This thesis describes the collection, analysis and interpretation of data on sensible heat transfer into the atmosphere from three sparsely vegetated sites: a vineyard and legume crop in Spain, and a savannah bush site in Niger. The viability of using measurements of the variance of air temperature to determine sensible heat flux is investigated. Monin-Obukhov similarity theory is reviewed, with particular emphasis on its limitations and asymptotes. The physical interpretation and relative magnitudes of zero-plane displacement and roughness length for heat and momentum transfer are examined. A heat flux measurement system based on measuring fluctuations of temperature is developed, and its results compared with eddy correlation measurements in both Spain and Niger. The surface temperatures of the various components of a sparsely vegetated surface are compared with the area-averaged radiometric temperature. It is shown that, for sparsely vegetated surfaces, this radiometric surface temperature may be much lower than the "aerodynamic" surface temperature required by similarity theory. Values of Z_0h, the roughness length for heat transfer, are calculated for all three sites. These are found to be smaller than for uniform vegetation, and to vary with wind speed by several orders of magnitude. A review of the physics of heat and momentum transfer is undertaken to explain this phenomenon. It is demonstrated that Z_0h is a function of both heat and momentum transfer, and that it can be expected to vary with wind speed. This effect is masked for uniform vegetation, but is amplified for sparse vegetation by the relatively low efficiency of heat transfer. This explains the observed behaviour of Z_Oh on the three field sites. Historical measurements of Z_0 and Z_0h over a variety of surfaces are reviewed and reinterpreted in terms of heat and momentum transfer properties.

The links between climate and permafrost are well known, but the precise nature of the relationship between air and ground temperatures remains poorly understood, particularly in complex mountain environments. Although previous studies indicate that elevation and potential incoming solar radiation (PISR) are the two leading factors contributing to the existence of permafrost at a given location, additional factors may also contribute significantly to the existence of mountain permafrost, including vegetation cover, snow accumulation and the degree to which individual mountain landscapes are prone to air temperature inversions. Current mountain permafrost models consider only elevation and aspect, and have not been able to deal with inversion effects in a systematic fashion. This thesis explores the relationship between air and ground surface temperatures and the presence of surface-based inversions at 27 sites within the Wolf Creek basin and surrounding area between 2001 and 2006, as a first step in developing an improved permafrost distribution TTOP model. The TTOP model describes the relationship between the mean annual air temperature and the temperature at the top of permafrost in terms of the surface and thermal offsets (Smith and Riseborough, 2002). Key components of this model are n-factors which relate air and ground climate by establishing the ratio between air and surface freezing (winter) and thawing (summer) degree-days, thus summarizing the surface energy balance on a seasonal basis. Here we examine (1) surface offsets and (2) freezing and thawing n-factor variability at a number of sites through altitudinal treeline in the southern Yukon. Thawing n-factors (nt) measured at individual sites remained relatively constant from one year to the next and may be related to land cover. During the winter, the insulating effect of a thick snow cover results in higher surface temperatures, while thin snow cover results in low surface temperatures more closely related to the winter air temperatures. The application of n-factor modeling techniques within the permafrost region, and the verification of these techniques for a range of natural surfaces, is essential to the determination of the thermal and physical response to potential climate warming in permafrost regions. The presence of temperature inversions presents a unique challenge to permafrost probability mapping in mountainous terrain. While elsewhere the existence of permafrost can be linearly related to elevation, the presence of frequent inversions challenges this assumption, affecting permafrost distribution in ways that the current modeling techniques cannot accurately predict. At sites across the Yukon, inversion-prone sites were predominantly situated in U-shaped valleys, although open slopes, mid-slope ridges and plains were also identified. Within the Wolf Creek basin and surrounding area, inversion episodes have a measurable effect on local air temperatures, occurring during the fall and winter seasons along the Mount Sima trail, and year-round in the palsa valley. Within the discontinuous permafrost zone, where average surface temperatures are often close to zero, even a relatively small change in temperature in the context of future climate change could have a widespread impact on permafrost distribution.

