Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 167-179). / The daily heating of the ocean by the sun can create a stably stratified near-surface layer when the winds are slight and solar insolation is strong. This type of shallow stable layer is called a Diurnal Warm Layer (DWL). This thesis examines the physics and dynamics of DWLs from observations of the subtropical North Atlantic Ocean associated with the Salinity Processes in the Upper ocean Regional Study (SPURS-I). Momentum transferred from the atmosphere to the ocean through wind stress becomes trapped within the DWL, generating shear across the layer. During SPURS-I, strong diurnal shear across the DWL was coincident with enhanced turbulent kinetic energy (TKE) dissipation ([epsilon], [epsilon] > 10⁻⁵ W/kg) observed from glider microstructure profiles of the near-surface. However, a scale analysis demonstrated that surface forcing, including diurnal shear, could not be the sole mechanism for the enhanced TKE dissipation. High-frequency internal waves ([omega] >> f) were observed in the upper ocean during the daytime within the DWL. Internal waves are able to transfer energy from the deep ocean into the DWL through the unstratified remnant mixed layer, which is the intervening layer between the DWL and seasonal thermocline. As the strength of the stratification of the DWL increases, so does the shear caused by the tunneling internal waves. The analysis demonstrates that internal waves can generate strong enough shear to cause a shear-induced instability, and are a plausible source of the observed enhanced TKE dissipation. Vertically-varying horizontal transport across the upper ocean occurs because a diurnal current exists within the DWL, but not in the unstratified remnant mixed layer below. Therefore, when a DWL is present, the water within DWL is horizontally transported a different distance than the water below. Coupled with nocturnal convection that mixes the DWL with the unstratified layer at night, this cycle is a mechanism for submesoscale (1-10 km) lateral diffusion across the upper ocean. Estimates of a horizontal diffusion coefficient are similar in magnitude to current estimates of submesoscale diffusion based on observations, and are likely an important source of horizontal diffusion in the upper ocean. / by Alec Setnor Bogdanoff. / Ph. D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2006. / Includes bibliographical references (p. 297-311). / The physical and biological forces that drive zooplankton distribution and patchiness in an antarctic continental shelf region were examined, with particular emphasis on the Antarctic krill, Euphausia superba. This was accomplished by the application of acoustic, video, and environmental sensors during surveys of the region in and around Marguerite Bay, west of the Antarctic Peninsula, in the falls and winters of 2001 and 2002. An important component of the research involved the development and verification of methods for extracting estimates of ecologically-meaningful quantities from measurements of scattered sound. The distribution of acoustic volume backscattering at the single frequency of 120 kHz was first examined as an index of the overall biomass of zooplankton. Distinct spatial and seasonal patterns were observed that coincided with advective features. Improved parameterization was then achieved for a theoretical model of Antarctic krill target strength, the quantity necessary in scaling measurements of scattered sound to estimates of abundance, through direct measurement of all necessary model parameters for krill sampled in the study region and survey period. / (cont.) Methods were developed for identifying and delineating krill aggregations, allowing the distribution of krill to be distinguished from that of the overall zooplankton community. Additional methods were developed and verified for estimating the length, abundance, and biomass of krill in each acoustically-identified aggregation. These methods were applied to multi-frequency acoustic survey data, demonstrating strong seasonal, inter-annual, and spatial variability in the distribution of krill biomass. Highest biomass was consistently associated with regions close to land where temperatures at depth were cool. Finally, the morphology, internal structure, and vertical position of individual krill aggregations were examined. The observed patterns of variability in aggregation characteristics between day and night, regions of high versus low food availability, and in the presence or absence of predators, together reinforced the conclusion that aggregation and diel vertical migration represent strategies to avoid visual predators, while also allowing the krill access to shallowly-distributed food resources. The various findings of this work have important implications to the fields of zooplankton acoustics and Antarctic krill ecology, especially in relation to the interactions of the krill with its predators. / by Gareth L. Lawson. / Ph.D.