Stormwater runoff is a major environmental concern, particularly in urban environments. Trends in managing stormwater have evolved (and continue to evolve) from a quantity only approach into a sustainable approach, which integrates quantity, quality, the environment, and aesthetics. Best management practices (BMPs) and Low Impact Development (LID) are two well-documented techniques capable of managing to sustainable standards. There are a number of stormwater models available to design professionals today. However, there are few which integrate site-scale BMP/LID analysis in a simplified fashion. The purpose of this study is to determine if there is a demand in the design profession for simplified stormwater modeling tools to help designers make informed decisions about integrating BMP/LID strategies into site plans. A Web-based questionnaire was administered to a group of design professionals to determine their knowledge of BMPs and their technological needs and preferences in meeting stormwater goals and requirements.

Diclofenac (DCF) and other emerging contaminants have been found in environments worldwide. These contaminants may enter the environment due to the application of treated wastewater, biosolids and direct excrement related to veterinary application. Leakage from the soils toward the groundwater is largely controlled by sorption and microbial degradation. Most studies on the environmental fate of DCF have focused on degradation during wastewater treatment processes. However, little is known about their behavior in soil. In this study, the combined effect of adsorption and degradation of diclofenac has been investigated in four (4) 24 ft3 agricultural soil-filled beds designed to mimic natural vegetated soil environments, enhanced via controlled wetting and drying cycles. Contour bund installation on slopes of 5, 10, 15 and 20° were mimicked in the beds. Results showed that the soil environment was a strong inhibitor to the leaching of DCF through the soil. Saturating slopes via contour bund application however can lead to landslides that may impact structures and human life. A feasible contour bund installation site was investigated and found that 20° slopes under saturated conditions resulted in an unsafe factor of safety and is not encouraged as a solution for stormwater management. The effect of contour bund application on slopes under 15° at the installation site can potentially increase removal of emerging contaminants, thereby protecting groundwater resources without endangering life or property.

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Modern geodynamic modeling is more complex than ever, and has been used to answer questions about Earth pertaining to the dynamics of the convecting mantle and core, layers humans have never directly interacted with. While the insights gleaned from these models cannot be argued, it is important to ensure calculations are understood and behaving correctly according to known math and physics. Here I perform several thermal 3-D spherical shell tests using the geodynamic code ASPECT, and compare the results against the legacy code CitcomS. I find that these two codes match to within 1.0% using a number of parameters. The application of geodynamic modeling is also traditionally to expand our understanding of Earth; however, even with a scarcity of data modern methods can provide insight into other planetary bodies. I use machine learning to show that coronae, circular features on the surface of the planet Venus, are not randomly distributed. I suggest the idea of coronae being fed by secondary mantle plumes in connected clusters. The entirety of the Venusian surface is poorly understood as well, with a large percentage being topographically smooth and much younger than the planet's hypothesized age. I use modeling to test the hypothesis of a large impact being responsible for a major resurfacing event in Venus's history, and find three distinct scenarios following impact: relatively little change, some localized change evolving into resurfacing through geologic time, or large-scale overturn and injection of heat deep into the Venusian mantle. / Doctor of Philosophy / Modern geodynamic modeling has been used to answer questions about Earth in wide-ranging fields. Despite technological improvements, it is important to ensure the calculations are understood and behaving correctly. Here I perform several tests using a code called ASPECT and compare the results against another code, CitcomS. I find that the two codes are in good agreement. Application of these techniques is also traditionally done for Earth, but modern methods can provide insight into other planets or moons as well. Coronae are circular features on the surface of Venus that are poorly understood. I use machine learning to show that these are not randomly distributed, and suggest a mechanism for the formation of clusters of coronae. The surface of Venus is also strange: it is both too flat and too young based on current ideas in planetary science. I use modeling to test whether a large impact could cause the details of Venus's surface we see today.

Phosphoenolpyruvate carboxykinase (PEPCK) and phosphoenolpyruvate carboxylase (Pepc) are two important CO₂-fixation enzymes which share a similar reaction mechanism. Both operate through a lid-gated active site and have a hypothesized enol-pyruvate intermediate in their catalytic pathway. While PEPCK is an important metabolic enzyme in animals and plays a broad role in cataplerosis, gluconeogenesis and glyceroneogenesis, Pepc reaction in plants catalyzes the first committed step in CO₂ fixation in CAM and C₄ plants via Rubisco. We are studying the structure-function aspects of both enzymes, with a goal of discovering new elements in these enzymes which can modulate catalysis. We have undertaken an interdisciplinary approach for this work and have shown that a combination of experimental and computational techniques can be complementary and can provide novel information. We have determined that in human PEPCK, Tyr235 forms an anion-quadrupole interaction with the carboxylate of PEP and thus positions the latter with respect to the enzyme-bound Mn²+ for optimal phosphoryl transfer and catalysis. We have also identified Pro82 as a catalytically influential residue in this enzyme. Using molecular dynamics simulations we have noted that absence of ligands induces active-site lid opening in GTP-PEPCKS and we have made the first observation of the intermediary structures of the lid opening event, the dynamics of which is an important element that controls GTP-PEPCK catalysis. We have determined the first three-dimensional crystal structure of an archaeal-type Pepc, i.e. C. perfringens PepcA. Our experimental data also provide information about the oligomerization of PepcAs and reveal that aspartate inhibits the C. perfringens enzyme competitively compared to the allosteric inhibition in Pepcs. Structure-based modeling has led to the identification of putative aspartate- and bicarbonate-binding residues in C. perfringens PepcA, of which Arg82, His11, Ser201, Arg390, Lys340, Arg342 and Arg344 probably play an important role. / Ph. D.

