with 0.50 g rl even with daily resuspension. Between 0.10 and 0.25 g rl, K. brevis survival and recovery depended on the interplay of clay loading, the frequency of resuspension, and duration of contact prior to the first resuspension event. For A. anophagefferens, the RE did not exceed 40% for any clay at 0.25 g rl even in combination with coagulants and flocculants. The highest removal was achieved by thoroughly mixing the clay slurry (e.g. phosphatic clay) into the cell culture. The RE by phosphatic clay varied significantly in a survey consisting of 17 different species from five algal classes. Moreover, the removal trends varied substantially with increasing cell concentration. For example, cell removal increased with increasing clay loading and cell concentration for K. brevis. However, RE dropped below 70% when cell concentration was 〈 1000 cell ml-1 for clay loadings up to 0.50 g rl. This suggested that a critical number of organisms should be present for clays to remain effective. Similarly, enhanced removal with increasing cell concentration was also found in Akashiwo sanguinea (formerly Gymnodinium sanguineum), Heterosigma akashiwo and Heterocapsa triquetra. In the six remaining species, RE initially increased then decreased, or RE remained constant as more cells were treated. The removal pattern among the species at comparable cell numbers did not correlate with the cross-sectional area (R2 = 0.23), swimming speed (R2 = 0.04), or a type of cell covering (i.e. theca, silica frustule). However, when the total collision frequency coefficients were calculated (including collisions due to cell motility) over the interval when clays were 〈 50 μm, these values correlated well with the empirical RB's for the flagellated species (R2 = 0.90). These results suggested that collisions due to cell motility may be important during the early stages of aggregation when clay sizes are relatively small (i.e. near the surface where the clay layer is initially added). The electrophoretic mobility (EPM) of marine microalgae displayed a small range of negative values. While the values were smaller that those reported from freshwater species, these results confirmed earlier assumptions that marine species carry a negative charge like their freshwater counterparts. In addition, these results also revealed that the stabilities of cell suspensions in seawater are not controlled by charge neutralization. However, these measurements did not provide direct information on why one species was more readily removed over another by a given clay mineral (e.g. phosphatic clay). The EPM of clays in freshwater also exhibited predictable negative values, with montmorillonites showing the highest stability and phosphatic clays the lowest. Kaolinite and zeolite displayed a range of intermediate values. These differences vanished when the clays were suspended in natural seawater (29.6 salinity), reducing the surface charge to a small range of negative values. This effect occurred even at 1116 of the final salinity (1.85 salinity). Viewed alone, these results did not provide direct information on why one clay mineral worked better than another against a given algal species (e.g. K. brevis). Kinetic and modelling experiments using K. brevis and three minerals revealed some distinct patterns in aggregation and settling among the clays, including how they removed the organisms. After dispersing on the surface, phosphatic clays aggregated quickly by virtue of low stability (low EPM). Cell removal coincided with the onset of settling. Also, kaolinite aggregated quickly and was controlled by size as well as stability. However, cell removal followed clay settling over 40 min, after which cell removal decreased yielding only 46% RE. Bentonite aggregated slowly over 90 min due to its high stability (high EPM), but produced a number of large voluminous flocs that steadily removed the algae. The sinking rate of flocs increased as cells became incorporated, but the onset of settling was delayed when cells were present in phosphatic clay and kaolinite due to a predicted reduction in aggregate density. The process of kinetics and sedimentation were modelled using first order equations for all mineral-algae combinations. Finally, phosphatic clays demonstrated the ability to selectively remove K. brevis in a mixed culture with the dinoflagellate, Prorocentrum micans, or the diatom, Skeletonema costatum. While the RE's were generally comparable to individual cultures, the RE of either species increased in the presence of the other, especially for K. brevis. Similar results were observed in mesocosm studies using a natural assemblage during a Karenia bloom. In fact, the RE of K. brevis were higher than would be predicted from single species laboratory studies given its low initial concentration. Overall, this research demonstrated the effectiveness of clay treatment against a number of HAB species in the U.S. This work also provided new insights into the aggregation phenomenon between minerals and living algal cells by focusing on the physical (cell size), chemical and behavioral (i.e. motility) properties of both particle types, the effect of particle concentration, and the aggregation kinetics of the clay-algae system.

Description: This work has been funded by the following: EPA Grant CR827090, Florida Institute of Phosphate Research Grant 99-03-138, Florida Fish and Wildlife Conservation Commission, Contracts MR266, 99157 and Purchase Order No. S7701 615727, Sholley Foundation, and the Cove Point Foundation. Scholarships to the author were provided by the Ford Foundation, and the Education Office of 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 February 2001

Description: The importance of the persistence of multiple inlets in coastal systems is fundamental for issues such as water quality, navigability, and beach/barrier stability. In long embayments, having extended residence times, the stability of multiple inlets can be important for more efficient flushing and water exchange between the embayment and the ocean. Many approaches have been used to analyze inlet stability, but have focused on single rather than multiple tidal inlet systems, relying solely on measured data to describe and predict the behavior of tidal inlets and/or suggesting empirical stability relationships between inlet morphology and inlet/bay hydrodynamics. At present, the only multiple tidal inlet stability model available combines a linear analytical model for the flow and an empirical relationship for equilibrium, suggesting that multiple inlet systems are unstable and ultimately all inlets will close or, at best, one will remain open. Focusing on shallow multiple tidal inlet systems and in particular on Ria Formosa, a shallow coastal lagoon in the south of Portugal known to have maintained persistently multiple inlets in a historical time scale, the morphodynamic and hydrodynamic response to disturbances in the physical characteristics of the lagoon and inlets was studied through a) the analysis of historical data of the region, b) the analysis of tidal data (velocity and water surface elevation) collected in the study site, and c) through the numerical modeling of the system hydrodynamics under various inlet scenarios (using RMA-2V, a vertically averaged finite element model), with emphasis on the contribution of the hydrodynamic response (changes in tidal prism, residual discharge and current, sediment transport capacity, tidal distortion, and cross-sectional averaged maximum velocity) to maintain the multiple inlets open. The model results show that multiple tidal inlet systems can exhibit stable inlet configurations, and that the strong hydrodynamic interaction between inlets, as well as the non-linear distortion of the tide, play a major role in multiple inlet persistence. Some of the results and findings are specific to Ria Formosa, and others can be generalized and used to identify processes contributing to stability in shallow systems with multiple inlets servicing a single embayment.

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 2001

Description: A comparison of monthly biogeochemical measurements made from 1993 to 1995, combined with hydrography and satellite altimetry, was used to observe the impacts of nine eddy events on primary productivity and particle flux in the Sargasso Sea. Measurements of primary production, thorium-234 flux, nitrate+nitrite, and photosynthetic pigments made at the US JGOFS Bermuda Atlantic Time-series Study (BATS) site were used. During the three years of this study, four out of six high thorium- 234 flux events over 1000 dpm/m2/d occurred during the passage of an eddy. Primary production nearly as high as the spring bloom maximum was observed in two modewater eddies (May 1993 and July 1995). The 1994 spring bloom at BATS was suppressed by the passage of an anticyclone. Distinct phytoplankton community shifts were observed in mode-water eddies, which had an increased percentage diatoms and dinoflagelletes, and in cyclones, which had an increased percentage cyanobacteria (excluding Prochlorococcus). The difference in the observations of mode-water eddies and cyclones may result from the age of the eddy, which was very important to the biological response. In general, eddies that were one to two months old elicited a large biological response; eddies that were three months old may show a biological response and were accompanied by high thorium flux measurements; eddies that were four months old or older did not show a biological response or high thorium flux. Our conceptual model depicting the importance of temporal changes during eddy upwelling and decay fit the observations well in all 7 upwelling eddies. Additional information is needed to determine the importance of deeper mixed layers and winter mixing to the magnitude of the eddy impacts. Also, sampling generally captured only the beginning, end, and lor edge of an eddy due to the monthly to semi-monthly frequency of the measurements made at BATS. Lagrangian studies, higher resolution time-series, and/or more spatial coverage is needed to provide additional information for improved C and N budgets in the Sargasso Sea and to complete our understanding of the temporal changes that occur in an eddy.

Description: Funding for this work was provided by NASA and NSF through the JGOFS Synthesis and Modeling 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 2009

Description: Estimates of natural climate variability during the past millennium provide a frame of reference in which to assess the significance of recent changes. This thesis investigates new methods of reconstructing low-latitude sea surface temperature (SST) and hydrography, and combines these methods with traditional techniques to improve the present understanding of western North Atlantic climate variability. A new strontium/calcium (Sr/Ca) - SST calibration is derived for Atlantic Montastrea corals. This calibration shows that Montastrea Sr/Ca is a promising SST proxy if the effect of coral growth is considered. Further analyses of coral growth using Computed Axial Tomography (CAT) imaging indicate growth in Siderastrea corals varies inversely with SST on interannual timescales. A 440-year reconstruction of low-latitude western North Atlantic SST based on this relationship suggests the largest cooling of the last few centuries occurred from ~1650-1730 A.D., and was ~1ºC cooler than today. Sporadic multidecadal variability in this record is inconsistent with evidence for a persistent 65-80 year North Atlantic SST oscillation. Volcanic and anthropogenic radiative forcing are identified as important sources of externally-forced SST variability, with the latter accounting for most of the 20th century warming trend. An 1800-year reconstruction of SST and hydrography near the Gulf Stream also suggests SSTs remained within about 1ºC of modern values. This cooling is small relative to other regional proxy records and may reflect the influence of internal oceanic and atmospheric circulation. Simulations with an atmospheric general circulation model (AGCM) indicate that the magnitude of cooling estimated by proxy records is consistent with tropical hydrologic proxy records.

Description: Funding for this research was provided by a National Science Foundation Graduate Student Fellowship, National Science Foundation grants OCE-0402728, OCE-0623364, ATM-033746, the WHOI Ocean and Climate Change Institute, the WHOI Ocean Ventures Fund, the WHOI Ocean Life Institute, the MIT Student Assistance Fund, award number USA-0002, made by King Abdullah University of Science and Technology (KAUST), and the Inter-American Institute for Global Change Research.

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 1979

Description: Concern with the impact of human activities on the coastal region of the world's oceans has elicited interest in the so-called "coastal boundary layer"-that band of water adjacent to the coast where ocean currents adjust to the presence of a boundary. Within this zone, roughly 10 km wide, several physical processes appear to be important. One of these, the tides, is of particular interest because their deterministic nature allows unusually thorough analysis from short time series, and because they tend to obscure the other processes. The Coastal Boundary Layer Transect (COBOLT) experiment was conducted within 12 km of the south shore of Long Island, New York to elucidate the characteristics of the coastal boundary layer in the Middle Atlantic Bight. Analysis of data from this experiment shows that 35% of the kinetic energy of currents averaged over the 30 m depth are due to the semidiurnal and diurnal tides. The tidal ellipses, show considerable vertical structure. Near-surface tidal ellipses rotate in the clockwise direction for semidiurnal and diurnal tides, while near-bottom ellipses rotate in the counterclockwise direction for the semidiurnal tide. The angle between the major axis of the ellipse and the local coastline decreases downward for semidiurnal and increases downward for diurnal tides. The major axis of the tidal ellipse formed from the depth averaged semidiurnal currents is not parallel to the local shoreline but is oriented at an angle of -15 degrees. This orientation "tilt" is a consequence of the onshore flux of energy which is computed to be about 800 watts/m. A constant eddy viscosity model with a slippery bottom boundary condition reproduces the main features observed in the vertical structure of both semidiurnal and diurnal tidal ellipses. Another model employing long, rotational, gravity waves (Sverdrup waves) and an absorbing coastline explains the ellipse orientations and onshore energy flux as a consequence of energy dissipation in shallow water. Finally, an analytical model with realistic topography suggests that tidal dissipation may occur very close (2-3 km) to the shore. Internal tidal oscillations primarily occur at diurnal frequencies in the COBOLT data. Analysis suggests that this energy may be Doppler-shifted to higher frequencies by the mean currents of the coastal region. These motions are trapped to the shore and are almost exclusively first baroclinic mode internal waves.

Description: This work was supported by the Department of Energy under Brookhaven National Laboratory subcontract numbers 325373-8 and 359133-S.

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 2009.

Description: Tropical cyclone activity over the last 5000 years is investigated using overwash sediments from coastal lagoons on the islands of Vieques, Puerto Rico and Koshikijima, Japan. A simple sediment transport model can reproduce the landward fining deposits observed at Vieques, and reveals that although the record exhibits centennial-tomillennial changes in hurricane overwash frequency, the magnitude of these flooding events has remained relatively constant. Stochastic simulations of hurricane overwash show that breaks in activity at Vieques are extremely long and unlikely to occur under the current hurricane climatology and the present barrier morphology. Periods of less frequent hurricane deposition at Vieques are contemporaneous with intervals of increased El Niño occurrences and reduced precipitation in West Africa, suggesting a dominant influence by these two climatic phenomena. Hiatuses in overwash activity between 3600- to-2500 and 1000-500 years ago are longer than what is generated by overwash simulations under a constant El Niño-like state, indicating that mechanisms in addition to variability in the El Niño/Southern Oscillation are required to completely produce the overwash variability at Vieques. Periods of low overwash activity at Vieques are concurrent with increased overwash activity at Kamikoshiki and may indicate a correspondence between tropical cyclone activity in the western Northern Atlantic and the western North Pacific.

Description: Funding for this research was provided by the Earth Systems History Program of the National Science Foundation, the Risk Prediction Initiative, the National Geographic Society, the Andrew W. Mellon Foundation Endowed Fund for Innovative Research, and graduate student fellowships from the Coastal Ocean Institute at Woods Hole Oceanographic Institution and the United States Geological Survey.

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 2008

Description: The mechanisms of faunal dispersal across ocean basins are key unknowns toward understanding of the modern biogeography and biodiversity of deep-sea fauna. Seamounts are considered to play a defining role in faunal evolution, acting as regional centers of speciation, “stepping-stones” for dispersal, and/or refugia for deep-sea populations. The overarching goal of this dissertation was to examine the role of seamounts in structuring marine biodiversity and biogeography. This study focused on North Atlantic seamounts, specifically the New England seamount chain, the Corner Rise seamounts, and Muir seamount, areas damaged and threatened by deep-sea fisheries and currently a focus of conservation efforts. Videographic analyses of biological community structure revealed distinct faunal assemblages, dominated by the Porifera, Cnidaria, and Echinodermata and structured by geographic region, depth regions (with apparent taxonomic breaks at 1300 m, 2300 m, and 2600 m), and substrate type (including natural/anthropogenic and abiotic substrates and biotic substrates). Amongst these assemblages, seven highly specific coral host- invertebrate associate relationships were identified. To investigate whether or not these broad community patterns were discernible at a genetic level, the 16S mtDNA gene was utilized as a genetic “barcode” within the Class Ophiuroidea, through which 22 putative species were identified, including four target species (Asteroschema clavigera, Ophiocreas oedipus, Ophioplinthaca abyssalis, and Ophioplinthaca chelys) for subsequent population genetic studies. Analyses of mitochondrial 16S and COI gene sequences revealed evidence for recent population expansion and estimates of recent high gene flow across all four species throughout the North Atlantic seamount region. However, genetic differentiation within populations of A. clavigera and O. chelys within seamount regions was significant, suggesting that historical diversification has been mediated by a long-distance dispersal mechanism that homogenizes this genetic signal on a regional scale. In addition, comparisons of all ophiuroid populations revealed no congruent pattern of historical migration amongst seamounts, which may also be attributed to the varying levels of host specificity and reproductive strategy of each ophiuroid species. These results will guide future studies and conservation efforts to protect seamount communities vulnerable to deep-sea fishery activities.

Description: Financial support was provided by the Ocean Life Institute, Deep-Ocean Exploration Institute, and Academic Programs Office of the Woods Hole Oceanographic Institution, the Census of Marine Life for Seamounts (CenSeam) through their mini-grant program (Grant #12301), the Office of Ocean Exploration, National Oceanic and Atmospheric Administration (NA05OAR4601054) and the National Science Foundation (OCE-0624627; OCE-0451983; OCE-0647612).

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 2008

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

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 1983

Description: Brook trout (Salvelinus fontinalis) raised from eggs under two photoperiod and two feeding regimes were tested for physiological changes preparatory for transition from freshwater to seawater. Size, age, growth rate, photoperiod, and diel rhythms were examined for possible influences on plasma osmolarity, [Na+], [Cl-], [K+], [Mg2+], thyroxine concentration, hematocrit, and gill Na+,K+-ATPase activity of brook trout in freshwater. Significant diel cycles were found in plasma osmolarity, (Na+] and thyroxine concentration. Significant size and/or age related changes occurred for plasma osmolarity, [Na+], [K+] and hematocrit, but could explain little of their total variation (0.02 〈 r2 〈0.18). A sexually dimorphic response to photoperiod was observed in hematocrit for both mature and immature fish, with hematocrit of mature females declining in autumn and hematocrit of immature males increasing in autumn. Gill Na+,K+-ATPase activity did not respond to photoperiod or feeding treatment and showed no change with size or age. Plasma thyroxine levels responded to feeding and photoperiod treatment. There was a significant correlation between the percent mean difference in plasma thyroxine and the mean difference in growth rate between high and low feed fish (r2 = 0.51), suggesting a relationship between thyroxine and growth. In 11 experiments over 1.5 yrs, brook trout were gradually exposed to 32 ppt seawater for 20 d to investigate the ontogeny of salinity tolerance. A single experiment examined daily changes in plasma osmolarity, [Na+], [Cl-], [K+], [Mg2+], thyroxine, hematocrit and gill Na+,K+-ATPase during adaptation to 10 ppt, 20 ppt and 32 ppt. Size was the primary determinant of seawater survival (r2 = 0.77); the effect of size on seawater survival slowed after fish reached a fork length of 14 cm. The effect of age on seawater. survival (r2 = 0.65) was through its covariance with size. Photoperiod affected seawater survival only through its influence on the timing of male maturation, which decreased salinity tolerance. Hypoosmoregulation of plasma osmolarity, [Na+], [Cl-], [K+], [Mg2+] and hematocrit increased linearly with size over the entire range of sizes (6-32 cm). Gill Na+,K+-ATPase activity after 20 d in seawater decreased with increasing size of brook trout, possibly reflecting decreased demand for active ion transport in larger fish. Plasma thyroxine concentrations generally declined in seawater, but no definitive role of this hormone in seawater adaptation was found. Size dependent survival and osmoregulatory ability of brook trout is compared to other salmonids and a conceptual model is developed. Decreased salinity tolerance and hypoosmoregulatory ability was found in mature male brook trout and was not found in females or immature males. Lowered salinity tolerance of adult males becomes acute during autumn photoperiod when normal spawning occurs. Plasma [Cl-], [Mg2+], osmolarity and hematocrit are significantly higher in mature males after transfer to seawater, relative to mature females. It is postulated that reduced adult male hypoosmoregulatory ability explains skewed sex ratios in anadromous populations, limits the extent of anadromy, and was a significant phase in the evolution of extended salmonid migration. Anadromous brook trout of Riviere a la Truite, Quebec, were examined for physiological changes associated with salmonid smoltification, and compared to non-anadromous brook trout of the Matamek River. There were no significant differences in plasma thyroxine concentration, gill Na+,K+-ATPase activity, hematocrit or osmoregulatory ability of anadromous and non-anadromous brook trout. Moisture content was significantly different between fish from the two river systems, but had the same pattern of declining moisture content as summer progressed. Silver coloration of brook trout in Riviere a la Truite was significantly associated with larger fish and higher gill Na+,K+-ATPase activity, but not with changes in plasma thyroxine, moisture content, hematocrit or condition factor. Silver coloration was absent in Matamek River brook trout. Brook trout at high salinity estuarine sites had significantly greater gill Na+,K+-ATPase activity and hypoosmoregulatory ability than brook trout at low salinity sites. Atlantic salmon (Salmo salar) in high salinity estuarine sites had significantly higher plasma thyroxine and gill Na+,K+-ATPase activity than brook trout. The results indicate that smoltification is relatively undeveloped in brook trout and that estuarine residence is important in salinity adaptation and eventual seaward migration.