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references (p. 43-45). / Grain size is an important material property that has significant effects on the viscosity, dominant deformation mechanism, attenuation, and shear wave velocity of the oceanic upper mantle. Several studies have investigated the kinetics of grain size evolution, but have yet to incorporate these evolution equations into large-scale flow models of the oceanic upper mantle. We construct self-consistent 1.5-D steady-state Couette flow models for the oceanic upper mantle to constrain how grain size evolves with depth assuming a composite diffusion-dislocation creep rheology. We investigate the importance of water content by examining end-member models for a dry, wet, and dehydrated mantle (with dehydration above -60-70 km depth). We find that grain size increases with depth, and varies with both plate age and water content. Specifically, the dehydration model predicts a grain size of -11 mm at a depth of 150 km for 75 Myr-old oceanic mantle. This results in a viscosity of -1019 Pa s, consistent with estimates from geoid and glacial rebound studies. We also find that deformation is dominated by dislocation creep beneath -60-70 km depth, in agreement with observations of seismic anisotropy in the oceanic upper mantle. The calculated grain size profiles are input into a Burger's model system to calculate seismic quality factor (Q) and shear wave velocity (Vs). For ages older than 50 Myrs, we find that Q and Vs predicted by the dehydration case best match seismic reference models for Q and the low seismic shear wave velocity zone (LVZ) observed in the oceanic upper mantle. / by James R. Elsenbeck, II. / S.M.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (p. 239-244). / In biology, the importance of fluid drag, diffusion, and heat transfer both internally and externally, suggest the boundary layer as an important subject of investigation, however, the complexities of biological systems present significant and unique challenges to analysis by experimental fluid dynamics. In this investigation, a system for automatically profiling the boundary layer over free-swimming, deforming bodies was developed and the boundary layer over rigid and live mackerel, bluefish, scup and eel was profiled. The profiling system combined robotics, particle imaging velocimetry, a custom particle tracking code, and an automatic boundary layer analysis code. Over 100,000 image pairs of flow in the boundary layer were acquired in swimming fish alone, making spatial and temporal ensemble averaging possible. A flat plate boundary layer was profiled and compared to known laminar and turbulent boundary layer theory. In general, profiles resembled those of Blasius for sub-critical length Reynolds numbers, Rex. Transition to a turbulent boundary layer was observed near the expected critical Rex and subsequent profiles agreed well with the law of the wall. The flat plate analysis demonstrated that the particle tracking and boundary layer analysis algorithms were highly accurate. / (cont.) In rigid fish, separation of flow was clearly evident and the boundary layer transitioned to turbulent at lower Rex than in swimming fish and the flat plate. Wall shear stress, [tao]o, forward of separation was slightly higher than flat plate values. Friction drag in rigid and swimming fish was determined by integrating [tao]o over the surface of the fish. The analysis was facilitated by the definition of the relative local coefficient of friction. In general, there was no significant difference in friction drag between the rigid-body and swimming cases. In swimming, separation was, on average, delayed. Therefore, pressure drag was estimated on the basis of thickness ratio and used to calculate an upper-bound total drag on a swimming fish. Total drag was used to determine the required muscle power output during swimming and compare that with existing muscle power data. [tau]o and boundary layer thickness oscillated with undulatory phase. The magnitude of oscillation appears to be linked to body wave amplitude. / by Erik J. Anderson. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / Includes bibliographical references. / 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. / (cont.) 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. / by Ari Daniel Shapiro. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2000. / Includes bibliographical references (p. 207-219). / Processes affecting organic carbon distribution and composition can control the speciation of organic contaminants such as polychlorinated biphenyls (PCBs) and ultimately determine their residence time in a particular environment. In marine systems, the microbial loop influences organic carbon dynamics by recycling a significant fraction of dissolved and particulate organic matter. The goal of this thesis was to understand how these recycling processes affect chlorobiphenyl (CB) cycling in marine systems by monitoring CB dynamics among organic carbon pools represented by dissolved organic matter, bacterial prey and phagotrophic protozoan grazers. Initially, I studied the extent to which a protozoan grazer (Uronema sp.-10[micro]m ciliate) equilibrated with aqueous PCBs within 2-3 hours. Initial calculations predicted rapid equilibration via passive diffusion. Experimentally, no difference in equilibration time was noted between grazing and non-grazing protozoa, indicating that diffusion was the primary uptake pathway for these organisms. The results were extended to determine the transition size of an organism where the rates of diffusive and ingested uptake are equivalent (100-500[micro]m). Disassociation rate constants were estimated for complexes of CB congeners and dissolved organic carbon (DOC). CB-DOC complexes enhanced the diffusive uptake rate constant for Tenax resin and, by inference, protozoan grazers. In the second phase of this work, concentrations of surfactants, organic carbon and cells were monitored over time in protozoan cultures. The effects of bacterial growth substrate and protozoan species were examined. Surfactants increased during protozoan exponential growth while total DOC concentrations decreased. Production of / (cont.) surface-active material in ciliate cultures was significantly higher than in flagellate cultures, and all protozoan cultures were higher than the bacterial control. Common headspace vessels were then used to compare and contrast the affinity of protozoan and bacterial culture filtrates (<0.2[micro]m) for PCBs relative to a seawater control. Affinities were normalized to bulk DOC and surfactant concentrations to determine underlying relationships among these parameters. Values of equilibrium partition coefficients (K[oc]) ranged from 10⁴·⁶ in Vineyard Sound seawater to 10⁵·⁴ and 10⁵·⁵ in protist cultures, indicating that "grazer-enhanced" DOM was a better sorbent for PCBs than DOM in bacterial controls and Vineyard Sound seawater. / by Elizabeth Belle Kujawinski. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references. / Present-day expeditionary oceanography is beginning to shift from a focus on short-term ship and submersible deployments to an ocean observatory mode where long-term temporally-focused studies are feasible. As a result, a critical need for in situ chemical sensors is evolving. New sensors take a significant amount of time to develop; thus, the evaluation of techniques in the laboratory for use in the ocean environment is becoming increasingly important. Laser-induced breakdown spectroscopy (LIBS) possesses many of the characteristics required for such in situ chemical sensing, and is a promising technique for field measurements in extreme environments. Although many LIBS researchers have focused their work on liquid jets or surfaces, little attention has been paid to bulk liquid analysis, and especially to the effect of oceanic pressures on LIBS signals. In this work, laboratory experiments validate the LIBS technique in a simulated deep ocean environment to pressures up to 2.76 x 10⁷ Pa. A key focus of this work is the validation that select elements important for understanding hydrothermal vent fluid chemistry (Na, Ca, Mn, Mg, K, and Li) are detectable using LIBS. A data processing scheme that accurately deals with the extreme nature of laser-induced plasma formation was developed that allows for statistically accurate comparisons of spectra. The use of both single and double pulse LIBS for high pressure bulk aqueous solutions is explored and the system parameters needed for the detection of the key analytes are optimized. Using both single and double pulse LIBS, the limits of detection were found to be higher than expected as a result of the spectrometer used in this experimentation. However, the results of this validation show that LIBS possesses the characteristics to be a viable chemical sensing method for in situ analyte detection in high pressure environments like the deep ocean. / by Anna Pauline Miranda Michel. / Ph.D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The 21st century warming and acidification of tropical oceans will impact the structure and function of coral reef ecosystems. Consequently, conservation efforts are increasingly focused on identifying and protecting reef communities that demonstrate resilience to these changes. In this thesis, I develop a scientific framework for identifying climate change resilience in coral communities and, using Palau's coral reefs as a case study, demonstrate the application of this