Denitrification in coastal sediments is a process of significant scientific interest and a major concern in coastal management. Reliable estimates of denitrification in coastal ecosystems are unavailable due in large part to a lack of understanding of the factors affecting spatial and temporal variability. The following studies are put forward as an attempt to help fill that gap in our understanding of this critical environmental process. These studies were conducted to test the hypotheses that significant spatial and temporal variability exists in the denitrification potential of coastal and continental shelf sediments of the Gulf of Mexico and that this variability is governed by environmental parameters including dissolved inorganic nitrogen, sediment organic composition, sediment porosity, bottom water dissolved oxygen concentration, sediment nitrification, and water temperature. Studies were conducted in two systems representing end member states in terms of anthropogenic nutrient loading. Apalachicola Bay, FL is relatively pristine estuary. The Louisiana Continental Shelf (LCS) is subject to the discharge of the Mississippi River and is the location of the largest area anthropogenic bottom water hypoxia in the Western Hemisphere. Sediment porosity was found to be the single most important factor relating to the spatial variability of denitrification potential. Sediment organic composition was closely correlated with denitrification potential in Apalachicola Bay but not on the Louisiana Continental Shelf. The effect of porosity on denitrification potential does not appear to be a function of sediment organic composition and may be due to the catalytic enhancement of microbial metabolism by mineral surfaces. Denitrification potential was generally higher on the Louisiana Continental Shelf than in Apalachicola Bay, FL. Seasonal variability in denitrification was observed both in Apalachicola Bay and on the LCS with peak rates occurring in the summer months. Significant inter annual variability in denitrification potential and its relationship to nitrification potential were observed on the LCS. These inter-annual differences are likely the result of the higher rate of nitrogen delivery from the Mississippi River in 2001 as compared to 2000. Higher nutrient loading in 2001 reduced the dependence of denitrifiers on nitrifiers allowing the two processes to become uncoupled. Thus, it appears that variability in the climactic factors that drive nutrient loading regulates the inter-annual variability in peak summer denitrification while seasonal factors such as temperature and primary productivity drive shorter-term seasonal changes in nitrogen cycling. Alternatively, contemporaneous spatial variability in denitrification potential seems to be driven by differences in sediment porosity that control bacterial abundance through the enhanced catalytic activity of mineral surfaces. Use of the acetylene block method for determining denitrification potential is discussed, including an assessment of the legitimate uses of this metabolic inhibitor as well as a discussion of the interpretation of such data. / 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 16, 2003. / Hypoxia, Nitrogen, Denitrification, Apalachicola / Includes bibliographical references. / Jeffrey Chanton, Professor Co-Directing Dissertation; Lita Proctor, Professor Co-Directing Dissertation; David Balkwill, Outside Committee Member; Joel Kostka, Committee Member; Richard Iverson, Committee Member.

The wind speed and wind stress over the Southern Ocean (SO) is compared from the QSCAT, COAPS, ERA-Int, JRA25 and NCEP2. From the results of comparison, NCEP2 seems to poorly represent wind speed in the SO. In the summer months, the difference of wind speed and wind stress between products is small while the bias during winter is larger. Also, the difference increases in the high latitudes, close to the sea-ice zone. South of 55°S, COAPS has weaker correlation of wind stress with reanalysis data. The major reasons of differences between products are associated with the impact of seaice and the differences of resolution, assimilation and parameters chosen from models. From the validation by ship data, ERA-Int fits the QSCAT and ship wind speed best in the SO. The large RMS difference of Ekman pumping between products is connected to wind variance, eddy kinetic energy (EKE), especially in the South Atlantic Ocean and South Indian Ocean during fall and winter. This implies that the difference between products may result in different responses of simulated storm activities. / A Thesis submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester, 2009. / July 7, 2009. / ECMWF, QuikSCAT, NCEP, Reanalysis, Satellite Data, Wind, Southern Ocean / Includes bibliographical references. / Kevin Speer, Professor Directing Thesis; Mark Bourassa, Committee Member; Carol Anne Clayson, Committee Member; Jeff Chanton, Committee Member.