Description: I gratefully acknowledge the financial support of the W.H.O.I. education office, the Tai Ping foundation and the U.S. Department of Commerce Sea Grant 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 August 1983

Description: Three cytochrome P-450 forms were highly purified (8-12 nmol/mg) from the hepatic microsomes of the untreated coastal marine fish Stenotomus chrysops (scup) by detergent solubilization and column chromatography. Scup cytochromes P-450A, P-450B and P-450E (labeled in order of elution from the first ion exchange column) had distinct spectroscopic properties, substrate profiles and minimum molecular weights on SDS-polyacrylamide gels (52.7, 45.9 and 54.3 K, respectively). The three purified cytochrome P-450 isozymes yielded different peptide maps when digested with a-chymotrypsin or S. aureus V8 protease. An additional hemoprotein fraction called cytochrome P-450 fraction D was also resolved and partially purified. This cytochrome P-450 preparation was characterized by a red shift in the CO-ligated, reduced difference spectrum with a chromophore near 451 nm. The scup NADPH-cytochrome P-450 reductase was purified to electrophoretic homogeneity (Mr = 82.6 K), had a specific activity of 45-60 U/mg with cytochrome c and contained both FAD and FMN. Scup cytochrome P-450E (Mr = 54.3 K) is the major aryl hydrocarbon hydroxylating form in untreated hepatic microsomes as judged by both its abundance (30-50% of the total resolved cytochromes P-450) and catalytic activity with benzo[a]pyrene (turnover number = 0.9 nmol product/nmol P-450/min). Further, reconstituted cytochrome P-450E was inhibited 70-80% by 100 uM 7, 8-benzoflavone in catalytic assays, similar to the 80-90% inhibition of benzo[a]pyrene hydroxylase in microsomal incubations. Analysis of benzo[a]pyrene products derived from reconstitutions of purified cytochrome P-450E revealed that greater than 50% of the oxidation occurred at benzo-ring positions, like the product profile observed in incubations with microsomes. The molecular weight of the purified cytochrome P-450E is identical to the major microsomal hemoprotein induced by 3-methylcholanthrene pretreatment, suggesting cytochrome P-450E is the major aromatic hydrocarbon-inducible cytochrome P-450 form in scup. Rabbit antisera raised against purified scup cytochrome P-450E reacts in Ouchterlony diffusion analysis with cytochrome P-450E antigenic determinants in microsomes but not purified cytochrome P-450A. Further, the antisera cross-reacts with an apparent 3-methylcholanthrene-inducible cytochrome P-450 isozyme purified from trout liver (TLM-4a; Williams and Buhler, Compo Biochem. Physiol. 7SC: 25-32, 1983), giving a pattern of fusion without visible-spurring in Ouchterlony analysis. These observations imply common antigenic determinants for the apparent major 3-methylchoianthrene-inducible cytochrome P-450 forms in trout and scup. Monooxygenase reconstitution experiments indicated that purified scup cytochrome P-450A actively hydroxylated testosterone at the 6ß position (turnover number = 0.8 nmol/min/nmol cytochrome P-450). Reconstituted cytochrome P-450B oxidized testosterone at two different sites tentatively identified as the 2-a and l5-a positions (total turnover number = 0.07 min-1). Cytochrome P-450 fraction D produced several metabolites upon reconstitution (sum turnover number = 0.2 min-1) including two chromatographically similar to 16a- and 16ß-hydroxytestosterone. Reconstituted cytochrome P-450E was a poor catalyst of testosterone hydroxylase but the only detectable product was 6 ß-hydroxytestosterone (turnover number = 0.04 min-1). However, besides benzo[a]pyrene, reconstituted cytochrome P-450E was active with 7-ethoxycoumarin, acetanilide and 7,8-benzoflavone as substrates. Addition of purified scup cytochrome b5 to monooxygenase reconstitutions had a stimulatory effect on some catalytic rates. The magnitude of the cytochrome b5 stimulation depended on the P-450 isozyme and the substrate used in the reconstitution; cytochrome P-450A was generally influenced by the presence of cytochrome b5. This rate stimulation was greater than the effect obtained with purified rabbit liver cytochrome b5. In an extreme example, cytochrome P-450E was completely inactive in reconstitutions of 7-ethoxyresorufin O-deethylase (an activity associated in microsomes with aromatic hydrocarbon induction) in the presence or absence of rabbit cytochrome b5 but the addition of scup cytochrome b5 to the reconstitution led to an observed O-deethylation rate of 7.0 min-1. It is uncertain whether these cytochrome b5 effects are exhibited in microsomes or in vivo but the stimulation in reconstitutions appears to be important in the evaluation of catalytic activity with purified isozymes.

Description: Financial support for my investigations was gleaned in part from a NSF Pre-doctoral Fellowship, the WHOI Education Office, WHOI Coastal Research Center grant 67.08, NSF grant OCE 80-18569 (J. S.) and NIH grant GM 21643 (C. W.).

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 2008

Description: Inspired by the swimming abilities of marine animals, this thesis presents "Finnegan the RoboTurtle", an autonomous underwater vehicle (AUV) powered entirely by four flapping foils. Biomimetic actuation is shown to produce dramatic improvements in AUV maneuvering at cruising speeds, while simultaneously allowing for agility at low speeds. Using control algorithms linear in the modified Rodrigues parameters to support large angle maneuvers, the vehicle is successfully controlled in banked and twisting turns, exceeding the best reported AUV turning performance by more than a factor of two; a minimum turning radius of 0.7BL, and the ability to avoid walls detected〉 1.8BL ahead, are found for cruising speeds of 0.75BL/S, with a maximum heading rate of 400 / S recorded. Observations of "Myrtle", a 250kg Green sea turtle (Chelonia mydas) at the New England Aquarium, are detailed; along with steady swimming, Myrtle is observed performing 1800 level turns and rapidly actuating pitch to control depth and speed. Limb kinematics for the level turning maneuver are replicated by Finnegan, and turning rates comparable to those of the turtle are achieved. Foil kinematics which produce approximately sinusoidal nominal angle of attack trace are shown to improve turning performance by as much as 25%; the effect is achieved despite limited knowledge of the flow field. Finally, tests with a single foil are used to demonstrate that biomimetically inspired inline motion can allow oscillating foils utilizing a power/recovery style stroke to generate as much as 90% of the thrust from a power/power stroke style motion.

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 2001

Description: Improving the performance of modular, low-cost autonomous underwater vehicles (AUVs) in such applications as long-range oceanographic survey, autonomous docking, and shallow-water mine countermeasures requires improving the vehicles' maneuvering precision and battery life. These goals can be achieved through the improvement of the vehicle control system. A vehicle dynamics model based on a combination of theory and empirical data would provide an efficient platform for vehicle control system development, and an alternative to the typical trial-and-error method of vehicle control system field tuning. As there exists no standard procedure for vehicle modeling in industry, the simulation of each vehicle system represents a new challenge. Developed by von Alt and associates at the Woods Hole Oceanographic Institute, the REMUS AUV is a small, low-cost platform serving in a range of oceanographic applications. This thesis describes the development and verification of a six degree of freedom, non-linear simulation model for the REMUS vehicle, the first such model for this platform. In this model, the external forces and moments resulting from hydrostatics, hydrodynamic lift and drag, added mass, and the control inputs of the vehicle propeller and fins are all defined in terms of vehicle coefficients. This thesis describes the derivation of these coefficients in detail. The equations determining the coefficients, as well as those describing the vehicle rigid-body dynamics, are left in non-linear form. to better simulate the inherently non-linear behavior of the vehicle. Simulation of the vehicle motion is achieved through numeric integration of the equations of motion. The simulator output is then checked against vehicle dynamics data collected in experiments performed at sea. The simulator is shown to accurately model the motion of the vehicle.

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 2001

Description: This thesis presents methods to analyze the function of vocalizations of the bottlenose dolphin, Tursiops truncatus. The thesis uses the social interaction as the basic unit of analysis, and maintains a deliberate focus on quantitative and replicable analyses throughout. A method for determining identity of the vocalizing animal in a lagoon was developed. This method combined passive acoustic localization with video sampling to determine which animal vocalized. It fills an urgent need for unbiased identification of vocalizations of undisturbed dolphins where details of social interactions can be followed without affecting the behavior of the subjects. This method was implemented in a captive lagoon with 6 dolphins: two adult females, their two male calves, and a juvenile male and a juvenile female. This thesis also reviews the current state of analysis of the bottlenose dolphin acoustic repertoire, highlighting the need for a detailed, quantitative, and consistent study of the entire vocal repertoire. It does not attempt to do a comprehensive repertoire study, but uses several new quantitative methods to parameterize vocalizations and relate these to behavior from dolphins. Vocalizations within the lagoon tended to occur around the time of onset of behaviors produced by the focal dolphin. A comparison of vocalizations during affiliative and agonistic interactions revealed that the association of group vocalizations with the behavior of a focal animal was related to agonistic but not affiliative interactions. Using the localization/video method, vocalizations in a time window around submissive behaviors were localized and classified as having come from either dolphins engaged in the interaction or dolphins not engaged in the interaction. Vocalizations were emitted by interactants more often than expected, and by non-interactants less often than expected. Use of different vocalization types was found to vary depending on the context of the agonistic interaction. In addition, the sequence of vocalizations with respect to behaviors within the interaction mattered, with more vocalizations occurring after than before submissive behaviors. These results demonstrated that group-based analyses of vocalizations are insufficient and one must use techniques designed to focus on the level of the interaction in order to study communication and social behavior in dolphins.

Description: Funding was provided by the Waikoloa Marine Life fund, Grant No. IBN-9975523 from the National Science Foundation, a graduate student fellowship for R. Thomas from the National Science Foundation, and an Ocean Ventures Fund Grant for R. Thomas 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 June 2009

Description: Iron availability and primary productivity in the oceans are intricately linked through photosynthesis. At the global scale we understand how iron addition induces phytoplankton blooms through meso-scale iron-addition experiments. At the atomic scale, we can describe the length and type of bonds that connect iron atoms to components of photosystem I, the most efficient light-harvesting complex in nature. Yet, we know little of how iron influences microbial diversity and distribution in the open ocean. In this study, we assess the influence of iron on the ecology of the numerically abundant marine cyanobacterium, Prochlorococcus. With its minimal genome and ubiquity in the global ocean, Prochlorococcus represents a model system in which to study the dynamics of the link between iron and primary productivity. To this end, we tested the iron physiology of two closely-related Prochlorococcus ecotypes. MED4 is adapted to high-light environments while MIT9313 lives best in low-light conditions. We determined that MIT9313 is capable of surviving at low iron concentrations that completely inhibit MED4. Furthermore, concentrations of Fe’ that inhibit growth in culture are sufficient to support Prochlorococcus growth in the field, which raises questions about the species of iron available to Prochlorococcus. We then examined the molecular basis for the ability of MIT9313 to grow at lower iron concentrations than MED4 by assessing whole-genome transcription in response to changes in iron availability in the two ecotypes. Genes that were differentially expressed fell into two categories: those that are shared by all (Prochlorococcus core genome) and those that are not (non-core genome). Only three genes shared between MED4 and MIT9313 were iron-responsive in both strains. We then tested the iron physiology of picocyanobacteria in the field and found that Synechococcus is iron-stressed in samples where Prochlorococcus is not. Finally, we propose a method to measure how iron stress in Prochlorococcus changes over natural gradients of iron in the oligotrophic ocean by quantifying transcription of the iron-stress induced gene, isiB. Taken together, our studies demonstrate that iron metabolism influences the ecology of Prochlorococcus both by contributing to its diversity and distinguishing it from other marine cyanobacteria.

Description: This work was supported by grants from the Gordon and Betty Moore Foundation (#495 and #495.01), the National Science Foundation (OCE-0425602), the Center for Microbial Oceanography: Research and Education established by the National Science Foundation (Z792093-02), and the Department of Energy (DE-FG02-07ER64506 and DE-FG02-08ER64516) to Sallie W. Chisholm. In addition, the work was supported by grants to Mak A. Saito from the Office of Naval Research (N00014-05-1-0704), National Science Foundation Center for Microbial Oceanography: Research and Education (Z792384), National Science Foundation Environmental Genomics Program (0723667), and National Science Foundation Chemical Oceanography Program (OCE-0752271 and OCE-0452883).

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 2009

Description: The application of elemental and isotopic metal palaeoredox tracers to the geologic past rests on an understanding of modern metal cycles. This study reevaluates the surface-cycling of Mo and Re in near-surface reservoirs. Revised river averages of Mo and Re are 1.8- and 7.9-fold larger than previous estimates. The river concentrations of 8.0 nmol Mo kg−1 and 11.2 pmol Re kg−1 (pre-anthropogenic), result in shorter seawater response times of 4.4×105 yr (τMo) and 1.3×105 yr (τRe pre-anthropogenic). These metals, especially Re, are more sensitive to changing source and sink fluxes than previously thought. Evaluation of Mo and Re concentrations in high temperature fluids from the Manus Basin indicate that Re is essentially absent from the hydrothermal end member and Mo is present at concentrations considerably lower than ambient seawater. The sink fluxes represented by hydrothermal circulation are negligible in comparison to the revised river source fluxes. Anthropogenic contributions to the Re flux to seawater are seen in the high concentrations of certain impacted water samples such as those associated with mining sites. It may also be seen in a significant, variable, Re enrichment feature in the Hudson River estuary. This Re enrichment feature is not the result of estuarine mixing or the remobilization of sediment-hosted Re. On the basis of a Re - SO2− 4 correlation we are able to quantify and correct for the anthropogenic Re, which corresponds to ~33% of the modern river average. This study documents the development of an analytical method for stable Re isotopes. Though complicated by analyte requirements and 187Re – 187Os decay, Re isotope measurements have a reproducibility of ±0.05h for analyte concentrations of 20 ng Re mL−1. Total Re isotopic variability to date is 0.9h. This includes 0.3h across five commercially available Re products, and 0.5h across a black shale weathering profile. δ187Re variability across the weathering profile was systematic with the most weathered samples showing the most significant 187Re depletions. The Re isotopic weathering profile is well described by both two-component mixing and Rayleigh fractionation. There are currently insufficient data to discriminate between the two models.

Description: We would like to acknowledge financial support from NSF-EAR grant 0519387 and from the WHOI Academic Programs Office as well as support for the WHOI Plasma Mass Spectrometry Facility from NSF-EAR/IF grants 0318137 and 0651366.

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 2009

Description: A study of the ecology of fish endemic to hydrothermal vents on the East Pacific Rise was undertaken utilizing a variety of techniques, focusing on the bythitid Thermichthys hollisi. Stable isotope and gut content analyses were used to elucidate prey choice and trophic relationships. Otolith chemical signatures were investigated to determine whether this technique could be utilized to examine life history strategy and habitat use. Chemical characteristics of preferred fish habitat and gene expression responses habitat chemistry were explored. Gut contents indicated that T. hollisi specimens were actively feeding upon a combination of brachyuran crabs, Alvinocaris shrimp, polychaetes, and zoarcid fish with the majority of fish containing evidence of crustacean prey. Carbon, nitrogen, and sulfur stable isotopic measurements support a chemosynthetically based prey source and place T. hollisi in the uppermost trophic levels of vent communities. The influence of exposure to hydrothermal fluids was apparent in otoliths from both species of vent fish, most noticeably within the relatively elevated Sr:Ca and depleted Mg:Ca ratios. Otolith chemistry suggested that the zoarcid Thermarces cerberus experiences greater direct exposure to diffuse fluids than does T. hollisi, which is concurrent with apparent habitat preferences. Isotopic patterns across the span of the otolith suggested that T. cerberus spends its entire life within the vent system. In contrast, it appeared that T. hollisi exists outside of the influence of hydrothermal activity for some early portion of its life-cycle. Time-lapse photography and in situ electrochemistry indicated that T. hollisi are preferentially utilizing fish holes where there are elevated temperatures and sulfide levels, and variable oxygen levels in comparison to ambient bottom water. A fragment of Cu, Zn superoxide dismutase was successfully amplified from T. hollisi mRNA, but there were no differences in expression levels between tissue types or among individuals within the small sample examined. In general, it appears that T. hollisi is both influenced by and may exert a greater influence on hydrothermal vent communities to a greater degree than initially hypothesized.

Description: I was the recipient of a 2003 MIT Presidential Fellowship, a 2004-2007 National Defense Science and Engineering Graduate Fellowship, and received support from the Woods Hole Oceanographic Institution Academic Programs Office as well as National Science Foundation’s Office of Polar Programs (ANT-073965) support to TMS. Funding for my research was provided in part by the National Science Foundation (OCE-032726 and OCE-0324232), the National Oceanic and Atmospheric Administration’s Office of Ocean Exploration and Research (Award Nos. NA03OAR4600110, NA16RP2390, and NA 04OAR4600049) support to TMS and a 2008 Lerner-Gray Grant for Marine Research from the Lerner Gray Memorial Fund of the American Museum of Natural History support to KLB.

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 2009

Description: Mode filtering is most commonly implemented using the sampled mode shape or pseudoinverse algorithms. Buck et al placed these techniques in the context of a broader maximum a posteriori (MAP) framework. However, the MAP algorithm requires that the signal and noise statistics be known a priori. Adaptive array processing algorithms are candidates for improving performance without the need for a priori signal and noise statistics. A variant of the physically constrained, maximum likelihood (PCML) algorithm is developed for mode filtering that achieves the same performance as the MAP mode filter yet does not need a priori knowledge of the signal and noise statistics. The central innovation of this adaptive mode filter is that the received signal's sample covariance matrix, as estimated by the algorithm, is constrained to be that which can be physically realized given a modal propagation model and an appropriate noise model. The first simulation presented in this thesis models the acoustic pressure field as a complex Gaussian random vector and compares the performance of the pseudoinverse, reduced rank pseudoinverse, sampled mode shape, PCML minimum power distortionless response (MPDR), PCML-MAP, and MAP mode filters. The PCML-MAP filter performs as well as the MAP filter without the need for a priori data statistics. The PCML-MPDR filter performs nearly as well as the MAP filter as well, and avoids a sawtooth pattern that occurs with the reduced rank pseudoinverse filter. The second simulation presented models the underwater environment and broadband communication setup of the Shallow Water 2006 (SW06) experiment. Data processing results are presented from the Shallow Water 2006 experiment, showing the reduced sensitivity of the PCML-MPDR filter to white noise compared with the reduced rank pseudoinverse filter. Lastly, a linear, decision-directed, RLS equalizer is used to combine the response of several modes and its performance is compared with an equalizer applied directly to the data received on each hydrophone.

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 November 1992

Description: This thesis examines the degradation pathways of chlorophyll in the Black Sea water column and sediments. Measurements are made of total chlorophyll in sediment traps from two locations and depths in the water column, and at two locations in surface sediments. Individual chlorophyll degradation products are also identified. This data is used to construct a mass balance of chlorophyll production and sedimentation showing the major pathways for chlorophyll loss and the ultimate sedimentary sinks. The distribution of chlorophyll degradation products is also analyzed down core and related to environmental changes in the Black Sea Several new sinks for chlorophyll degradation products are identified. Steryl esters of pyropheophorbide-a are identified in sediment trap and sediment samples. It is thought that these compounds are formed during grazing. In sediment traps it is found that the distribution of the sterols esterified to pyropheophorbide-a change with season and that the sterols esterified are related to the distribution of sterols synthesized by the phytoplankton living in the photic zone at the time of production. Analysis of pyropheophorbide-a steryl esters in sediments shows the distribution of sterols to be quantitatively and qualitatively more similar to the distribution of free sterols in sediment traps than in sediments. The esterification of the sterols to pyropheophorbide-a apparently prevents the preferential removal of 4-desmethylsterols relative to 4-methylsterols during degradation of the sterol esters. Chlorophyll degradation products which are incorporated into high molecular weight material and material which is only accessible with strong acid are also identified. The chlorophyll degradation products incorporated into these structures represent only a few percent of the total structure. In the high molecular weight material, only phorbins derived from chlorophyll-a are identifies, where as in the acid extractable material, porphyrins are also identified. In surface sediments, the acid extractable chlorophyll degradations products and the solvent extractable macromolecular chlorophyll degradation products each comprise approximately 30% of total sedimentary chlorophyll degradation products. The acid extractable chlorophyll degradation products are identified in sediment trap samples, and evidence is presented for the occurrence of the solvent extractable macromolecular chlorophyll degradation products in sediment trap samples. Using data from sediment traps, sediments, and the literature, a mass balance of chlorophyll flux, degradation, and accumulation in the Black Sea is presented. In the photic zone, chlorophyll degradation products are either destroyed by photo-oxidation and grazing, or they are transported into the anoxic water column in large, rapidly sinking particles. Once the chlorophyll degradation products have reached the anoxic water column, they survive to be deposited in the underlying sediments. As a comparison, 25 times more total organic carbon reaches the anoxic water column than does total phorbin, but 75% of total organic carbon which reaches the anoxic water column is degraded, either in the anoxic water column or in the very surface sediments. Though a larger percentage of total organic carbon passes out of the photic zone, the phorbin macrocycle appears to be more stable under anoxic conditions than is total organic carbon. The chlorophyll which can be detected below the chemocline of the Black Sea in the form of chlorophyll degradation products will survive to be deposited in surface sediments. Once in sediments, chlorophyll degradation products are found in four different reservoirs: phorbin steryl esters, free phorbins, solvent extractable macromolecular chlorophyll degradation products, and acid extractable chlorophyll degradation products. Evidence for the occurrence of porphyrins in surface Black Sea sediments is also presented. The distribution of chlorophyll degradation products in Unit I Black Sea sediments varies greatly with sediment depth. The concentration of total phorbin generally increases with increasing burial depth, but the concentrations of the individual chlorophyll degradation products vary in a manner which is both dissimilar to total phorbin and to each other. No parent/daughter relationships for the chlorophyll degradation products are indicated by the data. The distribution of sterols esterified to pyropheophorbide-a changes with sediment depth with the largest qualitative changes occurring in strata where the total phorbin concentration shows the largest quantitative changes. It is suggested that the variations seen in the esterified sterols are related to changes in the phytoplankton community over time. From the presented data, it is also suggested that total phorbin concentration, normalized to total organic carbon, in Black Sea Unit I sediments is related to paleoprimary production. Several conclusions are drawn from the work presented in this thesis. There is approximately 3 times more chlorophyll-derived phorbin in Black Sea sediments than can be accounted for when considering only individual pheopigments, and therefore the sedimentary degradation of chlorophyll is much more complex than previously thought. In the anoxic sediments of the Black Sea, the total phorbin distribution can be accounted for with organically extractable high molecular weight degradation products, pyropheophorbide steryl esters, pheopigments, and acid extractable chlorophyll degradation products. The sterol distribution in the pyropheophorbide steryl esters may preserve the sterol distribution in surface waters as synthesized by the phytoplankton, and pyropheophorbide steryl esters are preserved in sediments over the long term.

Description: The work in this thesis was funded by grants from the Woods Hole Oceanographic Institution's Ocean Ventures Fund and the National Science Foundation contract numbers OCE88-14398, OCE90-17626, and OCE92-01178.

