A method for estimating deep, depth independent current variability is described. The procedure uses XBT derived dynamic heights to remove the near surface signal from altimetric sea surface height (SSH). The difference between SSH and dynamic height is operationally defined as barotropic height (BRT). Currents are obtained from BRT slopes using the geostrophic balance. The method requires the variability below the deepest XBT measurement to be small. Results are restricted to temporal variability, as geoid uncertainties in the SSH data render absolute current estimations impossible. The technique is originally developed for use in the Atlantic Western Boundary Current (WBC). Comprehensive verification of the methodology requires simultaneous SSH, XBT and current meter measurements. There are no available Atlantic data sets that meet these requisites. The alternative is to use synthetic data from the CLIPPER Atlantic model (1=6o resolution). Correlation (r) between estimated and modelled near bottom velocities in WBC areas of interest vary from 0.7 to 0.8. Further tests are conducted with observed data from the Shikoku Basin boundary current in southern Japan, where the method is capable of reproducing the directly measured near bottom current variability (r = 0:6). The procedure is also tested using north Pacific (5o ¡ 55oN) data from the OCCAM model. Correlations between model derived and BRT estimated velocities are around r = 0:7 for the Shikoku Basin northern boundary and for the Pacific WBC. Values reach r = 0:9 in large areas of the basin's interior, specially over smooth topography. The above method is used to generate time series of the barotropic variability in two areas of the Atlantic Western Boundary. One site is located at 38oN, inshore of the Gulf Stream. The other is at 8oS, off the Brazilian coast. Both series are a approximately 6 years long. Empirical Orthogonal Function analysis results conducted on SSH and sea surface temperature data are used to confirm the feasibility of applying the method in the chosen South Atlantic area. Currents are compared to scatterometer derived local along-shore wind stress and basin wide wind stress curl. In both areas, current variability is significantly correlated to basin averaged wind stress curl and and also to local along-shore wind stress. The relationship between currents and wind curl is coherent with the WBC response to interior Sverdrup flow. We propose that local wind stress exerts control over the flow by divergence of the Ekman flow at the coast. In the north, the variability is dominated by interannual oscillations of the wind curl. The effects of the local stress are secondary and have annual frequency. Both wind stress curl and along-shore wind are significantly correlated to the currents on the southern site, but the local effect appears to be the dominant forcing. The main observed results are confirmed by data from a numerical model with 1=6o horizontal resolution. / A Dissertation Submitted to the Department of Oceanography in Partial FulfiLlment of the Requirements for the Degree of Doctor of Philosophy. / Spring Semester, 2004. / November 7, 2003. / TOPEX, Atlantic, Western Boundary, Variability / Includes bibliographical references. / Georges L. Weatherly, Professor Directing Thesis; Steven L. Blumsack, Outside Committee Member; William M. Landing, Committee Member; Doron Nof, Committee Member; James O'Brien, Committee Member; Kevin Speer, Committee Member.

The variations in the sea breeze are examined both diurnally and interannually along the panhandle of Florida during the boreal summer season. A climatology of sea breeze cross sections is calculated eight times daily between the years 1979 and 2001 to examine diurnal differences. The cross sections are created using very high resolution dynamically downscaled analyses from the NCEP-DOE (R2) and the ECMWF ERA-40 for the southeast U.S. The high resolution downscaled product is validated with other independent observations to show fidelity. Results from these diurnal analyses show that the sea breeze and precipitation peak at 4:00 p.m. The interannual variability of the sea breeze is examined with respect to the Atlantic Warm Pool (AWP). Composites consisting of Climate Prediction Center (CPC) precipitation observations are created based on the size of the AWP. These composites show that the strongest low-frequency signal is a negative anomaly along the panhandle. Therefore, model composite cross sections are primarily along the 30.5°N latitude. The cause of the negative anomaly is related to the subtropical high, which undergoes an eastward shift and a decrease in intensity for large AWP years. These changes in the subtropical high lead to a more cyclonic large-scale low-level flow for large AWP years as Sverdrup vorticity balance indicates. This study finds that this synoptic flow pattern will suppress the sea breeze circulation and lessen precipitation amounts over the panhandle region. / A Thesis Submitted to the Department of Earth, Ocean, and Atmospheric Science in Partial Fulfillment of the Requirements for the Degree of Master of Science. / Summer Semester, 2011. / April 28, 2011. / Bermuda High, Atlantic Warm Pool, Sverdrup Vorticity Balance, interannual variations / Includes bibliographical references. / Vasubandhu Misra, Professor Directing Thesis; James J. O’Brien, Professor Co-Directing Thesis; Henry Fuelberg, Committee Member; Mark Bourassa, Committee Member.

