Dissertations / Theses on the topic 'Transit and Residence Times'

Deteriorating water quality in the face of a rising demand for agricultural products triggered interest in the groundwater resources of the Najd dessert, an arid region of southern Oman. Groundwater in this area usually is abstracted from one of the largest aquifers on the Arabian Peninsula, the Umm Er Radhuma aquifer. Increased discharge stands in contrast to limited precipitation: the monsoon is an annual event but it is regionally limited; cyclones infrequently occur within the range of three to seven years. Both are possible sources for groundwater recharge in the Najd. With these preconditions in mind, the present study investigates recharge to the Najd groundwaters as part of an active flow system and evaluates the mean residence time in the deep groundwaters. The tools of choice are a groundwater flow model combined with environmental isotope tracer data. The two-dimensional flow model replicates the characteristics of the aquifer system from the potential recharge area in the south (Dhofar Mountains) to the discharge area in the north (Sabkha Umm as Sammim). The south-to-north gradients and the observed artesian heads in the confined aquifer are reproduced. Simulation results indicate that changes between wet and dry periods caused transient responses in heads and head gradients lasting for several thousand years. Based on the used parameters the model calibration indicated, that a recharge rate of around 4 mm a−1 is sufficient to reproduce current groundwater levels. Since rising groundwater levels were documented after cyclone Keila in November 2011, modern recharge evidently occurs. 36-Cl concentrations and dissolved-helium concentrations indicate that the deep groundwaters in the central Najd are up to 550,000 years old. Thus, radiocarbon values indicating groundwater residence times for the central Najd up to 20,000 years and the northern Najd up to 35,000 years underestimate the groundwater residence times and seem to have been strongly affected by mixing during sampling. Decreasing 36-Cl and increasing 4-He concentrations confirm the expected trend in the direction of groundwater flow and prove to be more robust tracers for age dating of Najd groundwaters. Backward pathline tracking was used to simulate the groundwater ages. The tracking results show that a total porosity value between 15 and 20 % is consistent with the range of the observed chlorine-36 and heliumbased ages. The results and parameters obtained in the present study provide the basis for future 3D-groundwater models designed to evaluate the water resources available to the Najd’s agricultural complex. In addition, the developed 2D-model allows for studies of paleoclimate scenarios and their influence on the groundwater regime
Ein steigender Bedarf nach landwirtschaftlichen Produkten - und damit Wasser - bei gleichzeitiger Abnahme des verfügbaren Wassers in Qualität und Menge in den bisherigen Anbaugebieten, führt zu einer intensiven Nutzung der Grundwasserressourcen der ariden Najd-Region in der Provinz Dhofar, im Süden des Sultanats Oman. Als Quelle dienen die Grundwasservorräte des Umm Er Radhuma-Aquifers, einer der Hauptaquifere auf der arabischen Halbinsel. Der steigenden Nutzung stehen mit dem jährlichen Monsoon, der regional limitiert ist, und unrgelmässigen, zwischen 3 und 7 Jahren auftretenden Unwettern (Zyklonniederschlag) nur begrenzte Niederschlagsmengen als Quellen für eine mögliche Zufuhr von Wasser (Grundwasserneubildung) zum Aquifersystem gegenüber. Der Ansatz der vorliegenden Arbeit besteht darin, mit Hilfe eines Grundwassermodells und der Einbeziehung von Umweltisotopen das tiefe und zur Nutzung geförderte Grundwasser in der Najd-Region als Teil eines aktiven Fließsystemes zu untersuchen und mittlere Verweilzeiten des Grundwassers abzuleiten. Ein 2D-Grundwassermodell entlang einer Fließlinie vom Dhofar Gebirge im Süden zur Sabkha Umm as Sammim im Nordosten wurde entwickelt. Das Modell reproduziert den Süd-Nord-Gradienten als auch den aufwärts gerichteten Gradienten mit höheren Grundwasserständen in den tiefen Grundwasserleitern. Die Simulationen zeigen, dass der Wechsel von ariden und humiden Phasen (wenig bzw. viel Grundwasserneubildung) zu Veränderungen der Grundwasseroberfläche führt die mehrere tausend Jahre anhalten können. Das kalibrierte Grundwassermodel zeigt, dass mit einer Neubildungsrate von 4 mm a−1 die natürlichen Grundwasserverhältnisse im Najd abgebildet werden können. Dass eine moderne Grundwasserneubildung stattfindet, konnte mittels Loggermessungen anhand steigender Grundwasserstände im tiefen Aquifersystem nach dem Extremunwetter im November 2011 (Zyklon Keila) eindeutig nachgewiesen werden. Die Analyse der 36Cl- und 4He-Konzentrationen zeigt, dass die tiefen Grundwasser im zentralen Najdgebiet bis 550 000 Jahren alt sein können. Das bedeutet allerdings, dass die über 14C Daten berechneten Grundwasseralter mit ca. 20 000 Jahren für das zentrale Najdgebiet und bis zu 35 000 Jahren für den nördlichen Najd, die Grundwasseralter deutlich unterschätzen. Die abnehmenden 36Cl und ansteigenden 4He Konzentrationen zeigen den erwarteten Trend in Grundwasserfließrichtung und können als aussagefähige Tracer für die Bewertung der Verweilzeiten und Alter des fossilen Grundwassers der Najd-Region angesehen werden. Mit Hilfe des Partickeltrackings wurden die Grundwasseralter, basierend auf den Isotopentracern, im Grundwassermodel simuliert. Die Porosität wurde dabei für das Aquifesystem mit Werten zwischen 15 und 20 % bestimmt. Die generierten Parameter und das gewonnene Systemverständnis sind eine wichtige Basis für zukünftige 3D-Modellstudien welche die Verfügbarkeit der Wasserresourcen im Najd untersuchen werden. Weitere Anwendungen für das in dieser Studie aufgebaute 2D-Modell sind Untersuchungen zum Paläoklima und dessen Einfluss auf das Grundwassersystem