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 1990

Description: Theory and observations of deep circulation in the near-equatorial Atlantic, Indian and Pacific Oceans are reviewed. Flow of deep and bottom water in the near-equatorial Indian and Pacific oceans, the two oceans with only a southern source of bottom water, is described through analysis of recent CTD data. Zero-velocity surfaces are chosen through use of water-mass properties and transports are estimated. Effects of basin geometry, bottom bathymetry and vertical diffusivity as well as a model meridional inertial current on a sloping bottom near the equator are all discussed in conjunction with the flow patterns inferred from observations. In the western equatorial Indian Ocean, repeat CTD surveys in the Somali Basin at the height of subsequent northeast and southwest monsoons show only small differences in the strength of the circulation of the bottom water (potential temperature θ ≤1.2°C). A deep western boundary current (DWBC) carrying about 4x106 m3 s-1 of this water is observed moving north along the continental rise of Africa at 3°S. The cross-equatorial sections suggest that the current turns eastward at the equator. The northern sections show a large mass of the coldest water in the interior east of the Chain Ridge, augmenting the evidence that the DWBC observed south of the equator turns east at the equator rather than remaining on the boundary, and feeds the interior circulation in the northern part of the basin from the equator. The circulation of deep water (1.2°C〈 θ ≤ 1.7°C) in the Somali and Arabian Basins is also analyzed. A DWBC flowing southward along the Carlsberg ridge in the Arabian Basin is described. In the central equatorial Pacific Ocean a recent zonal CTD section at 10°N, allows estimation that 5.0x106 m3 s-1 of Lower Circumpolar Water (LCPW, θ ≤ 1.2°C) moves northward as a DWBC along the Caroline Seamounts in the East Mariana Basin. In the Central Pacific Basin, 8.1x106 m3 s-1 of LCPW is estimated to move northward along the Marshal Seamounts as a DWBC at this latitude. An estimated 4.7x106 m3 s-1 of the LCPW moves back southward across 10°N in the Northeast Pacific Basin along the western flank of the East Pacific Rise and an equatorial jet is observed to flow westward from 138°W to 148°W shifting south of the Line Islands at 2.5°S, 159°W. The net northward flow of LCPW across 10°N in the Pacific Ocean is estimated at 8.4x106 m3 s-I. The net southward flow of the silica-rich North Pacific Deep Water (NPDW, 1.2 〈 θ ≤ 2.0°C) in the central Pacific Ocean estimated at 2.7x106 m3 s-1 is also discussed. In the Indian Ocean, the eastward equatorial flow in the the bottom water of the Somali Basin differs from the prediction of a flat-bottom uniform-upwelling Stommel-Arons calculation with realistic basin geometry and source location. The behavior of a uniform potential vorticity meridional jet on a sloping bottom is examined in an attempt to explain the observed behavior at the equator. The inertial jet does not cross the equator in a physically plausible fashion owing to the constraint of conservation of potential vorticity. Mass and heat budgets for the bottom water of the Somali Basin are of interest with respect to the equatorial feature. Upwelling through the θ = 1.2°C surface is estimated at 12±4x10-5 cm s-1 and a rough heat budget for the deep Somali Basin results in an estimate of vertical diffusivity of 9±5 cm2 s-1 at 3800 m. Numerical model results indicate that large vertical diffusivities result in eastward jets in the bottom water at the equator. In the Pacific Ocean the DWBC observed flowing northward south of the equator crosses the equator with transport nearly intact, albeit split into two at 10°N by the tortuous bathymetry. However the southward flow along the East Pacific Rise in the Northeast Pacific Basin and the westward equatorial jet this flow feeds are puzzling. The basin depth decreases equatorward and eastward, which may allow some southeastward flow in the Stommel-Arons framework. However, the equatorial jet is still unexplained. The estimated vertical velocity and diffusivity at 3600 db of 2±2x10-5 cm s-1 and 4±3 cm2 s-1 for the area between 12°8 and 10°N are much smaller than estimates in the Somali Basin. Thus the two oceans, similar in their single southern source of bottom water, have DWBC's which behave remarkably differently near the equator. In the Somali Basin of the Indian Ocean the DWBC appears to turn eastward at the equator, with large vertical upwelling velocity and large vertical diffusivity estimates for the bottom water of the basin. In the Pacific Ocean the DWBC appears to cross the equator, but there is a puzzling westward flowing equatorial jet in the bottom water of the Northeast Pacific Basin.

Description: The author began this research in the M.I.T.-W.H.O.I Joint Program while supported by the U. S. Offce of Naval Research through a Secretary of the Navy Graduate Fellowship in Oceanography. Support for collection and analysis of the data taken during R.R.S. Charles Darwin cruises 86-19 and 87-25 was provided by the U. S. National Science Foundation under grants OCE8800135 and OCE8513825 to D. B. Olson at the University of Miami and by the U. S. Offce of Naval Research under contract N00014-87-K-0001, NR083-004 and grant N00014-89-J-1076 to B. A. Warren at W.H.O.I. Collection of data taken during R.Y. Moana Wave cruise 89- 3 was supp6rted by the U. S. National Science Foundation under grant OCE881691O to H. L. Bryden and J. M. Toole at W.H.O.I. Collection of data taken during the U.S.-P.R.C. Toga cruises was supported by N.O.A.A. under grant NA85AA-DACU7.

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 2009.

Description: The radionuclides 231Pa and 230Th, produced in the water column and removed from the ocean by particle scavenging and burial in sediments, offer a means for paleoceanographers to examine past dynamics of both water column and sedimentary processes. I show for the first time that a state of balance exists between 230Th production and burial in the Central Arctic basins, based on measured sedimentary 230Thxs inventories in box cores, establishing this nuclide’s utility as a paleoceanographic indicator of sedimentary processes and as a normalization tool. I present the first 230Th-normalized particle fluxes calculated for the central Arctic: vertical particle fluxes were extremely low during the late glacial, rose during the deglaciation due to particle inputs from shelf inundation, increased productivity and ice-rafted debris, and fell again following the establishment of interglacial conditions. A major event of lateral sediment redistribution, inferred from surplus 230Thxs inventories, occurred in the Makarov Basin during the deglaciation and may have been due to destabilization of slope and shelf sediments as sea level rose. I present the first high-resolution, radiocarbon-dated downcore records of sedimentary 231Pa/230Th from the Arctic Ocean. Low ratios indicate that 231Pa was exported from all sites during the late glacial period, with export decreasing during the deglaciation and Holocene. 231Pa/230Th measurements in cores from three continental slope sites show no evidence for a 231Pa sink related to boundary scavenging on the continental slopes. Holocene 231Pa/230Th ratios show a very significant variation by depth, with strong export of 231Pa at deep sites but little or no export at shallow sites, a result which echoes findings for the South Atlantic and the Pacific. The Arctic thus appears fundamentally similar to other ocean basins in its 231Pa and 230Th dynamics, despite its peculiar qualities of sea ice cover, low particle flux, and relatively isolated deep waters.

Description: My graduate work has been funded by NSF grants OCE-0402565 and OCE- 0550637 to Jerry McManus, ARC-0520073 to Bill Curry, and OCE-0118126 to Daniel McCorkle. My graduate education was also supported by an IODP Schlanger Ocean Drilling Fellowship, WHOI Fellowships from the WHOI Academic Programs Office, and an MIT Presidential Fellowship.

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 February 2009

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

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 2002

Description: Sound propagation in shallow water is highly dependent on the interaction of the sound field with the bottom. In order to fully understand this problem, it is necessary to obtain reliable estimates of bottom geoacoustic properties that can be used in acoustic propagation codes. In this thesis, perturbative inversion methods and exact inverse methods are discussed as a means for inferring geoacoustic properties of the bottom. For each of these methods, the input data to the inversion is the horizontal wavenumber spectrum of a point-source acoustic field. The main thrust of the thesis work concerns extracting horizontal wavenumber content for fully three-dimensionally varying waveguide environments. In this context, a high-resolution autoregressive (AR) spectral estimator was applied to determine wavenumber content for short aperture data. As part of this work, the AR estimator was examined for its ability to detect discrete wavenumbers in the presence of noise and also to resolve closely spaced wavenumbers for short aperture data. As part of a geoacoustic inversion workshop, the estimator was applied to extract horizontal wavenumber content for synthetic pressure field data with range-varying geoacoustic properties in the sediment. The resulting wavenumber content was used as input data to a perturbative inverse algorithm to determine the sound speed profile in the sediment. It was shown using the high-resolution wavenumber estimator that both the shape and location of the range-variability in the sediment could be determined. The estimator was also applied to determine wavenumbers for synthetic data where the water column sound speed contained temporal variations due to the presence of internal waves. It was shown that reliable estimates of horizontal wavenumbers could be obtained that are consistent with the boundary conditions of the waveguide. The Modal Mapping Experiment (MOMAX), an experimental method for measuring the full spatial variability of a propagating sound field and its corresponding modal content in two-dimensions, is also discussed. The AR estimator is applied to extract modal content from the real data and interpreted with respect to source/receiver motion and geometry. For a moving source, it is shown that the wavenumber content is Doppler shifted. A method is then described that allows the direct measure of modal group velocities from Doppler shifted wavenumber spectra. Finally, numerical studies are presented addressing the practical issues associated with using MOMAX type data in the exact inversion method of Gelfand-Levitan.

Description: I am especially grateful to ONR for providing the funding for me to do this work.

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 1982

Description: The development of nonlinear surface and internal wave groups is investigated. Surface wave evolution was observed in an unusually long wave channel as a function of steepness and group length. Dissipation and frequency downshifting were important characteristics of the long-time evolution. The amplitude and phase modulations were obtained using the Hilbert transform and specified as an initial condition to the cubic nonlinear Schrodinger equation, which was solved numerically. This equation is known to govern the slowly varying complex modulation envelope of gravity waves on deep water. When dissipation was included, the model compared quite well with the observations. Phase modulation was used to interpret the long-time behavior, using the phase evolution of exact asymptotic solutions as a guide. The wave groups exhibited a long-time coherence but not the recurrence predicted by the inviscid theory. An oceanic field study of the generation of groups of large amplitude internal waves by stratified tidal flow over a submarine ridge indicates that the large amplitude and asymmetry of the topography are critical in determining the type of flow response. The calculated Froude numbers response length scale and duration differ markedly between the two phases of the tide due to the asymmetry.

Description: Research assistantship provided by the Office of Naval Research contract no. N00014-80-C-0273

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 2002

Description: Predictions of deposition rate are integral to the transport of many constituents including contaminants, organic matter, and larvae. Review of the literature demonstrates a general appreciation for the potential control of deposition by bed roughness, but no direct tests involving flat sediment beds. Understanding the mechanisms at work for flat sediment beds would provide the basis for exploring more complicated bed conditions and the incorporation of other transport processes, such as bioturbation and bedload transport. Generally, fine particle deposition rates are assumed to be equivalent to the suspension settling velocity, therefore, deposition rates in excess of settling are considered enhanced. Flume observations of deposition were made using treatments that covered a wide range of flow, particle, and bed conditions. Specific treatments demonstrated large enhancements (up to eight times settling). Delivery of particles to the interface is important, but models based on delivery alone failed to predict the observed enhancement. This necessitated the development of a new model based on a balance between delivery and filtration in the bed. Interfacial diffusion was chosen as a model for particle delivery. Filtration of particles by the bed is a useful framework for retention, but the shear in the interstitial flow may introduce additional factors not included in traditional filtration experiments. The model performed well in prediction of flow conditions, but there remained a discrepancy between predictions and observed deposition rate, especially for treatments with significant enhancement. Fluid flow predictions by the model,; such as slip at the sediment water interface and fluid penetration into the sediment, appeared to be supported by flume experiments. Therefore, failure to predict the magnitude of enhancement was attributed to far greater filtration efficiencies for the sediment water interface than those measured in sediment columns. Emerging techniques to directly measure fluid and particle motion at the interface could reveal these mechanisms. The observation of enhanced deposition to flat sediment beds reinforces the importance of permeable sediments to the mediation of transport from the water column to the sediment bed.

Description: The Education Office at the Woods Hole Oceanographic Institution coordinated and provided funding for much of my time here. Additional support has been provided by the Andrew W. Mellon Foundation, the Cooperative Institute for Climate and Ocean Research (CICOR), and the Offce of Naval Research under grant numbers N00014-97-1-0556 (STRATAFORM Plume Study Moored Observations: Data Analysis and Modeling), N00014-96-1-0953 (Graduate Student Training in Engineering: Instrumenting the Continental Shelf Wave Bottom Boundary Layer), and N00014-94-1-0713 (Coupled Biological, Geological and Hydrodynamical Processes Associated with Fine-Particle Transport & Accumulation in the Coastal Ocean).

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 2009

Description: The Basin Acoustic Seamount Scattering Experiment (BASSEX) of 2004 was conducted to measure forward-scattering around the Kermit-Roosevelt Seamount Complex in the Northeast Pacific. The BASSEX experiment was focused on the bathymetric effects on acoustic propagation, in particular, on direct blockage, horizontal refraction, diffraction, and scattering by the seamounts. A towed hydrophone array, with 64 sensors cut for 250Hz (3m spacing), was used to measure the signals transmitted from the aforementioned broadband sources at many locations around the Kermit-Roosevelt and Elvis seamounts. Utilizing the measured broadband signals from the towed array, the size of the shadow zone was obtained. The measured data in the BASSEX experiment strongly support the understanding of the complicated phenomena of sound propagation around the seamounts. In addition, the experimental data could be used to validate current 2D and 3D theoretical models and develop new models to properly realize the sound propagation with such complicated phenomena. In this thesis, the reconciliation between the measured pulse arrivals from the BASSEX experiment and various two-dimensional (2D) and three-dimensional (3D) theoretical models is carried out to investigate the physical characteristics of the sound propagation around seamounts: First, the 2D Parabolic Equation (PE) model and the 2D ray tracing model are used to reconcile each ray arrival with the BASSEX experiment in terms of arrival time and grazing angle. We construct a sound speed field database based on the sound speed profiles from the BASSEX experiment, World Ocean Atlas (WOA) 2005, and CTD casts using the objective analysis. Second, 3D broadband sound propagation around a conical seamount is investigated numerically using the 3D spectral coupled-mode model (W. Luo, PhD Thesis, MIT, 2007). Since the calculation of 3D broadband pulses with the spectral coupledmode model requires extensive computation time, a parallel program is developed with a clustered computing system to obtain results in reasonable time. The validation of the 3D spectral coupled-mode model is performed by a series of comparisons between the various 2D and 3D models for a shallow-water waveguide. The Kermit-Roosevelt seamount is modeled by a simple conical seamount for the 3D model. The computed 3D broadband pulses for the modeled conical seamount are compared with those from the BASSEX experiment and the 2D PE simulation. Through this analysis, we examine the limit of the application of the sound propagation models and improve the efficiency of the 3D sound propagation model using parallel computing to obtain a broadband pulse in a reasonable amount of 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 2009

Description: Driven by commercial promise, the carbon nanotube (CNT) industry is growing rapidly, yet little is known about the potential environmental impacts of these novel materials. In particular, there are no methods to detect CNTs in environmental matrices (e.g., sediment) and thus, there is no way to study their transport or gauge ecological exposure. Thermal methods were developed to quantify CNTs in coastal sediments down to 10 ug per sample, which is sufficient to for CNTs in laboratory air, but not sufficient to measure contemporary levels of CNTs in the environment (which were estimated to be present at pg g-1 sediment levels using a dynamic mass balance model). In addition to the CNTs themselves, potential impacts of CNT production were assessed by monitoring emissions from a representative synthesis. An ethene-fed chemical vapor deposition process generated several compounds of environmental concern, including the greenhouse gas, methane, the hazardous pollutants, benzene and 1,3-butadiene, and toxic polycyclic aromatic hydrocarbons. By identifying critical CNT precursors (alkynes), I delivered these compounds without thermal pre-treatment and achieved rapid CNT growth. This approach reduced carbonaceous emissions by more than an order of magnitude, and lowered initial feedstock requirements and energetic demands by at least 20%, without sacrificing CNT yield.

Description: National Science Foundation (NSF) Graduate Research Fellowship Program, NSF OCE-0221181, the Seaver Institute, the Martin Family Society of Fellows for Sustainability, Arunas and Pam Chesonis through MIT’s Earth System Initiative, and the WHOI 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 June 2009

Description: Trichodesmium spp. are considered the dominant nitrogen (N) fixing cyanobacteria in tropical and subtropical oceans, regimes frequently characterized by low iron (Fe). Limited information exists about what levels of Fe limit Trichodesmium N fixation. I developed a diagnostic for Fe limitation using quantitative reverse transcription PCR (qRT-PCR) of the Fe stress response gene isiB, which encodes for flavodoxin a non-Fe containing substitute for ferredoxin. I determined that high isiB gene expression corresponded to cell-specific reductions in N fixation rates in both phylogenetic clades of Trichodesmium grown on varying levels of Fe. Using these laboratory-determined thresholds, I assessed Fe limitation of Trichodesmium from the Sargasso Sea, equatorial Atlantic Ocean and Western Pacific Warm Pool in conjunction with other analytical measurements (N, phosphorus (P) and dissolved Fe (〈0.4μm filtered)). I found widespread Fe limitation in Trichodesmium from the Pacific Ocean and minimal expression in the North Atlantic Ocean. I also found an inverse correlation between isiB expression and dissolved Fe:P ratios in seawater and data suggesting that most dissolved Fe in seawater, including organic ligand-bound Fe, is available to Trichodesmium. These data support and refine previous model predictions and demonstrate, in situ, the importance of Fe to the marine N cycle.

Description: Henry Houghton Fund, the Center for BioInorganic Chemistry, the National Science Foundation (grants OCE- 0220945 and OCE-0623499), a National Defense Science and Engineering Graduate 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 June 2009

Description: My thesis covers two general circulation problems that involve the stability of largescale oceanic flows and the importance of non-local effects. The first problem examines the stability of meridional boundary currents, which are found on both sides of most ocean basins because of the presence of continents. A linear stability analysis of a meridional boundary current on the beta-plane is performed using a quasi-geostrophic model in order to determine the existence of radiating instabilities, a type of instability that propagates energy away from its origin region by exciting Rossby waves and can thus act as a source of eddy energy for the ocean interior. It is found that radiating instabilities are commonly found in both eastern and western boundary currents. However, there are some significant differences that make eastern boundary currents more interesting from a radiation point of view. They possess a larger number of radiating modes, characterized by horizontal wavenumbers which would make them appear like zonal jets as they propagate into the ocean interior. The second problem examines the circulation in a nonlinear thermally-forced two-layer quasi-geostrophic ocean. The only driving force for the circulation in the model is a cross-isopycnal flux parameterized as interface relaxation. This forcing is similar to the radiative damping used commonly in atmospheric models, except that it is applied to the ocean circulation in a closed basin and is meant to represent the large-scale thermal forcing acting on the oceans. It is found that in the strongly nonlinear regime a substantial, not directly thermally-driven barotropic circulation is generated. Its variability in the limit of weak bottom drag is dominated by high-frequency barotropic basin modes. It is demonstrated that the excitation of basin normal modes has significant consequences for the mean state of the system and its variability, conclusions that are likely to apply for any other system whose variability is dominated by basin modes, no matter the forcing. A linear stability analysis performed on a wind- and a thermally-forced double-gyre circulation reveals that under certain conditions the basin modes can arise from local instabilities of the flow.

Description: I was supported through a graduate research assistantship from the National Science Foundation Grant OCE-0423975 and the Woods Hole Oceanographic Institution 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 May 1984

Description: Part one of this thesis discusses the structure of the thermocline and the current pattern within a two-layer model. The corresponding flow field is explored as the amount of water in the upper layer is gradually reduced (or as the wind stress is gradually increased). In the model, when the amount of water in the upper layer is less than a first critical value, the lower layer outcrops near the middle of the western boundary. A dynamically consistent picture includes a whole loop of boundary currents, which surround the outcropping zone completely and have quite different structures. In addition to the boundary currents found in previous models, there is an isolated western boundary current (i.e. bounded on one side by the wall and on the other by a streamline along which the upper layer thickness vanishes), an internal boundary current and possibly isolated northern/southern boundary currents. Within the limitations of the two-layer model, the isolated western boundary current appears to represent the Labrador Current while the internal boundary current may represent the North Atlantic Current. A first baroclinic mode of water mass exchange occurs across the ZWCL (zero-wind-curl-line). When the amount of water in the upper layer is less than a second critical value, the upper layer separates from the eastern wall and becomes a warm water pool in the south-west corner of the basin. Under this warm water pool is the ventilated lower layer. The sea surface density distribution is not specified; it is determined from a consistent dynamical and mass balance. Implicit in this model is the assumption that advection dominates in the mixed layer. The subtropical gyre and the subpolar gyre combine asymmetrically with respect to the ZWCL. Chapter I discusses the case when the lower layer depth is infinite. Chapter II discusses the case when the lower layer depth is finite. In the Addendum the climatological meaning of this two-layer model is discussed. Part two of this thesis concerns the use of a continuously stratified model to represent the thermocline and current structures in subtropical/subpolar basins. The ideal fluid thermocline equation system Is a nonlinear, non-strict hyperbolic system. In an Addendum to Chapter III the mathematical properties of this equation system are studied and a proper way of formulating boundary value problems is discussed. Although the equations are not of standard type, so that no firm conclusions about the existence and uniqueness of solutions have been drawn, some possible approaches to properly posed boundary value problem are suggested. Chapter III presents some simple numerical solutions of the ideal fluid thermocline equation for a subtropical gyre and a subtropical/subpolar basin using one of these approaches. Our model predicts the continuous three dimensional thermocline and current structures in a continuously stratified wind-driven ocean. The upper surface density and Ekman pumping velocity are specified as input data; in addition, the functional form of the potential vorticity is specified. The present model emphasizes the idea that the ideal fluid thermocline model is incomplete. The potential vorticity distribution can not be determined within this idealized model. This suggests that the diffusion and upwelling/downwelling within the western boundary current and the outcropping zone in the north-west corner are important parts of the entire circulation system.

Description: This work was supported by NSF Grant 80-19260-0CE.

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 1984

Description: The principal objectives of the present study are: (1) to investigate sodium transport across the midgut as well as the hindgut of Callinectes sapidus and the functioning of these two regions of the gut in osmotic and ionic regulation of the animal, and (2) to elucidate the mechanism of glucose absorption across the midgut of C. sapidus and to assess its role in nutrient absorption. The transport processes across the gut tissues were studied with an in vitro perfusion technique. I demonstrated a net mucosal to serosal sodium transport across the midgut of C. sapidus. This net flux was within the same order of magnitude as the fluxes of isolated gut tissues of many other animal species. The flux displayed saturation kinetics and was ouabain-sensitive. The flux did not vary with environmental salinity, thus providing no evidence for an active regulatory role of the midgut in sodium balance. A reduction of passive permeability with salinity, however, was suggested. There was no measurable net sodium transport across the hindgut of the animal. The midgut of C. sapidus was also capable of net transmural glucose absorption. The net flux was considerably less than the fluxes reported in mammalian intestine. The unidirectional mucosal to serosal glucose flux was depressed by metabolic inhibitors, the absence of mucosal Na+, and the presence of mucosal phlorizin or serosal ouabain. The flux was also decreased by the presence of mucosal D-galactose, but not D-fructose or L-glucose. The net glucose flux followed Michaelis-Menten kinetics. The mucosal glucose uptake by the midgut was composed of two processes: a sodium-dependent, saturable component, and a sodium-indenpendent, non-saturable counterpart. The kinetic characteristics of the uptake suggest that the midgut does not play a major role in total nutrient absorption. Nutrients taken up by the midgut may be largely utilized to provide energy for other physiological functions served by this tissue. Thin layer chromatographic analyses showed that whereas most glucose appeared as phosphorylated forms upon entering the midgut, free glucose was translocated across the tissue. These results suggest that the mucosal and serosal membrane transport processes are coupled to phosphorylation-dephosphorylation mechanisms, respectively. An alternative hypothesis is the presence of a high-affinity glucose carrier in the serosal border of the midgut.