Large portions of the world ocean are less productive than they should be based on their nutrient concentrations. Dubbed high-nutrient low-chlorophyll (HNLC) regions, primary productivity in these areas may be limited by any number of factors including high zooplankton grazing rates as well as light and silicon limitation but, in general, iron (Fe) appears to most often be the factor limiting production. With approximately 30% of the world ocean comprised of Fe-limited HNLC waters, it is clear that the input of Fe to these waters, and its subsequent bioavailability, has an important role in stimulating primary productivity and lowering pCO2 possibly moderating the rise of atmospheric CO2 concentrations and therefore could influence the planet's climate. The work described in this dissertation represents an effort to characterize the elemental solubility, including Fe, of marine aerosols. The research was conducted on four oceanographic research cruises in the North Atlantic and Pacific Oceans. In total, over 170 aerosol samples were collected in both total and size-fractionated samples. Precipitation events were sampled when possible to characterize the wet deposition of marine aerosols. The data will constrain estimates of aerosol Fe deposition to HNLC regions and improve models of the global carbon cycle. Elemental solubilities were measured using both seawater and ultrapure deionized water leaching methods under trace metal clean conditions. Leaching of the aerosol samples was conducted using a rapid exposure, small volume technique. Ultrapure deionized water leaches were analyzed directly by high resolution inductively coupled plasma mass spectrometer (HR-ICP-MS), a relatively simple analysis technique. Soluble Fe in seawater leaches was analyzed by HR-ICP-MS following column extraction. Additionally, soluble aerosol Fe(II) was measured on four of the cruises. The sampling and analytical methods will be discussed in this dissertation and the results compared with similar studies of aerosol chemistry. The relationship between seawater and deionized water leaching was investigated to evaluate the applicability of the relatively simple ultrapure water technique to prediction of aerosol solubility in seawater. Elemental solubility behavior was analyzed within the context of a host of potential controlling factors including aerosol acidity, source region, and elemental composition among others. The results from these research cruises suggest that aerosol Fe solubility is relatively consistent globally. The solubility of aerosol Fe in deionized water was calculated to be ~12% and ~9% in filtered surface seawater. Aerosol Fe solubility percentage showed no significant correlation with the concentration of acidic aerosol species. The episodic nature of dust events was apparent from the highly variable measured concentrations of aerosol material and no apparent first order relationship existed between the concentration of crustal aerosol species (i.e. Fe) and their respective concentrations in the surface ocean. A robust relationship was found between the concentrations of the ultrapure deionized water and seawater soluble aerosol Fe and a predictive power law equation was derived. / A Dissertation submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2008. / June 4, 2008. / Aerosol Solubility, Mineral Dust, Atlantic Ocean, Pacific Ocean, Aluminum, Iron / Includes bibliographical references. / William M. Landing, Professor Directing Dissertation; Henry Fuelberg, Outside Committee Member; William Burnett, Committee Member; Joel Kostka, Committee Member; Thorsten Dittmar, Committee Member.

This study addresses the issue of global and regional cloud cover forecasts. Using a suite of global models, the multimodel superensemble forecasts are constructed for total cloud coverage and layered (low, middle, and high) cloud coverage out to 7 days (168 hours). The experiments were conducted on a 1° latitude by 1° longitude spatial grid at a 24 hour temporal resolution. The multimodel superensemble carries a training and a forecast phase. Several training periods were used to determine an optimal training phase. The total period of this study includes October 2006 through February 2007. Clouds from the International Satellite Cloud Climatology Project (ISCCP) were used for training and cloud validations. The metrics for the forecast evaluation include the root mean square errors, spatial correlations, and equitable threat scores. The results show a significant improvement (~25%) of the multimodel superensemble forecasts compared to those from the member models forecasts, as well as their ensemble mean for the global and regional domains. / A Thesis submitted to the Department of Meteorology in partial fulfillment of the requirements for the degree of Master of Science. / Summer Semester, 2010. / April 20, 2010. / Cloud Forecasting, Superensemble / Includes bibliographical references. / T. N. Krishnamurti, Professor Co-Directing Thesis; Paul Ruscher, Professor Co-Directing Thesis; Guosheng Liu, Committee Member; Vasu Misra, Committee Member.

