cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7274/25541077.v1
title: Laboratory and Numerical Simulation of Tsunami Inundation in a Coastal Urban Area

description: In recent years tsunamis have been recognized as one of the most catastrophic natural disasters in the world, highlighted by the 2004 Indian Ocean tsunami and the 2011 Tohoku earthquake and tsunami. However, both physical and numerical studies on tsunami wave inundation impact on a coastal urban area remain limited. For example, laboratory experiments on tsunami interaction with multiple coastal structures are relatively few, and numerical studies are more focused on the bare-earth conditions rather than the coastal urban topography. The objective of this dissertation is to study the influence of coastal structures on the tsunami wave inundation and loading within an urban area both numerically and physically. Two separate laboratory experiments were conducted to evaluate the numerical model performance within a coastal urban topography, as well as to collect data on the tsunami wave loading within a structural array sheltered by a partial wall. Another numerical simulation was performed to study the tsunami inundation and flow velocity within a structural array sheltered by a partially standing seawall. Results from the laboratory and numerical simulations on the coastal urban topography suggest that tsunami inundation and flow velocity can be significantly impacted by the arrangement of nearby coastal structures, and variation in results exists among different numerical models. The physical and numerical studies on the structural array sheltered by a partial wall demonstrate the sheltering effect among structures as the clearance and sheltering angle by another structure can largely affect the wave loading, inundation, and flow velocity at a certain location. Results from this dissertation provide better understanding on the tsunami behavior within a coastal urban area with dense structures and offer insights on how to improve the numerical simulations as well as disaster planning within a coastal urban area.
DOI: 10.7274/25565247
title: Redox and Speciation Behavior of Plutonium in Mineralogically Complex Systems: The Role of Aluminum-Substitution in Iron (Oxyhydr)Oxides

description: Plutonium (Pu) is a radiotoxic element that is present in used nuclear fuel and reprocessing products, and at legacy contaminated sites. To address existing waste inventories and environmental contamination, it is essential to understand Pu fate and transport in subsurface environments, which is tied to its rich redox aquatic chemistry.
Predictive geochemical models are necessary for the long-term performance assessments of nuclear waste repositories and radionuclide migration in contaminated sites. However, current models do not accurately predict actinide behavior under field conditions and legacy contaminated sites, and do not account for complexity in mineral assemblages, such as significant metal impurities or substitution. 
In this work, we studied mineralogically complex systems where Pu(V/VI) is the sorbate and Aluminum-substituted hematite (a-Fe2O3), or Aluminum-substituted goethite (a-FeOOH) are the sorbents. Using synchrotron-based high-energy resolution fluorescence detection X-ray absorption near-edge structure (HERFD-XANES) and extended X-ray absorption fine structure (EXAFS) spectroscopies targeting the M4 and L3 edges of Pu, we quantified of the extent of Pu surface-mediated reduction from Pu(V/VI) to Pu(IV), and the determined the Pu speciation in systems where controlled mineral complexity in iron oxides is induced.
We found that Al-substitution in both hematite and goethite generates electronic changes and lattice distortions, and it slows down the sorption and ensuing reduction of Pu in short timescales. However, as the systems approached steady state, the extent of surface-mediated reduction to Pu(IV) was very similar to non-substituted iron (oxyhydr)oxides. We also found that Al-substitution in hematite and goethite leads to an increase in defects in the crystal morphology, which impacts the sequestration of Pu. In terms of Pu speciation, we found that at relatively high concentrations, precipitation of PuO2 nanoparticles occurs readily on the surface of corundum (a-Al2O3), while PuO2 nanoparticles and sorbed Pu species co-exist on the surface of hematite and Al-substituted hematite.
DOI: 10.7274/25565247.v1
title: Redox and Speciation Behavior of Plutonium in Mineralogically Complex Systems: The Role of Aluminum-Substitution in Iron (Oxyhydr)Oxides