The objectives of this research were to provide a better understanding of particle motion in cascading rotary dryers. This would lead to more soundly based design procedures. Experiments were performed, to check the validity of a proposed design method for dryers operating in the under-loaded and design loaded conditions developed by Matchett and Baker, on a pilot plant rig at Teesside Polytechnic using wheat and sand in the absence of airflow. The model considers the particles to move in two parallel phases, the airborne phase contains the material in flight and the dense phase contains the remaining material which is caught on the flights and on the bottom of the drum. There is continuous Interchange of material between the two phases. A dimensionless number, dense phase velocity number 'a', has been defined which is a measure of the axial velocity of the material in the dense phase of the drum. The 'a' values were found to be in agreement with existing data and were found to be dependent on material and not on dryer speed or slope. Photographic studies of the dryer internals suggested that the assumption of a constant 0 value (measure of flight loading) In the original model was not valid and that 4) varied with number of flights. A model was developed to predict 0 which worked extremely well for large number of flights. The existing design model was therefore modified to take account of the variation In 4). However, the paired t-test Indicated that at 5% level of significance there was no difference between the original and the modified model, even though the modified model is physically more realistic. It is, however, recommended that the models be tested on a large number of flights and also large equipment, because It is expected that with a large number of flights there will be differences between the two models and the 0 model will be superior. The 'a' and am (the am value is a modified form of the 'a' value which takes into account the variation in flight loading) values were found to be Independent of operating conditions, flight angle and also dryer size but were dependent on material. The 'a' and am values were proportional to 1/number of flights. Particle motion in the dense is by bouncing, rolling and sliding, but the high dense phase velocity numbers obtained with zero flights (ar) suggested ii that rolling and sliding are the important mechanisms of the dense phase motion and may be far more important than bouncing. A model has also been developed to study the over-loaded regime. In the over-loaded regime It was found that dryer speed, slope, material and number of flights affected the dense phase motion and a simple relationship between the over-loaded dense phase velocity number (ao) and number of flights could not be developed with the limited data. Particle motion In the over-loaded regime was found to be very complex. The ao values could be predicted to within ± 35%. Estimates have been made of the transition holdup, marking the change from under-loaded to over-loaded behaviour, but It was found that the prediction of the transition holdup is also complex and could be predicted to within ± 45%. The am values could be predicted to an accuracy of ± 10%. Thus suggesting that the ao and the transition holdup numbers are not so reliable. Future work has been recommended particularly in the over-loaded regime and also on the transition region since it was found that the particle motion in these regions was complex. It has also been suggested that the models be tested in large Industrial units with and without air flow.