A composite study is presented analyzing the influence of upper-tropospheric troughs on the evolution of precipitation in twelve Atlantic tropical cyclones (TCs) between the years 2000 – 2005. The TRMM Multi-Satellite Precipitation Analysis (TMPA) is used to examine the enhancement of precipitation within a 24 h window centered on trough interaction (TI) time in a shear-vector relative coordinate system. Eddy angular momentum flux convergence (EFC) computed from European Centre for Medium-Range Weather Forecasts (ECMWF) operational analyses is employed to objectively determine the initiation of a TI while adding insight, along with vertical wind shear, into the intensification of TC vortices. The relative roles of the dynamics (EFC and vertical wind shear) and thermodynamics (moist static energy potential) in TIs are outlined in the context of precipitation enhancement that provides quantitative insight into the "good trough"/"bad trough" paradigm. The largest precipitation rates and enhancements are found in the down-shear left quadrant of the storm, consistent with previous studies of convective asymmetries. Maximum mean enhancement values of 1.4 mm/h are found at the 200 km radius in the down-shear left quadrant. Results indicate that the largest precipitation enhancements occur with "medium" TIs; comprised of EFC values between 17 – 22 (m/s)/day and vertical wind shear Sensitivity tests on the upper vertical wind shear boundary reveal the importance of using the tropopause for wind shear computations when a TC enters mid-latitude regions. Changes in radial mean precipitation ranging from 29 – 40 % across all storm quadrants are found when using the tropopause as the upper boundary on the shear vector. Tests on the lower boundary using QuikSCAT ocean surface wind vectors expose large sensitivities on the precipitation ranging from 42 – 60 % indicating that the standard level of 850 hPa, outside of the boundary layer in most storms, is more physically reliable for computing vertical wind shear. These results should help to improve TC quantitative precipitation forecasting (QPF) as operational forecasters routinely rely on crude statistical methods and rules of thumb for forecasting TC precipitation. / A Thesis submitted to the Department of Meteorology in partial fulfillment of the requirements for the degree of Master of Science. / Spring Semester, 2007. / January 25, 2007. / Satellites, Precipitation, Tropical Cyclones, Troughs / Includes bibliographical references. / Mark Bourassa, Professor Directing Thesis; Robert Hart, Committee Member; Philip Cunningham, Committee Member; Henry Fuelberg, Committee Member.

Despite the fact that latent heating in cloud systems drives many atmospheric circulations, including tropical cyclones, little is known of its magnitude and structure due in large part to inadequate observations. In this work, a reasonably high-resolution (2 km), four-dimensional airborne Doppler radar retrieval of the latent heat of condensation is presented for rapidly intensifying Hurricane Guillermo (1997). Several advancements in the retrieval algorithm are shown including: (1) analyzing the scheme within the dynamically consistent framework of a numerical model, (2) identifying algorithm sensitivities through the use of ancillary data sources and (3) developing a precipitation budget storage term parameterization. The determination of the saturation state is shown to be an important part of the algorithm for updrafts of ~ 5 m s-1 or less. The uncertainties in the magnitude of the retrieved heating are dominated by errors in the vertical velocity. Using a combination of error propagation and Monte Carlo uncertainty techniques, biases were found to be small, and randomly distributed errors in the heating magnitude were ~16 % for updrafts greater than 5 m s-1 and ~156 % for updrafts of 1 m s- 1. The impact of the retrievals is assessed by inserting the heating into realistic numerical simulations at 2 km resolution and comparing the generated wind structure to the Doppler radar observations of Guillermo. Results show that using the latent heat retrievals outperforms a simulation that relies on a state-of-the-art microphysics scheme (Reisner and Jeffery 2009), in terms of wind speed root-mean-square errors, explained variance and eye/eyewall structure. The incorrect transport of water vapor (a function of the sub-grid model and the numerical approximations to advection) and the restrictions on the magnitude of heat release that ensure the present model's stability are suggested as sources of error in the simulation without the retrievals. Motivated by the latent heat retrievals, the dynamics of vortex axisymmetrization from the perspective of thermal anomalies is investigated using an idealized, non-linear atmospheric model (HIGRAD). Attempts at reproducing the results of previous work (Nolan and Grasso 2003; NG03) revealed a discrepancy with the impacts of purely asymmetric forcing. While NG03 found that purely asymmetric heating led to a negligible, largely negative impact on the vortex intensification, in the present study the impacts of asymmetries are found to have an important, largely positive role. Absolute angular momentum budgets revealed that the essential difference between the present work and that of NG03 was the existence of a significant, axisymmetric secondary circulation in the basic-state vortex used in the HIGRAD simulations. This secondary circulation was larger than that present in NG03's simulations. The spin-up of the vortex caused by the asymmetric thermal anomalies was dominated by the axisymmetric fluxes of angular momentum at all times, indicating fundamentally different evolution of asymmetries in the presence of radial flow. Radial momentum budgets were performed to elucidate the mechanisms responsible for the formation of the physically significant secondary circulation. Results show that explicit (sub-grid) diffusion in the model was producing a gradient wind imbalance, which drives a radial inflow and associated secondary circulation in an attempt to re-gain balance. In addition, the production of vorticity anomalies from the asymmetric heating was found to be sensitive to the eddy diffusivity, with large differences between HIGRAD and the widely used WRF model for the exact same value of this uncertain parameter. / A Dissertation submitted to the Department of Earth, Ocean and Atmospheric Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2010. / August 25, 2010. / Hurricanes, Doppler Radar, Latent Heat, Axisymmetrization, Diffusion, Numerical Modeling / Includes bibliographical references. / Mark Bourassa, Professor Directing Dissertation; Michael Navon, University Representative; Robert Hart, Committee Member; Ming Cai, Committee Member; Xiaolei Zou, Committee Member.

