Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2008. / Includes bibliographical references (p. 159-170). / 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. / (cont) 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 EKEF 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. / by Matthew R. Walter. / S.M.

Thesis (M.S.)--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), 2003. / Includes bibliographical references (p. 181-191). / In this thesis I have endeavored to determine the factors and physical processes that controlled SST and thermocline depth at 10⁰N, 125⁰W during the Pan Amer- ican 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. / by J. Thomas Farrar. / M.S.

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. / The marine carbon cycle plays an important role in regulating Earth's climate. The vastness of the open ocean and the large variability in the coastal ocean provide obstacles to accurately quantify storage and transport of inorganic carbon within marine ecosystems and between marine and other earth systems. Thus far, the open ocean has been the only true net sink of anthropogenic carbon dioxide (Canthro) emissions. However, ocean storage of Canthro is not uniformly distributed. Changes in water chemistry in the Northeast Pacific were quantified to estimate the amount of Canthro stored in this region over the last decade. This additional Canthro was found to cause acidification and aragonite saturation horizon shoaling at rates towards the higher end of those found in Pacific and Atlantic Ocean basins, making the Northeast Pacific one of the most sensitive regions to the invasion of anthropogenic carbon dioxide. Due to large variability in biogeochemical signals in coastal oceans, it is challenging to accurately assess carbon fluxes across different boundaries, such as tidal exchange between coastal wetlands and coastal oceans. Coastal salt marshes have been suggested to be a large net CO₂ sink, thus designated as a type of "blue carbon." However, accurate and dynamic estimates of carbon fluxes to and from tidal marshes are still premature, particularly carbon fluxes from marshes to the coastal ocean via tidal exchange, often referred to as marsh lateral fluxes. In this thesis, lateral total alkalinity (TA) and dissolved inorganic carbon (DIC) export fluxes were realistically quantified using high frequency time-series, in situ data. High-resolution fluxes permitted a closer look at how marsh generated TA and DIC are being exported over diurnal, spring-neap, and seasonal scales. I investigated the best way to capture variability of marsh exports via traditional bottle sampling and assessed uncertainties associated with different sampling strategies. Marsh TA and DIC exports significantly modified buffering capacity of coastal waters. This work contains the first realistic estimate of TA exports from a tidal salt marsh. Accurate estimates of DIC and TA fluxes indicate the significance of salt marshes to the coastal carbon and alkalinity budgets. / by Sophie Ning-Shin Chu. / 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. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references. / 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. / by Jonathan N. Blythe. / 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), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references. / Nitrogen (N) species in hydrothermal vent fluids serve as both a nutrient and energy source for the chemosynthetic ecosystems surrounding deep-sea vents. While numerous pathways have been identified in which N-species can be produced and consumed in the context of submarine hydrothermal vent systems, their exact nature has been largely limited to interpretation of variations in concentrations. This thesis applies stable isotope approaches to further constrain the sources and fate of N-species in deep-sea vents across a variety of geological settings. First, I discuss isotope fractionation and reaction kinetics during abiotic reduction of nitrate (NO₃⁻) to ammonium ([sigma]NH₄⁺ = NH₃+NH₄⁺) under hydrothermal conditions. Results of lab experiments conducted at high temperatures and pressures revealed a wide degree of N isotope fractionation as affected by temperature, fluid/rock ratio, and pH-all which exert control over reaction rates. / Moreover, a clear pattern in terms of reaction products can be discerned with the reaction producing [sigma]NH₄⁺ only at high pH, but both [sigma]NH₄⁺ and N₂ at low pH. This challenges previous assumptions that NO₃⁻ is always quantitatively converted to NH₄⁺ during submarine hydrothermal circulation. Next, I report measurements of [sigma]NH₄⁺ concentrations and N isotopic composition ([delta]¹⁵N[subscript NH4]) from vent fluid samples, together with the largest compilation to date of these measurements made from other studies of deep-sea vent systems for comparison. The importance of different processes at sediment-influenced and unsedimented systems are discussed with a focus on how they ultimately yield observed vent [sigma]NH₄⁺ values. / Notable findings include the role that phase separation might play under some conditions and a description of how an unsedimented site from Mid-Cayman Rise with unexpectedly high NH4+ may be uniquely influenced by N₂ reduction to [sigma]NH₄⁺. Lastly, I explore [sigma]NH₄⁺ dynamics in the context of low-temperature vent sites at 9°50'N East Pacific Rise to investigate dynamics of microbially-mediated N transformations. Through both measurements of natural samples, as well as isotopic characterization of N species from incubation experiments and model simulations thereof, an exceptionally high variability observed in [delta]¹⁵N[subscript NH4] values emphasizes the complexity of these microbe-rich systems. / In sum, this thesis highlights the role of microbial processes in low temperature systems, demonstrates a more mechanistic understanding of lesser-understood abiotic N reactions and improves the coverage of available data on deep-sea vent [sigma]NH₄⁺ measurements. / by Chawalit "Net" Charoenpong. / Ph. D. / 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)