The formation of cold core filaments on an idealized continental shelf is investigated using a numerical model to simulate the ocean's response to surface cooling. A horizontal density gradient forms because of uneven buoyancy loss due to the sloping bottom, and this gradient induces an alongshelf current in thermal wind balance, that in time becomes unstable. As the instabilities grow, filaments, and later eddies, are generated so that dense water near the coast is mixed offshore. Scaling arguments of the filament wavelength indicate that the current is baroclinically unstable, and an analytical model of the frontal expansion with time is in very good agreement with the simulations. This study was inspired by satellite observations of sea surface temperature on the West Florida Shelf during the winter months, in which it is clearly seen that cold core filaments extend from a thermal front. Numerical experiments are therefore designed to allow for reliable comparisons with conditions in this region. / A Dissertation submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2004. / December 5, 2003. / Eddies, Baroclinic Instability, Filaments, Numerical Modeling, Shelf / Includes bibliographical references. / James J. O’Brien, Professor Directing Dissertation; Steven L. Blumsack, Outside Committee Member; Doron Nof, Committee Member; Allan J. Clarke, Committee Member; William Landing, Committee Member; Steven L. Morey, Committee Member.

The Floridan Aquifer consists of a series of conduits within a limestone matrix. Pollutants from sinking streams can be carried into the contiguous matrix and remain there after a short stay in the conduits. This retention, called sequestration, can significantly influence the transport and fate of the pollutants. A laboratory simulation has been performed in a flushable apparatus to study sequestration mechanisms and solute transport in the aquifer, in which glass beads represented the limestone matrix and NaCl acted as a solute, or a tracer. Two categories of experiments were performed for sequestration, simulating the alteration of the hydrological seasons, referred to as shear flow and radial flow respectively. Each experiment included three coherent phases: 1) the sequestration, 2) the release of the sequestered solute, and 3) the mixing-transport of the released solute by the conduit flow. An indirect methodology measuring the breakthrough curves (BTCs) was used to obtain the sequestration volume and tracer distribution in the porous medium. The leading and secondary sequestration mechanisms and their magnitudes were resolved for both categories. Gelhar and Collin's approximate analytical solution was used to model the radial-flow sequestration. The releasing process from the medium was modeled by an advection-dispersion equation. An advection model for the mixing-transport of the released tracer was solved analytically through characteristics using a parameter method; a better advection-dispersion model incorporating conduit dispersion was also developed and solved numerically. The model of shear-flow sequestration is mechanism-oriented. For large Reynolds numbers, Re, the distributions of the sequestered tracer were simulated by a semi-Lagragian advection model with particle tracking; for small Re, a two-stage diffusion model was used. The tracer distribution in the medium for high and intermediate Re was also inverted from the measured BTCs. The successful regeneration of the distribution of sequestered tracer in the medium, the tracer flux at the conduit wall and the BTCs shows that these models are effective in describing groundwater flow and solute interaction between a conduit and matrix, and provide a potential capability for prediction of solute transport and retention in a karstic aquifer. / A Dissertation submitted to the Program in Geophysical Fluid Dynamics in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2004. / November 1, 2004. / Transport, Aquifer, Contaminant, Groundwater, Karst, Breakthrough Curve / Includes bibliographical references. / David E. Loper, Professor Directing Dissertation; Gordon Erlebacher, Outside Committee Member; Ruby E. Krishnamurti, Committee Member; Amy B. Chan Hilton, Committee Member; Sergio Fagherazzi, Committee Member.