description: Plutonium (Pu) is a radiotoxic element that is present in used nuclear fuel and reprocessing products, and at legacy contaminated sites. To address existing waste inventories and environmental contamination, it is essential to understand Pu fate and transport in subsurface environments, which is tied to its rich redox aquatic chemistry.
Predictive geochemical models are necessary for the long-term performance assessments of nuclear waste repositories and radionuclide migration in contaminated sites. However, current models do not accurately predict actinide behavior under field conditions and legacy contaminated sites, and do not account for complexity in mineral assemblages, such as significant metal impurities or substitution. 
In this work, we studied mineralogically complex systems where Pu(V/VI) is the sorbate and Aluminum-substituted hematite (a-Fe2O3), or Aluminum-substituted goethite (a-FeOOH) are the sorbents. Using synchrotron-based high-energy resolution fluorescence detection X-ray absorption near-edge structure (HERFD-XANES) and extended X-ray absorption fine structure (EXAFS) spectroscopies targeting the M4 and L3 edges of Pu, we quantified of the extent of Pu surface-mediated reduction from Pu(V/VI) to Pu(IV), and the determined the Pu speciation in systems where controlled mineral complexity in iron oxides is induced.
We found that Al-substitution in both hematite and goethite generates electronic changes and lattice distortions, and it slows down the sorption and ensuing reduction of Pu in short timescales. However, as the systems approached steady state, the extent of surface-mediated reduction to Pu(IV) was very similar to non-substituted iron (oxyhydr)oxides. We also found that Al-substitution in hematite and goethite leads to an increase in defects in the crystal morphology, which impacts the sequestration of Pu. In terms of Pu speciation, we found that at relatively high concentrations, precipitation of PuO2 nanoparticles occurs readily on the surface of corundum (a-Al2O3), while PuO2 nanoparticles and sorbed Pu species co-exist on the surface of hematite and Al-substituted hematite.
DOI: 10.7274/25571523
title: The Lifecycle of Marine Fog in the Coastal Zone

description: Fog is a collection of suspended water droplets or ice crystals in the atmospheric boundary layer that appears under favourable dynamic, thermodynamic, chemical, and surface conditions with visibility less than 1 km. Fog negatively affects society due to its ability to reduce visibility, which leads to economic losses of the same enormity of tornadoes. Notwithstanding extensive research, the ability to predict fog accurately is limited. Coastal fog is particularly difficult to predict because of the complex interactions between the lower atmosphere, upper ocean, and land surface. This dissertation presents several cases studies that aim to improve the understanding of coastal fog. The first part of the dissertation investigates a captivating fog dissipation event that was observed during the ’Fog and Turbulence Interactions in the Marine Atmosphere’ (FATIMA) project’s Grand Banks field campaign in the North Atlantic, where a fog-free region appeared immediately downstream of an islet (Sable Island) as fog advected past it. The second part concerns a mixing-fog event that appeared during the C-FOG field campaign off the coast of Newfoundland, Canada, where an oceanic cold front collided with a peninsula to produce misty/foggy conditions. In the third part of the dissertation, to aid fog prediction using numerical weather prediction models, a comprehensive set of laboratory experiments was conducted to quantify mixing as a function of the obstacle height.
DOI: 10.7274/25571523.v1
title: The Lifecycle of Marine Fog in the Coastal Zone

description: Fog is a collection of suspended water droplets or ice crystals in the atmospheric boundary layer that appears under favourable dynamic, thermodynamic, chemical, and surface conditions with visibility less than 1 km. Fog negatively affects society due to its ability to reduce visibility, which leads to economic losses of the same enormity of tornadoes. Notwithstanding extensive research, the ability to predict fog accurately is limited. Coastal fog is particularly difficult to predict because of the complex interactions between the lower atmosphere, upper ocean, and land surface. This dissertation presents several cases studies that aim to improve the understanding of coastal fog. The first part of the dissertation investigates a captivating fog dissipation event that was observed during the ’Fog and Turbulence Interactions in the Marine Atmosphere’ (FATIMA) project’s Grand Banks field campaign in the North Atlantic, where a fog-free region appeared immediately downstream of an islet (Sable Island) as fog advected past it. The second part concerns a mixing-fog event that appeared during the C-FOG field campaign off the coast of Newfoundland, Canada, where an oceanic cold front collided with a peninsula to produce misty/foggy conditions. In the third part of the dissertation, to aid fog prediction using numerical weather prediction models, a comprehensive set of laboratory experiments was conducted to quantify mixing as a function of the obstacle height.
DOI: 10.7274/25586229
title: Effect of Low-Frequency Ultrasound on Antibiotic Susceptibility of <em>Pseudomonas aeruginosa </em>Biofilms

