College of Science Theses and Dissertations
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Browsing College of Science Theses and Dissertations by Department "Physical and Environmental Sciences"
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Item An analysis of emergency management agencies gis data for planning 9-1-1 services for the border counties of the lower Rio Grande Valley(2017-08) Nino, Orlando; Smith, Richard; Jeffress, Gary; Huang, YuxiaTexas 9-1-1 entities collect data that can be used to gain knowledge on 9-1-1 call patterns and trends. It is ideal to know these issues too efficiently maximize monies appropriated to local emergency management agencies. This research will analyze 9-1-1 calls and two police departments calls for service using Geographic Information Science (GIS). This information provided by multiple emergency management agencies to better plan 9-1-1 services in the border counties of the Rio Grande Valley. The data that was used is recorded daily by these agencies. Many emergency management organizations keep their own GIS data in-house and they need to be analyzed with 9-1-1 data. Analyzing various GIS databases can yield better results, in finding correlation within each dataset, hotspots and inadequate data collection. These results can then be used by the organizations that contributed the data and shared to all stakeholders.Item Applying segmentation and neural networks to detect and quantify marine debris from aerial images captured by unmanned aerial system and mobile device(2018-08) Tran, Kieu; Conkle, Jeremy; Starek, Michael J.; Gibeaut, JamesMarine debris is a global issue with adverse impacts on the marine environment, wildlife, economy, and human health. Its presence on beaches may vary due to topography, hydrological conditions, proximity to litter sources, and the extent of beach use. Studies of these parameters on beach litter are essential for understanding spatial and temporal patterns; however, this work is labor-intensive and time-consuming. To overcome these obstacles while gaining higher spatial and temporal resolution data, two methods were developed (1) segmentation and (2) regions with convolutional neural networks (R-CNN) to detect and quantify marine macro-debris using high-resolution imagery. Data to develop and test the methods were collected using a small rotary Unmanned Aerial System (UAS) with an RGB sensor at various altitudes over a 100m section of sandy beach of Mustang Island, Texas. Images were processed through structure-from-motion photogrammetry to derive orthomosaics for each flight. Orthomosaics were then run through an image processing, and classification workflow developed for segmentation and delineation of imaged debris. The segmentation algorithm detected the most debris at the lowest altitude (215 of 341 total at 15m), with decreasing detections at 22m (101) and 35m (50). The second method applied deep learning object detection to smartphone images. Based on the dataset and the network architecture, R-CNN mean average precision can range from 31.4% to 66% (Girshick et al., 2014). Training for R-CNN consisted of three stages: extract region proposals, train AlexNet to classify objects, and train a bounding box regression model to locate the debris. Average precision for the Specifically Engineered Algorithm for Gathering and Understanding Litter Location (SEAGULL) detector was ~22%, meaning it has a low performance at detecting all the debris in the testing dataset and correctly predicting whether or not that region was debris or not. Object detection has been a challenging task for decades, and with a low overall debris detection accuracy, it needs to be further improved with the use of a larger dataset or adjusting the training parameters. Few studies have been published on this topic, but this work demonstrates that remote sensing with UAS has the potential to increase research efficiency.Item Assessing short-term sediment accretion rates and hydrological influences on a microtidal estuarine wetland: Mustang Island, TX(2015-12) Martinez, MelindaAs sea level rises there has been a growing concern whether salt marsh wetlands can withstand an accelerated rise in sea level by vertically accreting. Sediment accretion is a natural process that changes the elevation of the marsh surface relative to sea level. For a wetland to persist in the long-term, its accretion rate must at least match the rate of relative sea level rise. This study describes sedimentation rates in the estuarine wetlands located on Mustang Island, TX, a sandy barrier island. Sedimentation rates were measured bi-weekly from June 2014 to July 2015 using sediment plates and erosion pins, and over periods of 2.4 to 3.3 years (2012- 2014/2015) using horizon marker techniques. Water level loggers were used to assess hydrological controls on bi-weekly sedimentation patterns. Shallow cores (~15 cm) were collected from the horizon marker plots in August 2014 and July 2015. Vertical accretion rates were compared across different timescales including decadal rates determined using 137Cs from a previous study on Mustang Island, TX. Results indicated sediment accretion across the study area was not significantly influenced by hydrological patterns, with the exception of low marsh environments near tidal creeks (r2=0.52, p < 0.1). The most important factor in determining sediment deposition on sediment plates located near the main tidal creek was the number of flooding events, suggesting that deposition increases as frequency of flooding events increases. The total accumulation deposited on plates was dominated by inorganic sediments, suggesting there is a limit of detrital organic matter contribution for this area. Average vertical accretion using horizon markers was 8.15 ± 5.21 mm yr-1 in upland environments; 4.51 ± 5.21 mm yr-1 in high marsh environments; 3.36 ± 3.57 mm yr-1 in high flat environments; 11.92 ± 9.73 mm yr-1 in low marsh environments; and 1.88 ± 2.54 mm yr-1 in low flat environments. There was a significant difference in vertical accretion rates between both horizon markers and erosion pins, which provide annual-scale accretion rates, when compared to 137Cs, which provide decadal-scale accretion rates (p < 0.1). On average annual vertical accretion rates were 2.8 times higher than decadal rates. Differences