Urban waterways are highly vulnerable to bacterial contamination, which presents significant risks to public health and water quality. Common methodologies typically measure the total concentration of fecal indicator bacteria (FIB) but are unable to address the complex sources of contamination contributing to the overall bacterial load. This study established chip-based digital polymerase chain reaction (cdPCR) techniques for microbial source tracking to unveil the origins of Escherichia coli (E. coli). Along with a simultaneous analysis of physicochemical water quality indicators, an assessment was conducted using host-associated genetic markers that indicate fecal sources from humans (HF183/BacR287), ruminants (Rum2Bac), dogs (DG3), and birds (GFD) in the lower portion of Rock Creek River (RCR) in the District of Columbia, United States. Stream samples were collected twice a month (n = 24) and after rain events (n = 6) from three sites along the RCR in the district area that feature a mix of highly developed urban areas and park surface regions. Approximately 50% of the stream samples (n = 96) were found to be impaired, exceeding the district's single sample maximum assessment level (410 MPN/100 ml) for E. coli. Herein, we adopted a multi-scale characterization of the relationship of cultural E. coli with host-associated markers, the regression with in-stream physiochemical constituents, the distinction between sampling sites, and the correlation with sizeable land cover categories. In Chapter 1, a comprehensive overview of MST methods is presented. This chapter summarizes the development of MST, categorizes common MST techniques into library-dependent versus library-independent and culture-dependent versus culture-independent groups, and provides a brief history of the advancements in molecular instrumentation used for culture-independent methods. In Chapter 2, consistently elevated E. coli levels were observed at all sites during wet weather, highlighting the substantial impact of storm runoff on water quality deterioration. Among the four molecular markers tested, HF183/BacR287, which indicates human-associated contamination, was particularly prevalent, with the highest frequency found in one of the tributaries. The second marker, derived from avian sources (GFD), showed a moderate to low frequency across the sites. Detection of the ruminant- and dog-specific markers was sporadic at all three sites. Correlation and regression analyses involving E. coli, molecular markers, and physicochemical constituents revealed significant statistical relationships. Notably, turbidity and flow were useful indicators for quickly assessing bacterial contamination. These findings emphasize the importance of reducing microbial contributions from runoff in watershed areas to urban streams during wet weather. The methods and findings of this study are expected to assist stormwater management and regulatory agencies in developing best management practices (BMP) to protect the water quality of urban streams. In Chapter 3, a strong association of E. coli with low-intensity developed land was established, but this association to forested areas at smaller spatial scales. The HF183/BacR287 marker exhibited similar trends, reinforcing its role as a reliable indicator of E. coli contamination sources. This study highlights the value of MST markers in identifying sources of microbial contamination. It provides important insights for managing water quality across various land cover types and changing weather conditions. In Chapter 4, the scalability of cdPCR to cell equivalents was investigated. By transforming scaled cdPCR DNA copies, the study revealed that 3,153 DNA copies per 100 mL of human-associated HF183BacR287 corresponded to the same regulatory threshold as cultured E. coli, enabling direct comparison between cdPCR and Colilert methods for contamination detection. This approach highlights the potential of cdPCR as a complementary tool to traditional methods in MST studies, offering a more detailed and efficient approach for water quality monitoring and management. In Chapter 5, a summary of the results is presented, and a perspective of future research direction is proposed. / Doctor of Philosophy / Urban waterways are highly susceptible to bacterial contamination, which can pose serious risks to public health and water quality. Traditional methods for monitoring bacterial contamination typically focus on measuring total levels of fecal indicator bacteria (FIB), but they are incapable of distinguishing the bacterial sources. This study aimed to fill that gap by using advanced techniques to trace the origins of Escherichia coli (E. coli) contamination in an urban creek in Washington, D.C. This study utilized a chip-based digital PCR (cdPCR) system to identify fecal pollution from various sources, including humans, animals, and wildlife. Throughout the study, water samples were collected from three sites along the creek within the district area during both dry weather and after rainstorms. The results indicated that approximately half of the samples had E. coli levels exceeding safe limits, particularly following rainfall, highlighting the significant impact of stormwater runoff on water quality. Among the identified sources of contamination, human-associated pollution was the most prevalent, followed by contamination from birds. The study also combined analysis of water quality indicators, such as turbidity and flow. Strong correlations between E. coli levels, molecular markers, and certain water quality indicators were observed, which can help in quickly assessing water contamination. This research underscores the potential of molecular techniques, like cdPCR, to accurately identify the sources of bacterial contamination in urban waterways. The findings can aid in better management of stormwater runoff and inform efforts to improve water quality in urban streams. Additionally, the study provides valuable insights into how land use, such as urban development and forest cover, can influence bacterial contamination, offering a more comprehensive understanding of the environmental factors contributing to water pollution.