Description: This research was supported by the WHOI Ocean Industries Program, and the U.S. Department of Commerce, National Oceanic and Atmospheric Administration under Grant No. NA80-AA-D-0077 (R/P-B).

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 2009

Description: Trichodesmium is a colonial, N2-fixing cyanobacterium found in tropical oceans. Species of Trichodesmium are genetically similar but several species exist together in the same waters. In order to coexist, Trichodesmium spp. may occupy different niche spaces through differential utilization of resources such as nutrients and light, and through responses to physical characteristics such as temperature and turbulence. To investigate niche differentiation in Trichodesmium, I characterized cultured strains of Trichodesmium, identified and enumerated Trichodesmium clades in the field, and investigated P stress and N2 fixation in field populations. Species of Trichodesmium grouped into two clades based on sequences from 16S rDNA, the internal transcribed spacer (ITS), and the heterocyst differentiation gene hetR. Clade I contained Trichodesmium erythraeum and Trichodesmium contortum, and clade II contained Trichodesmium thiebautii, Trichodesmium tenue, Trichodesmium hildebrandtii, and Trichodesmium pelagicum. Each clade was morphologically diverse, but species within each clade had similar pigmentation. I developed a quantitative polymerase chain reaction (qPCR) method to distinguish between these two clades. In field populations of the Atlantic and Pacific Oceans, the qPCR method revealed that clade II Trichodesmium spp. were more prominent than clade I in the open ocean. Concentrations of Trichodesmium did not correlate with nutrient concentrations, but clade I had wider temperature and depth distributions than clade II. Temperature and light are physical characteristics that may define niche spaces for species of Trichodesmium. Clade I and II concentrations correlated with each other in the Pacific but not in the Atlantic, indicating that the two clades were limited by the same factors in the Pacific while different factors were limiting the abundance of the two clades in the Atlantic. Trichodesmium populations in the North Atlantic were more P stressed and had higher N2 fixation rates than populations in the western Pacific. While nutrient concentrations didn’t directly correlate with Trichodesmium concentrations, the contrasting nutrient regimes found in the Atlantic and Pacific Oceans might influence distributions of the two clades differently. Unraveling the differences among species of Trichodesmium begins to explain their coexistence and enables us to understand factors controlling global N2 fixation.

Description: National Science Foundation (NSF) Biocomplexity Program Grant (OCE-0323332); the Center for Microbial Oceanography Research and Education (C-MORE), an NSF Science and Technology Center (EF-0424599); the Woods Hole Oceanographic Institution (WHOI) Ocean Life Institute (OLI) grant to J. Waterbury, 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 2009.

Description: This thesis examines the nature of eddy-mean flow interactions in western boundary current jets and recirculation gyre dynamics from both theoretical and observational perspectives. It includes theoretical studies of eddy-mean flow interactions in idealized configurations relevant to western boundary current jet systems, namely (i) a study of the mechanism by which eddies generated from a localized forcing drive mean recirculation gyres through the process of nonlinear rectification; and (ii) a study of the role of eddies in the downstream evolution of a baroclinic jet subject to mixed instabilities. It also includes an observational analysis to characterize eddy-mean flow interactions in the Kuroshio Extension using data from the downstream location of maximum eddy kinetic energy in the jet. New insights are presented into a rectification mechanism by which eddies drive the recirculation gyres observed in western boundary current systems. Via this mechanism, eddies drive the recirculations by an up-gradient eddy potential vorticity flux inside a localized region of eddy activity. The effectiveness of the process depends on the properties of the energy radiation from the region, which in turn depends on the population of waves excited. In the zonally-evolving western boundary current jet, eddies also act to stabilize the unstable jet through down-gradient potential vorticity fluxes. In this configuration, the role of eddies depends critically on their downstream location relative to where the unstable time-mean jet first becomes stabilized by the eddy activity. The zonal advection of eddy activity from upstream of this location is fundamental to the mechanism permitting the eddies to drive the mean flows. Observational results are presented that provide the first clear evidence of a northern recirculation gyre in the Kuroshio Extension, as well as support for the hypothesis that the recirculations are, at least partially, eddy-driven. Support for the idealized studies’ relevance to the oceanic regime is provided both by indications that various model simplifications are appropriate to the observed system, as well as by demonstrated consistencies between model predictions and observational results in the downstream development of time-mean and eddy properties.

Description: Funding was for this research and my education was provided by the MIT Presidential Fellowship and NSF grants OCE-0220161 and OCE-0825550. The financial assistance of the Houghton Fund, the MIT Student Assistance Fund, and WHOI Academic Programs is also gratefully acknowledged.

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 2009

Description: To explore the ability of melting mafic lithologies to produce alkaline ocean-island basalts (OIB), an experimental study was carried out measuring clinopyroxene (Cpx)- melt and garnet (Gt)-melt partition coefficients during silica-poor garnet pyroxenite melting for a suite of trace elements, including U and Th, at 2.5GPa and 1420-1450°C. Partition coefficients range from 0.0083±0.0006 to 0.020±0.002 for Th and 0.0094±0.0006 to 0.024±0.002 for U in Cpx, and are 0.0032±0.0004 for Th and 0.013±0.002 for U in Gt. Forward-melting calculations using these experimental results to model time-dependent uranium-series isotopes do not support the presence of a fixed quantity of garnet pyroxenite in the source of OIB. To use U-series isotopes to further constrain mantle heterogeneity and the timing and nature of melting and melt transport processes, U-Th-Pa-Ra disequilibria, radiogenic isotopes, and trace-element compositions were measured for the slow-spreading Arctic mid-ocean ridges (MOR). A focused case study of 33 young (〈10ka) MOR basalts (MORB) from the shallow endmember of the global ridge system, the Kolbeinsey Ridge (67°05’-70°26’N) found that unaltered Kolbeinsey MORB have universally high (230Th/238U) (1.165-1.296) and relatively uniform (230Th/232Th) (1.196-1.324), εNd (8.43- 10.49), 87Sr/86Sr (0.70274-0.70301), εHf (16.59-19.56), and Pb isotopes (e.g. 208Pb/206Pb = 2.043-2.095). This suggests a homogeneous mantle source and a long peridotite melting column produces the thick Kolbeinsey crust. Trace element ratios suggest a young, depleted mantle source. Data from the slow- to ultraslow Mohns and Knipovich Ridges north of Kolbeinsey form a sloped array, and (230Th/232Th) correlates systematically with radiogenic isotopic variations. These data are readily reproduced by models for heterogeneous mantle melting. MORB from 85ºE on the global ultraslow-spreading endmember Gakkel Ridge are homogeneously depleted with low (230Th/238U) and high (226Ra/230Th) that lie along a global negative correlation. Arctic data support a global mantle temperature control on mean (230Th/238U).

Description: This work was made possible through funding support from the National Defense Science and Engineering Graduate Fellowship Program, from the Academic Programs Office, from the WHOI and MIT student travel assistance funds, and from National Science Foundation grant OCE-0422278 to K.W.W.S.

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 2009

Description: Marine cyanobacteria in the genus Synechococcus are widely distributed and contribute significantly to global primary productivity. In many parts of the ocean their growth is limited by a lack of iron, an essential nutrient that is virtually insoluble in seawater. To overcome this, Synechococcus have evolved a number of strategies to acquire iron. Gene distribution, metagenomics and a novel immunological flow cytometry assay in the Costa Rica Upwelling Dome were used to estimate the importance of Fe stress. Genomic and metagenomic measures suggest that iron limitation is, paradoxically, more severe in coastal and upwelling areas than in the open ocean, where iron is less abundant. A serological assay found significant differences in the vertical distribution of the Fe stress protein IdiA over just a few meters. Despite average surface ocean iron concentrations of just 0.07 nM, most marine oligotrophic cyanobacteria lack iron-binding siderophores that are present in many heterotrophic marine bacteria. Siderophores are widely distributed in the surface ocean and compose an important portion of the pool of natural ligands that bind 〉99% of all soluble Fe. In bottle incubations from the Sargasso Sea we found the addition of Fe complexed to an excess of the siderophore desferrioxamine B (DFB) limited Synechococcus growth and stimulated the growth of heterotrophic bacteria in a concentration dependent manner. Laboratory work revealed that excess DFB decreased Synechococcus growth beyond Fe-limited controls at concentrations as low as 20-40 nM. The inhibition was aggravated by light but it could be reversed by the addition of Fe. The DFB inhibition could not be explained by thermodynamic or kinetic models of Fe’ or co-limitation with other metals. DFB may interact with some aspect of cellular physiology to directly inhibit cyanobacterial growth.

Description: Funding for this research was provided by Grant NSF-OCE0352241 from the National Science Foundation to Eric A. Webb and grants 495 and 495.01 from the Gordon and Betty Moore Foundation, grants DE-F602-07ER64506 and DE-F602- 08ER64516 from the Department of Energy, and grant Z792093-02 (C-MORE) from the University of Hawaii, to Sallie W. Chisholm.

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 January 1982

Description: A comparison between predicted and measured damping controlled dynamic response of an operational single pile platform (AMOCO's South Marsh Island Block 33B platform) is presented. In the predictive analysis, a finite element model of the structure and a theoretical assessment of damping phenomena are combined with a response prediction method which utilizes the principle of reciprocity of ocean waves. The result is a versatile expression for the estimation of the dynamic response fatigue life of a platform in a directionally spread sea. In addition, the data analysis performed on wind, wave and response time histories, recorded in March, 1980, is carefully described. A method is presented which uses biaxial accelerometer data to infer platform modal orientations and to estimate wave spreading. Finally, modal natural frequencies and damping ratios are estimated using the Maximum Entropy Method (MEM) of spectral analysis. Good agreement between predicted and estimated response characteristics is attained.

Description: This research was sponsored by the Branch of Marine Oil and Gas Operations of the United States Geological Survey, Department of the Interior, and the Joint Program in Oceanographic Engineering between the Massachusetts Institute of Technology and 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 December 2001

Description: I used direct measurements of nitrogen gas (N2) fluxes and a 15N stable isotope tracer to determine the contribution of denitrification to salt marsh sediment N cycling. Denitrification in salt marsh tidal creekbottoms is a major sink for groundwater nitrate of terrestrial origin. I studied creekbottom denitrification by direct measurements of N2 fluxes in closed chambers against a low-N2 background. I undertook experiments and simulation modeling of sediment N2 fluxes in closed chambers to optimize the key experimental parameters of this approach. Denitrification in these sediments was driven by the degradation of labile organic matter pools which are depleted during long incubations. Sediment thickness was the most important parameter controlling the required incubation time. Errors of up to 13% with gas headspaces and 80% with water headspaces resulted from headspace N2 accumulation and the resulting collapse of the sediment-water diffusion gradient. These errors could be eliminated by using headspaces of sufficient thickness. Headspace flushing to reduce ammonium accumulation did not affect denitrification rates, but caused transient disturbance of N2 flux rates. Direct measurements of O2, CO2, N2, and inorganic N fluxes from the sediments of a salt marsh tidal creek were made in order to examine the interaction of denitrification with the carbon, oxygen, and N cycles. Organic carbon concentration and lability were the primary controls on metabolic rates. CO2/N flux ratios averaged 6.1, indicating respiration driven by algal biomass. Allochthonous denitrification accounted for 39% of total sediment denitrification (2.7 mol N m-2 yr-I). 46% of remineraIized ammonium was denitrified, while the contribution of autochthonous denitrification to O2 and CO2 fluxes was 18% and 10%, respectively. A 15N-ammonium tracer was used to study competition between plants and nitrifying bacteria for remineralized ammonium. In undisturbed sediments of Spartina alterniflora, plant uptake out-competed nitrification-denitrification, with plant uptake accounting for 66% of remineralized ammonium during the growing season. Under N fertilization (15.5 mol m-2 yr-1), both plant N uptake and denitrification increased, but denitrification dominated, accounting for 72% of the available N. When plant uptake was hydrologically suppressed, nitrification-denitrification was stimulated by the excess N, shifting the competitive balance toward denitrification.

Description: Financial support came through the generosity of the Education Department at WHOI, the Coastal Systems Group at the School for Marine Science and Technology, University of Massachusetts, the Reinhart Coastal Research Center, and the Biology Department at WHOI.

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 February 2001

Description: I study the exchange between a boundary current and flanking horizontal recirculations in a 'sliced-cylinder' rotating tank laboratory experiment. Two flow configurations are investigated: a single recirculation and a double, figure-8, recirculation. The latter case involves a hyperbolic point, while the former does not. I investigate the stirring and mixing under both steady and unsteady forcing. I quantify the mixing in each case using effective diffusivity, Keff, and a corollary effective length, Leff, as derived by Nakamura (1995, 1996). This approach involves diagnosing the geometric complexity of a tracer field. Geometric complexity is indicative of advective stirring. Because stirring creates high gradients, flows with high advective stirring also have high diffusion, and stronger overall mixing. I calculate effective length from images of dye in the tank and find much higher values of Leff in the unsteady hyperbolic cases than in the other cases. Slight unsteadiness in flows involving hyperbolic points gives rise to a chaotic advection mechanism known as 'lobe dynamics'. These lobes carry fluid in and out of the recirculations, acting as extremely effective stirring mechanisms. I demonstrate the existence of these exchange lobes in the unsteady hyperbolic (figure-8) flow. The velocity field in the tank is calculated utilizing particle image velocimetry (PIV) techniques and a time series U(t) demonstrates the (forced) unsteadiness in the flow. Images of dye in the tank show exchange lobes forming at this same forcing period, and caring fluid in and out of the recirculation. Based on the results of these experiments, I am able to confirm that, at least in this controlled environment, basic geometry has a profound effect on the mixing effectiveness of a recirculation. I demonstrate radically increased stirring and mixing in the unsteady hyperbolic flow as compared to steady flows and flows without hyperbolic points. Recirculations are ubiquitous in the world ocean; they occur on a variety of scales, in many different configurations, and at all depths. Some of these configurations involve hyperbolic points, while others do not. Chaotic advection via lobe exchange may be an important component of the mixing at multiple locations in the ocean where hyperbolic recirculation geometries exist.

Description: I am grateful for funding provided by a National Defense Science and Engineering Graduate Fellowship and for funding from ONR #N00014-99-1-0258 and NSF #OCE-9616949

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 1982

Description: The dynamics of steady and unsteady channel flow over large obstacles is studied analytically and numerically in an attempt to determine the applicability of classical hydraulic concepts to such flows. The study is motivated by a need to understand the influence of deep ocean straits and sills on the abyssal circulation. Three types of channel flow are considered: nonrotating one dimensional (Chapter 2); semigeostrophic, constant potential vorticity (Chapter 3); and dispersive, zero potential vorticity (Chapter 4). In each case the discussion centers around the time-dependent adjustment that occurs as a result of sudden obtrusion of an obstacle into a uniform initial flow or the oscillatory upstream forcing of a steady flow over topography. For nondispersive (nonrotating or semigeostrophic) flow, nonlinear adjustment to obstacle obtrusion is examined using a characteristic formulation and numerical results obtained from a Lax-Wendroff scheme. The adjustment process and asymptotic state are found to depend upon the height of the obstacle bO in relation to a critical height bc and a blocking height bb. For bO 〈 bc 〈 bb, isolated packets of nondispersive (long gravity or Kelvin) waves are generated which propagate away from the obstacle, leaving the far field unaffected. For bc 〈 bO 〈 bb, a bore is generated which moves upstream and partially blocks the flow. In the semigeostrophic case, the potential vorticity of the flow is changed by the bore at a rate proportional to the differential rate of energy dissipation along the line of breakage. For bb 〈 bO the flow is completely blocked. Dispersive results in the parameter range bO 〈 bc are obtained from a linear model of the adjustment that results from obstacle obtrusion into a uniform, rotating-channel flow. The results depend on the initial Froude number Fd (based on the Kelvin wave speed). The dispersive modes set up a decaying response about the obstacle if Fd 〈 1 and (possibly resonant) lee waves if Fd 〉 1. However, the far-field upstream response is found to depend on the behavior of the nondispersive Kelvin modes and is therefore nil. Nonlinear steady solutions to nondispersive flow are obtained through direct integration of the equations of motion. The characteristic formulation is used to evaluate the stability of various steady solutions with respect to small disturbances. Of the four types of steady solution, the one in which hydraulic control occurs is found to be the most stable. This is verified by numerical experiments in which the steady, controlled flow is perturbed by disturbances generated upstream. If the topography is complicated (contains more than sill, say), then controlled flows may become destabilized and oscillations may be excited near the topography. The transmission across the obstacle of energy associated with upstream-forced oscillations is studied using a reflection theory for small amplitude waves. The theory assumes quasi-steady flow over the obstacle and is accurate for waves long compared to the obstacle. For nonrotating flow, the reflection coefficients are bounded below by a value of 1/3. For semigeostrophic flow, however, the reflection coefficient can be arbitrarily small for large values of potential vorticity. This is explained as a result of the boundary-layer character of the semigeostrophic flow.

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 1982

Description: In an effort to understand the more general mechanisms and rates of pre-depositional reactions that transform organic matter, the types and relevant time scales of reactions that transform carotenoid pigments in the oceanic water column were studied. Suspended particulate matter collected from surface waters of Buzzards Bay, Massachusetts and the Peru upwelling system has a carotenoid distribution reflecting the phytoplanktonic source of the material. The carotenoid distribution of sediment trap samples collected in these same areas was dominated by transformation products. Fucoxanthin, the primary carotenoid of marine diatoms, typically constituted 77-100% of the total fucopigments in suspended particulate material. In sediment trap samples this pigment constituted only 4-85% of the total. The remaining 15-96% of the pigments consisted of the fucoxanthin transformations products: free alcohols (2-94%), dehydrates (0-6%), and opened epoxides (0-19%). Preliminary results suggest that carotenoid esters are hydrolyzed to free alcohols at a rate determined by the turnover of primary productivity. The dehydrated and epoxide opened intermediates of fucoxanthin represent products of transformation reactions that operate over much longer time scales (0.1-10 yrs). Dehydration and epoxide opening are not significant water column transformations, but are important in surface sediments.

Description: This research was supported by the Ocean Sciences Section, National Science Foundation grants OCE 79-25352 and OCE 81-18436, the Office of Naval Research Contract N00014-74-Co-262NR 083-004, the Woods Hole Coastal Research Center project 25 000067 04, and a Woods Hole Oceanographic Institution Student 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 May 1980

Description: This study of particulate matter in the water column and the underlying surface sediments verifies the occurrence of local, present-day resuspension in the deep sea. The location of the major portion of this work was the South Iceland Rise, a region influenced by the flow of Norwegian Sea Overflow Water. Measured current velocities exceeded 20 cm/sec in the axis of the bottom current for the duration of the deployments, approximately two weeks. Particulate matter was sampled with Niskin bottles, to obtain the standing crop of suspended matter and with sediment traps, to obtain the material in flux through the water column. Box cores were taken to obtain surface sediment samples for comparison with the trap samples. Suspended particulate matter (SPM) and light-scattering studies demonstrate that in the Iceland Rise area the correlation of the L-DGO nephelometer to concentration of SPM differs between clear water and the nepheloid layer. Correlations of light scattering to SPM concentration also differ regionally, but for predicting concentration from light scattering, regression lines at two locations are indistinguishable. Particle size distributions have lower variance in the nepheloid layer than those in clear water which have roughly equal volumes of material in logarithmically increasing size grades from 1-20 μm. Apparent density differences between SPM in clear water and the nepheloid layer are not distinguishable in the Iceland Rise study; apparent densities increase in the nepheloid layer in the western North Atlantic. An apparent density of 1.1 g/cm3 adequately separates clear water from nepheloid layer samples in this region. Compositional variations seen between clear water and the nepheloid layer include a decrease in small coccoliths and an increase in clays and mineral matter. These compositional variations are more dramatic in the western North Atlantic region, due to dissolution of carbonate at the seafloor, later resuspended into the nepheloid layer. Sedimentological evidence of resuspension and redistribution of material are: 1) presence of sediment drifts throughout the Iceland Basin; 2) occurrence of coarse, glacial age sediments beneath the axis of the bottom current; and 3) differences in mineralogy, carbonate and organic carbon contents between surface sediments beneath the bottom current and those in a channel. A comparison of the vertical flux of material measured by sediment traps at 500 meters above bottom (mab) with the accumulation rate in cores, shows that the present-day surface input is an order of magnitude smaller than the accumulation rate. This observation suggests transport of material into some sections of the region by bottom currents or by turbidity currents. The horizontal flux of particulate matter into and out of the region by the bottom current is 100 kg/sec. This material may contribute to the formation of Gardar sediment drift downstream. The trends in % CaC03 and % organic carbon through the water column and in the surface sediments suggest that dissolution of carbonate and decomposition and consumption of organic carbon occurs primarily at the seafloor. These data also suggest preferential preservation at channel stations and/or preferential erosion beneath the bottom current. A comparison of sediment-trap samples with box-core surface samples further supports present-day resuspension. Benthic foraminifera, iron-oxidicoated planktonic foraminifera and the glacial, subpolar planktonic foraminifera (Neogloboquadrina pachyderma (sinistral)) in traps at 10,100 and a few specimens at 500 mab, provide conclusive evidence for local resuspension. The coarse fraction (〉125 μm) of the sediment trap material collected at 10 mab comprises 21-34% of the samples Calculations indicate that this material is locally derived (few kilometers) resuspended material.

Description: This work was financially supported by the Woods Hole Oceanographic Institution, ONR through contracts N00014-79-C-00-7l NR 083-004, N00014-74-C0262 NR 083-004, and N00014-75-C-029l and ERDA through contracts 13-7923 and 13-2559.