between annual and decadal accretion rates are mostly attributed to shallow sediment compaction within the top 3 cm of the wetland surface. Variation in wetland vertical accretion rates increased significantly going from decadal (± 0.41 mm) to annual (± 2.87 mm) to annualized biweekly rates (± 9.60 mm). Annual-scale accretion rates measured using horizon markers in low marsh and upland environments appear to be keeping up with relative sea level rise (RSLR), which is 5.27 ± 0.48 mm yr-1 as measured since the 1950’s at a nearby tide gauge. However horizon marker vertical accretion rates in tidal flats and high marsh environments are not sufficient to overcome sea level rise. Vertical accretion rates were positively correlated with organic and inorganic accretion for all horizon markers (p < 0.1); however, the relative contribution of organic matter decreases as inorganic matter increases. Our findings anticipate environmental shifts in habitats with accretion rates below RSLR. Furthermore, vertical accretion was dominated by inorganic matter, making the wetlands reliant on constant wind and episodic storms to transport sediment to the area. Importantly, these data suggest that storm-induced sedimentation acts to stabilize coastal wetlands and helps certain environments cope with RSLR, but is not sufficient to prevent shifts in the relative composition of the wetland.Item Assessing the influence of genotypic diversity on sulfur dynamics in the seagrass halodule wrightii using stable isotope analysis(2022-07-19) Girard, Allyson; Larkin, Patrick; Abdulla, Hussain; Felix, JosephCoastal development and other mounting anthropogenic pressures are threatening valuable seagrass habitats. The greatest risks posed to seagrasses are the effects of coastal eutrophication, which stimulates primary productivity and ultimately supplies abundant organic matter to marine sediments. The decomposition of this material is initially facilitated by aerobic microorganisms, depleting dissolved oxygen and generating anoxic conditions. Under these conditions, anaerobic microorganisms such as sulfate-reducing bacteria begin to dominate the degradation process, which reduce sulfate (SO42-) to sulfide (H2S) for energy production. The accumulation of H2S in marine sediments is problematic for seagrasses, as this molecule can be highly toxic. Yet, seagrasses can withstand relatively high concentrations of H2S in their environments. Stable isotope analyses have been used to investigate sulfide intrusion in seagrass meadows, as the unique isotopic signature of sediment-derived sulfur can be used to trace the uptake of H2S and its distribution throughout the plant. This technique has allowed the study of factors that may influence sulfide production and intrusion, such as reduced light availability, organic matter enrichment, and high temperatures. However, few studies have examined the biological or biochemical features that enable seagrasses to withstand relatively high sedimentary sulfide levels. One biological feature that may help confer resistance is population genetic diversity, which has been identified as an important trait in the survival and performance of seagrass meadows under environmental stress. In general, genetic diversity is thought to play an important role in population resistance to environmental disturbance, as a wider assortment of functional traits encoded at the molecular level results in a variety of phenotypes likely to possess morphological and physiological differences that are complementary. This genotypic complementarity may extend to biochemical strategies associated with tolerance to, or detoxification of, H2S. The purpose of this study was to determine whether sulfide intrusion differs between genotypes of the seagrass Halodule wrightii, a prominent species in the Gulf of Mexico. Further, as the sulfur isotopic composition of marine sediments and seagrass vegetation is known to exhibit high spatial variability, this study also sought to assess sulfide intrusion between populations from distinct sites along the Texas Gulf Coast. Stable isotope data was used to infer the proportion of sulfur in H. wrightii tissues that was derived from sedimentary sulfide, while total sulfur (TS) data was also considered to understand the extent of sulfur accumulation within the plant. H. wrightii genotypes were determined by screening each sample at a series of microsatellite loci previously identified for this species. Although no difference in sulfide intrusion was observed between genotypes, sulfide uptake and distribution was significantly different between the three study sites. The results offer important insight to the effect of local conditions on sulfide intrusion in seagrass meadows and may guide future investigations concerned with the influence of genotypic diversity on H2S metabolism in seagrasses.Item Assessment of Sulfide Intrusion and Genotypic Diversity in the Seagrass Halodule Wrightii from the Texas Gulf Coast(2019-12) Rubiano-Rincon, Sebastian; Larkin, Patrick D.; Coffin, Richard; Hu, XinpingSeagrasses are marine angiosperms that provide key ecological services to coastal areas. Unfortunately, seagrasses are experiencing a progressive decline, driven by natural and anthropogenic stressors, including sulfide (H2S) intrusion from high sediment sulfide concentrations. Seagrasses cope with sulfides through avoidance (reoxidation in the sediment) or tolerance (assimilation by tissues). Previous studies also suggested that seagrass response to environmental stress can be influenced and benefit from having genotypic (clonal) diversity. Although these mechanisms have been studied in some species, few have examined sulfide intrusion and its relation to genotypic diversity in seagrasses from the Texas Gulf Coast. In this study, we used stable sulfur isotopes and a microsatellite-based DNA marker assay to assess sulfide intrusion in the seagrass Halodule wrightii and investigate whether genotypic diversity plays a role in its response to sulfide stress. We found a gradient in δ34S values (-5.58 ± 0.54‰ to 13.58 ± 0.30‰), from roots to leaves, suggesting that H2S enters through underground tissues and is then distributed throughout the plant. The presence of sulfide-derived sulfur in varying proportions (15% to 76%) among the leaf, rhizome and root tissues