In non-rotating fluids, boundary-layer separation occurs when the nearly inviscid flow just outside a viscous boundary-layer experiences an appreciable deceleration due to a region of adverse pressure gradient. The fluid ceases to flow along the boundary due to a flow recirculation region close to the boundary. The flow is then said to be "detached." In recent decades, attention has shifted to the study of boundary-layer separation in a rotating reference frame due to its significance in Geophysical Fluid Dynamics (GFD). Since the Earth is a rotating sphere, the so-called β-plane approximation f = f0 + βy is often used to account for the inherent meridional variation of the Coriolis parameter, f, while still solving the governing equations on a plane. Numerical simulations of currents on the β-plane have been useful in understanding ocean currents such as the Gulf Stream, the Brazil Current, and the Antarctic Circumpolar Current to name a few. In this thesis, we first consider the problem of prograde flow past a cylindrical obstacle on the β-plane. The problem is governed by the barotropic vorticity equation and is solved using a numerical method that is a combination of a finite difference method and a spectral method. A modified form of the β-plane approximation is proposed to avoid computational difficulties. Results are given and discussed for flow past a circular cylinder at selected Reynolds numbers (Re) and non-dimensional β-parameters (β^). Results are then given and discussed for flow past an elliptic cylinder of a fixed aspect ratio (r = 0.2) and at two angles of inclination (90°, 15°) at selected Re and β^. In general, it is found that the β-effect acts to suppress boundary-layer separation and to allow Rossby waves to form in the exterior flow field. In the asymmetrical case of an inclined elliptic cylinder, the β-effect was found to constrain the region of vortex shedding to a small region near the trailing edge of the cylinder. The shed vortices were found to propagate around the trailing edge instead of in the expected downstream direction, as observed in the non-rotating case. The second problem considered in this thesis is the separation of western boundary currents from a curved coastline. This problem is also governed by the barotropic vorticity equation, and it is solved on an idealized model domain suitable for investigating the effects that boundary curvature has on the tendency of a boundary current to separate. The numerical method employed is a two-dimensional Chebyshev spectral collocation method and yields high order accuracy that helps to better resolve the boundary-layer dynamics in comparison to low-order methods. Results are given for a selection of boundary curvatures, non-dimensional β-parameters (β^), Reynolds numbers (Re), and Munk Numbers (Mu). In general, it is found than an increase in β^ will act to suppress boundary-layer separation. However, a sufficiently sharp obstacle can overcome the β-effect and force the boundary current to separate regardless of the value of β^. It is also found that in the inertial limit (small Mu, large Re) the flow region to the east of the primary boundary current is dominated by strong wave interactions and large eddies which form as a result of shear instabilities. In an interesting case of the inertial limit, strong waves were found to interact with the separation region, causing it to expand and propagate to the east as a large eddy. This idealized the mechanism by which western boundary currents such as the Gulf Stream generate eddies in the world's oceans.

In non-rotating fluids, boundary-layer separation occurs when the nearly inviscid flow just outside a viscous boundary-layer experiences an appreciable deceleration due to a region of adverse pressure gradient. The fluid ceases to flow along the boundary due to a flow recirculation region close to the boundary. The flow is then said to be "detached." In recent decades, attention has shifted to the study of boundary-layer separation in a rotating reference frame due to its significance in Geophysical Fluid Dynamics (GFD). Since the Earth is a rotating sphere, the so-called β-plane approximation f = f0 + βy is often used to account for the inherent meridional variation of the Coriolis parameter, f, while still solving the governing equations on a plane. Numerical simulations of currents on the β-plane have been useful in understanding ocean currents such as the Gulf Stream, the Brazil Current, and the Antarctic Circumpolar Current to name a few. In this thesis, we first consider the problem of prograde flow past a cylindrical obstacle on the β-plane. The problem is governed by the barotropic vorticity equation and is solved using a numerical method that is a combination of a finite difference method and a spectral method. A modified form of the β-plane approximation is proposed to avoid computational difficulties. Results are given and discussed for flow past a circular cylinder at selected Reynolds numbers (Re) and non-dimensional β-parameters (β^). Results are then given and discussed for flow past an elliptic cylinder of a fixed aspect ratio (r = 0.2) and at two angles of inclination (90°, 15°) at selected Re and β^. In general, it is found that the β-effect acts to suppress boundary-layer separation and to allow Rossby waves to form in the exterior flow field. In the asymmetrical case of an inclined elliptic cylinder, the β-effect was found to constrain the region of vortex shedding to a small region near the trailing edge of the cylinder. The shed vortices were found to propagate around the trailing edge instead of in the expected downstream direction, as observed in the non-rotating case. The second problem considered in this thesis is the separation of western boundary currents from a curved coastline. This problem is also governed by the barotropic vorticity equation, and it is solved on an idealized model domain suitable for investigating the effects that boundary curvature has on the tendency of a boundary current to separate. The numerical method employed is a two-dimensional Chebyshev spectral collocation method and yields high order accuracy that helps to better resolve the boundary-layer dynamics in comparison to low-order methods. Results are given for a selection of boundary curvatures, non-dimensional β-parameters (β^), Reynolds numbers (Re), and Munk Numbers (Mu). In general, it is found than an increase in β^ will act to suppress boundary-layer separation. However, a sufficiently sharp obstacle can overcome the β-effect and force the boundary current to separate regardless of the value of β^. It is also found that in the inertial limit (small Mu, large Re) the flow region to the east of the primary boundary current is dominated by strong wave interactions and large eddies which form as a result of shear instabilities. In an interesting case of the inertial limit, strong waves were found to interact with the separation region, causing it to expand and propagate to the east as a large eddy. This idealized the mechanism by which western boundary currents such as the Gulf Stream generate eddies in the world's oceans.