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 2007.

Description: The water circulation and evolution of water temperature over the inner continental shelf are investigated using observations of water velocity, temperature, density, and bottom pressure; surface gravity waves; wind stress; and heat flux between the ocean and atmosphere during 2001-2007. When waves are small, cross-shelf wind stress is the dominant mechanism driving cross-shelf circulation. The along-shelf wind stress does not drive a substantial cross-shelf circulation. The response to a given wind stress is stronger in summer than winter. The cross-shelf transport in the surface layer during winter agrees with a two-dimensional, unstratified model. During large waves and onshore winds the cross-shelf velocity is nearly vertically uniform, because the wind- and wave-driven shears cancel. During large waves and offshore winds the velocity is strongly vertically sheared because the wind- and wave-driven shears have the same sign. The subtidal, depth-average cross-shelf momentum balance is a combination of geostrophic balance and a coastal set-up and set-down balance driven by the cross-shelf wind stress. The estimated wave radiation stress gradient is also large. The dominant along-shelf momentum balance is between the wind stress and pressure gradient, but the bottom stress, acceleration, Coriolis, Hasselmann wave stress, and nonlinear advection are not negligible. The fluctuating along-shelf pressure gradient is a local sea level response to wind forcing, not a remotely generated pressure gradient. In summer, the water is persistently cooled due to a mean upwelling circulation. The cross-shelf heat flux nearly balances the strong surface heating throughout midsummer, so the water temperature is almost constant. The along-shelf heat flux divergence is apparently small. In winter, the change in water temperature is closer to that expected due to the surface cooling. Heat transport due to surface gravity waves is substantial.

Description: My last three years of thesis work were supported by National Aeronautics and Space Administration Headquarters under the Earth System Science Fellowship Grant NNG04GQ14H, and by WHOI Academic Programs Fellowship Funds. I also benefited from the freedom of a Clare Boothe Luce Fellowship during my first year in the Joint Program, which allowed me more time than is usual to explore different research topics before choosing an advisor. This research was also funded by the National Aeronautics and Space Administration under grant NNG04GL03G and the Ocean Sciences Division of the National Science Foundation under grants OCE-0241292 and OCE-0548961. The Martha's Vineyard Coastal Observatory is partly funded by the Woods Hole Oceanographic Institution and the Jewett/EDUC/Harrison Foundation. The ADCP deployments at CBLAST site F were funded by National Science Foundation Small Grant for Exploratory Research OCE-0337892. Ship time for deployment and recovery of the F ADCP was provided by Robert Weller through Office of Naval Research contracts N00014-01-1-0029 and N00014-05-10090 for the Low-Wind Component of the Coupled Boundary Layers Air-Sea Transfer Experiment.

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 1976

Description: Analytical methods have been developed for the determination of iodate, iodide and particulate iodine in sea water. Iodate is converted to tri-iodide and the absorbance of tri-iodide at 353 nm is measured. The precision of this method is ca. ±3%. Iodide is first separated from most other anions by an AG 1-x8 anion exchange column and then precipitated as palladous iodide with elemental palladium as the carrier. The precipitate is analyzed by neutron activation analysis. The precision of the method is ±5% and the reagent blank is 0.005 uM. Marine suspended matter is collected by passing sea water under pressure through a 0.6 u (37 mm diameter) Nuclepore filter. The iodine content of the particles is determined by neutron activation analysis. The method has excellent reproducibility and the filter blank is ca. 3 ng. Iodate is depleted in the surface waters of the Equatorial Atlantic. The depletion is more pronounced than in the Argentine Basin and possibly reflects the higher productivity in the equatorial area. Superimposed on this feature, a thin lens of water, of a few tens of meters thick and with high iodate concentrations, can be traced across the Atlantic. Along the equator, this lens occurs at 80 m at 33˚W and rises upwards to 55 m at 10˚W and it coincides with a core of highly saline water which is characteristic of the Equatorial Undercurrent. Longitudinal sections reflect the complexity of the equatorial current system. At least three cores of water with high iodate concentrations may be identified. These waters may be transported to the equatorial region from the highly productive areas along the north-western and western African coasts and the Amazon plume. In anoxic basins, the concentration of iodide increases rapidly in the mixing zone from 0.02 uM to 0.44 uM in the Cariaco Trench and from 0.01 uM to 0.23 uM in the Black Sea. The iodate concentration, meanwhile. decreases to zero. A maximum in the total iodine to salinity ratio is observed just above the oxygen-sulfide interface (15 to 17 nmoles/g); it is suggestive of particle dissolution in a strong pycnocline. Below the interface, the total iodine to salinity ratio is constant at 12.3 nmoles/g in the anoxic zone of the Cariaco Trench, whereas, in the Black Sea, it increases with depth from 10.0 to 19.4 nmoles/g and suggests a possible flux of iodide from the sediments. By considering the distribution of iodate and iodide in oxic and anoxic basins and our present analytical capability, the lower limit of the pE of the oceans is estimated to be 10.7. Thermodynamic considerations further suggest that the iodide-iodate couple is a poor indica tor for the pE of the oceans with a limited usable range of 10.0 to 10.7. In the Gulf of Maine during the winter of 1974 to 1975. the effect of winter mixing was conspicuous. Uniform concentrations of iodide and iodate were observed in the mixed layer above the sill. The absence of a depletion of iodate and the low iodide concentration (0.04 uM) in the surface waters reflect the low biological activity in this region during winters. Profiles of particulate iodine are characterized by high concentrations in the euphotic zone (〉5 ng/kg), and lower concentrations (〈 2 ng/kg) at greater depths. Occasionally, high concentrations have also been observed in the nepheloid layer. The iodine-containing particles are probably biogenic. A section in the Western Atlantic from 75°N to 55˚S shows evidence of the transport of particles along isopycnals and the re-suspension of surface sediments to considerable distance from the bottom. The standing crops in the top 200 m may be qualitatively correlated with the primary productivity. Thermodynamic considerations show that iodide is a metastable form at the pH of sea water. Laboratory studies fail to show the oxidation of iodide at measurable rates. Elemental iodine is unstable in sea water and undergoes hydrolysis to form hypoiodous acid in seconds. Hypoiodous acid is also unstable and has a life time of minutes to hours. It may react with organic compounds to form iodinated derivatives or it may be reduced to iodide by a reducing agent. The disproportionation of hypoiodite to form iodate seems to be a slower process. A possible chemical cycle for iodine in the marine environment is proposed.

Description: This work was supported at various phases by NSF Grant GA-13574, NSF-IDOE Grant GX 33295, NSF Grant DES 74- 22292 and by a research fellowship 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 September 2007

Description: Present-day expeditionary oceanography is beginning to shift from a focus on short- term ship and submersible deployments to an ocean observatory mode where long- term temporally-focused studies are feasible. As a result, a critical need for in situ chemical sensors is evolving. New sensors take a significant amount of time to develop; thus, the evaluation of techniques in the laboratory for use in the ocean environment is becoming increasingly important. Laser-induced breakdown spectroscopy (LIBS) possesses many of the characteristics required for such in situ chemical sensing, and is a promising technique for field measurements in extreme environments. Although many LIBS researchers have focused their work on liquid jets or surfaces, little at- tention has been paid to bulk liquid analysis, and especially to the effect of oceanic pressures on LIBS signals. In this work, laboratory experiments validate the LIBS technique in a simulated deep ocean environment to pressures up to 2.76 × 107 Pa. A key focus of this work is the validation that select elements important for understand- ing hydrothermal vent fluid chemistry (Na, Ca, Mn, Mg, K, and Li) are detectable using LIBS. A data processing scheme that accurately deals with the extreme nature of laser-induced plasma formation was developed that allows for statistically accu- rate comparisons of spectra. The use of both single and double pulse LIBS for high pressure bulk aqueous solutions is explored and the system parameters needed for the detection of the key analytes are optimized. Using both single and double pulse LIBS, the limits of detection were found to be higher than expected as a result of the spectrometer used in this experimentation. However, the results of this validation show that LIBS possesses the characteristics to be a viable chemical sensing method for in situ analyte detection in high pressure environments like the deep ocean.

Description: National Science Foundation for support of this research under grants OCE0352278 and OCE0352242. Additional support was received from WHOI’s Deep Ocean Exploration Institute who awarded this research with two grants. The WHOI Ocean Ventures Fund and the Department of Defense

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 1993

Description: Dimethylsulfide (DMS) plays a central role in the transfer of sulfur from the ocean to the atmosphere, and ultimately to land. The most abundant volatile organosulfur compound in seawater, DMS is believed to account for the bulk of the sea-to-air biogenic sulfur flux. DMS has also been implicated as the major precursor of submicron-sized sulfate aerosol over the ocean. This aerosol acts as an effective site for cloud droplet condensation, suggesting a possibly important role for DMS in marine cloud formation. In the ocean, the precursor of DMS is presumed to be the zwitterionic sulfonium compound dimethylsulfoniopropionate (DMSP), a common osmoticum in certain classes of marine algae. While some algae can cleave DMSP intracellularly to form DMS, correlation of DMS concentrations with indicators of algal productivity on a local scale is poor. This thesis focuses on an alternative pathway of DMS formation: microbial cleavage of dissolved (extracellular) DMSP. In laboratory studies, bacteria able to cleave DMSP to form DMS were isolated from seawater by a DMSP enrichment technique, and the kinetics of DMSP uptake and DMS production were examined closely in pure cultures of a bacterial isolate from the Sargasso Sea. The isolate could grow with both DMSP and acrylic acid, one of the products of DMSP cleavage, as the sole source of carbon and energy, and the enzyme catalyzing DMSP cleavage appeared to be induced by both of these compounds. Kinetic parameters were estimated for DMSP uptake and cleavage by whole cells. Comparison of the 16S rRNA sequence of this isolate with that of known eubacteria showed that it was most closely related to Erythrobacter longus, an aerobic, bacteriochlorophyll-containing member of the α proteobacteria. DMS production from dissolved DMSP, along with microbial DMSP and DMS removal, was investigated in seawater incubation experiments with the goal of establishing turnover times for DMSP and DMS. These were determined to be on the order of days in both coastal (Vineyard Sound) and oligotrophic (Sargasso Sea) seawater. Loss of DMSP from the dissolved phase always occurred more rapidly than production of DMS; on average, microbial removal processes turned DMSP over on timescales of less than a day. This suggests that processes which do not result in DMS production, such as demethylation, may be important sinks for DMSP. Kinetic parameters for DMSP uptake and DMS production varied, possibly as a function of season. However, more data are needed to assess the seasonal dependence of this process. These results imply that microbial production of DMS from dissolved DMSP is likely to be a quantitatively significant mode of DMS formation in both coastal and oligotrophic marine environments. Timescales of DMS turnover with respect to this process are comparable to published estimates of DMS turnover times due to biological consumption, indicating that coupling between these two microbially-mediated processes may constitute an important control on oceanic DMS levels.

Description: Financial support for this work was provided by the NASA Graduate Student Researchers Program (NGT-50456), NASA (NAGW-606), NSF (OCE-902532), the Ocean Ventures 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 September 2007

Description: This thesis covers a comprehensive analysis of long-range, deep-ocean, low-frequency, sound propagation experimental results obtained from the North Pacific Ocean. The statistics of acoustic fields after propagation through internal-wave-induced sound-speed fluctuations are explored experimentally and theoretically. The thesis starts with the investigation of the North Pacific Acoustic Laboratory 98-99 data by exploring the space-time scales of ocean sound speed variability and the contributions from different frequency bands. The validity of the Garret & Munk internal-wave model is checked in the upper ocean of the eastern North Pacific. All these results impose hard bounds on the strength and characteristic scales of sound speed fluctuations one might expect in this region of the North Pacific for both internal-wave band fluctuations and mesoscale band fluctuations. The thesis then presents a detailed analysis of the low frequency, broadband sound arrivals obtained in the North Pacific Ocean. The observed acoustic variability is compared with acoustic predictions based on the weak fluctuation theory of Rytov, and direct parabolic equation Monte Carlo simulations. The comparisons show that a resonance condition exists between the local acoustic ray and the internal wave field such that only the internal-waves whose crests are parallel to the local ray path will contribute to acoustic scattering: This effect leads to an important filtering of the acoustic spectra relative to the internal-wave spectra. We believe that this is the first observational evidence for the acoustic ray and internal wave resonance. Finally, the thesis examined the evolution with distance, of the acoustic arrival pattern of the off-axis sound source transmissions in the Long-range Ocean Acoustic Propagation EXperiment. The observations of mean intensity time-fronts are compared to the deterministic ray, parabolic equation (with/without internal waves) and (one-way coupled) normal mode calculations. It is found the diffraction effect is dominant in the shorter-range transmission. In the longer range, the (internal wave) scattering effect smears the energy in both the spatial and temporal scales and thus has a dominant role in the finale region.

Description: The funding that made this research possible came from the Office of Naval Research, 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 November 1980

Description: Plankton samples have been carefully collected from a variety of marine environments under the rigorous conditions necessary to prevent contamination for major and trace-chemical analysis. Immediately after collection, the samples were subjected to a series of physical and chemical leaching-decomposition experiments designed to identify the major and trace element composition of particulate carrier phases. Elements examined through some or all of these experiments were: C, N, P, Mg, Ca, Si, Fe, Mn, Ni, Cu, Cd, Al, Ba, and Zn. Emphasis was placed on the identification of trace element/major element ratios in the biogenic materials. The majority of the trace elements in the samples were directly associated with the non-skeletal organic phases of the plankton. These associations included a very labile fraction which was rapidly released into seawater and a more refractory fraction which involved specific metal-organic binding. Calcium carbonate and opal were not significant carriers for any of the trace elements studied. A refractory phase containing Al and Fe in terrigenous ratios was present in all samples, even from the more remote marine locations. The concentration of this carrier phase within the plankton samples varied in proportion to the estimated rate of supply of terrigenous matter and in opposition to the rate of production of the biogenic particulate matter. The aluminosilicates contributed insignificant amounts to the other trace elements studied. A trace concentration of particulate Al was identified which was more labile and associated with the organic fractions of the samples. Variations in the surface water concentrations of dissolved Cu, Ni, Cd, and Zn with respect to P are compared to the ratios measured in the plankton samples and their regeneration products. The trace element/major element ratios ,in the residual plankton materials can be combined with estimates of the carrier fluxes to account for the transport of trace elements required to maintain their deep enrichment. A variety of processes determining the geochemical cycles of specific trace elements were identified. As much as 50% of the Cd, Ni, Mn, and P are rapidly released from plankton and recycled within the surface ocean. During this process, the metal/P ratio in the residual particles must decrease by 10-30% for Cd and increase by a factor of 2-4 for Ni and Cu to balance their deep enrichments. Although Mn is taken up and regenerated by plankton, the magnitude of this process is small with respect to other non-biogenic Mn fluxes and has very little influence on its dissolved distribution. The Ba content of all known surface carriers is insufficient to account for the deep enrichment of Ba. A secondary concentration process results in the formation of significant particulate Ba within the upper thermocline.

Description: Portions of the data in this research have been collected under the NSF grant DES 75-03826 and ONR grant N00014-80-C-0273. I have been supported for the last three years on an NSF National Needs Graduate Traineeship to the MIT-WHOI Joint Program. Ship time was generously provided by various principal investigators of the NSF Galapagos Hydrothermal research program and the NSF-IDOE MANOP program.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Philosophy and the Woods Hole Oceanographic Institution November 1980

Description: Suspended particulate matter was collected by sediment traps deployed in the Sargasso Sea (Site S2), the north equatorial Atlantic (Site E), the north equatorial Pacific (Site P), and the Panama Basin (STIE Site). Additional samples of suspended particles were obtained by in situ filtration at Site F., at the STIE Site, and in the Guatemala Basin. Concentrations of dissolved Th and Pa were determined by extraction onto manganese dioxide adsorbers at Site P, at a second site in the Sargasso Sea (Site D), at the STIE Site and in the Guatemala Basin. Sediment samples were obtained from cores taken near Sites E and P. Results have shown unequivocally that suspended particulate matter in the open ocean preferentially scavenges Th relative to Pa. This behavior could not have been predicted from the known physical chemistry of Th and Pa. Dissolved 230Th/231Pa activity ratios were 3-5 at Sites P and D and 3-8 at the STIE Site. In contrast, unsupported 230Th/231Pa ratios were 22-35 (average 29.7 for 7 samples) in sediment-trap samples from greater than 2000 m at Sites S2, E and P. Ratios were lower in particulate matter sampled at shallower depths. Particles filtered at 3600 m and 5000 m at Site E had ratios of 50 and 40. In contrast to the open ocean samples described above, samples collected by six sediment traps at depths of 667-3791 m in the Panama Basin had unsupported 230Th/231Pa ratios of 4-8, and the deepest samples had the lowest ratios. Fractionation of Th and Pa that was observed at the three open ocean sites either does not occur or occurs to a very limited extent in the Panama Basin. Particulate 230Th/231Pa ratios were negatively correlated with the concentration of suspended particles. However, variable scavenging rates, as indicated by variable particle concentration, do not completely control the ratio at which Th and Pa are scavenged from solution. Major biogenic and inorganic components of trapped material were found in approximately the same proportions in the STIE samples and in samples from Sites E and S2. Lower 230Th/231Pa ratios found in the STIE samples must therefore result from subtle changes in the chemical properties of the particles. Consideration of 230Th/23lPa ratios in several depositional environments indicates that no single factor controls the ratio at which Th and Pa are adsorbed from seawater. Fluxes of 210Th and 231Pa were less than their rates of production in the overlying water column in every trap at Sites S2, E, and P. In the Panama Basin, fluxes measured with the same traps were greater than or equal to their rates of production. These results are a strong indication that even extremely reactive elements such as Th and Pa are redistributed within the oceans. Redistribution occurs because variable scavenging rates in different environments set up horizontal concentration gradients. Horizontal mixing processes produce a net horizontal transport of Th and Pa from areas of 1ow scavenging rates to areas of high scavenging rates. Protactinium is redistributed to a greater extent than Th. Fluxes of 230Th can be used to set lower limits for horizonttal transport of Pa even when absolute trapping efficiencies of the sediment traps are not known. Less than 50% of the Pa produced at the open ocean sites is removed from the water column by scavenging to settling particles. The remainder is removed by horizontal transport to other environments. At Sites E and P, 230Th/231Pa ratios were identical in the deepest sediment trap sample and in surface sediments. However, 230Th/232Th and 231Pa/232Th ratios were 2.5 times higher in trapped particles than in surface sediments. The 230Th/232Th ratios were 5.5 times higher in particles filtered at 3600 m and 5000 m at Site E than in surface sediments. This observation is best explained by dissolution of most of the 230Th and 231Pa scavenged by settling particles during remineralization of labile biogenic phases. The behaviors of certain other radioisotopes were also studied. 232Th is present only in detrital mineral components of trapped material. Concentrations of 232Th in trapped particles correlate closely with Al and K, at ratios approaching that of average shale or crustal abundances at Site E and P and basalts at the STIE Site. High specifìc activities of 228Th and 239+240Pu were found in sediment trap samples throughout the water column at Sites E and P and in the Panama Basin. The dominant source of these isotopes is near the sea surface and also near the sea floor in the case of 228Th. Thus it appears that the bulk of the trapped material is recently derived from the sea surface where it incorporates these isotopes,with little loss during rapid transit through the water column. A bioauthigenic form of particulate uranium is produced at the sea surface and remineralized in the deep ocean along with its labile carrier phase(s). This flux of uranium to the deep ocean is 0.25-1.0 dpm/cm2103 years, which is insufficient to cause a measurable concentration gradient in the uranium distribution within the mixing time of the oceans. Increased concentrations and fluxes of particulate uranium were not found in the eastern equatorial North Pacific under areas of an intense oxygen minimum. Therefore, reduction of uranium to the tetravalent state with subsequent scavenging to settling particles in oxygen minima is not a mechanism removing uranium from the oceans.

Description: Financial support for parts of this work have come from many sources, including: National Science Foundation Grants OCE-7826318, OCE-7825724, and OCE-7727004; Department of Energy Contract EY-76-S-02-3566; a Cottrell Research Grant from the Research Corporation; the WHOI Ocean Industries Program; a fellowship from the WHOI Education Office, and the Paul Fye Fellowship

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 May 1982

Description: Seismic refraction experiments have been used extensively in the past thirty five years in investigations of the structure of the oceanic crust. The longer range of the refraction or wide angle reflection technique, on the order of tens of kilometers, permits a deeper and wider area of examination, although with less resolution, than the spatially limited seismic reflection experiment. Observations of arrivals from the Mohorovicic discontinuity, at an average depth of seven kilometers below the sea floor, are routinely made. The major focus in interpreting refraction data has been the analysis of travel time/range data and the "inversion" of this data for the purpose of determining a velocity versus depth profile of the crust. The most frequent application of this procedure is the geophysicist's use of velocities for postulating geologic structures and rock types below the sediment (Christensen & Salisbury, 1975). Another area using refraction data, less widely seen, falls into the ocean acoustician's domain. In studying the behaviour of sound in the ocean, the sea floor is often modelled as a boundary with a half space below, and with some form of reflection characteristic and/or loss mechanism. If acoustic energy, upon encountering the bottom, was either reflected or transmitted directly, this would be appropriate, and the determination of reflection and transmission coefficients for the sea-sediment interface would probably be sufficient. However, sound energy does penetrate beneath the sea floor and is both reflected and refracted back to the water. In an active acoustical experiment, especially at longer ranges, a significant amount of the received energy may come from waves that have interacted with the earth's crust and have been reinjected into the water. Since these arrivals can be detected in the ocean, their study is of concern for the acoustician. The role of bottom interaction, especially at low frequencies, is now an area of intense research activity in modelling acoustic propagation. In particular, in the language of the sonar engineer, the TL, or transmission loss, of this energy is of major importance for i) predicting the character of the sound field at a receiver in future experiments, ii) for comparing crustal loss with the better known TL of paths remaining primarily in the water layer, and iii) expanding the role of arrival amplitudes in inversion theory. Just as there may be a number of possib1e paths in the sea between a source and receiver, each with a different loss characteristic, trajectories in the crust are variegated and exhibit different TL behaviors. It is important to be able to differentiate the energy partitioned among the different paths, and to determine which paths are most important. Resolving the locus of a particular acoustic path is intimately tied to the problem of determining the velocity structure of a medium. To the limits of the geometrical optics approximation of acoustic behaviour, sometimes sorely pressed at low frequencies, a completely detailed knowledge of sound speed variations, both laterally and with depth, plus known source characteristics and attenuation losses in the medium, enables one in principle to predict signals observed at a receiver. For an ocean acoustician, the requirement of environmental knowledge of the sound speed profiles, both in water and crust, needed to predict the amplitude and timing of data, is clearly very burdensome. In the past twenty five years, however, models of the oceanic crust have been formulated which are statistically consistent over much of the oceans. These models divide the crust into three or more horizontal layers with certain average thicknesses and velocities (Raitt, 1963). At least within the confines of these models, if a typical transmission loss were known for each of these layers, an acoustician can make predictions of the expected strength and timing of crustal arrivals at other stations. Most of this environmental information has been obtained from refraction and/or wide angle reflection data, usually via travel time analysis. Little has been done in developing models accounting for amplitude dependence.