indicates they are able to assimilate it into non-toxic, metabolic forms. Although sulfide intrusion did not significantly vary among the different genotypes (P > 0.05), this seagrass population had signs of being genetically diverse, indicating that it has the necessary genetic material to face and resist environmental stress. We hope that this study serves as the basis for further exploration of the genetics of sulfur assimilation and metabolism in seagrasses.Item Associations between chlorophyll and wind forcing in the Gulf of Mexico derived from satellite observations(2015-08) Trnka, Maureen C.The Gulf of Mexico supports many industries that rely on its natural resources. Primary production is required to sustain fish populations and contributes to ocean carbon exchange. Ocean color satellites make it possible to observe large geographic areas; however, an individual sensor has limited coverage. The GlobColour project merges observations from multiple satellites into a single product. The purpose of this study is to use GlobColour and QuikSCAT to investigate the seasonal and non-seasonal associations between chlorophyll and wind from 2000-2008 in the Gulf of Mexico. An overview of the Gulf of Mexico’s physical setting, circulation, and main features is presented. The Gulf is divided into: Interior Basin, West Florida Shelf, Louisiana-Texas Shelf, Tamaulipas-Veracruz Shelf, Bay of Campeche, and Campeche Bank. Phytoplankton biomass is discussed in the context of nutrient-transport mechanisms including coastal upwelling, Ekman pumping, horizontal advection, and vertical turbulent mixing. Seasonal associations are evaluated between chlorophyll and wind using Empirical Orthogonal Functions and Singular Value Decomposition. Chlorophyll has strong seasonal variability over the shelves. The interior variability of chlorophyll and wind speed is in-phase with annual periodicity, increasing in winter and decreasing in summer. Strong winter winds increase the upward turbulent transport of nutrients into the mixed layer. The northern chlorophyll variability has a dipole with increased anomalies over the Western Shelf and decreased anomalies around the Mississippi mouth; associated with intensified easterly winds. Non-seasonal anomalies of chlorophyll and wind are similarly investigated. Increases in wind speed are associated with chlorophyll increases over the Campeche Bank, Bay of Campeche, and West Florida Shelf; the mechanism is upward entrainment of nutrients by turbulent mixing. Northerly winds are associated with coastal upwelling in the Bay of Campeche, offshore advection in the west, and a chlorophyll dipole across the Mississippi mouth. The non-seasonal coupled patterns are predominantly intraseasonal and spatially coherent with interannual modulations. This study is the first to apply a merged ocean color product to research in the Gulf of Mexico. Overall, this project provides baseline information on the seasonal and non-seasonal variability of chlorophyll and winds, identifies statistical associations, and proposes dynamical mechanisms.Item Beach geomorphology and Kemp’s Ridley (lepidochelys kempii) nest site selection along Padre Island, Tx, USA(2018-05) Culver, Michelle F.; Gibeaut, James C.; Starek, Michael J.; Tissot, Philippe; Shaver, Donna J.The Kemp’s ridley sea turtle (Lepidochelys kempii) is the most endangered sea turtle species in the world, largely due to historic take of eggs at the primary nesting beach in Mexico, loss of juveniles and adults incidental to fisheries operations, and the limited geographic range of its nesting habitat. In the USA, the majority of nesting occurs along Padre Island in Texas. There has been limited research regarding the connection between beach geomorphology and Kemp’s ridley nesting patterns, but studies concerning other sea turtle species suggest that certain beach geomorphology variables, such as beach slope and width, influence nest site selection. This research addresses the literature gap by quantifying the terrestrial habitat variability of the Kemp’s ridley and investigating the connection between beach geomorphology characteristics and Kemp’s ridley nesting preferences on Padre Island, Texas, USA. Beach geomorphology characteristics, such as beach slope and dune peak height, were extracted from airborne topographic lidar data collected annually along the Texas coast from 2009 through 2012. The coordinates of observed Kemp’s ridley nests from corresponding years were integrated with the geomorphic data, which was then statistically analyzed using generalized linear models and random forest models. These models were successful in predicting Kemp’s ridley nest presence. The top generalized linear models explained 40-46% of nest presence variability with a relatively low prediction error. The final random forest model was superior in performance in comparison to the generalized linear models, with a true positive rate above 85%. Nest elevation, distance from shoreline, maximum dune slope, and average beach slope were the significant variables in the top two generalized linear models and the relatively most important variables in the random forest model, with elevation and distance from shoreline being the most influential in each. Kemp’s ridleys nested at a median elevation of 1.04 m above mean sea level and a median distance from shoreline of 12.79 m, which corresponds to the area directly below the potential vegetation line, which is defined as the lowest elevation where dune plants may persist. Kemp’s ridleys also exhibited a preference for a limited range of the study area and avoided nesting on beaches with extreme values for maximum dune slope, average beach slope, and beach width. This study provides new information regarding Kemp’s ridley terrestrial habitat and nesting preferences that have many applications for species conservation and management.Item Benthic macrofauna community response to salinity in the San Antonio and Matagorda Bay systems, Texas(2017-05) Ehrmann, Hannah; Montagna, Paul A.; Pollack, Jennifer Beseres; Sterba-Boatwright, BlairThe aim of this study was to quantify the effects of salinity on ecosystem health in Matagorda and San Antonio Bay systems, using benthic macrofauna communities as biological indicators of ecosystem integrity. Benthic and discrete water quality samples