Water is the elementary component of life on Earth, and quantifying this resource is critical to understanding ecosystem viability on planetary, continental, and local scales. In a simplified partition of the Earthfs freshwater resources, 75% is ice at the north and south poles, 25% is groundwater, and 0.01% exists in lakes and streams. Mean transit time is a robust description of groundwater volume within the discrete aquifers that together make up the 25% of Earthfs freshwater. Mean transit time can be estimated using environmental tracer concentrations in springs and gaining streams. That is because springs and streams are locations where groundwater flow paths naturally converge. Converging flowpaths create discharge that is a flow]weighted mixture of water from the contributing aquifer. The age of that flow-weighted mixture is a good measure of the mean transit time of water as it discharges from the contributing aquifer. Mean transit time can be directly used to estimate the volume of groundwater storage in the aquifer.

Although simple in principle, there are several important topics that need to be considered when collecting and dating a broad mixture of flow paths. They include 1) the necessity for a basic conceptual perception of the investigated aquifer, 2) the non-conservative aspect of most age-dating environmental tracers once exposed to the atmosphere, and 3) the importance of estimating a transit-time distribution. These specific topics are discussed in this dissertation.

This dissertation presents a system-wide approach, based on genetic algorithms, for the optimization of transfer times for an entire bus transit system. Optimization of transfer times in a transit system is a complicated problem because of the large set of binary and discrete values involved. The combinatorial nature of the problem imposes a computational burden and makes it difficult to solve by classical mathematical programming methods. The genetic algorithm proposed in this research attempts to find an optimal solution for the transfer time optimization problem by searching for a combination of adjustments to the timetable for all the routes in the system. It makes use of existing scheduled timetables, ridership demand at all transfer locations, and takes into consideration the randomness of bus arrivals. Data from Broward County Transit are used to compute total transfer times. The proposed genetic algorithm-based approach proves to be capable of producing substantial time savings compared to the existing transfer times in a reasonable amount of time. The dissertation also addresses the issues related to spatial and temporal modeling, variability in bus arrival and departure times, walking time, as well as the integration of scheduling and ridership data.

A hydrographic dataset from the 2008-2009 Rivers Inlet Ecosystem Study (RIES) field program was used (a) to provide a more complete oceanographic description of Rivers Inlet, British Columbia and (b) to develop the first quantitative estimates of estuarine circulation and new production for this system. Water column observations show a highly stratified two-layer estuarine structure, particularly in the spring and summer months when river discharge and atmospheric heat inputs were high. The net air-sea heat flux had a seasonal range of approximately 220 Wm⁻² and peaked almost a month earlier in 2008 than in 2009. The main source of river input comes from the Wannock River. As temperatures begin to rise in the spring, the river discharge can suddenly increase by an order of magnitude (from about 100 m³ s⁻¹ to almost 1000 m³ s⁻¹) in less than two weeks. Residence times (ie. first-order estimates of estuarine circulation) were estimated for every cruise using salinity and temperature budgets in a two-layer box model parameterization of the flow structure. The results show that upper box residence times vary seasonally with river discharge; dropping from about 14 days in the winter to as low as 4 days in the spring at the freshet onset. An earlier flushing event in 2009 caused residence times to drop earlier and could have caused higher advection losses for phytoplankton in the early spring. Overall, residence times averaged to about 7 days for the upper layer and about 165 days for the lower layer during periods of high river discharge, and about twice that during periods of low river discharge. Deep water in the lower layer below the sill was renewed almost once a year in summer and was affected only by vertical diffusion during the rest of the year. Finally, a spring/summer new production estimate of 0.6-1.7 gCm⁻²d⁻¹ (which implies about 110-300 gCm⁻²y⁻¹ assuming no production during the other months) was obtained by combining transport estimates with observations of nutrients to infer a surface nitrate sink. This range compares well with independent estimates made in nearby regions.