Often the parameterization of the moisture roughness length is not seen as being important, as long as the parameterization seems reasonable; that is, it is within the rather considerable bounds of error for the data sets used to determine the parameterization. However, the choice of parameterization does influence height adjustments of humidity and calculations of turbulent heat fluxes. This paper focuses on the calculation of the turbulent heat fluxes using different parameterizations of roughness length. Five roughness length parameterizations are examined herein. These parameterizations include wall theory; the Clayson, Fairall, Curry parameterization; the Liu, Katsaros, Businger parameterization; Zilitinkevich et al. parameterization; and the COARE3.0 parameterization. Turbulent heat fluxes are calculated from each parameterization of the roughness length and are compared to observed turbulent heat flux values. The bulk latent heat flux estimates have a much better signal to noise ratio than the sensible heat fluxes, and are therefore the focus of the comparison to observations. This comparison indicates how to improve the proportionality in the above roughness length parameterizations, which are causing modeled turbulent heat flux magnitudes to be too large in four of the five parameterizations. The modeled turbulent heat fluxes are evaluated again after the modification of the parameterizations. Significant improvements in both the bias and the root mean square error (RMSE) are seen. Three parameterizations see roughly the same improvements of around 17Wm^-2 in the bias and roughly 10Wm^-2 in the RMSE. The largest improvements are in the Liu, Katsaros, Businger parameterization with bias improvements of over 45Wm^-2 and a RMSE reduction of nearly 32Wm^-2. / A Thesis submitted to the Department of Meteorology in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester, 2009. / October 29, 2009. / Boundary Layer Meteorology, Roughness Length Parameterization, Moisture Roughness Lengths / Includes bibliographical references. / Mark A. Bourassa, Professor Directing Thesis; Shawn R. Smith, Committee Member; Paul H. Ruscher, Committee Member; Paul D. Reasor, Committee Member.

This study focused on the effective use of a numerical climate model for agriculture in Florida, especially in the citrus farming region of the Florida peninsula, because of the impact of agriculture to Florida's economy. For the analyses of the ensemble, the climate models used in this study were the FSU/COAPS Global Spectral Model and FSU/COAPS Regional Spectral Model (FSU/COAPS RSM) coupled with a land-surface model. The multi-convective scheme method and variable initial conditions were used for the ensembles. Severe freezes impacting agriculture in Florida were associated with some major climate patterns, such as El Niño and Southern Oscillation (ENSO) and North Atlantic Oscillation (NAO). In the first part of this study, seasonal ensemble integrations of the regional model were examined for the tendencies of freezes in the Florida peninsula during each ENSO or NAO phase is examined. Mean excess values of minimum temperatures from thresholds on the basis of the Generalized Pareto Distribution (GPD), which represents the extreme data in a dataset, were used to analyze the freezes in the regional model. According to some previous studies, El Niño winters obtain fewer freezes than the other ENSO phases. Although the ensemble comprised only 19 winters, the ensemble found variability patterns in minimum temperatures in each climate phase similar to the findings in the previous studies which were based on the observed data. The FSU/COAPS RSM was coupled with Community Land Model 2.0 (CLM2), to represent the land-surface conditions. Although the coupling improved the temperature forecast of the RSM, it still has a cold bias and simulates smaller diurnal temperature changes than actually occur in southern Florida. Among the prescribed surface data, Leaf Area Index (LAI) for southern Florida in the CLM2 is lower than those observed by MODIS (Moderate Resolution Imaging Spectroradiometer). In the first experiment of this part, the sensitivity of the temperature forecast to the LAI in the climate models was investigated, by modifying the LAI data in the CLM2 based on the monthly MODIS observations. In the second experiment, newly created prescribed datasets of LAI and plant functional types for the CLM2 based on the MODIS observations were applied to the RSM. The substitution increased the diurnal temperature change in southern Florida slightly but almost consistently. / A Dissertation submitted to the Department of Meteorology in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2008. / July 3, 2008. / Ensemble Forecast, Climate Model / Includes bibliographical references. / James J. O’Brien, Professor Directing Dissertation; Ruby Krishnamurti, Outside Committee Member; Mark A. Bourassa, Committee Member; Ming Cai, Committee Member; Paul Ruscher, Committee Member; Timothy LaRow, Committee Member.