were taken monthly at five stations in the San Antonio and Matagorda Bays. Benthic macrofauna community dynamics were linked to salinity to infer the effects of freshwater inflow on the estuarine biotic communities. The benthic communities were classified into two groups based on different salinity habitat zones when salinity was above or below 11. Benthic metrics were significantly correlated with salinity, one-month lag, or two-month lag salinity in all bays. Peak abundances were observed in Carancahua and San Antonio Bays when salinities were 5 and 7 respectively, and peak diversity was observed in San Antonio Bay when salinity was 4. Diversity (Hill’s N1) increased throughout the salinity gradient in Tres Palacios and San Antonio Bays, as did abundance in Tres Palacios Bay. Overall, salinity was a driving factor for these communities. There is a need for hydrological restoration in many areas, and resources for restoration have been made available by the RESTORE Act. However, only small flows may be available to be set aside to maintain ecological health. The present study gives evidence that benthic communities are supported by low salinity habitats within the upper reaches of the San Antonio and Matagorda Bay Systems.Item Biomimetic iron complexes for the oxidation of C-H bonds in hydrocarbons(2021-12) Le, Uyen; Prakash, Jai; Billiot, Fereshteh; Holubowitch, NicolasWith the rapid growth in transportation and industry, petroleum and other types of fossil fuels (coal, heavy oil) are heavily used for energy production. The consumption of these types of energy resources pose a serious environmental concern because of the production of greenhouse gases such as carbon dioxide, methane, nitrous oxide, and chlorofluorocarbons (CFCs) which are the primary reasons for climate change. This makes the development of cheaper and cleaner energy more important in modern society. Conversion of methane into liquid fuel such as methanol has become a promising goal for future petrochemical derivatives and decreasing petroleum dependence. Methane is the primary component of natural gas which is highly abundant on earth. Methane is used as a raw material to produce methanol which is further used as fuel to generate electricity. However, the conversion of methane into methanol is carried out at high temperature and pressure and this process is energy consuming. This makes methane oxidation catalysts high in demand. In recent decades, transition metal complexes have proven to be efficient and powerful catalysts for various oxidative transformations. Specifically, mononuclear and di-nuclear metal complexes now are widely applied as catalysts for the oxidation of organic substrates and water. Transition metals such as Mn, Fe, Co, Ni and Cu have been recognized as cheap, environmentally friendly and effective catalysts for C-H activation. Specifically, iron is the most attractive metal because it’s very inexpensive (most earth-abundant transition metal), displays high oxidation states (required in catalysis), and is relatively non-toxic. In this research, we will design and develop routes for synthesizing iron complexes that can serve as cheap and efficient catalysts for methane oxidation (or C-H activation). This is the foundation for future research aiming at converting inert hydrocarbons into useful petrochemical derivatives.Item Characterization of single amino acid based surfactants undecanoic L-Isoleucine and undecanoic L-Norleucine in the presence of diamine counterions with varying chain lengths(2019-08) Maynard-Benson, Amber; Billiot, Eugene; Billiot, Fereshteh; Causgrove, TimothyTo understand chiral recognition and discrimination, single amino-acid-based surfactants undecanoic L-isoleucine and L-norleucine were synthesized and examined at various pHs with different counterions. Analysis was conducted utilizing different analytical instruments and techniques such as NMR and Capillary Electrophoresis (CE). Knowledge gained from this research will later be used to develop a database that will recognize behaviors of micelle systems and determine which parameters and materials will be most effective for enantiomeric separation.1 The focus of this particular study was to determine how varying the chain length of diamine counterions affects the properties of the surfactant. The following six counterions were investigated: 1,2-ethylenediamine, 1,3-diaminopropane, 1,4-diaminobutane, 1,5-diaminopentane, 1,6-diaminohexane, and sodium. Sodium was employed as the standard counterion for comparison. Early work was performed using arginine and lysine as counterions before shifting focus to the diamines; this data is also included as supplemental information. Data from this project has shown that the Critical Micelle Concentration (CMC) of surfactants is dependent upon the chain length of the diamine counterions. As the counterion chain length was increased, the CMC decreased. At pH 9 the CMC decreased from 12.19 mM undecanoic L-isoleucine with 1,2 ethylenediamine to a CMC of 2.00 mM for undecanoic Lisoleucine with 1,6 diaminohexane as the counterion. CE data showed that as the chain length of the counterion was increased, the enantiomers were resolved at a lower surfactant-counterion concentration. There was also improved chiral selectivity of BNA enantiomers in the presence of diamine counterions compared to the standard sodium. Based on previous literature, the micellar size also increased with a decrease in CMC as expected. The average hydrodynamic radius of undecanoic L-norleucine with 1,2-ethylenediamine at pH 10 was 9.17 Å compared to 24.52 Å for L-norleucine with 1,6 diaminohexane at pH 10.Item Characterization of the dipeptide based micellar systems undecanoic alanine-alanine and undecanoic alanine-glycine(2018-12) Maldonado, Savanna; Billiot, Fereshteh; Billiot, Eugene; Abdulla, HussainSurfactant are surface-active-agents, meaning surfactants have the ability to lower surface tension. In this research, two dipeptide surfactants undecanoic alanine-alanine and undecanoic alanine-glycine were studied to better understand their micellar systems. Variations of pH, temperature, surfactant concentration, and counterion type were examined to determine what effect, if any, changing these variables would have on micelle formation and chiral recognition. The counter ions examined in