Description: This work was supported under ONR contract N-00014-75-C-0852.

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 2008

Description: The subtidal circulation of the southeast Greenland shelf is described using a set of highresolution hydrographic and velocity transects occupied in summer 2004. The main feature present is the East Greenland Coastal Current (EGCC), a low-salinity, highvelocity jet with a wedge-shaped hydrographic structure characteristic of other surface buoyancy-driven currents. The EGCC was observed along the entire Greenland shelf south of Denmark Strait, while the transect north of the strait showed only a weak shelf flow. This observation, combined with evidence from chemical tracer measurements that imply the EGCC contains a significant Pacific Water signal, suggests that the EGCC is an inner branch of the polar-origin East Greenland Current (EGC). A set of idealized laboratory experiments on the interaction of a buoyant current with a submarine canyon also supported this hypothesis, showing that for the observed range of oceanic parameters, a buoyant current such as the EGC could exhibit both flow across the canyon mouth or into the canyon itself, setting the stage for EGCC formation. Repeat sections occupied at Cape Farewell between 1997 and 2004 show that the alongshelf wind stress can also have a strong influence on the structure and strength of the EGCC and EGC on timescales of 2-3 days. Accounting for the wind-induced effects, the volume transport of the combined EGC/EGCC system is found to be roughly constant (~2 Sv) over the study domain, from 68°N to Cape Farewell near 60°N. The corresponding freshwater transport increases by roughly 60% over this distance (59 to 96 mSv, referenced to a salinity of 34.8). This trend is explained by constructing a simple freshwater budget of the EGCC/EGC system that accounts for meltwater runoff, melting sea-ice and icebergs, and net precipitation minus evaporation. Variability on interannual timescales is examined by calculating the Pacific Water content in the EGC/EGCC from 1984-2004 in the vicinity of Denmark Strait. The PW content is found to correlate significantly with the Arctic Oscillation index, lagged by 9 years, suggesting that the Arctic Ocean circulation patterns bring varying amounts of Pacific Water to the North Atlantic via the EGC/EGCC.

Description: Funding for the cruise and analysis was provided by National Science Foundation grant OCE-0450658, which along with NSF grant OCE- 0095427 provided funds for my tuition and stipend as well.

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 February 2008

Description: I build on the deterministic phytoplankton growth model of Sosik et al. by introducing process error, which simulates real variation in population growth and inaccuracies in the structure of the matrix model. Adding a stochastic component allows me to use maximum likelihood methods of parameter estimation. I lay out the method used to calculate parameter estimates, confidence intervals, and estimated population growth rates, then use a simplified three-stage model to test the efficacy of this method with simulated observations. I repeat similar tests with the full model based on Sosik et al., then test this model with a set of data from a laboratory culture whose population growth rate was independently determined. In general, the parameter estimates I obtain for simulated data are better the lower the levels of stochasticity. Despite large confidence intervals around some model parameter estimates, the estimated population growth rates have relatively small confidence intervals. The parameter estimates I obtained for the laboratory data fell in a region of the parameter space that in general contains parameter sets that are difficult to estimate, although the estimated population growth rate was close to the independently determined value.

Description: My research was supported by MIT, the Woods Hole Oceanographic Institution, and a grant from the National Science Foundation (OCE-0530830).

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 2003

Description: In this thesis I have endeavored to determine the factors and physical processes that controlled SST and thermocline depth at 10°N, 125°W during the Pan American Climate Study (PACS) field program. Analysis based on the PACS data set, TOPEX/Poseidon sea surface height data, European Remote Sensing satellite wind data, and model simulations and experiments reveals that the dominant mechanisms affecting the thermocline depth and SST at the mooring site during the measurement period were local surface fluxes, Ekman pumping, and vertical mixing associated with enhancement of the vertical shear by strong near-inertial waves in the upper ocean superimposed upon intra-seasonal baroclinic Rossby waves and the large scale zonal flow.

Description: This work was funded under NOAA Grant NA17RJ1223 and I also gratefully acknowledge receipt of an MIT Presidential Fellowship in 2000-2001.

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 2003

Description: The incidence and known distribution of paralytic shellfish poisoning (PSP) have both increased dramatically in recent decades. A concurrent rise in bloom frequency and geographic range of PSP toxin-producing Alexandrium dinoflagellates explains the increase in PSP, but the reasons for changes in Alexandrium occurrence are unknown. This thesis explores the phylogeny, taxonomy, and biogeography of Alexandrium in light of this recent expansion. Alexandrium phylogeny was reconstructed through rDNA sequence analysis and compared to traditional morphological taxonomy. Alexandrium split into two groups, termed the α and ß clades. Interspecific relationships did not correlate with the morphological traits traditionally used to identify and group species, although other traits appeared phylogenetic ally conserved. The ability to produce toxins has been acquired and/or lost multiple times during Alexandrium evolution. Because most PSP events are caused by either the tamarensis or minutum complexes, the phylogeny, species definitions, and biogeography of each complex was examined. The morphospecies of the tamarensis complex, A. catenella, A. tamarense, and A. fundyense, did not represent valid species by the phylogenetic, biologic or morphological species concepts. Instead, five cryptic species were identified through phylogeny and mating incompatibility. A. universa and A. toxipotens contain all toxic strains, while A. mediterra, A. tamarensis and A. tasmanense contain only non-toxic isolates. Within the minutum group, A. lusitanicum and A. angustitabulatum were also not distinct species based on morphology and phylogeny while A. insuetum and A. tamutum were clearly distinct. Three new minutum group species were identified on the basis of morphology, phylogeny and prior research. Unlike the pattern found for the tamarensis complex, toxic and non-toxic A. minutum strains cannot be segregated based upon LSU sequences. The reconstructed biogeography of the tamarensis and minutum complexes indicate that both natural dispersal and human-assisted transportation of Alexandrium have caused the geographic spread. Human-assisted transport of toxic A. catenella-type cells from Asia to the Thau Lagoon, France, was demonstrated in chapter iv. This thesis demonstrates the importance of human action in the recent PSP increase, better defines species boundaries and provides an invaluable genetic database for tracking future Alexandrium spread and distinguishing between harmful and non-toxic Alexandrium blooms.

Description: Financial support was provided by the Woods Hole Oceanographic Institution, the MIT-WHOI Joint Program, a NSF doctoral fellowship, NOAA Grants No. NA960P0099, NA160P1438, NSF Grants No. OCE-9808173, OCE-9415536 and supported by the U.S. ECOHAB Program sponsored by NOAA, the U.S. EP A, NSF, NASA and ONR.

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 2003

Description: The cosmogenic radionuclide 10Be is a unique tracer of shallow sediment subduction in volcanic arcs. The range in 10Be enrichment in the Central American Volcanic Arc between Guatemala and Costa Rica is not controlled by variations in 10Be concentrations in subducting sediment seaward of the Middle America Trench. Sedimentary 10Be is correlated negatively with 143Nd/144Nd, illustrating that 10Be concentrations varied both between and within cores due to mixing between terrigenous clay and volcanic ash endmember components. This mixing behavior was determined to be a function of grain size controls on 10Be concentrations. A negative correlation of bulk sedimentary 10Be concentrations with median grain size and a positive correlation with the proportion of the sediment grains that were 〈32 μm in diameter demonstrated that high concentrations of 10Be in fine-grained, terrigenous sediments were diluted by larger grained volcanogenic material. The sharp decrease in 10Be enrichment in the Central American Volcanic Arc between southeastern Nicaragua and northwestern Costa Rica correlates with changes in fault structure in the subducting Cocos plate. Offshore of Nicaragua, extensional faults associated with plate bending have throw equal to or greater than the overlying subducting sediment thickness. These faults enable efficient subduction of the entire sediment package by preventing relocation of the décollement within the downgoing sediments. Offshore of Costa Rica, the reduction of fault relief results in basement faults that do not penetrate the overlying sediment. A conceptual model is proposed in which the absence of significant basement roughness allows the décollement to descend into the subducting sediment column, leading to subsequent underplating and therefore removal of the bulk of the sediment layer that contains 10Be. Basement fault relief was linearly related to plate curvature and trench depth. The systematic shoaling of the plate from southeastern Nicaragua to northwestern Costa Rica is not explained by changes in plate age for this region. Instead, it is hypothesized that the flexural shape of the plate offshore of southeastern Nicaragua and northwestern Costa Rica represents a lateral response to a buoyant load caused by the thick crust and elevated thermal regime in the Cocos plate offshore of southeastern Costa Rica.

Description: Funding for this work was provided by the National Science Foundation Graduate Research Fellowship, the WHOI Ocean Ventures Fund, the WHOI Deep Ocean Institute Graduate Fellowship, and Geological Society of America Graduate Research Grant #7179-02.

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 2003

Description: Groundwater discharge into estuaries and the coastal ocean is an important mechanism for the transport of dissolved chemical species to coastal waters. Because many dissolved species are present in groundwater in concentrations that are orders of magnitude higher than typical river concentrations, groundwater-borne nutrients and pollutants can have a substantial impact on the chemistry and biology of estuaries and the coastal ocean. However, direct fluxes of groundwater into the coastal ocean (submarine groundwater discharge, or SGD) can be difficult to quantify. Geochemical tracers of groundwater discharge can reflect the cumulative SGD flux from numerous small, widely dispersed, and perhaps ephemeral sources such as springs, seeps, and diffuse discharge. The natural radiocarbon content (Δ14C) of dissolved inorganic carbon (DIC) was developed as a tracer of fresh, terrestrially driven fluxes from confined aquifers. This Δ14C method was tested during five sampling periods from November 1999 to April 2002 in two small estuaries in southeastern North Carolina. In coastal North Carolina, fresh water artesian discharge is characterized by a low Δ14C signature acquired from the carbonate aquifer rock. Mixing models were used to evaluate the inputs from potential sources of DIC-Δ14C to each estuary, including seawater, springs, fresh water stream inputs, and salt marsh respiration DIC additions. These calculations showed that artesian discharge dominated the total fresh water input to these estuaries during nearly all sampling periods. These new Δ14C-based SGD estimates were compared with groundwater flux estimates derived from radium isotopes and from radon-222. It is clear that these tracers reflect different components of the total SGD. The fluxes of low-Δ14C and of 222Rn were dominated by artesian discharge. Estuarine 226Ra showed strong artesian influence, but also reflected the salt water SGD processes that controlled the other three radium isotopes. The flux of 228Ra seemed to reflect seepage from the terrestrial surficial aquifer as well as salt water recirculation through estuarine sediments. The fluxes of 224Ra and 223Ra were dominated by salt water recirculation through salt marsh sediments. This multi-tracer approach provides a comprehensive assessment of the various components contributing to the total SGD.

Description: This work was funded by grants from the Rinehart Coastal Research Center/Coastal Ocean Institute at WHOI (RCRC/COI Awards 25035057, 27040014 and 27040048), WHOI SeaGrant Project R/-47, the National Ocean Sciences Accelerator Mass Spectrometer at WHOI, and the WHOI Academic Programs Office and its 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 June 2003

Description: This thesis examines the evolution of a mud-dominated coastal sedimentary system on multiple time scales. Fine-grained systems exhibit different properties and behavior from sandy coasts, and have received relatively little research attention to date. Evidence is presented for shoreline accretion under energetic conditions associated with storms and winter cold fronts. The identification of energetic events as agents of coastal accretion stands in contrast to the traditional assumption that low-energy conditions are required for deposition of fine-grained sediment. Mudflat accretion is proposed to depend upon the presence of an unconsolidated mud sea floor immediately offshore, proximity to a fluvial sediment source, onshore winds, which generate waves that resuspend sediment and advect it shoreward, and a low tidal range. This study constrains the present influence of the Atchafalaya River on stratigraphic evolution of the inner continental shelf in western Louisiana. Sedimentary and acoustic data are used to identify the western limit of the distal Atchafalaya prodelta and to estimate the proportion of Atchafalaya River sediment that accumulates on the inner shelf seaward of Louisiana's chenier plain coast. The results demonstrate a link between sedimentary facies distribution on the inner shelf and patterns of accretion and shoreline retreat on the chenier plain coast.

Description: Among my funding sources was a two-year fellowship from the Clare Booth Luce Foundation. I have received research grants from the Geological Society of America Foundation (Grant 6873-01) and the American Association of Petroleum Geologists (Kenneth H. Crandall Memorial grant).

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 2003

Description: The presence of aqueous organic compounds derived from sedimentary organic matter has the potential to influence a range of chemical processes in hydrothermal vent environments. For example, hydrothermal alteration experiments indicate that alteration of organic-rich sediments leads to up to an order of magnitude more metals in solution than alteration of organic-poor basalt. This result is in contrast to traditional models for the evolution of vent fluids at sediment-covered mid-ocean ridge axis environments, and indicates the fundamental importance of including the effects of organic compounds in models of crustal alteration processes. However, in order to rigorously constrain their role in crustal alteration processes, quantitative information on the abundances and distributions of organic compounds in hydrothermal vent fluids is required. This thesis was undertaken to provide quantitative information on the distributions and stable carbon isotopic compositions of several low-molecular weight organic compounds (C1-C4 alkanes, C2-C3 alkenes, benzene and toluene) in fluids collected in July, 2000, at three sites on the northern Juan de Fuca Ridge: the Dead Dog and ODP Mound fields, which are located at Middle Valley, and the Main Endeavour Field, located on the Endeavour segment. At Middle Valley, the ridge axis is covered by up to 1.5 km of hemipelagic sediment containing up to 0.5 wt.% organic carbon. The Main Endeavour Field (MEF) is located approximately 70 km south of Middle Valley in a sediment-free ridge-crest environment, but previously measured high concentrations of NH3 and isotopically light CH4 relative to other bare-rock sites suggest that the chemical composition of these fluids is affected by sub-seafloor alteration of sedimentary material (LILLEY et al., 1993). Differences in the absolute and relative concentrations of NH3 and organic compounds and the stable carbon isotopic compositions of the C1-C3 organic compounds suggest that the three fields represent a continuum in terms of the extent of secondary alteration of the aqueous organic compounds, with the Dead Dog fluids the least altered, the MEF fluids the most altered and ODP Mound fluids in an intermediate state. At the two Middle Valley sites, the greater extent of alteration in the ODP Mound fluids as compared to the Dead Dog fluids is due either to higher temperatures in the subsurface reaction zone, or a greater residence time of the fluids at high temperatures. Higher reaction zone temperatures at the ODP Mound field than at the Dead Dog field are consistent with differences in endmember C1 concentrations between the two fields. The greater extent of alteration in the MEF fluids is caused by relatively oxidizing conditions in the subsurface reaction zone that promote faster reaction kinetics. Temperatures in the subsurface reaction zones calculated by assuming equilibrium among aqueous alkanes, alkenes and hydrogen are consistent with other inorganic indicators (C1 and Si concentrations) of temperature, indicating that metastable equilibrium among these compounds may be attained in natural systems. Isotopic equilibration among CH4 and CO2 appears to have been attained in ODP Mound fluids due to the high temperatures in the subsurface reaction zone and the approach to chemical equilibrium from excess methane. However, isotopic equilibrium between CH4 and CO2 was not attained in the MEF fluids, due to a short residence time of the fluids in the crust following late-stage addition of magmatic-derived CO2 to the fluids. Time series analysis indicate that Middle Valley fluid compositions are generally characterized by stable concentrations over the last decade. However, decreases in Br concentrations in Dead Dog fluids from 1990 to 2000 suggest that either a greater proportion of the fluids interact with basalt rather than sediments or that the sediment with which hydrothermal fluids interact is becoming exhausted. In contrast, the concentrations of H2 and H2S and the δ34S of H2S are quite different in fluids sampled from vents of differing ages at the ODP Mound field, despite their close spatial proximity. The observed variations are caused by the reaction of hydrogen-rich fluids within the ODP Mound massive sulfide to reduce pyrite to pyrrhotite during upflow. The replacement of pyrite by pyrrhotite is opposite to the reaction predicted during the weathering of sulfide minerals weather on the seafloor and reflects the real-time equilibration of the reduced fluids with mound mineralogy due to the very young age (〈2 years) venting from Spire vent. The presence of aqueous organic compounds therefore affects not only the inorganic chemical speciation in vent fluids, but can also control the mineralogy of associated sulfide deposits. These results also indicate that vent fluid compositions do not necessarily reflect conditions in the deep subsurface, but can be altered by reactions occurring in the shallow subsurface.

Description: This research was supported by grants to Jeffrey Seewald from the Petroleum Research Fund (323lO-AC2), administered by the American Chemical Society, the National Science Foundation (OCE-9618179, OCE-9906752, OCE-0136954) and the WHOI Green Technology 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 2003

Description: Inertial terms dominate the single-gyre ocean model and prevent western-intensification when the viscosity is small. This occurs long before the oceanically-appropriate parameter range. It is demonstrated here that the circulation is controlled if a mechanism for ultimate removal of vorticity exists, even if it is active only in a narrow region near the boundary. Vorticity removal is modeled here as a viscosity enhanced very near the solid boundaries to roughly parameterize missing boundary physics like topographic interaction and three dimensional turbulence over the shelf. This boundary-enhanced viscosity allows western-intensified mean flows even when the inertial boundary width, is much wider than the frictional region because eddies flux vorticity from within the interior streamlines to the frictional region for removal. Using boundary-enhanced viscosity, western-intensified calculations are possible with lower interior viscosity than in previous studies. Interesting behaviors result: a boundary-layer balance novel to the model, calculations with promise for eddy parameterization, eddy-driven gyres rotating opposite the wind, and temporal complexity including basin resonances. I also demonstrate that multiple-gyre calculations have weaker mean circulation than single-gyres with the same viscosity and subtropical forcing. Despite traditional understanding, almost no inter-gyre flux occurs if no-slip boundary conditions are used. The inter-gyre eddy flux is in control only with exactly symmetric gyres and free slip boundaries. Even without the inter-gyre flux, the multiple-gyre circulation is weak because of sinuous instabilities on the jet which are not present in the single-gyre model. These modes efficiently flux vorticity to the boundary and reduce the circulation without an inter-gyre flux, postponing inertial domination to much smaller viscosities. Then sinuous modes in combination with boundary-enhanced viscosity can control the circulation.

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 2003

Description: A novel distributed underwater acoustic networking (UAN) protocol suitable for ad-hoc deployments of both stationary and mobile nodes dispersed across a relatively wide coverage area is presented. Nodes are dynamically clustered in a distributed manner based on the estimated position of one-hop neighbor nodes within a shallow water environment. The spatial dynamic cellular clustering scheme allows scalable communication resource allocation and channel reuse similar in design to land-based cellular architectures, except devoid of the need for a centralized controlling infrastructure. Simulation results demonstrate that relatively high degrees of interference immunity, network connectivity, and network stability can be achieved despite the severe limitations of the underwater acoustic channel.

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 2008

Description: This thesis studies the dynamics of a rotating compressible gas sphere, driven by internal convection, as a model for the dynamics on the giant planets. We develop a new general circulation model for the Jovian atmosphere, based on the MITgcm dynamical core augmenting the nonhydrostatic model. The grid extends deep into the planet's interior allowing the model to compute the dynamics of a whole sphere of gas rather than a spherical shell (including the strong variations in gravity and the equation of state). Different from most previous 3D convection models, this model is anelastic rather than Boussinesq and thereby incorporates the full density variation of the planet. We show that the density gradients caused by convection drive the system away from an isentropic and therefore barotropic state as previously assumed, leading to significant baroclinic shear. This shear is concentrated mainly in the upper levels and associated with baroclinic compressibility effects. The interior flow organizes in large cyclonically rotating columnar eddies parallel to the rotation axis, which drive upgradient angular momentum eddy fluxes, generating the observed equatorial superrotation. Heat fluxes align with the axis of rotation, contributing to the observed flat meridional emission. We show the transition from weak convection cases with symmetric spiraling columnar modes similar to those found in previous analytic linear theory, to more turbulent cases which exhibit similar, though less regular and solely cyclonic, convection columns which manifest on the surface in the form of waves embedded within the superrotation. We develop a mechanical understanding of this system and scaling laws by studying simpler configurations and the dependence on physical properties such as the rotation period, bottom boundary location and forcing structure. These columnar cyclonic structures propagate eastward, driven by dynamics similar to that of a Rossby wave except that the restoring planetary vorticity gradient is in the opposite direction, due to the spherical geometry in the interior. We further study these interior dynamics using a simplified barotropic annulus model, which shows that the planetary vorticity radial variation causes the eddy angular momentum flux divergence, which drives the superrotating equatorial flow. In addition we study the interaction of the interior dynamics with a stable exterior weather layer, using a quasigeostrophic two layer channel model on a beta plane, where the columnar interior is therefore represented by a negative beta effect. We find that baroclinic instability of even a weak shear can drive strong, stable multiple zonal jets. For this model we find an analytic nonlinear solution, truncated to one growing mode, that exhibits a multiple jet meridional structure, driven by the nonlinear interaction between the eddies. Finally, given the density field from our 3D convection model we derive the high order gravitational spectra of Jupiter, which is a measurable quantity for the upcoming JUNO mission to Jupiter.

Description: Funding was provided by the MIT Presidential Fellowship, the Charney Fellowship, WHOI Academics Programs, NSF grants OPP-9910052, OCE-0137023, AST-0708106 and NASA grant NN-6066GC286.