High-level parallel programming approaches, such as OpenACC, have recently become popular in complex fluid dynamics research since they are cross-platform and easy to implement. OpenACC is a directive-based programming model that, unlike low-level programming models, abstracts the details of implementation on the GPU. Although OpenACC generally limits the performance of the GPU, this model significantly reduces the work required to port an existing code to any accelerator platform, including GPUs. The purpose of this research is twofold: to investigate the effectiveness of OpenACC in developing a portable and maintainable GPU-accelerated code, and to determine the capability of OpenACC to accelerate large, complex programs on the GPU. In both of these studies, the OpenACC implementation is optimized and extended to a multi-GPU implementation while maintaining a unified code base. OpenACC is shown as a viable option for GPU computing with CFD problems. In the first study, a CFD code that solves incompressible cavity flows is accelerated using OpenACC. Overlapping communication with computation improves performance for the multi-GPU implementation by up to 21%, achieving up to 400 times faster performance than a single CPU and 99% weak scalability efficiency with 32 GPUs. The second study ports the execution of a more complex CFD research code to the GPU using OpenACC. Challenges using OpenACC with modern Fortran are discussed. Three test cases are used to evaluate performance and scalability. The multi-GPU performance using 27 GPUs is up to 100 times faster than a single CPU and maintains a weak scalability efficiency of 95%. / Master of Science

Increased stormwater runoff due to urban development in the northern Shenandoah Valley (NSV) region of Virginia has prompted local officials and representatives to consider Low Impact Development (LID) as a stormwater management technique. LID is based on infiltrating stormwater runoff at the source through practices such as bioretention, rain gardens, and grass swales. The karst terrain that underlies the Shenandoah Valley presents a major barrier to the use of LID. Infiltration of surface runoff in karst landscapes may threaten groundwater quality and the stability of the bedrock. In 2004 the Center for Geospatial Information Technology (CGIT) at Virginia Tech developed an LID site suitability model for the NSV region incorporating karst as a key component in distinguishing unsuitable from suitable conditions for LID. But, due to the difficulty of mapping karst, the karst layer used in the site suitability model is very coarse in resolution, based primarily on carbonate versus non-carbonate rock. This study uses a 1:24,000 scale sinkhole map derived from sinkhole boundaries identified by geologist David Hubbard (1984) of the Virginia Department of Mines and Minerals (DMME) to develop a more detailed karst map for a sub-watershed of the NSV region. The analysis uses geospatial techniques to determine the relationship between sinkhole distribution and four major landscape factors: bedrock type, soil depth to bedrock, proximity to geologic faults, and proximity to surface streams. The analysis identified three major trends in sinkhole occurrence: (1) sinkholes are more abundant in relatively pure carbonate rocks of Ordivician age; (2) sinkhole occurrence increases with proximity to fault lines; and (3) sinkholes are sparse near streams, most abundant 600 to 1400 feet away from surface streams. Based on these findings a sinkhole susceptibility index was produced using weighted overlay analysis in ArcGIS. The sinkhole susceptibility index provides a more detailed karst layer for the LID site suitability maps and can be used by the NSV region as a predictive tool for future sinkhole occurrence. / Master of Science