this study were di-amine alkanes with a different number of methyl groups separating the amines. These counter ions are pH dependent and preliminary results have shown that pH effects the interaction of these counter ions with the amino acid polar head, and in turn effects the physical properties of the surfactants and their micellar behavior. Some of the properties examined include: the critical micelle concentration, Krafft temperature, enantiomeric separation of chiral compounds, hydrodynamic radius of the micelles as well as fraction bound of the surfactant and counterions to the micelles. These systems were studied using proton Nuclear Magnetic Resonance (NMR), Diffusion Order Spectroscopy (DOSY), Capillary Electrophoresis (CE) and a LabQuest 2 with attached conductivity and temperature probes. The results here provide a better insight on the behavior of these dipeptide micellar systems which will aid in future research.Item Characterizing vascular plant and algal community structure and biomass in the Nueces Delta (TX) salt marsh system(2016-12) Lawson, BenjaminPrimary producers are responsible for the majority of the services provided by salt marshes, such as nutrient uptake, carbon sequestration, and support for fisheries. The Nueces Delta, a salt marsh in southern Texas, has been severely affected by reduced freshwater inflow, resulting in an altered composition of dominant plant species and functionality of the habitat. This study determined if the primary production along the two main channels in the Nueces Delta was affected differently by restrictions of freshwater inflow. Vegetative and microalgal biomass were harvested monthly at three locations along each channel and correlated to environmental factors. Photosynthetic measurements were also performed to determine stress levels of species present. A concurrent evaluation of government monitoring methods was performed. The study period was marked by rainfall amounts that were double the long-term average and by high vascular plant growth. Vegetative biomass along the Delta Access Channel (422.16 g C m-2) was significantly less (p < 0.005) than that of the Rincon Channel (475.71 g C m-2), with the largest differences in late winter months. Reduced winter vegetation biomass in the Delta Access Channel was accompanied by elevated microalgal biomass compared to the Rincon Channel (p < 0.0001). Maximum quantum yield (Fv/F¬m) of all vascular plants and microalgae remained well below optimum throughout the study and did not differ significantly between channels. Explanatory models revealed warm temperatures and increased freshwater inflow were the most important factors governing vegetative biomass, while microalgae thrived under salinity extremes and cooler temperatures. These results indicate that vegetation in the Delta Access Channel is impacted to a greater extent by reduced freshwater inflow. The RAM protocol currently used by the Texas General Land Office was unable to detect differences between seasons or sites. However, this indicates robustness of the protocol instead of a failure. Normalized difference vegetation index (NDVI) calculated from hyperspectral measurements was able to detect seasonal variation. The lower Nueces Delta should continue to be monitored to verify long term hydrologic and vegetation trends. Water management of the system may require channelization modifications to enhance freshwater flow into the Delta Access Channel and improve overall primary production in the Nueces Delta.Item Chemistry at the glass transition: Fluorescence-detected proton transfer reactions(2019-05) Granfor, Keegan; Causgrove, Timothy P.; Larkin, Patrick; Abdulla, HussainMany liquids when cooled to cryogenic temperatures have the ability to take the form of a glassy substance; these are referred to as amorphous solids. As they are supercooled they do not form crystalline substances but rather an amorphous glass lacking in long-range structure. While the knowledge of these amorphous solids has been around for many years not much is known regarding the simplest physical and chemical processes that are allowed to occur within this glassy state. We introduce a new fluorescence-based temperature derivative spectroscopy methodology with the aim of discerning some of these physical and chemical attributes such as proton transfer in the glassy state. Proton transfer in a cryogenic sample is accomplished by exploiting the photolytic capabilities of o-nitrobenzaldehyde. When exposed to ultraviolet light, o-nitrobenzaldehyde is transformed to o-nitrosobenzoic acid which has a relatively large acid dissociation constant. Fluorescein, a simple fluorescent molecule, and o-nitrobenzaldehyde were dissolved in a glycerol/water mixture and cryogenically supercooled below the glass transition temperature. The sample was then exposed to ultraviolet light and measured fluorometrically for alterations in the spectra. This experiment was repeated at varying viscosities and with deuterated solvents for measuring isotopic effects. The spectra were fit to first-order rate kinetic Arrhenius style equations to determine the energy barriers associated with the proton transfer. Currently there is no documented use of temperature derivative spectroscopy using fluorometric based measurements to study dynamic processes and little if any information regarding simple chemical processes occurring within a supercooled glass sample. This research provides a more detailed picture of these processes as well as describe a new methodology for temperature derivative spectroscopic experimentsItem Comprehensive approach for dissolved organic matter chemical characterization using orbitrap fusion tribrid mass spectrometer coupled with ion and liquid chromatography techniques(2021-12) Bergmann, Daniela; Bergmann, Daniela; Abdulla, Hussain; Abdulla, Hussain; Coffin, Richard; Murgulet, Dorina; Coffin, Richard; Murgulet, DorinaDissolved organic matter (DOM) contains the largest active organic carbon in the global carbon cycle. Though it has been extensively studied, only <10% of DOM has been chemically characterized into individual dissolved compounds. DOM is one of the most complex mixtures in nature; it consists of thousands of compounds with various molecular compositions, functional groups, and physicochemical characteristics. This study