Chromophoric dissolved organic matter (CDOM) was quantified by colorimetric light absorption for five blackwater intermittent streams draining into sinks (swallets) connected to the Floridan Aquifer underlying the Woodville Karst Plain, Wakulla County, Florida. Munson Slough receives drainage from the city of Tallahassee and the other streams; Fisher Creek, Black Creek, Jump Creek, and Lost Creek drain the Apalachicola National Forest. Previously conducted dye trace injections have shown the disappearing waters contribute to the discharge of Wakulla Springs, a first magnitude spring. Stage-discharge rating curves were developed for Black Creek and Jump Creek. Wakulla Springs CDOM was determined using UV-VIS spectrophotometry with a 10 cm path length and correlated to total organic carbon concentrations. The year-long study period included a two-month long baseflow period, followed by 12 inches of precipitation, an increase in discharge from 400 cfs to 1700 cfs, and a 41- day recession curve for Wakulla Springs. The Wakulla Springs 2009 water clarity extremes contained 28 percent (poorest water clarity) to 0.5 percent (best water clarity) stream water. The total CDOM mass associated with the streams exceeds the Wakulla Springs mass following storm events, indicating that some mass bypasses Wakulla Springs or is stored in the matrix/conduit aquifer system to be later released. Total stream mass equals Wakulla Springs mass for low baseflow conditions, but for higher baseflow, Wakulla Springs mass exceeds the total stream mass, indicating Wakulla Springs is still discharging mass from the preceding storm. This delayed mass is either from aquifer matrix/conduit storage or from the slower Lost Creek pathway. The storm mass associated with any one stream exceeds the Wakulla Springs lower baseflow mass by 4 to 9 times (for the two lowest mass streams) and has the ability to affect Wakulla Springs water clarity without contribution from any other stream. All of the water filled caves connected to Wakulla Springs contribute CDOM, with wet conditions contributing 25-67 percent more CDOM. A Wakulla Springs transmittance of 99 percent would have a NAC254nm of 0.1 and a TOC concentration of 0.69 mg/l. With the Wakulla Springs baseflow CDOM mass range of 600-1000 kg/day, this concentration indicates that the Floridan Aquifer clear water baseflow discharge will need to be 350-600cfs (10-17cms) to provide the necessary dilution for the bottom of the Wakulla Springs basin to be viewed with the water clarity of historic times. Investigation of upgradient Floridan aquifer water use indicated no change for the potentiometric surface entering Florida, but declines up to 16 feet were noted for northern Leon County, based on the 2008 potentiometric surface. Groundwater withdrawals by municipalities, Consumptive Use Permits, and private wells totaled 14,500 MGY for Leon and Wakulla counties or 9 percent of the 164,000 MGY discharged by Wakulla Spring in 2009. A decline in precipitation for the most recent decade, 1999-2009, was noted that may contribute, but groundwater use is the most likely cause of the decreased water clarity water. Wakulla Springs has an increasing trend for total dissolved solids and specific conductivity indicating a greater contribution of deep Floridan Aquifer water. More research is needed to understand vertical and lateral upgradient flow within the Floridan Aquifer and the fluctuating controls that either direct creek water to Wakulla Springs or result in it bypassing Wakulla Springs. / A Thesis submitted to the Department of Earth, Ocean and Atmospheric Science in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester, 2010. / October 18, 2010. / water clarity, absorption coefficient, transmittance, spectrophotometer, colorimeter / Includes bibliographical references. / Stephen A. Kish, Professor Directing Thesis; William C. Parker, Committee Member; Ming Ye, Committee Member.

The wind-driven oceanic circulation in the presence of bottom topography that isopycnals intersect is examined in an idealized setting. A modified quasi-geostrophic (QG) model has been designed and implemented. The model allows staircase bottom topography: topographic breaks decompose the lateral domain into subdomains consisting of fixed numbers of layers. Topographic shelves are placed within small (order Rossby number) vertical distances from the undisturbed layer interfaces. Each shelf can have topographic variations of the same scale. An elliptic solver inverting potential vorticity into geostrophic stream functions was designed based on the Capacitance matrix method. Solutions are matched at the topographic breaks by adding fictitious potential vorticity sources. The model has been tested against the problem of trapped topographic waves over a cliff. The results obtained for small-steepness disturbances agree with a weakly non-linear theory developed by Dewar and Leonov. Steeper disturbances break in a way that favors on shelf eddy detachment and transport of undiluted properties onto the shelf. The model has been further applied to the basin-scale wind-driven circulation problem in a 3-layer configuration with a continental shelf in the western part of the domain. Double-gyre wind forcing has been considered. The topographic shelves are responsible for dynamics absent in classical idealized eddy resolving QG models which have been the preferred numerical tool for the study of low frequency intrinsic ocean variability. The top-layer flow interacts with the shelf topography by means of vortex tube stretching and vorticity dissipation due to bottom drag. This mechanism reduces the role of horizontal friction as a controlling factor in the dynamics.The results obtained for different parameter regimes (free-slip, no-slip boundary condition, different values of the viscosity) show reduced sensitivity to the type of dynamic boundary condition, compared to classical results. The intrinsic variability of the flow is affected by the new mechanism of on- and off shelf transport of potential vorticity. The role of horizontal friction is again reduced, as shown by the modeling results. Spatiotemporal patterns of the variability have been analyzed. Most of the patterns are insensitive to the type of boundary condition (free-slip vs. no-slip), and qualitatively resemble classical no-slip results. / A Dissertation submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2005. / May 31, 2005. / Wind-Driven Circulation, Decadal Climate Variability, Ocean Intrinsic Variability, Finite Topography, Trapped Topographic Waves / Includes bibliographical references. / William K. Dewar, Professor Directing Thesis; Ionel Michael Navon, Outside Committee Member; Allan J. Clarke, Committee Member; William M. Landing, Committee Member; James C. McWilliams, Committee Member; Doron Nof, Committee Member; Melvin E. Stern, Committee Member.