Radio-frequency microelectromechanical systems (RF~MEMS) are highly miniaturized devices intended to switch, modulate, filter or tune electrical signals from DC to microwave frequencies. The micromachining techniques used to fabricate these components are based on the standard clean-room manufacturing processes for high-volume integrated semiconductor circuits. RF~MEMS switches are characterized by their high isolation, low insertion loss, large bandwidth and by their unparalleled signal linearity. They are relatively simple to control, are very small and have almost zero power consumption. Despite these benefits, RF~MEMS switches are not yet seen in commercial products because of reliability issues, limits in signal power handling and questions in packaging and integration. Also, the actuation voltages are typically too high for electronics applications and require additional drive circuitry. This thesis presents a novel MEMS switch concept based on an S-shaped film actuator, which consists of a thin and flexible membrane rolling between a top and a bottom electrode. The special design makes it possible to have high RF isolation due to the large contact distance in the off-state, while maintaining low operation voltages due to the zipper-like movement of the electrostatic dual-actuator. The switch comprises two separately fabricated parts which allows simple integration even with RF circuits incompatible with certain MEMS fabrication processes. The two parts are assembled by chip or wafer bonding which results in an encapsulated, ready-to-dice package. The thesis discusses the concept of the switch and reports on the successful fabrication and evaluation of prototype devices. Furthermore, this thesis presents research results in wafer-level packaging of (RF) MEMS devices by full-wafer bonding with an adhesive intermediate layer, which is structured before bonding to create defined cavities for housing MEMS devices. This technique has the advantage of simple, robust and low temperature fabrication, and is highly tolerant to surface non-uniformities and particles in the bonding interface. It allows cavities with a height of up to many tens of micrometers to be created directly in the bonding interface. In contrast to conventional wafer-level packaging methods with individual chip-capping, the encapsulation is done using a single wafer-bonding step. The thesis investigates the process parameters for patterned adhesive wafer bonding with benzocyclobutene, describes the fabrication of glass lid packages based on this technique, and introduces a method to create through-wafer electrical interconnections in glass substrates by a two-step etch technique, involving powder-blasting and chemical etching. Also, it discusses a technique of improving the hermetic properties of adhesive bonded structures by additional passivation layers. Finally, it presents a method to substantially improve the bond strength of patterned adhesive bonding by using the solid/liquid phase combination of a patterned polymer layer with a contact-printed thin adhesive film. / QC 20100617

Le but de cette thèse est de sonder la flexibilité de NCp7 et de Δ(-)PBS, deux bio-molécules impliquées dans le second saut de brin de la transcription inverse du VIH. Deux stratégies expérimentales ont été mises en place. Un nouveau montage de spectroscopie ultra-rapide de fluorescence par down-conversion a été construit. Les dynamiques de quenching de la 2-aminopurine (2Ap), insérée en position 6, 8 et 10 de la boucle Δ(-)PBS ont pu être entièrement résolues à une résolution sub-ps. Pour chaque position, 4 temps de vie ont été révélés. Des mesures d'anisotropie confirment que les deux composantes < 5 ps sont liées à un empilement de la 2Ap avec les Guanines avoisinantes. Cet empilement est site-spécifique, prouvé par l'augmentation significative de leurs amplitudes lorsque la 2Ap est située près de la tige (position 10). La faible proportion de conformations reliées à un quenching collisionnel est significative de la faible exposition des 2Ap au solvant et de l'encombrement général de la boucle. La seconde approche avait pour but d'étudier l'effet du repliement du squelette protéique de [35-50] NCp7 autour de son atome de zinc par CID et par LID. Les spectres CID de la protéine nue sont expliqués par le modèle du proton mobile et une description détaillée d'un schéma de fragmentation spécifique autour du Tryptophane (Trp) a été soulignée, attribué une Lysine voisine. Un seul fragment issu de l'excitation à 266 nm a été identifié, son apparition entre en compétition avec les fragments CID du Trp. L'effet général du repliement autour du Zinc se traduit par une augmentation du taux de fragmentation autour du Trp et par une perte de spécificité pour le reste du spectre.Les flexibilités de Δ(-)PBS et NCp7 ont été respectivement évaluées par spectroscopie ultra-rapide de type down-conversion et par spectrométrie en phase gazeuse. La première méthode nécessite l'utilisation d'une sonde fluorescente non invasive, la 2-aminopurine (2Ap), placée en position 6, 8 et 10 de la boucle Δ(-)PBS. Notre résolution temporelle permet de résoudre entièrement les dynamiques locales de quenching et d'anisotropie de la 2Ap. Les composantes liées au quenching statique et quenching collisionnel ont été discriminées et révèlent les degrés d'empilement / encombrement locaux de la boucle. L'effet du repliement de [35-50] NCp7 autour de son atome de zinc a été étudié par CID et par LID à 266 nm. La protéine nue présente un interessant shéma de fragmentation autour du Tryptophane (Trp), exalté par la complexation avec le zinc, au prix une perte de spécificité pour le reste du spectre. Un seul fragment LID a été identifié, un mécanisme de sa formation est proposé. / This thesis aims to probe the flexibility of NCp7 and Δ(-)PBS, two biomolecules involved in the second strand transfer of the HIV's reverse transcription. We brought to the front two original experimental methods. A new ultrafast fluorescence down-conversion setup has been built, suitable for biological chromophore investigations. The quenching dynamics of 2-aminopurine (2Ap), site-mutated at the positions 6, 8 and 10 of Δ(-)PBS loop, were completely resolved under a ps scale. For each location, 4 decay times, were highlighted. Further anisotropy measurements confirmed that the two < 5 ps components correspond to stacking interactions of 2Ap with neighbouring Guanines. The site-specific aspect of the stacking were supported by a significant increase of their relative amplitudes when 2Ap were cloesly located to the stem (position 10). The minor portion of conformations involved with ps to ns collisional quenching suggests a low exposure of 2Ap towards the solvent as well as a general restriction of the loop. The second method planned to investigate the effet of the zinc-folding on [35-50] NCp7's peptidic backbone, thanks to CID and LID. The CID-generated spectra of the bare peptide were explained by the mobile proton model, and an exhaustive tryptophan (Trp) fragmentation pattern was described, mainly due to a neighbouring Lysin effects. Only one LID-fragment has been identified upon 266 nm excitation, probably created through a pathway competing with the generation of Trp fragments by CID. The main aspects related to zinc-folding are a general enhancement of the fragmentation ratios related to Trp and a loss of specificity for the remaining mass spectra parts.Δ(-)PBS et NCp7 has been respectively investigated by ultrafast down-conversion spectroscopy and gas-phase spectrometry. The first method implies the use of a non invasive fluorescent probe, named 2 aminopurine (2Ap), site mutated in position 6, 8 et 10 of the Δ(-)PBS loop. Our time resolution allows to fully depict the local quenching dynamics and anisotropy decays. The component related to static and collisional has been solved, thus describing different stacking degrees as well as local restrictions. The effect of [35-50] NCp7 folding around its zinc atom has been studied by CID and 266 nm LID. The bare protein displays an interesting fragmentation pathway around its Tryptophan (Trp), enhanced with zinc complexation, at the cost of a loss of specificity for the remaining mass spectra parts. Only one LID fragment has been identified, its occurence has been interpreted.