introduced a more comprehensive DOM characterization method by coupling both Ion Chromatography and Liquid Chromatography with high accuracy mass and resolution mass spectrometer. Estuarine DOM samples were and analyzed by Orbitrap Fusion Tribrid mass spectrometer (OT-FT-MS) coupled to both Ion Chromatography (IC) in negative mode and Liquid Chromatography (LC) in positive mode. This combination allows us to cover various DOM compounds ranging from highly cationic to highly anionic molecules. On-the-fly mass calibration of the Orbitrap at every scan by utilizing the “lock mass” function in the OT-FT-MS assures high mass accuracy throughout the whole sample run by a post-column introduction of internal labeled standards. A pooled quality control sample was used to increase reproducibility by applying systematic error removal using the random forest (SERRF) technique. The on-the-fly internal calibration application was tested on standard mixes before applying to actual DOM samples. In LC, the mass accuracy for the standards was consistently below +1.0ppm, and in IC below -4.0ppm, giving the OT-FT-MS the potential of reaching the massaccuracy of the Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR-MS). Once “lock mass” was established, estuarine surface water DOMsamples were analyzed in negative and positive modes. LC coupled to the OT-FT-MS for positive mode detection resulted in 915 compounds including 53 peptides and deaminated peptides that were identified through an in-house mass list comparison. IC coupled to the OT-FT-MS for negative mode detection resulted in 1432 extra compounds and including 361 deaminated peptides. Comparing the number of compounds detected shows the importance of analyzing both detection modes and the promising results of using IC in negative mode. A random forest-based normalization termed SERRF was compared to the traditional way of data normalization constant sum technique. Although constant sum provides already meaningful PCA data, SERRF assured a tight cluster of all Quality Control (QC). In IC mode, the relative standard deviation of QC samples was as high as 34.1% and corrected to 4.4% with SERRF, and in LC, the relative standard deviation was corrected from 28.1% to 3.9%. A combination of IC, LC, “lock mass”, and SERRF with the OT-FT-MS provides reliable and comprehensive approaches for DOM molecular characterization.Item Computational chemistry study of iron-based complexes for aqueous redox flow batteries(2021-08) Nguyen, Giang Thi Hoang; Holubowitch, Nicolas; Billiot, Fereshteh; Causgrove, TimothyRedox flow batteries (RFBs) are a new kind of battery with a great potential to store electricity from renewable energy sources like solar, wind, and tidal on a large scale. This project aims to discover new RFB active compounds that are eco-friendly and inexpensive to produce compared to vanadium, which is the current active compound for most commercial RFBs. This research focuses on iron-based organometallic complexes which are promising inexpensive and long-lived catholytes for aqueous RFBs. The long-term goal of this project is to discover new active compounds for aqueous redox flow battery (RFB). When iron binds with bipyridine (a common ligand for organometallic complexes), it gives stability at near-neutral pH and high discharge potential (high energy density) relative to uncompleted ferrous/ferric ions. However, there are two major challenges with Iron tris(2,2’-bipyridine): low aqueous solubility and dimerization. In this research project, computational chemistry, mainly density functional theory (DFT), will be applied to predict properties of Iron tris(2,2’-bipyridine) for RFBs. Redox potentials are best predicted via computation of Gibbs free energies in a Born-Haber thermodynamic cycle. Due to a variety of functionals and basis sets that serve as inputs for quantum chemistry calculations, different approximations including BP89, PBE, PBE0, B3LYP, BHLYP, B3PW91 and CAM-B3LYP were performed to match redox potential and structural determinations from DFT with actual lab data. As a result, PBE0 functional with LANL2DZ/def2-TZVP basis set gave the most accurate information. Hence, it is applied for deeper study about molecular orbitals, electrostatic potential, and the highest occupied (HOMO) and lowest unoccupied molecular orbital (LUMO) In the pursuit of new RFB compounds, it is critical to understand the relationship of molecular structure, functional group properties, and electronic properties. Redox potential of 13 derivatives of bipyridine were calculated. We were able to plot the effects of substituents on bipyridine ligand on the complex’s redox potentials by applying Hammett equation. In addition, dimerization of Fe(bpy)3SO4, which leads to poor voltage efficiencies in batteries with this catholyte is studied in this research. Due to spin-crossover of the charged (oxidized) Fe (III) complex, it changes structural, vibrational, electronic, and magnetic properties of the molecule. Hence, it forms a dimer during discharge which leads to a drop in voltage efficiency. Preventing dimerization is important in RFB research because it maintain total voltage output of the redox flow battery. Due to spin-crossover phenomenon, broken symmetry was applied to describe the magnetic properties of dimer which is antiferromagnetic. In addition, the dimer undergoes two electron reductions to regenerate two Febpy2+ monomers, thus a modified Born-Haber thermodynamic cycle is applied in discharge reaction to estimate discharge potential of dimer.Item Constraining alkalinity sources to a secondary bay in South Texas(2016-08) Trevino, Melissa; Murgulet, DorinaSubmarine groundwater discharge (SGD) is an important pathway for solute transfer from land to sea. With recent atmospheric carbon dioxide (CO2) increase, global concerns over oceanic and estuarine acidification have ascended. To better understand the natural ability of estuaries to buffer decreasing pH levels and assist in ocean acidification mitigation studies, overlooked sources of total alkalinity (TA) need to be considered. This study investigates TA changes in Nueces Bay (a secondary bay adjacent to Corpus Christi Bay in the Gulf of Mexico), at scales spanning from hours to seasonal, by incorporating submarine groundwater discharge (SGD) rates. TA concentrations within