Thesis (Ocean E.)--Joint program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering and Woods Hole Oceanographic Institution), 1999. / Includes bibliographical references (p. 127-128). / Acoustic coded signaling offers potentially significant improvements over traditional "toneburst" methods in many underwater applications where error due to noise and multipath interference is a problem. In this thesis, the use of these spread spectrum techniques is analyzed for navigation of the REMUS autonomous underwater vehicle. The accuracy of the current system using Turyn and Barker sequences, as well as toneburst, is quantified, and the sources of the remaining error are examined. / by Benjamin Kerbin Evans. / Ocean E.

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), 2005. / Includes bibliographical references. / The geographic distribution and dynamics of coastal benthic populations are shaped by physical - biological interactions affecting larval dispersal and the demography of juvenile and adult individuals. This thesis focused on nearshore patterns of larval distribution and regional patterns in demography of intertidal barnacles in Southern and Baja California. Horizontal and vertical distributions, and the mortality rates of larvae, were assessed from short term (i.e. days) small- scale observations (0.1-1 km) in nearshore waters. Observations on spatial variability of adult barnacle demography were gathered over 1.5 years at scales of hundreds of kilometers. Stage-specific horizontal distributions and nearshore current measurements suggested that larvae of Balanus g-landula and Chthamalus spp. may experience limited dispersal. High mortality rates could further limit travel distances and the exchange of individuals among disjunct populations. Data on vertical distributions indicated that nauplii and cyprids of Balanus nubilus and Pollicipes polymerus occur at different depths. Nauplii remained near the surface at all times, whereas cyprids occurred in the bottom half of the water column. / (cont.) Such distributions, combined with vertical variability in horizontal flows, might cause the observed horizontal segregation of nauplii and cyprids. Differences in survival, growth rate, size structure, and per capita fertility of adult Balanus glandula were observed between Dana Point (Southern California) and Punta Baja (Baja California), a site located near the species' southern limit of distribution. Effects of spatial differences in demography on population persistence were assessed with a stage-structured matrix model. Model analyses indicated that the Punta Baja population is more susceptible to environmental stochasticity and more prone to local extinction than populations located further north. This thesis emphasizes the importance of characterizing factors that affect the dynamics of benthic populations at multiple spatial-temporal scales, and the usefulness of small scale high- frequency observations of nearshore phenomena, especially in relation with the dispersal of larvae. / by Fabián J. Tapia. / Ph.D.

Thesis (Ph. D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science; and the Woods Hole Oceanographic Institution), 2006. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Also issued in pages. Barker Engineering Library copy: issued in pages. / Includes bibliographical references (leaves 193-[201]). / The first part of the dissertation investigates the application of the theory of large random matrices to high-dimensional inference problems when the samples are drawn from a multivariate normal distribution. A longstanding problem in sensor array processing is addressed by designing an estimator for the number of signals in white noise that dramatically outperforms that proposed by Wax and Kailath. This methodology is extended to develop new parametric techniques for testing and estimation. Unlike techniques found in the literature, these exhibit robustness to high-dimensionality, sample size constraints and eigenvector misspecification. By interpreting the eigenvalues of the sample covariance matrix as an interacting particle system, the existence of a phase transition phenomenon in the largest ("signal") eigenvalue is derived using heuristic arguments. This exposes a fundamental limit on the identifiability of low-level signals due to sample size constraints when using the sample eigenvalues alone. The analysis is extended to address a problem in sensor array processing, posed by Baggeroer and Cox, on the distribution of the outputs of the Capon-MVDR beamformer when the sample covariance matrix is diagonally loaded. / (cont.) The second part of the dissertation investigates the limiting distribution of the eigenvalues and eigenvectors of a broader class of random matrices. A powerful method is proposed that expands the reach of the theory beyond the special cases of matrices with Gaussian entries; this simultaneously establishes a framework for computational (non-commutative) "free probability" theory. The class of "algebraic" random matrices is defined and the generators of this class are specified. Algebraicity of a random matrix sequence is shown to act as a certificate of the computability of the limiting eigenvalue distribution and, for a subclass, the limiting conditional "eigenvector distribution." The limiting moments of algebraic random matrix sequences, when they exist, are shown to satisfy a finite depth linear recursion so that they may often be efficiently enumerated in closed form. The method is applied to predict the deterioration in the quality of the sample eigenvectors of large algebraic empirical covariance matrices due to sample size constraints. / by Rajesh Rao Nadakuditi. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2009. / Includes bibliographical references. / 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 (<0.4[mu]m 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. / by Phoebe Dreux Chappell. / S.M.

Thesis (Ph.D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2000. / Includes bibliographical references (p. 299-312). / by Sean Patrick McKenna. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2006. / Includes bibliographical references. / Two years of moored oceanographic and automatic weather station data which span the winter ice seasons of 2001-2003 within Marguerite Bay on the western Antarctic Peninsula (wAP) shelf were collected as part of the Southern Ocean Global Ocean Ecosystems Dynamics program. In order to characterize the ice environment in the region, a novel methodology is developed for determining ice coverage, draft and velocity from moored upward-looking acoustic Doppler current profiler data. A linear momentum balance shows the importance of internal ice stresses in the observed motion of the ice pack. Strong inertial, not tidal, motions were observed in both the sea ice and upper ocean. Estimates of upward diapycnal fluxes of heat and salt from the Upper Circumpolar Deep Water to the surface mixed layer indicate almost no contribution from double diffusive convection. A one-dimensional vertical mixed layer model adapted for investigation of mixing beneath an ice-covered ocean indicates that the initial wind event, rather than subsequent inertial shear, causes the majority of the mixing. This work points towards episodic wind-forced shear at the base of the mixed layer coupled with static instability from brine rejection due to ice production as a major factor in mixing on the wAP shelf. / by Jason Hyatt. / Ph.D.

