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Publication Novel photobioreactor systems for characterizing algal behavior in outdoor-simulating environments(Colorado School of Mines. Arthur Lakes Library, 2024)This thesis presents the development of a series of progressively sophisticated novel photobioreactors for cultivating photosynthetic microorganisms in outdoor-simulating environments. The reactors have been created with the needs of the organisms as well as the lab and scientists in mind for characterizing high productivity candidate strains for outdoor farming of valuable resources. They control four major components (or selections thereof) of managing photosynthetic growth: illumination, temperature control, gas administration, and liquids handling. Light drives the photosynthetic apparatus, temperature dictates the rates of many physiochemical processes, the dissolved gas environment determines concentration gradients the cells must work with or against for electron fixation, and the liquid environment impacts salinity, nutrient availability, and homogeneity. In outdoor situations, these conditions can swing diurnally, with weather, and at different locations of the pond, resulting in unexpected behaviors compared to traditional flask-grown cultures. It is a costly and time-constrained endeavor to test strains outdoors, so to enable more rapid experimentation indoors, these reactors were developed. They are capable of simulating diurnal outdoor light intensities and temperature swings, controlling pH, and performing liquid additions and subtractions like what would be seen in operation at an outdoor facility. This enables characterization of outdoor candidate strains indoors during off-seasons and alleviates much of the manual labor associated with caring for each individual culture.Publication Advanced numerical methods for simulating advection-diffusion equations using parallelized Lagrangian particle tracking algorithms(Colorado School of Mines. Arthur Lakes Library, 2024)Lagrangian particle tracking schemes allow a wide range of flow and transport processes to be simulated accurately, but a major challenge is numerically implementing the inter-particle interactions in an efficient manner. Such methods were originally derived from a probabilistic or first-principles perspective and have previously lacked a more rigorous derivation arising directly from the underlying advection-diffusion-reaction equation (ADRE). Herein, we provide a rigorous derivation of the MTPT method as a Lagrangian approximation of solutions to the ADRE. Numerically, this research describes the development of multi-dimensional, parallelized domain decomposition (DDC) strategies for mass-transfer particle tracking (MTPT) methods in which particles exchange mass dynamically. We show that this method can be efficiently parallelized by employing large numbers of CPU cores to accelerate run times. We first validate the approach and our theoretical predictions by focusing our efforts on a well known benchmark problem with pure diffusion, where analytical solutions in any number of dimensions are well established. We are then able to extend these studies to more complex systems where analytic solutions may not exist. In particular, the MTPT methods we use can simulate systems with highly heterogeneous velocity fields and non-constant hydrodynamic dispersion. This combination of capabilities allows us to validate and expand on the existing lamella theory that describes concentration evolution via kinematic stretching, which is currently limited to a constant-dispersion assumption. Given the capability of our particle tracking methods to simultaneously simulate mixing and spreading via a velocity-dependent, hydrodynamic dispersion tensor, this research explores the existing assumptions of lamella theory and exhibits expanded high performance computing (HPC) techniques for load balancing and computationally efficiency.Publication Industrial microalgal characterization and enhancement for a sustainable future(Colorado School of Mines. Arthur Lakes Library, 2024)Microalgae are compelling renewable resources because of their rich biomass composition, with applications including biofuels, bioplastics, and nutraceuticals. However, economically viable industrial algal cultivation requires improved biomass productivity, stress tolerance, and product yield. This work addresses the need for better industrial microalgal strains. First, adaptive laboratory evolution (ALE) of Nitzschia inconspicua was utilized to increase high temperature tolerance. Second, biomass characterization and genetic engineering of Picochlorum celeri were deployed to better understand composition and carbon usage. Nitzschia inconspicua is a diatomic microalga with high relative lipid content, making it a promising platform for sustainable aviation fuel (SAF). ALE was conducted to increase the temperature tolerance of N. inconspicua to 37.5 °C, a lethal temperature to the parent (WT) strain. Clonal isolation of the adapted strain resulted in two unique clones with increased cell size (~20 μm) relative to adapted strain prior to clonal isolation, indicative that a sexual cycle occurred. Preliminary outdoor pond data showed increased productivity of adapted clones compared to WT, enabling more viable SAF production from this strain. Picochlorum celeri TG2 is a green microalga with rapid growth in high light, high CO2, and seawater. To characterize potential applications, a detailed biomass analysis was conducted. Nutrient-replete P. celeri contained protein-rich biomass. Gradual nitrogen restriction shifted biomass from primarily proteins to carbohydrates as cells transitioned into storage metabolite production. Hyper saline (2X) cultivation resulted in increased levels of the amino acid proline, which putatively acts as an osmolyte. This identification of biomass components yields critical information that informs how this strain might be utilized for renewable product production. While P. celeri shows high biomass productivity with high CO2 supplementation, growth is slow in air. To understand carbon usage in P. celeri, eight carbonic anhydrases were identified through BLAST investigation and four of these characterized through transformation of fluorescently-tagged carbonic anhydrase constructs. By using confocal imaging, carbonic anhydrases were experimentally localized throughout the cell. Targeted CRISPR/Cas9 knock-out of several carbonic anhydrases revealed unique stationary phase functionalities for these enzymes. This work enables future engineering of more efficient P. celeri carbon usage, facilitating more economically viable algal