the bay fluctuated from December 2014 to December 2015 (December, 2014: 2527.6 µM; March, 2015: 2341.0 µM; June, 2015: 2765.1 µM; September, 2015: 2869.8 µM; December, 2015: 2638.6 µM). These observed changes in TA among the sampling events were mostly affected by different rates of SGD and biogeochemical reactions, while discharge from Nueces River was only important after significant rain events and flooding (June 2015), increasing the average TA (March, 2015: 2341.0 µM to June, 2015: 2765.1 µM) of the bay. Dry periods (March 2015) indicated consumption of DIC in the form of calcification may occur at some locations. SGD rates are the highest during the dry seasons (March 2015: 9.2 · 10-1 m3/d), thus there is an increased export of TA from groundwater. SGD, also has a lag effect post flooding (September-2015 to December-2015), as discharge at the shoreline increased (north shoreline of the Nueces Bay: 6.5 · 10-1 to 9.0 · 10-1 m3/d; south shoreline: 4.5 · 10-1 to 8.8 · 10-1 m3/d) and elevated SGD-derived TA input. Under unimpaired conditions, Nueces River would likely have a significant role on the bay’s alkalinity given the high groundwater contribution of alkalinity (1.2 · 107 µM/m2/d). This research shows that influences on TA fluctuations in an estuary may be spotty and not necessarily revealed by simple spatial analyses regardless of the sampling resolution. Hourly time series analyses are necessary to understand endogenous processes influencing alkalinity especially in estuaries with limited riverine inflows.Item Contamination risk and geophysical signature of abandoned wells in the gulf coast aquifer system, Texas(2021-12) Penchala, Tejaswini; Mohamed, Ahmed; Murgulet, Dorina; Smith-Engle, JenniferOver the years, many oil and gas wells have been abandoned, without proper plugging, around homes, farms, industrial sites, and urban areas. These abandoned wells are potentially becoming pathways for groundwater contamination through short-circuiting between aquifer units. The primary goal of this research is to create a risk map for the Texas Gulf Coast Aquifer (GCA, area: 108 x 103 km2) showing locations that are prone to groundwater contamination due to the presence of abandoned oil and gas wells. For this purpose, a Generalized Linear Regression model (GLR) was constructed and calibrated using the Geographic Information Systems (GIS) environment. Model inputs included well locations, surface lithology, locations of petroleum storage tanks, superfund points, wastewater outfalls, landfill sites, surface reservoirs, slope, stream density, and rainfall rates. Some of the abandoned wells might be buried underground over the years, identifying these wells is important to plug and eliminate their risk of contamination. To help identifying the buried wells, different geophysical datasets (magnetic, electromagnetic) were acquired and processed to explore their geophysical signature. The geophysical data was collected at the TAMU-CC's geophysical test site, where multiple well covers and steel drums were installed at various depths. Modelling results indicated that 11.53% of the total area of the GCA region is under high risk of groundwater contamination, whereas 43.79% of the area is at moderate risk, 31.05% of the area is at low risk, and 13.61% of the area is at no risk. The high-risk zones are mostly concentrated in the central part of the GCA region (Liberty, Jefferson, Jackson, Live Oak, Zapata, Washington, Calhoun, Chamber, and McMullen counties) and the risk-free zones in the southern part (Duval, Jim Hogg, Webb, Kenedy, Brooks, Lavaca, and Polk counties). Geophysical investigations indicated that both magnetic and electromagnetic anomalies were mainly generated, and correlated with the locations of, the buried drums (45,450–45,700 nT for magnetic, 226–254 mS/m for electromagnetic). Relatively lower magnetic and electromagnetic anomalies are associated with the locations of the well covers (45,200–45,400 nT for magnetic, 210 –222 mS/m for electromagnetic). Our research results could be utilized by decision makers to develop enhanced mitigation scenarios for risks associated with abandoned wells in Texas and around the globe.Item Dazed and confused: pesticides alter physiology, behavior, and predator-prey interactions of juvenile and adult blue crabs (Callinectes sapidus)(2017-05) Schroeder-Spain, Kaitlyn J; Smee, Delbert Lee; Shirley, Thomas; Wetz, Michael S.; Zimba, Paul V.; Deis, DonaldToxicants (i.e., pesticides) and predators may have large and interacting effects on natural communities by removing species (lethal effect) or by altering organismal physiology or behavior (sublethal effect). Studies evaluating the effects of sublethal concentrations of pesticide mixtures are limited, especially in coastal systems [1]. The purpose of this dissertation research was to investigate both lethal and sublethal effects of realistic pesticide exposure scenarios on two life-stages (juvenile and adult) of an important invertebrate estuarine predator, prey, and fishery species, the blue crab (Callinectes sapidus). Importantly, blue crab populations are declining throughout the U.S., but the potential role of pesticides in declines remains largely unexplored. In a series of laboratory experiments, I investigated: (1) lethal and sublethal effects of a single exposure to carbaryl (carbamate), malathion (organophosphate) and resmethrin (pyrethroid) + PBO (synergist), individually and in mixtures, on juvenile and adult blue crab survival and neuromuscular functioning by measuring changes in mortality, righting time (RT), and eyestalk reflexes. These responses serve as a proxy for the direct effects of exposure on survival and indirect effects on coordinated behaviors critical to blue crab survival (e.g., predator escape or foraging). Pesticides were selected because they are three of the mostly commonly used throughout the U.S. and have different modes of action. Effects observed at the organismal level were subsequently evaluated and linked with changes in (2) predator-prey interactions (mesocosms), and (3) physiological responses (enzyme assays). Lastly, (4) differences in susceptibility between juvenile (post-planktonic) and adult life-stages were also evaluated in behavioral and predator-prey experiments. Sublethal, legally allowable concentrations of individual