Dopamine replacement therapy is the main method of treating Parkinson’s Disease (PD), however over time this treatment causes increasingly abnormal, involuntary movements. This symptom, known as Levodopa-Induced-Dyskinesia (LID) is associated with aberrant, high frequency oscillations (HFOs) in the motor cortex and basal ganglia, as demonstrated with implanted electrodes in human Parkinson’s patients as well as in a rat model of Parkinson’s Disease. However, despite efforts to determine if the same high frequency oscillations are also present during dyskinesia in the widespread 6-OHDA mouse model of Parkinson’s Disease, studies have been unable to do so. By building and implanting a 64-channel multi-electrode array into a unilateral 6-OHDA lesioned mouse, we were able to record HFOs at 80Hz and &gt;100Hz in the motor cortex, basal ganglia and thalamus in the lesioned hemisphere during LID. We also recorded bilateral HFOs at &gt;100Hz in the intact hemisphere. With this work we show that the same HFOs that are present in the motor cortex and basal ganglia of rats and humans are also present in mice during dyskinesia. This work will act to further validate the 6-OHDA PD-model in mice and provide opportunities to investigate new treatments for Parkinson’s Disease, dyskinesia and other neurological conditions. It will also serve as a model to study a purposed mechanism underlying the information processing in populations of neurons. / Dopaminbehandling är den mest förekommande metoden för att behandla Parkinsons sjukdom men detta orsakar dessvärre en bieffekt i form av gradvis förvärrande ofrivilliga rörelser. Detta beteendemönster kallas för Levodopa-Inducerad-Dyskinesi (LID) och med hjälp av elektrodimplantat i hjärnan, på parkinsonpatienter och djurmodeller av parkinsons, har man kunnat se att beteendet är förknippat med högfrekventa oscilleringar (HFO) av hjärnaktivitet i motorcortex och basala ganglierna. Trots försök att kartlägga om dessa högfrekventa oscilleringar också är närvarande i den populära 6-OHDA musmodellen av Parkinsons sjukdom, så har man hittills inte lyckats demonstrera detta. Genom att bygga och implantera ett elektrodimplantat med 64 kanaler i en ensidigt-leisonerad 6-OHDA musmodell av Parkinsons sjukdom så kunde vi åskådliggöra HFO i motor cortex, basala ganglierna och thalamus i den lesionerade hjärnhalvan under LID. Vi kunde också påvisa HFO som sträckte sig över till den intakta hjärnhalvan, med frekvenser över 100 Hz. Denna forskning ger stöd att 6-OHDA modellen för Parkinsons i möss är valid och ger möjlighet till nya metoder att utforska och behandla Parkinsons, dyskinesi och andra neurologiska åkommor. Studien lägger också grunden för framtida studier som ämnar att undersöka föreslagna mekanismer bakom sättet populationer av neuroner bearbetar information. / ingår i ett projekt finansierat av Vetenskapsrådet #2018-02717