Thesis: M.B.A., Massachusetts Institute of Technology, Sloan School of Management, 2014. In conjunction with the Leaders for Global Operations Program at MIT.
Thesis: S.M., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2014. In conjunction with the Leaders for Global Operations Program at MIT.
Cataloged from PDF version of thesis.
Includes bibliographical references (page 85).
with delays on the road and variabilities introduced by the major participants in the process, ie: distribution centers, drivers, etc. These sources of variability also make it difficult to measure the impact changes in transit time have on on-time performance. This paper focuses on trying to identify indicators of variability and incorporates them into quantile regression forest, a black box forecasting model, that will provide estimated scheduled transit times for a given probability of on-time arrival at the destination. With the use of Amazon's Q1 & Q2 2013 linehaul data, an analysis on performance trends based on length of haul were categorized to develop an understanding linehauls in North America. The outbound transportation team at Amazon faces the complex trade off between providing a sufficient amount of scheduled transit time to ensure ontime delivery to destination and the utilization rate of a truck. The ability to quantify how changes in scheduled transit time impact the performance of a particular linehaul allows transportation managers to assess this trade off. The paper explores a machine learning regression technique called quantile regression forests. The model was developed in R using the quantregforest package. It incorporates numerous factors about linehaul including: origin, destination, historical reporting on sources of late to arrivals, time to depart from origin and time of departure. The strengths of this black box model are in its ability to handle a large amount of data and continuously update its predicting structure to provide more accurate recommendations. Quantile regression forests also enable the user to specify the ontime performance percentage, p, that he/she wants the model to predict based on historical data. The final model at p = 95% provided a weight mean absolute percent error of 4.57% and a root mean square error of 2.22%. A four-week pilot was conducted to validate these predictions and the results are discussed.
by Gold Truong.
M.B.A.
S.M.

Anthropogenic Climate Change is amongst the greatest challenges of human civilization. A key area that will play a large role in mitigating its effects are clean fossil fuel applications. Clean coal combustion is one such application with an urgent timeline. This can be achieved with an oxygen-fired pressurized fluidized bed combustor with downstream carbon capture and sequestration. In relation to pressurized fluidization processes, understanding the influence of pressure on bed hydrodynamics and in turn their effect on parameters including fuel residence time is essential. For the proposed combustor, the heat exchanger boiler tubes are submerged in the fluidized bed such that the effect of a horizontal tube bank on the fuel residence time is also of great importance. The main focus of present work was to evaluate the impact of gas velocity, pressure, presence of a tube bank and fuel feed rate on the average fuel residence time. Experiments were conducted under cold flow conditions in a pilot-scale pressurized fluidized bed with an inner diameter of 0.15 m. The fluidization material was relatively large glass beads (1.0 mm in diameter) while the fuel particles were simulated with smaller glass beads (40 to 138 μm in diameter), susceptible to entrainment. Operating pressures and superficial gas velocities tested were between 101.3 and 1200 kPa and 0.4 and 1.1 m/s respectively. To simulate coal combustors, experiments were then conducted in a continuous mode where the fuel particles were continuously fed to the fluidized bed of large particles over a desired period of time. Downstream, entrained particles were continuously captured to determine the entrainment rate and mass of fuel particles inside the fluidized bed at steady state, which yielded the average fuel residence time. The combination of elevated pressure with the tube bank present was found to enhance gas bubble break up and reduce the average gas bubble size. In turn, this increased the average fuel residence time of 83 μm particles by nearly 3 fold to a value of 77 s in comparison to 27 s at atmospheric pressure. The effect of gas velocity was not found to be statistically significant under the range tested. Similarly the effect of increased fuel feed rate by 50% neither had a statistically significant impact.