bioproducts.Publication Bedrock and surficial geology of the southern half of the Montezuma 7.5' quadrangle, central Colorado Front Range, Colorado, USA(Colorado School of Mines. Arthur Lakes Library, 2024)The purpose of this study was to create a 1:24,000 scale geologic map of the southern half of the Montezuma 7.5’ quadrangle in the central Colorado Front Range, and to investigate the Paleo- and Mesoproterozoic history of the area. The Paleoproterozoic geologic history in the southwestern United States is characterized by the Yavapai (~1.71-1.68 Ga) and Mazatzal (~1.65-1.60 Ga) orogenies, which both involved terrane accretion along the southeastern margin of Laurentia. Within the last two decades, evidence for a Mesoproterozoic orogeny, the ~1.48 -1.35 Ga orogeny has been recognized in northern New Mexico and Arizona, and more recently in Colorado. Mesoproterozoic deformation and metamorphism based on metamorphic monazite growth between ~1.43 Ga and ~1.42 Ga has previously been recognized in some areas of the Montezuma quadrangle and the Mount Blue Sky quadrangle east of it. Bedrock geologic mapping, structural analysis, and U-Pb LA-ICP-MS zircon geochronology was used to interpret the structural history of the southern half of the Montezuma quadrangle further. In addition, younger brittle structures and Quaternary surficial deposits in the area were mapped and analyzed. The main metamorphic lithologies in the study area are Paleoproterozoic biotite-sillimanite gneiss/schist, biotite-quartz gneiss/schist, and hornblende gneiss. These are intruded by Mesoproterozoic granitoid plutonic rocks and local satellite intrusions related to the ~39.7 Ga Montezuma stock. The Paleoproterozoic rocks are deformed by isoclinal F1 folds in various orientations. These are overprinted by D2 structures, which include tight to open NW-trending folds that are best observed in the western half of the field area. West-trending tight to open F3 folds are best recognized in the eastern half of the field area. F3 folds are consistent with W- and E-trending folds in the Mount Blue Sky quadrangle, the Wet Mountains in southern Colorado, and the Picuris Mountains in northern New Mexico. D2, and possibly D1 structures are interpreted as younger than ~1.75 Ga based on the maximum depositional age of a previously dated quartzite in the Montezuma quadrangle. More specifically, D2 deformation is interpreted as ~1.68 Ga based on previously analyzed in situ metamorphic monazite grains. U-Pb zircon of a granitic dike deformed by an F2 fold in the southern half of the Montezuma quadrangle, analyzed in this study, yielded an imprecise Paleoproterozoic age, but is generally within uncertainty of the ~1.68 Ga monazite ages. These ages are also consistent with the age of D1 deformation near the Idaho Springs-Ralston Shear Zone, ~40 km north of the Montezuma quadrangle, and D2 deformation in the Mount Blue Sky quadrangle. D3 deformation is interpreted as ~1.43-1.42 Ga, based on previously analyzed in situ metamorphic monazite grains aligned with F3 fold axial planes in the Montezuma quadrangle. U-Pb LA-ICP-MS zircon analysis of a granitoid in the southeast corner of the Montezuma quadrangle indicates that it is a phase of the magnesian ~1.443 Ga Mount Blue Sky batholith, and not part of the ~1.1 Ga Pikes Peak batholith or the ~1.7 Ga Routt plutonic suite, as previously interpreted. NW-dipping tectonic foliations in the batholith suggest that NW-directed shortening occurred during or after ~1.443 Ga, probably as a result of the Picuris orogeny, because no ductile deformation is known to have occurred in the central Colorado Front Range after that time. The Montezuma stock yielded a ~39.8 Ma crystallization age with Proterozoic inherited zircons. Glacial deposits of the Pinedale glaciation are present throughout the southern half of the Montezuma quadrangle. Late middle Pleistocene Bull Lake-age glacial signatures are preserved on higher interfluve ridges as bedrock-etched trimlines and glaciofluvial benches, but deposits have been mainly reworked and deposited into lower topographic positions by late Pleistocene glaciation as Pinedale till.Publication At the intersection of land use, flooding, and social vulnerability: a case study of New Orleans, Louisiana(Colorado School of Mines. Arthur Lakes Library, 2024)Urban flooding is becoming more frequent and severe due to the effects of climate change, underscoring the urgent need for effective flood risk management. Flood susceptibility maps are tools that assess the likelihood and potential impacts of various flood scenarios. They are generally used for flood risk management in coastal cities like New Orleans, Louisiana, which face recurring flooding events. This thesis presents a comprehensive investigation into the factors that have influenced flood risk in New Orleans – a city with a history marked by catastrophic flooding events. Storms that overpower drainage systems and natural basins often lead to urban floods (Hirabayashi et al., 2021), which bring significant risks like infrastructure damage, economic setbacks, and loss of life, the latter being the second most common cause of weather-related deaths in the United States (Han & Sharif, 2021). Furthermore, this research seeks to generate risk maps that show the risk profile of communities (at the census tract level) at the overlap of flood risk, social vulnerability index (SVI), and land use and land cover (LULC) change between 2005 and 2023. Employing satellite imagery and geospatial analysis, the study uses the Modified Normalized Difference Vegetation Index (MNDWI) to indirectly evaluate flood risks and the Normalized Difference Vegetation Index (NDVI) to assist in the assessment of land cover classification through time. Toward these objectives, thematic mapping and geospatial analysis were used to generate a map overlay of flood risk, SVI, and LULC in New Orleans. Integrating satellite observations with SVI calculations allows for a comprehensive view of flood dynamics and social vulnerability in a major urban setting, examining the relationship between natural and built environments and their effects on flood risks. The final composite products provided insight into zones where past resilience-building and risk-reduction efforts have reduced vulnerability and zones requiring intervention. The findings convey how integrated data-driven analysis can inform urban infrastructure and policy development, advancing discussions on urban resilience and the nuanced understanding of interactions between urban settings and flood risks and potentially aiding in the implementation of adaptive strategies to build resilience in New Orleans.