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 2008

Description: The work was motivated by studies of Austin and Lentz (2002) and Pedlosky (2007). The above mentioned works considered two different responses of the stratified flow to a downwelling favorable wind forcing. The first study investigated a time dependent flow with a formation of a constantly expanding relatively well mixed region near the shore and the second considered a steady flow that arises when an offshore varying wind is applied. In my thesis I use ROMS to determine which type of response will take place based on the wind amplitude near the coast. It was demonstrated that if the value of the wind is much smaller than the critical value (determined by the stratification, the rotation rate and the horizontal diffusivity) then the flow is steady (the bbl case) and similar to the one investigated by Pedlosky. If the wind is of the order, or larger than, the critical value then the response is time dependent (the pool case) and similar to the one described by Austin and Lentz. The resulting flow structure of each response was also investigated. I examined the sensitivity of the bbl response to variations in the background vertical diffusivity, the initial stratification and the bottom slope. It was shown that a higher background vertical diffusivity, a higher stratification and a shallower bottom slope correspond to thinner (vertically) and narrower (horizontally) bbl. For the pool case the time dependent structure was also examined, using a number of idealized models. It was shown that the rate of the pool region expansion is a complex function of the local wind stress amplitude and the local depth.

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 2008

Description: Coupled ocean/atmosphere simulations exhibit systematicwarm biases over the SouthWest African (SWA) coastal region. Recent investigations indicate that coastal ocean dynamics may play an important role in determining the SST patterns, but none of them provide a detailed analysis. In this study, I analyze simulations produced both by coupled models and by idealized models. Then results are interpreted on the basis of a theoretical framework. Finally the conclusion is reached that the insufficient resolution of the ocean component in the coupled model is responsible for the warm biases over the SWA coastal region. The coarse resolution used in the ocean model has an artificially stretched coastal side-wall boundary layer, which induces a smaller upwelling velocity in the boundary layer. The vertical heat transport decreases even when the volume transport is unchanged because of its nonlinear relationship with the magnitude of the upwelling velocity. Based on the scaling of the idealized model simulations, a simplified calculation shows that the vertical heat transport is inversely proportional to the zonal resolution over the coastal region. Therefore, increasing the horizontal resolution can considerably improve the coastal SST simulation, and better resolve the coastal dynamics.

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 2008

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

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 2002

Description: This thesis investigates the complexities of acoustic scattering by finite bodies in general and by fish in particular through the development of an advanced acoustic scattering model and detailed laboratory acoustic measurements. A general acoustic scattering model is developed that is accurate and numerically effcient for a wide range of frequencies, angles of orientation, irregular axisymmetric shapes and boundary conditions. The model presented is an extension of a two-dimensional conformal mapping approach to scattering by irregular, finite-length bodies of revolution. An extensive series of broadband acoustic backscattering measurements has been conducted involving alewife fish (Alosa pseudoharengus), which are morphologically similar to the Atlantic herring (Clupea harengus). A greater-than-octave bandwidth (40-95 kHz), shaped, linearly swept, frequency modulated signal was used to insonify live, adult alewife that were tethered while being rotated in 1-degree increments over all angles of orientation in two planes of rotation (lateral and dorsal/ventral). Spectral analysis correlates frequency dependencies to morphology and orientation. Pulse compression processing temporally resolves multiple returns from each individual which show good correlation with size and orientation, and demonstrate that there exists more than one significant scattering feature in the animaL. Imaging technologies used to exactly measure the morphology of the scattering features of fish include very highresolution Phase Contrast X-rays (PCX) and Computerized Tomography (CT) scans, which are used for morphological evaluation and incorporation into the scattering modeL. Studies such as this one, which combine scattering models with high-resolution morphological information and high-quality laboratory data, are crucial to the quantitative use of acoustics in the ocean.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy and the Woods Hole Oceanographic Institution February 1982

Description: In this thesis, seismic waves generated by sources ranging from 2.7 kg shots of TNT to magnitude 5 earthquakes are studied in order to determine the seismic activity and crustal structure of the Orozco transform fault. Most of the data were collected by a network of 29 ocean bottom seismometers (OBS) and hydrophones (OBH) which were deployed as part of project ROSE (Rivera Ocean Seismic Experiment). Additional information is provided by magnetic anomaly and bathymetric data collected during and prior to ROSE and by teleseismic earthquakes recorded by the WWSSN (Worldwide Seismic Station Network). In Chapter II, the tectonic setting, bathymetry and teleseismic history of the Orozco Fracture Zone are summarized. Covering an area of 90 x 90 km which includes ridges and troughs trending both parallel and perpendicular to the present spreading direction (approximately east-west), the bathymetry of the transform portion of the fracture zone does not resemble that of other transform faults which have been studied in detail. A detailed study of one of the largest teleseismic earthquakes (mb=5.1) indicates right lateral strike-slip faulting with a strike parallel to the present spreading direction and a focal depth of less than 5 km. The moment sum from teleseismic earthquakes suggests an average fault width of at most a few kilometers. Because the teleseismic earthquake locations are too imprecise to define the present plate boundary and the magnetic anomaly data are too sparse to resolve the recent tectonic history, more questions are raised than are answered by the results in this chapter. These questions provide the focus for the study of the ROSE data. Chapter III contains an examination of the transfer function between seafloor motion and data recorded by the MIT OBS. The response of the recording system is determined and the coupling of the OBS to the seafloor during tests at two nearshore sites is analysed. Applying these results to the ROSE data, we conclude that the ground motion in the absence of the instrument can be adequately determined for at least one of the MIT OBS deployed during ROSE. Hypocentral parameters for 70 earthquakes, calculated for an assumed laterally homogeneous velocity structure which was adapted from the results of several refraction surveys in the area, are presented in Chapter IV. Because of the large number of stations in the ROSE network, the epicentral locations, focal depths and source mechanisms are determined with a precision unprecedented in marine microseismic work. Relative to the assumed model, most horizontal errors are less than ±1 km; vertical errors are somewhat larger. All epicenters are within the transform region of the Orozco Fracture Zone. About half of the epicenters define a narrow line of activity parallel to the spreading direction and situated along a deep topographic trough which forms the northern boundary of the transform zone (region 1). Most well determined depths are very shallow (〈4km) and no shallowing of activity is observed as the rise-transform intersection is approached. In fact, the deepest depths (4-10km) are for earthquakes within 10 km of the intersection; these apparent depth differences are supported by the waveforms recorded a t the MIT OBS. First motion polarities for all but two of the earthquakes in region 1 are compatible with right lateral strike-slip faulting along a nearly vertical plane striking parallel to the spreading direct ion. Another zone of activity is observed in the central part of the transform (region 2). The apparent horizontal and vertical distribution of activity is more scattered than for the first group and the first motion radiation patterns of these events do not appear to be compatible with any known fault mechanism. No difference can be resolved between the stress drops or b values in the two regions. In Chapter V, lateral variations in the crustal structure within the transform region are determined and the effect of these structures on the results of the previous chapter is evaluated. Several data sources provide information on different aspects of the crustal structure. Incident angles and azimuths of body waves from shots and earthquakes measured at one of the MIT OSS show systematic deflections from the angles expected for a laterally homogeneous structure. The effect of various factors on the observed angles and azimuths is discussed and it is concluded that at least some of the deflection reflects regional lateral velocity heterogeneity. Structures which can explain the observations are found by tracing rays through three dimensional velocity grids. High velocities are inferred at upper mantle depths beneath a shallow, north-south trending ridge to the west of the OBS, suggesting that the crust under the ridge is no thicker, and perhaps thinner, than the surrounding crust. Observations from sources in region 2 suggest the presence of a low velocity zone in the central transform between the sources and the receiver. That the presence of such a body provides answers to several of the questions raised in Chapter IV about the hypocenters and mechanisms of earthquakes in region 2 is circumstantial evidence supporting this model. These proposed structures do not significantly affect the hypocenters and fault plane solutions for sources in region 1. The crustal velocity structure beneath the north-south trending ridges in the central transform and outside of the transform zone is determined by travel time and amplitude modeling of the data from several lines of small shots recorded at WHOI OBH. Outside of the transform zone, a velocity-depth structure typical of oceanic crust throughout the world oceans is found from three unreversed profiles: a 1 to 2 km thick layer in which the velocity increases from about 3 to 6.7 km/sec overlies a 4 to 4.5 km thick layer with a nearly constant velocity of 6.8 km/sec. A reversed profile over one of the north-south trending ridges, on the other hand, indicates an anomalous velocity structure with a gradient of 0.5 sec-1 throughout most of the crust ( from 5.25 km/sec to 7.15 km/sec over 3.5 km). A decrease in the gradient at the base of the crust to about 0.1 sec-1 and a thin, higher gradient layer in the upper few hundred meters are also required to fit the travel time and amplitude data. A total crustal thickness of about 5.4 km is obtained. An upper mantle velocity of 8.0 to 8.13 km/sec throughout much of the transform zone is determined from travel times of large shots of TNT recorded at MIT and WHOI instruments. "Relocations" of the large shots relative to the velocity model assumed in Chapter IV support the conclusion from the ray tracing that results from region 2 may be systematically biased because of lateral velocity heterogeneity whereas results from region 1 are not affected. In the last chapter, the results on crustal structure and seismicity are combined in order to define the present plate boundary and to speculate on the history of the present configuration.

Description: This research was supported by the Office of Naval Research, under contracts N00014-75-C-0291 and N00014-80-C-0273

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 2002

Description: We have investigated the near liquidus phase relations of a primitive absarokite from the Mascota region in Western Mexico. Sample M.102 was chosen because it has high MgO contents, a high Mg# and F090 olivine phenocrysts, indicating it is primitive mantle melt. High-pressure experiments on a synthetic analogue of the absarokite composition with a H2O content of either -1 7 wt% or -5.1 wt% were cared out in a piston cylinder apparatus. The composition with -1.7 wt% H2O is multiply saturated with olivine and orthopyroxene as liquidus phases at 1.6 GPa and 1400°C. At the same pressure clinopyroxene appears 30°C below the liquidus. With a H2O content of -5.1 wt% composition M.102 is multiply saturated with olivine and orthopyroxene on the liquidus at 1.7 GPa and 1300°C. Assuming batch melting, we suggest that absarokite M.102 segregated from a depleted lherzolite or harburgite residue at depth -50 km depth in the mantle wedge. Unlike most lavas in the region, the absarokite has not ponded and fractionated at the crust mantle interface (-35-40 km), and the temperatures of multiple saturation indicate that the mantle wedge beneath the Jalisco block is hotter than previously thought. The low degree batch melting of an original metasomatised harzburgite source, can produce the observed trace element abundances. The liquidus phase relations are not consistent with the presence of non-peridotitic veins at the depth of last equilibration. Therefore, we propose that the Mascota absarokites segregated at an apparent melt fraction of less than 5% from a depleted peridotitic source. They initially formed by a small degree of melting of a metasomatised original source at greater depth.

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 2002

Description: This thesis investigates the evolution of lithospheric deformation and crustal structure from continental margins to mid-ocean ridges. The first part (Ch. 2) examines the style of segmentation along the U.S. East Coast Margin and investigates the relationship between incipient margin structure and segmentation at the modem Mid-Atlantic Ridge. The second part (Chs. 3-5) focuses on the mechanics of faulting in extending lithosphere. In Ch. 3, I show that the incorporation of a strain-rate softening rheology in continuum models results in localized zones of high strain rate that are not imposed a priori and develop in response to the rheology and boundar conditions. I then use this approach to quantify the effects of thermal state, crustal thickness, and crustal rheology on the predicted style of extension deformation. The mechanics of fault initiation and propagation along mid-ocean ridge segments is investigated in Ch. 4. Two modes of fault development are identified: Mode C faults that initiate near the center of a segment and Mode E faults that initiate at the segment ends. Numerical results from Ch. 5 predict that over time scales longer than a typical earhquake cycle transform faults behave as zones of significant weakness. Furthermore, these models indicate that Mode E faults formed at the inside-comer of a ridge-transform intersection wil experience preferential growth relative to faults formed at the conjugate outside-comer due to their proximity to the weak transform zone. Finally, the last par of this thesis (Ch. 6) presents a new method to quantify the relationship between the seismic velocity and composition of igneous rocks. A direct relationship is derived to relate V p to major element composition and typical velocity-depth profiles are used to calculate compositional bounds for the lower continental, margin, and oceanic crust.

Description: Funding was provided by NASA through grants NAG5-3264, NAG5-4806, NAG5-11113, and NAG5-9143, and by a National Defense Science and Engineering Graduate 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 April 1983

Description: Ocean acoustic tomography was proposed in 1978 by Munk and Wunsch as a possible technique for monitoring the evolution of temperature, density, and current fields over large regions. In 1981, the Ocean Tomography Group deployed four 224 Hz acoustic sources and five receivers in an array which fit within a box 300 km. on a side centered on 26°N, 70°W (southwest of Bermuda). The experiment was intended both to demonstrate the practicality of tomography as an observation tool and to extend the understanding of mesoscale evolution in the low-energy region far from the strong Gulf Stream recirculation. The propagation of 224 Hz sound energy in the ocean can be described as a set of rays traveling from source to receiver, with each ray taking a different path through the ocean in a vertical plane connecting the source and receiver. The sources transmitted a phase-coded signal which was processed at the receiver to produce a pulse at the time of arrival of the signal. Rays can be distinguished by their different pulse travel times, and these travel times change in response to variations in sound speed and current in the ocean through which the rays passed. In order to reconstruct the ocean variations from the observed travel time changes, it is necessary to specify models for both the variations and their effect on the travel times. The dependence of travel time on the oceanic sound speed and current fields can be calculated using ray paths traced by computer. The vertical structure of the sound speed and current fields in the ocean were modelled as a combination of Empirical Orthogonal Functions (EOFs) from MODE. The horizontal structure was continuous, but was constrained to have a gaussian covariance with a 100 km. e- folding scale. The resulting estimator closely resembles objective mapping as used in meteorology and physical oceanography. The tomographic system has at present only been used to estimate sound speed structure for comparison with the traditional measurements, especially the first two NOAA CTD surveys, but the method provides means for estimating density, temperature or velocity fields, and these will be produced in the future. The sound speed estimates made using the tomographic system match the traditional measurements to within the associated error bars, and there are several possibilities for improving the signal to noise ratio of the data. Given high-precision data, tomographic systems can resolve ocean structures at small scales, such as in the Gulf Stream, or at large scales, over entire ocean basins. Work is in progress to evaluate the usefulness of tomography as an observation tool in these applications.

Description: My support for the first 3 years came from an NSF graduate fellowship, and I was then supported as a research assistant by NSF Grant OCE-8017791.

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 2002

Description: Predictions of chlorophyll concentration from satellite ocean color are an indicator of phytoplankton primary productivity, with implications for foodweb structure, fisheries, and the global carbon cycle. Current models describing the relationship between optical properties and chlorophyll do not account for much of the optical variability observed in natural waters, because of the presence of seawater constituents that do not covary with phytoplankton pigment concentration. In an attempt to better understand variability in these models, the contributions of seawater constituents to ocean optical properties were investigated. A combination of Mie theory and flow cytometry was used to determine the diameter, complex refractive index (n+n'i), and optical cross-sections of individual particles, based on a method developed in the laboratory using phytoplankton cultures. Individual particle measurements were used to interpret variability in concurrently measured bulk optical properties in New England continental shelf waters in two seasons. The summed contribution to scattering of individual particles in the size range of 0.1-50 μm accounted for approximately the entire scattering coefficient measured independently using bulk methods. In surface waters in both seasons, the large diameters and n' of eukaryotic phytoplankton caused them to be the main particle contributors to both absorption and scattering. Minerals were the main contributor to backscattering, bb, in the spring, whereas in the summer both minerals and detritus contributed to bb. Synechococcus and heterotrophic bacteria were less important optically, contributing ≤11% each to attenuation in either season. The role of seawater constituents in determining remote sensing reflectance, Rrs, was determined using radiative transfer theory. Seasonal differences in the spectral shape of Rrs were contributed to approximately equally by eukaryotic phytoplankton absorption, dissolved absorption, and non-phytoplankton bb. A higher inverse wavelength dependence of non-phytoplankton bb in the summer was caused by the contribution of small detritus, in contrast to larger minerals in the spring. Measurements of bb and Rrs were compared to values from bio-optical models based on chlorophyll concentration. Differences in measured and modeled bb and Rrs were caused by higher dissolved absorption and higher backscattering efficiencies and scattering by non-phytoplankton than were assumed by the model.

Description: This work has been supported in par by: a NASA Earth System Science Fellowship to R. Green, ONR grants NOOOI4-95-1-0333 and NOOOI4-96-1-0965 to H. Sosik and R. Olson, and the 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 August 1980

Description: Observational evidence of seasonal variability below the main thermocline in the eastern North Atlantic is described, and a theoretical model of oceanic response to seasonally varying windstress forcing is constructed to assist in the interpretation of the observations. The observations are historical conductivity-temperature-depth data from the Bay of Biscay region (2° to 20°W, 42° to 52°N), a series of eleven cruises over the three years 1972 through 1974, spaced approximately three months apart. The analysis of the observations utilizes a new technique for identifying the adiabatically leveled density field corresponding to the observed density field. The distribution of salinity anomaly along the leveled surfaces is examined, as are the vertical displacements of observed density surfaces from the leveled reference surfaces, and the available potential energy. Seasonal variations in salinity anomaly and vertical displacement occur as westward propagating disturbances with zonal wavelength 390 (±50) km, phase 71 (±30) days from 1 January, and maximum amplitudes of ±30 ppm and ±20 db respectively. The leveled density field varies seasonally with an amplitude corresponding to a thermocline displacement of ±15 db. The observations are consistent with the predictions of a model in which an ocean of variable stratification with a surface mixed layer and an eastern boundary is forced by seasonal changes in a sinusoidal windstress pattern, when windstress parameters calculated from the observations of Bunker and Worthington (1976) are applied.

Description: This work was supported by the Office of Naval Research under contract N00014~76-C-197, NR 083-400.

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 1984

Description: The hypothesis that planktonic larvae of benthic invertebrates sink through the water like passive particles in turbulent flows near the seabed was tested in the field using several groups of geometrically different sediment trap designs. A priori predictions regarding the rank order that the various traps would collect larvae in the field were dictated from laboratory flume experiments to determine the relative particle collection efficiencies of traps. The flume flow was seeded with particles having fall velocities similar to those measured, in the laboratory, for nonswimming polychaete larvae. The flume flow speed (of ~10 cm/sec) was within the range of near-bottom current velocities measured during trap collecting intervals at the study site. In seven field experiments, each lasting from one to eleven days, trap collections of Mediomastus ambiseta (a polychaete worm) postlarvae, total bivalve larvae and postlarvae, sabellariid polychaete larvae, and enteropneust postlarvae generally fit the patterns predicted for passive particle collections between or among the trap designs. While the results were statistically more significant during some intervals than during others, the rank order of larval collections within each group of trap designs tested nearly always corresponded precisely to the rank order of passive particle collections by the traps in the flume experiments. Thus, the hypothesis that larvae sinking toward the seabed in the field and passive particles (with fall velocities similar to larvae) sinking in a flume are collected in the same rank order of abundance by near-bottom traps could not be falsified for collections of organisms from three invertebrate phyla. Collections of the polychaete, Pectinaria gouldii, and of metamorphosing seastar larvae between or among trap designs significantly differed from the patterns predicted for passive particle collections. A testable hypothesis to explain the Pectinaria collections involves unique hydrodynamic properties of these postlarvae, relative to the other organisms collected, and is consistent with the passive sinking hypothesis. Trap collections of the seastars may have resulted, at least in part, from larvae adhering to solid trap surfaces during metamorphosis. The passive sinking hypothesis could not be falsified in most of the field experiments conducted in this study. Thus, hydrodynamical processes must be included in any future studies of processes that determine patterns of larval settlement. However, passive sinking by larvae is not the explicit result of this experimental study. Other processes that could have produced the observed patterns of larval collections among the trap designs now must be tested against the passive sinking alternative hypothesis. However, much more information on the biology and ecology of the larvae collected in this study is required before future process oriented experiments can be designed. If larvae sink like passive particles to heights of ~50 cm above the seabed, as the results of this study suggest, then it is possible that larvae initially reach the seafloor at sites where particulates, with fall velocities similar to larvae, initially settle. This hypothesis requires experimental testing. Larvae may not remain at these initial settlement sites; however, after larvae initially reach the seafloor via passive physical processes, the larvae may redistribute by actively choosing a preferred microenvironment within that location, by actively swimming above the bottom or remaining on the sediment surface to be resuspended and transported away, by resuspension only during storm events, and/or by passively accumulating around microtopographic structures. As a precursor to the flume tests of traps, a theoretical analysis of the physical nature of trap biases was conducted. A dimensional analysis of the independent variables involved in the process of trapping particulates suggested that trap collection efficiencies should be a function primarily of trap Reynolds number, trap aspect ratio, the ratio of the fluid velocity to the particle fall velocity, and trap geometry. A review of data from previous studies that flume-tested various trap designs further suggested that particle collection efficiencies of cylindrical traps should decrease over some range of increasing trap Reynolds number, decrease over some range of decreasing particle fall velocity and increase over some range of increasing trap aspect ratio. Theoretical models were then provided to account for these effects. Flume tests, in the present study, of cylinders varying by one order of magnitude in trap Reynolds number supported one of the predictions: particle collection efficiencies of the cylinders decreased by a factor of two over this range of increasing trap Reynolds number. Results of this theoretical and experimental study of trap collection characteristics suggest that more flume experiments to quantitatively determine the nature of trap biases are required before flux estimates, using traps in the field, can be adequately interpreted.

Description: This research was funded by a National Science Foundation Dissertation Improvement Grant, A National Ocean Survey/Sea Grant Fellowship (NOAA, Dept. of Commerce Grant No. NA80-AA-D00077), a grant from the Coastal Research Laboratory at W.H.O.I., a grant from the Diving Equipment Manufactures Association, an Association for Women in Science Predoctoral Award, a National Science Foundation Grant (No. OCE-78-19820) to Dr. J. Frederick Grassle, the W.H.O.I. Education Program, and the U.S. Geological Survey (Woods Hole, MA).