Tableau d'honneur de la Faculté des études supérieures et postdoctorales, 2017-2018
Dans le cadre du projet PACES III pour la région de Chaudière-Appalaches, situé au sud de la ville de Québec, au Canada, l'étude présente une analyse approfondie de l’influence des dynamiques d’écoulement sur la qualité des eaux souterraines dans un contexte régional. L’écoulement régional, le transport d’âge et l'impact d'une faille sur la qualité de l'eau souterraine sont étudiés par l’entremise de modèles numériques bidimensionels. La combinaison des connaissances hydrogéologiques physiques et chimiques, y compris une analyse des concentrations de ¹⁴C dans les eaux souterraines échantillonnées, a conduit à l’ébauche d'un modèle conceptuel de l’écoulement régional. Ce dernier est mis à l’essais pas l’entremise d’un modèle d'écoulement numérique suivant une ligne d’écoulement régionale dans le plan 2D vertical à l’aide du logiciel FLONET. Le modèle est d'abord calibré à l’aide d’une méthode semi-automatisé qui utilise le logiciel PEST en comparant les charges simulés à la piézométrie régionale, et est validé par la comparaison des flux simulés à la recharge. Bien que le modèle affiche l’existence d’un écoulement régional profond, la région à l’étude apparaît être dominée par des systèmes d'écoulements locaux à des échelles maximales d'environ 5 km, avec un écoulement significatif dans le roc fracturé peu profond. L’écoulement actif se limitant à une profondeur maximale de 40 m à 60 m du roc fracturé, confirme que la géochimie des eaux souterraines échantillonnées à partir de puits résidentiels est susceptible d'être affectée par les eaux faisant parti de l’écoulement intermédiaire et régional. Le transport advectif-dispersif de l'âge est ensuite simulé avec le simulateur de transport TR2 et comparé aux temps de déplacement advectifs le long des lignes d’écoulements et à l'âge ¹⁴C des eaux échantillonnées. Enfin, l’influence de la faille de la Rivière Jacques Cartier sur le contexte hydrogéologique régional est étudiée à travers divers scénarios hypothétiques de perméabilité de faille.
As part of the PACES III project in the Chaudière-Appalaches region, south of Quebec City, Quebec, Canada, the study herein presents insights into the extent to which regional groundwater quality is shaped by flow dynamics. In this context, 2D numerical modelling is used to simulate regional flow, transport of groundwater age and the possible influence of a fault on groundwater quality. Combining physical and chemical hydrogeological knowledge, including an analysis of ¹⁴C concentrations in sampled groundwater, leads to the development of a regional conceptual flow model. The conceptual model is tested by representing the system with a two-dimensional numerical flow model oriented in the vertical plane roughly south-north towards the St. Lawrence River using the FLONET code. The model is first calibrated to regional piezometry through a semi-automated workflow using PEST and is then validated with average recharge values. Although some evidence for deeper regional flow exists, the area appears to be dominated by local flow systems on maximum length scales of about 5 km, with significant flow through the shallow fractured sedimentary rock aquifer. This regional scale flow model is also supported by the local hydrogeochemical signatures. Active flow appears contained within the top 40 m to 60 m of the fractured bedrock, which confirms that the geochemical signatures of groundwater sampled from residential wells are likely affected by the slow moving waters of the intermediate and regional flow systems. Advective-dispersive transport of groundwater age is then simulated with the TR2 transport model and compared with advective travel times and sampled ¹⁴C water ages. Finally, the possible role of the Jacques-Cartier River fault on regional flow dynamics is investigated by testing various fault permeability configurations.

In surface hydrology, much attention is paid to the effects of changing water fluxes, however there is less of a focus on the effects of changing energy fluxes. These energy fluxes are an important driver of many hydrological processes such as evapotranspiration and snow sublimation/ablation. The hypothesis that varying energy fluxes are important to the hydrological features of a catchment is tested by an experiment that involves calculating mean transit times for a number of catchments that drain different aspects of a large dome located in the Valles Caldera, New Mexico, called Redondo Peak. These catchments have different orientations and therefore receive different amounts of solar radiation. There is a general correlation between mean transit times, as determined by lumped-parameter convolution, and aspect, suggesting that in the Valles Caldera, transit times might be affected by a variety of features that are influenced by exposure to solar radiation, such as slope steepness, vegetation patterns, and soil depth. To put these transit times into context, I also used a distributed physically-based model to simulate a number of factors simultaneously to determine how hydrological features are influenced by aspect. This modeling excercise has illuminated the aspect-dependence of hydrological features such as the timing and intensity of snowmelt and soil moisture patterns, and it has quantified differences in energy and water fluxes on different aspects. These factors affect both water storage and water fluxes, and are therefore tied to transit times.