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), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references. / The architecture of coral reef ecosystems is composed of coral skeletons built from the mineral aragonite (CaCO3). Coral reefs are currently being threatened by ocean acidification (OA), which may lower calcification rates, reduce skeletal density, and increase aragonite dissolution. Crystallography and chemistry are what govern the materials properties of minerals, such solubility and strength. Thus, understanding the mineralogical nature of coral aragonite and how it forms are important for predicting bulk skeletal responses under climate change. Different models based on geochemical versus biological controls over coral skeleton biomineralization propose conflicting predictions about the fate of corals under OA. Rather than investigating the mechanism directly, I use a mineralogical approach to study the aragonite end-products of coral biomineralization. / I hypothesize that coral mineralogy and crystallography will lend insights into how coral aragonite crystals form and how sensitive coral aragonite material properties may be to OA. Here I compare the crystallography, bonding environments, and compositions of coral aragonite with aragonite produced by other organisms (mollusk), synthetically (abiogenic precipitation in aragonite-supersaturated seawater and freshwater), and in natural geological settings (abiogenic). Coral aragonite crystallography does not resemble mollusk aragonite (aragonite formed with a strong biological influence), but rather is identical to abiogenic synthetic aragonite precipitated from seawater. I predict that the material properties of coral aragonite are similar to that of abiogenic synthetic seawater aragonites and that coral aragonite formation is sensitive to surrounding seawater chemistry. / To test the effect OA on coral aragonites, I studied deep-sea corals from a natural [omega][subscript sw], gradient (1.15-1.44) in the Gulf of Mexico and shallow-water corals across a natural [omega][subscript sw] (2.3-3.7) and pH (7.84-8.05) gradient in Palau. Minor shifts in crystallography are expressed by coral aragonite in these natural systems, likely governed by skeletal calcite contents, density, and [omega] of the coral calcifying fluid. My results are most consistent with a geochemical model for biomineralization, which implies that coral calcification may be sensitive to OA. However, further work is required to determine whether the modest crystallographic shifts I observe are representative on a global scale and whether they could influence bulk skeletal material properties. / by Gabriela A. Farfan. / Ph. D. / 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)

Thesis: Thesis (Ph. D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 126-137). / Although seawater appears uniform at scales that humans often interact with and sample, the world that marine microbes inhabit can be highly heterogeneous, with numerous biological and physical processes giving rise to resource hotspots where nutrient concentrations exceed background levels by orders of magnitude. While the impact of this microscale heterogeneity has been investigated in the laboratory with microbial isolates and theoretical models, microbial ecologists have lacked adequate tools to interrogate microscale processes directly in the natural environment. Within this thesis I introduce three new technologies that enable interrogation of microbial processes at the microscale in natural marine communities. The IFCB-Sorter acquires images and sorts individual phytoplankton cells, directly from seawater, allowing studies exploring connections between the diversity of forms present in the plankton and genetic variability at the single-cell level. / The In Situ Chemotaxis Assay (ISCA) is a field-going microfluidic device designed to probe the distribution and role of motility behavior among microbes in aquatic environments. By creating microscale hotspots that simulate naturally occurring ones, the ISCA makes it possible to examine the role of microbial chemotaxis in resource acquisition, phytoplankton-bacteria interactions, and host-symbiont systems. Finally, the Millifluidic In Situ Enrichment (MISE) is an instrument that enables the study of rapid shifts in gene expression that permit microbial communities to exploit chemical hotspots in the ocean. The MISE subjects natural microbial communities to a chemical amendment and preserves their RNA in a minute-scale time series. / Leveraging an array of milliliter-volume wells, the MISE allows comparison of community gene expression in response to a chemical stimulus to that of a control, enabling elucidation of the strategies employed by marine microbes to survive and thrive in fluctuating environments. Together, this suite of instruments enables culture-independent examination of microbial life at the microscale and will empower microbial ecologists to develop a more holistic understanding of how interactions at the scale of individual microbes impact processes in marine ecosystems at a global scale. / by Bennett S. Lambert. / Thesis (Ph. D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution) / Thesis(Ph.D.)--JointPrograminAppliedOceanScienceandEngineering(MassachusettsInstituteofTechnology,DepartmentofCivilandEnvironmentalEngineering;andtheWoodsHoleOceanographicInstitution)