Gridded QuikSCAT data has been used to show that a strong confluence zone of the Southeast Pacific Intertropical Convergence Zone (SITCZ) existed in 2000 – 2002 during boreal spring, and the Panama wind jet contributes to its variability. Time series analysis of winds off the Gulf of Panama and convergence advection into the Southern Hemisphere (from 80W to 95W) show these winds kept the SE Trades out of the Northern Hemisphere and created a confluent zone in the Southern Hemisphere. A monthly averaged SITCZ is maintained by the deceleration of the SE Trades that flow from warm water toward the equatorial cold tongue, creating a speed convergent zone south of the equator. Images of wind trajectories show zonally orientated SE Trade winds that were deflected from a divergent zone parallel to the coast of South America converge with more meridional Trades over warm waters. Panamanian winds crossed into the Southern Hemisphere to contribute to this convergence. It is hypothesized that this confluent zone can be intensified by the Panamanian winds. In 2002, the SITCZ confluent zone occurred with more intense Panamanian gap flow than the previous two years. Cross equatorial SE Trades wrapped anti-cyclonically around a divergent pocket in the Northern Hemisphere and became southward winds, which allowed the Panamanian winds to enter the Southern Hemisphere and intensify the SITCZ. Variability in the Panamanian winds makes a substantial contribution to the evolution of the SITCZ. / A Thesis submitted to the Department of Meteorology in partial fulfillment of the requirements for the degree of Master of Science. / Summer Semester, 2004. / July 8, 2004. / Central American Wind Jets / Includes bibliographical references. / James J. O’Brien, Professor Directing Thesis; Mark. A. Bourassa, Committee Member; Guosheng Liu, Committee Member.

Dinoflagellates are unicellular, eukaryotic organisms that consist of both photosynthetic and non-photosynthetic species. The approximately 91 known species of bioluminescent dinoflagellates are the pre-dominate contributors to ocean surface bioluminescence. These species are distributed throughout the world, but are generally located in channels, seas, straits, and along coastlines. The bioluminescent properties of dinoflagellates can pose a threat for naval applications. Bioluminescence generated by submarine and SDV operations in coastal areas can result in increased vessel visibility. The initial steps of my research involved testing various chemical agents and physical factors that might be used to mitigate dinoflagellate bioluminescence in situ. I identified formaldehyde as the only chemical compound among many common compounds tested that successfully mitigated dinoflagellate bioluminescence. Formaldehyde was used in the form of formalin, a solution consisting of 37% formaldehyde and methanol as a stabilizing agent. Next, I performed experiments applying shear stress through a stirrer, and used photon counting to determine the extent and time-course of bioluminescence mitigation by formaldehyde in 1.0, 2.5, and 4.6 percent concentrations. Those concentrations were chosen to bracket the formaldehyde concentration commonly used to preserve phytoplankton samples. There was an initial, short-term burst in bioluminescence upon addition of formaldehyde, as formalin, to cultures of the two species before formaldehyde limited bioluminescence, presumably caused by denaturation of compounds in the bioluminescence apparatus. The initial burst lasted 34.6 seconds at 1.0 percent formaldehyde, 9.8 seconds at 2.5 percent formaldehyde, and 8.4 seconds at 4.6 percent formaldehyde for Lingulodinium polyedrum. After the initial burst, bioluminescence output of both Pyrocystis lunula and L. polyedrum was reduced by formaldehyde. For L. polyedrum, the effect was rapid for all concentrations tested, with a 100 percent bioluminescence reduction upon stirring one minute after formalin was added. Bioluminescence continued after administration of formalin, resulting in an afterglow effect for P. lunula. However, L. polyedrum, a species more typical of bioluminescent dinoflagellates found in marine waters compared to P. lunula, did not exhibit the afterglow effect after formalin administration. / A Thesis submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester, 2006. / August 4, 2006. / Calcium Channel, AI Hypothesis, Tensegrity Network, Scintillons, Phytoplankton, Luciferin, Luciferase, Shear Stress, Formalin, Action Potential / Includes bibliographical references. / Richard Iverson, Professor Directing Thesis; Markus Huettel, Committee Member; Behzad Mortazavi, Committee Member.