pesticides and pesticide mixtures negatively affected juvenile and adult blue crabs by (1) reducing survivorship and locomotor functioning, (2) altering predator-prey interactions via changes on foraging rates and increased vulnerability to predators, and (3) increasing metabolic costs (e.g., AChE synthesis). These findings underscore the importance of studying pesticide effects in an ecological context, as juvenile life-stages were not always the most vulnerable, some effects varied non-linearly with concentration, and interactions between individual pesticides in mixtures were not necessarily predicable based on individual exposures. Notably, blue crabs were most sensitive to exposures including pyrethroid (resmethrin) + PBO, which are representative of common co-components of vector control products. Pyrethroid use for mosquito abatement and disease control is expected to increase, and the application of such products near aquatic systems should be carefully evaluated. In blue crabs, behavioral changes (e.g., RT) provided a reliable and sensitive endpoint, indicating altered physiological (i.e., increased AChE activity) and predator-prey interactions (i.e., reduced foraging, increased vulnerability to predators) in the pesticide exposures studied. Results also highlight the importance of studying individual responses with increasing levels of biological organization, e.g., changes in species interactions, as increases in RT unexpectedly corresponded with increased consumption rates in juvenile crabs (e.g., hyperactivity, Chapter 2). In the context of fisheries management and environmental regulations, RT may be a useful endpoint when measured in combination with other responses to indicate chances of survival or altered trophic relationships [2, 3].Item Decision support tools for managing freshwater inflows(6/9/2013) Sprague, Paige; Montagna, Paul A.Estuaries are important transitional zones where freshwater and marine water meet and mix. This freshwater is referred to as freshwater inflows. Estuaries are the link between streams and rivers and the sea. Freshwater inflows provide nutrients, sediments, and regulate salinity levels. An estuary cannot properly function without freshwater inflows from rivers and streams. Landscape changes caused mainly by anthropogenic influences are altering the amount of freshwater inflows to estuaries. Humans are diverting fresh water from rivers and streams. As the human population grows and the strain on water resources continues, the ability to effectively manage freshwater inflows into estuaries is becoming increasingly important. The purpose of the current project was to design support tool frameworks for managing freshwater inflows to estuaries, then creating a web-based implementation of the decision support tool, and lastly, surveying stakeholders to gauge its effectiveness. There is a great need for decision support tools to provide science-based information to policy makers, managers, and stakeholders. A decision support system is a structured system that can be used to integrate ecosystem based management (EBM) strategies in an organized manner. A decision support system traditionally assimilates operations processing systems into a framework where all are easily accessible. Decision support systems aid managers in the decision-making process and support the transference of knowledge to all levels of the system. A review of structural components of decision support tools in general, and existing environmental decision support tools, provided guidance for the creation of a web-based decision support tool to inform managers regarding issues relating freshwater inflows to estuarine system health. The web-based decision support tool created here is called Inflows. This tool offers information on freshwater inflows and estuarine systems to users through the use of EBM strategies and web-based technology. Integration of this broad range of data, information, human components, and technology into useful management tools can help managers create effective strategies for managing freshwater inflows and protecting estuarine habitats.Item Defining essential fish habitat in an ecosystem context: practical identification and relevance to management(2019-08) Olsen, Zachary; Stunz, Gregory W.; Tolan, James; Montagna, Paul; Pollack, Jennifer Beseres; Rios, JoWhile traditional fisheries management has been that of a single species approach, ecosystem-based management would allow for greater confidence and efficiency in fisheries management decision making. However, there is no consensus regarding what ecosystem-based management would look like in practice. The goal of this dissertation was to create a conceptual framework that will guide the incorporation of habitat data into existing fisheries management paradigms. This framework consists of three focus areas: (1) functional examination of fisheries-habitat relationships, (2) identification of linkages from habitat to population level impacts, and (3) identification of relevant application to specific management scenarios. The Black Drum (Pogonias cromis) population in the Upper Laguna Madre (ULM) was used as a case study to exemplify the quantification of functional habitat relationships (focus area 1) and to further link stage-specific habitat relationships (e.g., nursery habitat) to the population dynamics of the full population (focus area 2). These analyses were conducted using data from fisheries independent bag seine surveys collected by Texas Parks and Wildlife Department. Relationships between habitat variables (salinity, water temperature, and dissolved oxygen) and juvenile vital rates (mortality and growth) were modeled and then employed in a stage-specific population model. The salinity – juvenile mortality relationship was found to substantially influence the finite rate of increase for the full population. Two specific application of habitat data in fisheries management decision making were then demonstrated (focus area 3). The first application used habitat suitability models for three estuarine species to examine changes in the extent and distribution of suitable habitat within three classes of estuary (positive, neutral, and negative) across three salinity regimes (low, moderate, and high). The second application was a formal decision support tool that used