description: Biofilms are complex communities of microorganisms generally attached to a surface and surrounded by a gel-like matrix of extracellular polymeric substances (EPS). This matrix provides protection and support to the biofilm community, shielding the microorganisms from environmental stresses, including antibiotics and host immune responses. Biofilms play significant roles in several aspects of human life and health. While they can be beneficial in certain environmental processes, biofilms are also associated with chronic infections. They exhibit high levels of antibiotic tolerance, contributing to the escalating antimicrobial-resistance health crisis.
The combination of low-frequency ultrasound (LFU) with antibiotics has emerged as a potential strategy to combat antimicrobial resistance. However, the mechanisms underlying this synergistic approach at both the biofilm and cellular levels remain poorly understood. This dissertation aims to elucidate these mechanisms through a series of comprehensive studies. 
Preliminary studies were conducted to verify the influence of LFU on antibiotic susceptibility of Pseudomonas aeruginosa biofilms, and to guide the subsequent research. Building upon these findings, a thorough analysis was performed to assess the impact of LFU on biofilm characteristics, including biofilm morphology and mechanical properties, and their subsequent influence on antibiotic susceptibility. Additionally, the effects of combined LFU and antibiotics on mucoid biofilms, relevant to cystic fibrosis infections, were explored. Furthermore, a 1-dimensional biofilm inactivation model was developed to probe potential mechanisms underlying the observed enhancement with LFU, suggesting changes in diffusion coefficient and biofilm cohesion. The enhanced inactivation of biofilms was characterized by an increase in antibiotic inactivation constants, resulting in shortened contact times for cell inactivation. This led to an exploration of cellular-level mechanisms, with a particular focus on the effect of LFU on efflux pumps, a key mechanism employed by cells to resist antibiotics. 
By achieving a better understanding of the combination of LFU and antibiotics, this research provides valuable insights into the management and treatment of biofilm-associated infections.
DOI: 10.7274/25586229.v1
title: Effect of Low-Frequency Ultrasound on Antibiotic Susceptibility of <em>Pseudomonas aeruginosa </em>Biofilms

description: Biofilms are complex communities of microorganisms generally attached to a surface and surrounded by a gel-like matrix of extracellular polymeric substances (EPS). This matrix provides protection and support to the biofilm community, shielding the microorganisms from environmental stresses, including antibiotics and host immune responses. Biofilms play significant roles in several aspects of human life and health. While they can be beneficial in certain environmental processes, biofilms are also associated with chronic infections. They exhibit high levels of antibiotic tolerance, contributing to the escalating antimicrobial-resistance health crisis.
The combination of low-frequency ultrasound (LFU) with antibiotics has emerged as a potential strategy to combat antimicrobial resistance. However, the mechanisms underlying this synergistic approach at both the biofilm and cellular levels remain poorly understood. This dissertation aims to elucidate these mechanisms through a series of comprehensive studies. 
Preliminary studies were conducted to verify the influence of LFU on antibiotic susceptibility of Pseudomonas aeruginosa biofilms, and to guide the subsequent research. Building upon these findings, a thorough analysis was performed to assess the impact of LFU on biofilm characteristics, including biofilm morphology and mechanical properties, and their subsequent influence on antibiotic susceptibility. Additionally, the effects of combined LFU and antibiotics on mucoid biofilms, relevant to cystic fibrosis infections, were explored. Furthermore, a 1-dimensional biofilm inactivation model was developed to probe potential mechanisms underlying the observed enhancement with LFU, suggesting changes in diffusion coefficient and biofilm cohesion. The enhanced inactivation of biofilms was characterized by an increase in antibiotic inactivation constants, resulting in shortened contact times for cell inactivation. This led to an exploration of cellular-level mechanisms, with a particular focus on the effect of LFU on efflux pumps, a key mechanism employed by cells to resist antibiotics. 
By achieving a better understanding of the combination of LFU and antibiotics, this research provides valuable insights into the management and treatment of biofilm-associated infections.
DOI: 10.7274/25595241
title: We Made A Breakthrough (Curve): How Immobile Zone Properties and Breakthrough Curves Inform One Another