approach. First, I use coral skeletal records to evaluate the sensitivity of coral communities to episodes of severe thermal stress. This information reveals coral reef communities that consistently exhibit weak responses to multiple high temperature events. Second, I evaluate coral reef community structure across a strong, natural pH gradient using metrics informed by laboratory ocean acidification studies. The coral communities of Palau's Rock Island reefs show a level of pH tolerance that is unique amongst reefs studied to date. Third, I conduct laboratory and field experiments to constrain the pH thresholds of these resilient corals and investigate potential mechanisms for pH tolerance. Finally, I combine archipelago-wide coral temperature and pH sensitivity data to construct climate change resilience indices. My study succeeds in identifying a small number of coral communities that have the potential to withstand 2 1st century climate change and highlights the spatial variability in community responses to ocean warming and acidification. Critically, I present a set of scientific tools and approaches for identifying resilient coral reef communities that has applicability to coral reefs worldwide. / by Hannah Catherine Barkley. / Ph. D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2006. / Includes bibliographical references (p. 197-206). / This thesis develops methods for estimating wideband shallow-water acoustic communication channels. The very shallow water wideband channel has three distinct features: large dimension caused by extensive delay spread; limited number of degrees of freedom (DOF) due to resolvable paths and inter-path correlations; and rapid fluctuations induced by scattering from the moving sea surface. Traditional LS estimation techniques often fail to reconcile the rapid fluctuations with the large dimensionality. Subspace based approaches with DOF reduction are confronted with unstable subspace structure subject to significant changes over a short period of time. Based on state-space channel modeling, the first part of this thesis develops algorithms that jointly estimate the channel as well as its dynamics. Algorithms based on the Extended Kalman Filter (EKF) and the Expectation Maximization (EM) approach respectively are developed. / (cont.) Analysis shows conceptual parallels, including an identical second-order innovation form shared by the EKF modification and the suboptimal EM, and the shared issue of parameter identifiability due to channel structure, reflected as parameter unobservability in EKF and insufficient excitation in EM. Modifications of both algorithms, including a two-model based EKF and a subspace EM algorithm which selectively track dominant taps and reduce prediction error, are proposed to overcome the identifiability issue. The second part of the thesis develops algorithms that explicitly find the sparse estimate of the delay-Doppler spread function. The study contributes to a better understanding of the channel physical constraints on algorithm design and potential performance improvement. It may also be generalized to other applications where dimensionality and variability collide. / by Weichang Li. / Ph.D.

Thesis (Ph.D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences and the Woods Hole Oceanographic Institution), 2000. / Vita. / Includes bibliographical references (leaves 266-286). / Phosphorus, an essential nutrient, is removed from the oceans only through burial with marine sediments. Organic phosphorus (Prog) constitutes an important fraction (ca. 25%) of total-P in marine sediments. However, given the inherent lability of primary Prog biochemicals, it is a puzzle that any Porg is preserved in marine sediments. The goal of this thesis was to address this apparent paradox by linking bulk and molecular-level Porg information. A newly-developed sequential extraction method, which isolates sedimentary Pol reservoirs based on solubility, was used in concert with Prog nuclear magnetic resonance spectroscopy (31P-NMR) to quantify Prog functional group concentrations. The coupled extraction/ 31P-NMR method was applied to three sediment cores from the Santa Barbara Basin, and the first-ever high-resolution depth profiles of molecular-level Porg distribution during diagenesis were generated. These depth profiles were used to consider regulation of Prog distribution by biomass abundance, chemical structure, and physical protection mechanisms. Biomass cannot account for more than a few percent of sedimentary Prog. No evidence for direct structural control on remineralization of Porg was found. Instead, sorptive protection appears to be an important mechanism for Prog preservation, and structure may act as a secondary control due to preferential sorption of specific Porg compound classes. / by Kirsten Lynn Laarkamp. / Ph.D.