Thesis (S.M.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (leaves 70-72). / The uncertainty in the determination of the momentum and scalar fluxes remains one of the main obstacles to accurate numerical forecasts in low to moderate wind conditions. For example, latent heat fluxes computed from data using direct covariance and bulk aerodynamic methods show that there is good agreement in unstable conditions when the latent heat flux values are generally positive. However, the agreement is relatively poor in stable conditions, particularly when the moisture flux is directed downward. If the direct covariance measurements are indeed accurate, then they clearly indicate that the bulk aerodynamic formula overestimate the downward moisture flux in stable conditions. As a result, comparisons of the Dalton number for unstable and stable conditions indicate a marked difference in value between the two stability regimes. Investigations done for this thesis used data taken primarily at the Air-Sea Interaction Tower (ASIT) during the Coupled Boundary Layers and Air-Sea Transfer (CBLAST) Experiment 2003 from the 20-27 August 2003. Other data from the shore based Martha's Vineyard Coastal Observatory (MVCO) and moored buoys in the vicinity of the ASIT were also incorporated. / (cont.) During this eight day period, the boundary layer was often characterized by light winds, a stably stratified surface layer and a swell dominated wave field. Additionally, the advection of warm moist air over cooler water resulted in fog formation and a downward flux of moisture on at least three occasions. Therefore, a primary objective of this thesis is to present a case study to investigate the cause of this shortcoming in the bulk formula under these conditions by examining the physical processes that are unique to these boundary layers. Particular attention will be paid to the behavior of the Dalton number in a stable marine atmospheric boundary layer under foggy conditions using insights derived from the study of fog formation and current flux parameterization methods. / by Robert Farrington Crofoot. / S.M.

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), February 2013. / "February 2013." Cataloged from PDF version of thesis. / Includes bibliographical references. / Intact polar diacylglycerolipids (IP-DAGs) were used to study microbial dynamics in the surface ocean. IP-DAGs from surface ocean seawater were quantified using high performance liquid chromatography-mass spectrometry (HPLC-MS), after first developing a sensitive, high throughput molecular ion independent triple quadrupole MS method for quantification. Using this analytical technique I examined the distribution of the nine most abundant classes of IPDAGs across the Mediterranean, and found that phospholipids as a percent of total IP-DAGs correlated with phosphate concentration. Furthermore, phospholipids were a higher percent of total particulate phosphorus where phosphate was higher, ranging from 1-14%. Thus IP-DAGs can play not only a significant but also a dynamic role in defining planktonic nutrient needs and cellular C:N:P ratios in the environment. Additionally, microcosm incubations were amended with phosphate and ammonium, and in the course of several days this elicited a shift in the ratios of IP-DAGs. This study was the first to demonstrate the dynamic response of membrane lipid composition to changes in nutrients in a natural, mixed planktonic community, and indicated that the change in IP-DAG ratios in response to changing nutrients may be a useful indicator of microbial nutrient stress. In the surface waters of the western North Atlantic I used three experimental approaches to identify the microbial sources of the nine most abundant classes of IP-DAGs. Phytoplankton are the primary source of one class of sulfolipid, sulfoquinovosyldiacylglycerol, and one class of betaine lipid, diacylglyceryl-trimethyl-homoserine, while heterotrophic bacteria are the dominant source of the phospholipids phosphatidylglycerol and phosphatidylethanolamine. In regrowth experiments in the Sargasso Sea and the North Pacific I demonstrated that phospholipid specific production rate is representative of heterotrophic bacterial cell specific growth rate. I measured phospholipid specific production rate and bacterial production rate using uptake of 3H-leucine (³H-Leu) and 3H-thymidine (³H-TdR) across the North Atlantic, across the Mediterranean, and in the North Pacific subtropical gyre. I found that phospholipid specific production rates estimate heterotrophic bacterial cell specific growth rates that are on the order of 1 per day, an order of magnitude faster than cell specific growth rates suggested by uptake of ³H-Leu and ³H-TdR. / by Kimberly J. Popendorf. / 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), 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 (S.M.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (p. 63-65). / Hydrothermal vents discharge superheated, mineral rich water into our oceans, thereby providing a habitat for exotic chemosynthetic biological communities. Hydrothermal fluids are convected upwards until they cool and reach density equilibrium, at which point they advect laterally with the current. The neutrally buoyant plume layer can have length scales on the order of several kilometers, and it therefore provides the best means to detect the presence of vent fields on the seafloor, which typically have length scales on the order of a few meters. This thesis uses field measurements of the velocity, temperature and particulate anomalies associated with the TAG hydrothermal plume to demonstrate that tidal currents exert a strong impact on the plume shape, and to provide new constraints on the thermal power of the TAG hydrothermal system. The results show that the power output of the TAG system is on the order of 6000 MW, which is up to two orders of magnitude greater than previous estimates, and that there is considerably more entrainment than had previously been assumed. / by Sacha Wichers. / S.M.