A karst aquifer is a carbonate aquifer where groundwater flow dominantly occurs through bedding planes, fractures, conduits, and caves created by and/or enlarged by dissolution. Conventional groundwater modeling methods assume that groundwater flow can be described by Darcian principles where primary porosity (i.e. matrix porosity) and laminar flow are dominant in the aquifer. However, in karst aquifers this assumption is inapplicable due to the dual porosity present in karst aquifers. While Darcian principles may apply to the matrix portion of the karst aquifer, they often do not apply to flow through conduits, where flow velocities can be great enough to invalidate the applicability of Darcy's Law. Thus, different methodologies must be used to model groundwater flow in karst aquifers. MODFLOW-CFP is a relatively new modeling program which accounts for turbulent and laminar flow in pipe like karst caves. In this study the methodology of MODFLOW-CFP is compared to several other methods to evaluate the accuracy that CFP can achieve when modeling flow in karst conditions at a laboratory and sub-regional scale. This study also briefly evaluates the program MT3DMS, to test its abilities for modeling contaminant transport in a karst aquifer analog at a laboratory scale. Results at the laboratory scale indicate that CFP is more accurate when compared to simulated results generated by MODFLOW 2005, and performs better when compared to a Navier-Stokes finite element model developed by Hua (2009). At the sub-regional scale, CFP is less accurate than the traditional MODFLOW-2000 model when comparing peak flow conditions for a simulated storm event. However, for total simulated flow for the storm event, CFP produces more accurate results than MODFLOW-2000. Regarding transport, MT3DMS can adequately simulate transport within karst at a laboratory scale. / 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. / Spring Semester, 2011. / March 18, 2011. / Includes bibliographical references. / Bill X. Hu, Professor Directing Thesis; Ming Ye, Committee Member; Stephen Kish, Committee Member.

A greatly expanded section of Holocene sediment was recovered at Site NBP0602-8 in the Firth of Tay near the tip of the West Antarctic Peninsula during the SHALDRIL II cruise aboard the R/V Nathaniel B. Palmer, 2006. Recovery in the four holes at this site was ~85%, with the exception of the uppermost eight meters of water saturated sediments. The next year the site was revisited during Cruise NBP0703 and a jumbo piston core (JPC 02) recovered sediment to 23 meters below seafloor to fill missing gaps in the upper section. Fossil diatoms have been proven to be highly useful in paleontological climate reconstruction. Therefore, this investigation is a down-core quantitative study of diatom assemblages from this Firth of Tay sequence to identify and constrain changes in paleoenvironmental events. The project provides evidence of an early deglaciation episode, the Mid-Holocene Climatic Optimum, and subsequent cooling and Neoglacial conditions that persist until the present. The Mid-Holocene Climatic Optimum delineated in this study correlates closely with the timing and duration of this event in Maxwell Bay, to the north. The same event is recorded in Palmer Deep on the opposite (west) side of the Antarctic Peninsula but with an earlier onset and longer duration. The Climatic Optimum recorded at the Firth of Tay is less pronounced than at the other two sites, however, due to the colder water stemming from the Weddell Sea Gyre. / A Thesis submitted to the Department of Geology in partial fulfillment of the requirements for the degree of Master of Science. / Spring Semester, 2010. / May 3, 2010. / Antarctic Peninsula, Firth of Tay Diatom, Mid-Holocene Climatic Optimum / Includes bibliographical references. / Sherwood W. Wise, Professor Directing Thesis; Anthony J. Arnold, Committee Member; Joseph F. Donoghue, Committee Member.