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references. / Under global climate change, our oceans are warming at an unprecedented rate. Increased temperatures represent a severe source of stress for many marine organisms. This thesis aims to understand how corals and anemones respond to changing temperatures across different timescales and investigates mechanisms that can facilitate persistence in light of environmental change, from selection and adaptation across generations to phenotypic plasticity within a single individual's lifespan. In this context, I explore three case studies of thermal stress in corals and anemones. I begin with massive Porites lobata corals from the central Pacific. Here, reefs that are most affected by El Niflo, such as Jarvis and the northeast Phoenix Islands maintain genetic diversity indicating recruitment from nearby reefs may occur. Yet, they show significant genetic differentiation (FsT) from farther areas, suggesting this dispersal may be limited. / Thermal variability in this region may also favor plasticity over adaptation, as we do not find differences in bleaching histories among genetic groups. Next, I investigate genetic connectivity and adaptation to chronically elevated temperatures across a natural temperature gradient within the Palauan archipelago. Combining genetic data and historical growth measurements from coral cores, I find that Palau's warmest reefs harbor unique genetic subpopulations of Porites lobata and find evidence for a genetic basis of their higher thermal tolerance. Lastly, I explore if parents can modulate parental effects to increase the thermal tolerance of their offspring over short time scales, using the estuarine anemone Nematostella vectensis. Indeed, I find parents exposed to increased temperatures quickly produce more thermally tolerant larvae. In fact, offspring from these Massachusetts parents show thermal thresholds that are indistinguishable from more southern populations. / This thesis highlights the ability and potential of corals and anemones to persist under variable conditions over different timescales. Nevertheless, a compelling effort to reduce rates of warming worldwide will be imperative to the survival and integrity of key marine ecosystems such as coral reefs. / Funding for this research came from the National Science Foundation (Awards OCE- 1537338, OCE-1605365, OCE-1220529, and OCE-1031971), the Link Foundation, Bermuda Institute of Ocean Sciences Grants-in-Aid, the Tiffany & Co. Foundation, the Nature Conservancy, the Dalio Foundation, Inc., through the Dalio Explore Fund, and Ray Dalio through the WHOI Access to the Sea Fund, all to Anne Cohen; and a Gordon and Betty Moore Foundation grant (#4033) to Ann Tarrant / by Hanny Elizabeth Rivera. / Ph. D. / Ph.D. Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution)

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2017 / Cataloged from PDF version of thesis. / Includes bibliographical references. / Waves, currents, and bathymetric change observed along 11 km of the southern shoreline of Martha's Vineyard include storm events, strong tidal flows (> 2 m/s), and an inlet migrating 2.5 km in ~7 years. A field-verified Delft3D numerical model developed for this system is used to examine the hydrodynamics in the nearshore and their effect on the migrating inlet. An initial numerical experiment showed that the observed 700 tidal modulation of wave direction in the nearshore was owing to interactions with tidal currents, and not to depth-induced refraction as waves propagated over complex shallow bathymetry. A second set of simulations focused on the separation of tidal currents from the southeast corner of Martha's Vineyard, showing the positive correlation between flow separation and sediment transport around a curved shoreline. Observations of waves, currents, and bathymetric change during hurricanes were reproduced in a third numerical experiment examining the competition between storm waves, which enhance inlet migration, and strong tidal currents, which scour the inlet and reduce migration rates. The combined field observations and simulations examined here demonstrate the importance of wave and tidal current forcings on morphological evolution at timescales of days to months. / by Julia A. Hopkins. / Ph. D. / Ph.D. Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution)

Thesis: S.M., 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), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 53-58). / The Arctic surface air temperature has warmed nearly twice as much as the global mean since the mid-20th century. Arctic sea ice has also been declining rapidly in recent decades. There is still discussion about how much of this Arctic amplification is caused by local factors, such as changes in surface albedo, versus remote factors, such as changes in heat transport from the midlatitudes. This thesis focuses mainly on the role of poleward heat transport on Arctic amplification. Most of the previous studies on this topic have defined ocean heat transport as the zonally averaged ocean heat transport at 65°N or 70°N, which ignores the physical pathways of heat into the Arctic and may include recirculation of heat in the North Atlantic. In this thesis, we define the ocean heat transport as the heat transport across five sections surrounding the Arctic, to create a closed domain in the Arctic. / Previous studies on Arctic amplification have used either a single model run or have compared results from a multi-model ensemble. While the multi-model ensemble approach may potentially average out biases in individual models, the ensemble spread confounds the model differences and the internal climate variability. In this thesis, we investigate the Arctic amplification in the Community Earth System Model version 1 (CESMi) Large Ensemble. The CESMI Large Ensemble includes 40 members that use the same model and external forcing, but different initializations. This simulates different climate trajectories that can occur in a given atmosphere-ocean-land-cryosphere system. We find that CESMI Large Ensemble projects a large increase towards the end of the 21st century in ocean heat transport into the Arctic, and that the increase in ocean heat transport is significantly correlated with Arctic amplification. / The main contributor to the increase in ocean heat transport is the increase across the Barents Sea Opening. The increase in Barents Sea Opening ocean heat transport is highly correlated with the decrease in sea ice in the Barents-Kara Sea region. We propose that this is because the increase in ocean heat transport melts the ice at the sea ice margin, which results in increased surface heat flux from the ocean and further local feedback through decreased surface albedo and increased cloud coverage. We also find that while the changes in atmosphere heat transport into the Arctic circle at 66.5 N are on the same order as the changes in ocean heat transport, they are not correlated with Arctic amplification. / by Laura Elizabeth Fleming. / S.M. / S.M. 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)