description: The prediction of solute transport through environmental and man-made systems is critical to the preservation of ecological and human health, influencing our ability to remediate contaminated rivers, protect groundwater aquifers, and permanently dispose of nuclear waste. However, natural environments tend to be rich in physical, biological, and chemical complexities, producing regions of negligible flow that retard transport and give rise to anomalous behaviors. Mobile-immobile models (MIMs) have successfully captured anomalous transport in different environments by accounting for simultaneous interactions between solutes and a collection of negligible-flow features. While effective, integrating retention over a host of features hinders our understanding of how any one feature affects transport. Through the use of physical experiments and numerical simulations, this thesis aims to (i) determine whether we can disentangle the role of individual immobile features on BTC dynamics and (ii) determine whether BTC features can be related back to specific retention mechanisms. We explore these questions in subsurface fracture networks, fluvial, and colloidal systems which, while quite diverse, can be similarly divided into mobile and immobile flow regions. We find that in subsurface fracture networks and streams, varying a single immobile zone characteristic (ie: thickness, substrate type, biofilm accumulation) exerts a noticeable signature on continuum scale transport. We then take initial steps in relating features of continuum scale data back to retention mechanisms in stream and colloidal systems by using regressive and inverse model- ing techniques. Although there is significant work ahead to establish a predictable relationship between individual immobile features and BTC behavior, this thesis lays the groundwork for such detailed analyses.
DOI: 10.7274/25595241.v1
title: We Made A Breakthrough (Curve): How Immobile Zone Properties and Breakthrough Curves Inform One Another

description: The prediction of solute transport through environmental and man-made systems is critical to the preservation of ecological and human health, influencing our ability to remediate contaminated rivers, protect groundwater aquifers, and permanently dispose of nuclear waste. However, natural environments tend to be rich in physical, biological, and chemical complexities, producing regions of negligible flow that retard transport and give rise to anomalous behaviors. Mobile-immobile models (MIMs) have successfully captured anomalous transport in different environments by accounting for simultaneous interactions between solutes and a collection of negligible-flow features. While effective, integrating retention over a host of features hinders our understanding of how any one feature affects transport. Through the use of physical experiments and numerical simulations, this thesis aims to (i) determine whether we can disentangle the role of individual immobile features on BTC dynamics and (ii) determine whether BTC features can be related back to specific retention mechanisms. We explore these questions in subsurface fracture networks, fluvial, and colloidal systems which, while quite diverse, can be similarly divided into mobile and immobile flow regions. We find that in subsurface fracture networks and streams, varying a single immobile zone characteristic (ie: thickness, substrate type, biofilm accumulation) exerts a noticeable signature on continuum scale transport. We then take initial steps in relating features of continuum scale data back to retention mechanisms in stream and colloidal systems by using regressive and inverse model- ing techniques. Although there is significant work ahead to establish a predictable relationship between individual immobile features and BTC behavior, this thesis lays the groundwork for such detailed analyses.
DOI: 10.7274/25608531
title: Bacterial Exudates: Characteristics and Role in Selenium Reduction

description: The goals of this research are to further our understanding of interactions between soluble bacterial exudates and selenium, and to determine how these interactions may affect the environmental behavior of Se. 