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 2008

Description: Chapter 1 presents the first published measurements of Sr-isotope variability in olivine-hosted melt inclusions. Melt inclusions in just two Samoan basalt hand samples exhibit most of the total Sr-isotope variability observed in Samoan lavas. Chapter 3 deals with the largest possible scales of mantle heterogeneity, and presents the highest magmatic 3He/4He (33.8 times atmospheric) discovered in Samoa and the southern hemisphere. Along with Samoa, the highest 3He/4He sample from each southern hemisphere high 3He/4He hotspot exhibits lower 143Nd/144Nd ratios than their counterparts in the northern hemisphere. Chapter 2 presents geochemical data for a suite of unusually enriched Samoan lavas. These highly enriched Samoan lavas have the highest 87Sr/86Sr values (0.72163) measured in oceanic hotspot lavas to date, and along with trace element ratios (low Ce/Pb and Nb/U ratios), provide a strong case for ancient recycled sediment in the Samoan mantle. Chapter 4 explores whether the eclogitic and peridotitic portions of ancient subducted oceanic plates can explain the anomalous titanium, tantalum and niobium (TITAN) enrichment in high 3He/4He ocean island basalts (OIBs). The peridotitic portion of ancient subducted plates can contribute high 3He/4He and, after processing in subduction zones, a refractory, rutile-bearing eclogite may contribute the positive TITAN anomalies.

Description: Funding was provided by a National Science Foundation Graduate Research Fellowship, the National Science Foundation grants EAR- 0509891 and EAR-0652707 to Stanley R. Hart, the Woods Hole Oceanographic Institution Academic Programs Office, the Woods Hole Oceanographic Institution Deep Ocean Exploration Institute, the Woods Hole Oceanographic Institution Coastal Ocean Institute, and the Ocean Ventures 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 2008.

Description: An increased understanding of heterotrophic bacterial strategies for acquiring nutrients and trace elements is critical for elucidating their impact on biogeochemical cycling in the ocean. It is estimated that iron is a limiting nutrient for phytoplankton growth in over 30% of the open ocean, but still little is known about bacterial strategies for iron acquisition. Siderophore (Fe ligand) production by bacteria may play a major role in influencing the bioavailability of iron in the ocean. Despite the importance of siderophores in the environment, only limited information from a select group of bacteria is available. On a cruise through the Costa Rica Dome (CRD) upwelling region in July 2005, a library of 867 isolates from five depth profiles inside and outside of the dome was obtained and screened for siderophore production using the Chrome Azurol-S (CAS) assay. Phylogenetic affiliation of 134 isolates was determined by sequencing the 16s rDNA gene, and determined that gamma proteobacteria such as Alteromonas, Pseudoalteromonas, Halomonas, and Marinobacter dominated the collection, while alpha-proteobacteria such as Roseobacter were also represented. The isolates obtained from stations in the CRD showed greater siderophore-producing capabilities between 55m and 100m while strains isolated from outside the CRD had shallower peak (~8-35m) production. Functional group determination showed that hydroxamate production dominated from 50-150m, while hydroxamate and catechol production is roughly equal in shallower waters. By characterizing the siderophores produced by these isolates and determining the genetic make-up of the population, these findings further our understanding of how heterotrophic microbes affect biogeochemical processes and the competitive nature of nutrient acquisition.

Description: I am grateful to my funding sources, National Science Foundation grants BO OCE- 0352241 "The Effect of Iron Bioavailability on Synechococcus diversity from a HNLC region to the Costa Rica upwelling dome" and CO-OCE-0452883 "Interactions of Cobalt and Iron with in situ Cyanobacterial Physiology in the South Atlantic and the Benguela Upwelling Region", the National Science Foundation Graduate Research Fellowship, and the Academic Programs office.

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 2008.

Description: Biogeochemical cycling of phosphate is a key component in the overall production rate of coastal ecosystems. Mineral phases in the near-shore sediments play a significant role in the return of phosphate remineralized in the upper sediments to the water column. Sequential Extraction (SEDEX) of the solid-phase associated PO4-3 yielded reservoir profiles of phosphate at three sites off of the Massachusetts coast. These extractions found Fe-associated PO4 to be the dominant phase associated with rapid porewater-solid P exchange. Additionally, a seasonal enrichment/depletion pattern of phosphate fluxes relative to total carbon was observed from the sediments. These observations established the behavior of phosphate in coastal sediments as interconnected with the ongoing Fe-cycling in the sediments as well.

Description: This work was made possible by sponsorship and funding provided by NOAA, (U.S. Department of Commerce (Grant # NA06OAR4170021, project # R/G-29)); National Science Foundation (Grant # OCE-0526389); WHOI / USGS Cooperative Agreement; and the WHOI Academic Programs Office.

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 June 1981

Description: Note: Pages 88-89 do not appear in original document.

Description: The multichannel Maximum Entropy Method (MEM) of spectral analysis is developed and applied in the dynamic analysis of offshore structures. Two different algorithms are implemented and compared with the conventional Blackman-Tukey method. These are (1) a direct on the data or Burg method and (2) a Yule-Walker or correlation function extension method. Cross-spectral estimates of magnitude, phase, coherence squared, and transfer function are calculated. These estimates are then used in mode shape identification of a triple decked, single caisson offshore platform. The superiority of the multichannel Maximum Entropy Methods relative to conventional spectral analysis techniques in calculating these cross-spectral estimates and evaluating mode shapes is demonstrated.

Description: This research was sponsored by the Branch of Marine Oil and Gas Operations of the United States Geological Survey, Department of the Interior and by the Massachusetts Institute of Technology/Woods Hole Oceanographic Institution Joint Program in Ocean Engineering

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 1982

Description: Mean long-isobath drift of the order 5 cm/sec has been observed on several continental shelves, e.g. in the Middle Atlantic Bight and in the Weddell Sea. A theoretical model is developed to explore the driving mechanism of this mean circulation. In the model, the velocity field is decomposed into a depth-independent bottom geostrophic component and a thermohaline component relative to the bottom. The latter can be calculated from the density field, and the former is described by a parabolic equation which expresses the tendency-to balance vorticity between bottom stress curl and vortex stretching. The near-bottom flow field is studied both analytically and numerically under forcing by wind, deep ocean flow, and long-isobath density differences. Model solutions are derived for circulations over a shelf/slope topography driven by wind stress, wind stress curl, and deep ocean currents. The resulting flow patterns show strong dependence on the topography. Over the continental slope, large bottom depth variation suppresses the flow driven by local forcing and insulates the slope region from circulations on the shelf and in the deep-ocean. Geochemical observations on the continental shelf and slope support the argument that the flow on the upper slope below the thermocline is weak. Under the condition of a vertically homogeneous layer below the thermocline, near-bottom density advection is mainly caused by the bottom geostrophic velocity field. Using the parabolic vorticity equation together with a density equation, circulations driven by coastal buoyancy flux and surface cooling are investigated. In the mid-shelf region, away from the coast and the shelf break, the density field is governed by Burgers' equation, which shows longshore self-advection of density perturbations and the formation of front with strong density gradient in the longshore direction. A dense water blob moves in the direction of Kelvin wave propagation. The direction is reversed for the movement of a light water blob. In the near-shore region, the light river water bottom is also self-advected in the direction of Kelvin wave propagation. For a heavy density anomaly at the coast, the initial movement is offshore, and the accumulation of dense water in the mid-shelf region leads to long-isobath propagation of density perturbations, similar to the case of a dense water blob. This theory sheds light on the bottom water movements in the Adriatic Sea, the Antarctic Continent, and the Middle Atlantic Bight. The model solutions are applied to the flow on the western North Atlantic shelf. Southwestward flow is produced near the coast by the self-advection of river water in winter and spring. The southwestward long-isobath propagation of thermal fronts caused by winter cooling contributes significantly to the mean circulation over the mid-shelf. It is suggested that density-driven current is an important component of the near-bottom mean circulation in the Middle Atlantic Bight in spring and summer.

Description: This work was supported by the Department of Energy through contract entitled Coastal-Shelf Transport and Diffusion.

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 1981

Description: Data demonstrating the presence and inducibility of the xenobiotic monooxygenase system in fish embryos and larvae are described. The ontogeny of benzo(a)pyrene monooxygenase (BPM) activity, and NADPH- and NADH-cytochrome c reductase activities, were followed in microsomes prepared from whole embryos of the estuarine killifish Fundulus heteroclitus. BPM activity was detectable as early as 4 days from fertilization, prior to the appearance of the liver rudiment, which indicates a substantial role for the extrahepatic tissues in xenobiotic metabolism in Fundulus embryos. At all stages assayed before hatching, BPM activity was uniformly low, but within 24 hours of hatching there was a 10-fold increase in specific activity. This increase was shown not to be age-dependent but required hatching, and was not an artifact of the presence of endogenous inhibitors in embryos. Both NADPH- and NADH-cytochrome c reductase activities were measurable at all stages assayed. The developmental patterns of these two reductases were distinct from each other and did not closely correlate with that of BPM activity. However, the functional involvement of the NADPH-cytochrome c reductase in monooxygenase activity was indicated by the inhibition of BPM activity by cytochrome c. The metabolism of benzo(a)pyrene by fractions prepared from whole Fundulus embryos and eleutheroembryos appears to be catalyzed by a typical cytochrome P-450 dependent monooxygenase. This activity is localized in the microsomal fraction, requires O2, NADPH and native enzyme, and is inhibited by CO. NADPH supports much higher activity than NADH. BPM activity was detectable in the livers of Fundulus eleutheroembryos, larvae and juveniles. The level of activity in Fundulus eleutheroembryo livers was about 1/4 the average adult activity. Specific activity rose continuously from the end of the embryonic period into the juvenile period when adult levels were approached. BPM activity was also measurable in the livers of brook trout (Salvelinus fontinalis) embryos and eleutheroembryos. The ontogenic pattern contrasted with that seen in Fundulus. At 6 and 1 days before hatching BPM specific activity in embryonic liver was close to the adult level. After hatching there was a 3-fold increase in activity, thus the livers of eleutheroembryos were considerably more active in metabolizing BP than those of adult brook trout. BPM activity was inducible in Fundulus embryos by both Aroclor 1254 and No.2 Fuel oii. Embryos were competent to respond to induction as early as 4 days from fertilization. In Fundulus eleutheroembryos, Aroclor 1254 induced BPM activity in both the liver and extrahepatic tissues. Aminopyrine N-demethylase activity was detectable in microsomes prepared from whole eleutheroembryos, but was not induced by Aroclor 1254. Neither NADPH- nor NADH-cytochrome c reductase activities were induced by Aroclor 1254 before hatching, but after hatching both activities were induced. A striking developmental change in the sensitivty of the induction response was observed in Fundulus. The tissue levels of PCBs necessary to produce a maximal induction of BPM activity were at least 5 times lower in post-hatching stages compared to prehatching stages. The relative insensitivity of the induction response prior to hatching may serve to protect embryos from damage from activated metabolites during organogenesis. Aroclor 1254 was also shown to induce BPM activity in brook trout embryonic liver. The data obtained with both Fundulus and brook trout indicate that levels of PCBs occurring in fish in contaminated environments are likely to induce the monooxygenase system during embryonic development. Metabolites of benzo( a) pyrene produced by microsomes prepared from adult Fundulus liver, and untreated and PCB exposed eleutheroembryos were analyzed by HPLC. Similar metabolite profiles were obtained in all cases, with a high proportion of benzo-ring dihydrodiols. The dihydrodiol peaks produced by e leutheroembryo microsomes were abolished by TCPO, indicating the presence of epoxide hydrolase. These results suggest that Fundulus embryos and eleutheroembryos can activate BP to the highly mutagenic trans-7, 8-dihydrodiol-9, 10-epoxides. Fish embryonic monooxygenase activity may play a role in pollutant-induced lesions, including teratogenic effects, by producing reactive and mutagenic metabolites during organodifferentiation.

Description: This work was supported by National Science Foundation grants OCE77-24517 and OCE80-18569.

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 September 1994

Description: This Paper explores the use of an extended Kalman filter to provide real-time estimates of underwater vehicle position and attitude. The types of previously available sensors are detailed including strapdown accelerometers, roll and pitch sensors, gyro and magnetic compasses, depth sensor, and various types of acoustic positioning systems. A doppler velocimeter is added to this sensor suite to improve the performance of the filter. As an integral part of the filter, magnetic compass and gyrocompass biases are estimated to improve vehicle heading accuracy. The filter is designed to account for numerous reallife complications. These include varying rates of sensor output, lengthy gaps in reception of position information, presence of non-Gaussian position fix errors (flyers), and varying probability density functions for sensor errors. Simulated data are used to test the filter with varying availability of data and accuracy of initial conditions, along with actual data from a deployment of the towed DSL-120 vehicle. The increased accuracy obtained by using the doppler velocimeter is emphasized.

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 2008

Description: Studying the social and cultural transmission of behavior among animals helps to identify patterns of interaction and information content flowing between individuals. Killer whales are likely to acquire traits culturally based on their population-specific feeding behaviors and group-distinctive vocal repertoires. I used digital tags to explore the contributions of individual Norwegian killer whales to group carousel feeding and the relationships between vocal and non-vocal activity. Periods of tail slapping to incapacitate herring during feeding were characterized by elevated movement variability, heightened vocal activity and call types containing additional orientation cues. Tail slaps produced by tagged animals were identified using a rapid pitch change and occurred primarily within 20m of the surface. Two simultaneously tagged animals maneuvered similarly when tail slapping within 60s of one another, indicating that the position and composition of the herring ball influenced their behavior. Two types of behavioral sequence preceding the tight circling of carousel feeding were apparent. First, the animals engaged in periods of directional swimming. They were silent in 2 of 3 instances, suggesting they may have located other foraging groups by eavesdropping. Second, tagged animals made broad horizontal loops as they dove in a manner consistent with corralling. All 4 of these occasions were accompanied by vocal activity, indicating that this and tail slapping may benefit from social communication. No significant relationship between the call types and the actual movement measurements was found. Killer whale vocalizations traditionally have been classified into discrete call types. Using human speech processing techniques, I considered that calls are alternatively comprised of shared segments that can be recombined to form the stereotyped and variable repertoire. In a classification experiment, the characterization of calls using the whole call, a set of unshared segments, or a set of shared segments yielded equivalent performance. The shared segments required less information to parse the same vocalizations, suggesting a more parsimonious system of representation. This closer examination of the movements and vocalizations of Norwegian killer whales, combined with future work on ontogeny and transmission, will inform our understanding of whether and how culture plays a role in achieving population-specific behaviors in this species.

Description: Funding sources: The Ocean Life Institute at WHOI and the National Geographic Society, the National Defense Science and Engineering Graduate Fellowship, a National Science Foundation Graduate Fellowship, the Academic Programs Office at WHOI and Dennis McLaughlin at MIT.

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 2003

Description: Male dolphins form stable, long-term alliances comparable to long-term relationships formed by terrestrial species. The goal of this thesis was to determine the effect of the formation of these alliances on vocal development. Comparing whistles produced in isolation revealed that alliance partners have similar whistles, while non-partners do not. Whistle similarity seen in alliance partners mirrors group-specific vocal convergence in stable groups of birds and bats. Males produce more variable whistles than females, and females have more stable whistle repertoires. Unlike males, females do not maintain the strong, stable relationships seen in male alliances. Increased vocal plasticity in males may be related to modifying whistle production while forming alliances. Females produced whistles that were less similar to other females than to males. Females may rely on whistle distinctiveness for mother-offspring recognition, while males may rely on whistle convergence to maintain specific social bonds. The whistles produced by an isolated individual may not represent its complete repertoire. A hydrophone array was used to record whistles of free-swimming, socializing individuals to compare to the whistles produced by those animals in isolation. There was no significant difference in the whistle repertoires of restrained vs. free-swimming dolphins for over 60% of the animals, and most produced at least one whistle type in both contexts. Therefore, animals use similar whistles in isolated and free-swimming conditions. Recordings of different social groups were examined to test if signature whistles function as contact calls. An allied male produced signature whistles most often when separated from his partner and least often when with his partner. Signature whistles were also highly individually distinctive, and therefore well suited as contact calls, while variant whistles were not. Separations and reunions between alliance partners were examined to determine if whistles are used to maintain contact between preferred associates. Most whistles recorded from separated males were signature whistles. The timing of whistle production was correlated with the timing of the maximum partner separation and the initiation of a reunion. Few whistles were produced as the partners separated. Therefore, whistles may initiate reunions between partners. This thesis demonstrates that free-ranging male dolphins use signature whistles in the same way as females and captive dolphins.

Description: Funding for this thesis was provided by the Grant No. 6456-99 from the National Geographic Society, Grant No. IBN-9975523 from the National Science Foundation, an NSF Dissertation Improvement grant, WHOI Ocean Ventures Fund, National Institutes of Health, SERDP Contract No. DACA72-01-C-0ll, Dolphin Quest, Chicago Zoological Society, and WHOI Academic Programs Departent, and ONR.

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 November 1981

Description: Radiolarians which settle through the oceanic water column were recovered from three stations (western Tropical Atlantic-Station E, central Tropical Pacific-Pi and Panama Basin-PB) using PARLUX sediment traps in moored arrays at several depths. The taxonomic diversities of the radiolarian assemblages in the sediment traps were very high. A total of 420 taxa, including 23 newly identified taxa, were found at the three stations; of these, 208 taxa were found at station E. The polycystine radiolarians generally reach the sea floor with little change in abundance or species composition, although slight skeletal dissolution occurs throughout their descent. The phaeodarian radiolarians, on the other hand, are largely dissolved within the water column; only a few species reach the sea-floor and these dissolve rapidly at the sediment-water interface. Most radiolarian skeletons sink as individuals through deep water columns without being incorporated into large biogenic aggregates. Because significant numbers of nassellarian and phaeodarian species are deep-water dwelling forms the diversity index of radiolarians increases with increasing depth in the mesopelagic zone. The vertical flux of the total radiolarians arriving at the trap depths (in x 103 individuals/m2/day) ranged from 16-24 (E), 0.6-17 (Pl), and 29-53 (PB). Of these on the average 25% and 69% of the total radiolarian flux is transported by Spumellaria and Nassellaria, respectively, while 5% is carried by Phaeodaria. The measured Si02 content of the skeletons averaged 91, 98 and 71% of measured weight for Spumellaria, Nassellaria and Phaeodaria, respectively. The supply of radiolarian silica (mg Si02/m2/day) to each trap depth ranged from 2.5-4.0 (E), 0.9-3.2 (Pl), and 5.7-10.4 (PB). The Radiolaria appear to be a significantly large portion of the Si02 flux in 〉63 pm size fraction and thus play an important role in the silica cycle. When the radiolarian fluxes at the three Stations are compared with Holocene radiolarian accumulation rates in the same areas it became apparent that several percent or less of the fluxes are preserved in the sediments in all cases and the rest is dissolved on the sea-floor. Estimated excess Si which is derived from Si02 dissolution on the sea-floor is fairly small relative to advective Si in the western North Atlantic and thus it appears to be insignificant to show any deviation in a simple mixing curve of deep water masses. Weight, length, width, projected area and volume of 58 radiolarian taxa were measured. The density contrast of radiolarians, relative to seawater, generally falls between 0.01 and 0.5 g/cm3. The sinking speed of 55 radiolarian taxa, measured in the laboratory at 3°C, ranged from 13 to 416 m/day. Despite the wide variety of morphology between the species, sinking speeds were best correlated with weight/shell among all the possible combinations of the examined variables. The estimated residence times of these taxa in the 5 km pelagic water column ranged from 2 weeks to 14 months. Large phaeodarians reached the water-sediment interface relatively quickly and ultimately dissolved on the sea floor. Small-sized taxa dissolved en route during sinking. The standing stock of 26 examined abundant taxa is on the order of 1 to 100 shells/m3. Total radiolarian standing stock ranges from about 450 shells/m3 at Stations Pl and E to 1200 shells/m3 at Station PB. The rate of production of total Radiolaria is calculated to be 77 to 225 shells/m3 /day. The turnover time for these species ranges from several days to one month depending on the species and the assumption of the depth interval used for the estimation.

Description: This thesis work has been supported by the National Science Foundation, Submarine Geology and Geophysics Program, Grant OCE80-l9386 and the Woods Hole Oceanographic Institution 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 September 2003

Description: Contamnant exposure has been associated with toxic effects in marine mammals. Studies on early biochemical and molecular responses prior to, but associated with, contaminant-induced toxicity will aid in understanding the susceptibility of cetaceans to such exposures. Cytochrome P450 1A1 (CYP1A1) induction by planar halogenated aromatic hydrocarbons, including certain polychlorinated biphenyls (PCBs), has been correlated with toxic effects in rodents. CYP1A1 expression was measured in multiple organs from beluga whales and white-sided dolphins and integument biopsies from bottlenose dolphins. Age and sex do not appear to influence CYP1A1 expression in these species. Mono-artha PCB concentrations were correlated with CYP1A1 in bottlenose dolphin integument and white-sided dolphin liver. White-sided dolphins, with PCBs concentrations six times higher than Arctic beluga, have lower hepatic CYP1A1 expression. Beluga whales thus appear very sensitive to the induction of CYP1A1 by PHAHs. These studies demonstrate that comparative studies between cetacean species, with reference to experimental work in model organisms, could determine the relative susceptibility of cetaceans to contaminant exposures. Aromatase is the enzyme responsible for estrogen production and recent studies suggest that PCBs may alter its activity or expression. We determined the sequence and characterized the catalytic properties of a cetacean aromatase, which was similar to other mammalian aromatases. Evolutionary analyses of vertebrate aromatases revealed striking functional conservation. Although much work is required, these data show that similar to CYP1A1, aromatase studies in other mammals are applicable to cetacean species. Experimental work in model organisms, coupled with careful studies with cetacean tissues, could infer the physiological role and transcriptional control of aromatase in cetacean species.

Description: Funding for this research was provided by the Natural Sciences and Engineering Research Council of Canada postgraduate scholarship B, the MIIWOI Joint Program, WHOI Sea Grant Project Number R/-162, NI Superfund Basic Research Program Grant P-42-ES07381, the WHOI Biology Department, and the International Whaling Commission's Pollution 2000+ program.