In Chapter 2, I discuss a study that tests whether soluble bacterial exudates can reduce aqueous Se(IV). Exudate solutions were isolated from three different model species of bacteria and tested for reductive activity to added Se(IV). The results show that some bacterial exudates reduce Se(IV), but that those from Shewanella oneidensis can not unless the cells are grown in the presence of aqueous Se(IV). The results also demonstrate that Se(IV) reduction by each of the exudate solutions involves exudate-hosted sulfhydryl binding.

Chapter 3 describes potentiometric titration experiments that were used to measure the concentrations of proton-active sites on the exudate molecules produced by several bacterial species as a function of soak time, and the chapter also reports the first measurements of sulfhydryl site concentrations on exudate molecules. The total binding site concentrations of the exudates are primarily controlled by DOC concentration, unlike sulfhydryl site concentrations, suggesting that production of sulfhydryl-site bearing exudates is primarily an active process.

The research reported in Chapter 4 uses comparative proteomics to identify candidate proteins that are responsible for the inducible Se(IV) reductase activity of soluble S. oneidensis exudates. Combining the control of S. oneidensis exudates’ inducible activity with knowledge of required characteristics for Se(IV) reduction allows us to narrow the list to six candidate proteins for further investigation.

The research in this dissertation demonstrates for the first time the ability of soluble bacterial exudates to reduce Se(IV) and suggests that Se(IV) binding onto sulfhydryl sites controls the reduction reaction. The research characterizes the total concentration of binding sites and the concentration of sulfhydryl sites specifically on exudate molecules, and it identifies six candidate proteins that are responsible for the observed Se(IV) reduction. Overall, the research presented here improves our understanding of Se(IV)-exudate reactions, and could be useful in refining environmental models of selenium behavior and developing bioremediation methods for selenium contamination.
DOI: 10.7274/25608531.v1
title: Bacterial Exudates: Characteristics and Role in Selenium Reduction

description: The goals of this research are to further our understanding of interactions between soluble bacterial exudates and selenium, and to determine how these interactions may affect the environmental behavior of Se. 

In Chapter 2, I discuss a study that tests whether soluble bacterial exudates can reduce aqueous Se(IV). Exudate solutions were isolated from three different model species of bacteria and tested for reductive activity to added Se(IV). The results show that some bacterial exudates reduce Se(IV), but that those from Shewanella oneidensis can not unless the cells are grown in the presence of aqueous Se(IV). The results also demonstrate that Se(IV) reduction by each of the exudate solutions involves exudate-hosted sulfhydryl binding.

Chapter 3 describes potentiometric titration experiments that were used to measure the concentrations of proton-active sites on the exudate molecules produced by several bacterial species as a function of soak time, and the chapter also reports the first measurements of sulfhydryl site concentrations on exudate molecules. The total binding site concentrations of the exudates are primarily controlled by DOC concentration, unlike sulfhydryl site concentrations, suggesting that production of sulfhydryl-site bearing exudates is primarily an active process.

The research reported in Chapter 4 uses comparative proteomics to identify candidate proteins that are responsible for the inducible Se(IV) reductase activity of soluble S. oneidensis exudates. Combining the control of S. oneidensis exudates’ inducible activity with knowledge of required characteristics for Se(IV) reduction allows us to narrow the list to six candidate proteins for further investigation.

The research in this dissertation demonstrates for the first time the ability of soluble bacterial exudates to reduce Se(IV) and suggests that Se(IV) binding onto sulfhydryl sites controls the reduction reaction. The research characterizes the total concentration of binding sites and the concentration of sulfhydryl sites specifically on exudate molecules, and it identifies six candidate proteins that are responsible for the observed Se(IV) reduction. Overall, the research presented here improves our understanding of Se(IV)-exudate reactions, and could be useful in refining environmental models of selenium behavior and developing bioremediation methods for selenium contamination.