Les grandes éruptions caldériques sont parmi les phénomènes les plus destructeurs de la Terre, mais les processus à l’origine des grands réservoirs de magma siliceux et pauvre en cristaux qui alimentent ces éruptions ne sont pas bien compris. Le temps de stockage de ces réservoirs dans la croûte supérieure a un intérêt particulier. De longs temps de stockage—jusqu’à 105 ans—ont été estimés en utilisant les temps de repos entre les éruptions et les âges radiométriques des cristaux qui se trouvent dans les produits éruptifs. Par contre, des travaux récents sur la diffusion dans des cristaux suggèrent que les réservoirs qui alimentent même les plus grandes éruptions peuvent se mettre en place pendant une période beaucoup plus courte—101–102 ans. Afin de répondre à cette question, j’ai étudié l’éruption dacitique de Cape Riva de Santorin, Grèce (>10km3, 22 ka). Pendant les 18.000 ans précédant cette éruption, une série de dômes et de coulées dacitiques a été émise, alternant avec des dépôts de ponce dacitique (le complexe de dômes de Therasia). Ces dacites ont des compositions similaires à celle qui a été émise pendant l’éruption de Cape Riva, et ont été décrites précédemment comme des « fuites » provenant du réservoir de Cape Riva pendant sa croissance. Cependant, le magma de Cape Riva est appauvri en éléments incompatibles (tels que K, Zr, La, Ce) par rapport au magma de Therasia, une différence qui apparaît également dans les cristaux de plagioclase. Cette différence ne peut pas être expliquée par des processus peu profonds, tels que la cristallisation fractionnée ou l’assimilation de la croûte, ce qui suggère que les magmas de Cape Riva et Therasia ont des origines différentes. En outre, il existe des arguments tendant à montrer que les dacites de Therasia n’ont pas été alimentées par un réservoir majoritairement liquide ayant eu une longue durée de vie. Il y a des variations non systématiques dans la composition du magma, les compostions des bords ainsi que les caractéristiques des cristaux de plagioclase tout au long de la séquence. De plus, les temps de résidence à haute température des cristaux de plagioclase et d’orthopyroxène estimés par des modèles de diffusion sont 101–102 ans. Ces temps sont courts par rapport au temps moyen entre éruptions (1.500 ans), ce qui suggère que les cristaux observés dans chaque coulée ne se sont formés que peu de temps avant l’éruption. Les différentes teneurs en éléments incompatibles indiquent qu’un nouveau magma s’est mis en place dans le système volcanique superficiel peu de temps avant l’éruption de Cape Riva. Cet apport de magma a eu lieu après la dernière éruption de Therasia, qui s’est produite <2.800±1.400 ans avant l’éruption de Cape Riva selon les âges 40Ar/39Ar. Les périphéries des cristaux de plagioclase présents dans la dacite de Cape Riva sont en équilibre avec une rhyodacite, avec une composition similaire à celui du verre de l’éruption. Cependant, les zonations dans les éléments majeurs et traces enregistrent des changements dans la composition du liquide magmatique pendant la croissance des cristaux. La composition du centre de la plupart des cristaux de plagioclase est la même que celle des bords ; toutefois ces cristaux sont souvent partiellement résorbés, et la croissance a repris avec du plagioclase plus calcique. Ces cycles se répètent jusqu’à trois fois. La relation étroite entre la teneur en anorthite, Sr et Ti des différentes zones suggère que la composition des plagioclases est corrélé avec la composition du liquide, allant de liquides dacitiques à rhyodacitiques. Des cristaux d’orthopyroxène révèlent une séquence similaire. Les motifs de zonation sont interprétés comme un témoin de la formation du réservoir de Cape Riva dans la croûte supérieure par le mélange de plusieurs magmas ayant des compositions diverses. Des modèles de diffusion de Mg dans le plagioclase et de Fe–Mg dans l’orthopyroxène suggèrent que ce mélange a eu lieu 101–102 ans avant l’éruption
Large, explosive, caldera-forming eruptions are amongst the most destructive phenomena on the planet, but the processes that allow the large bodies of crystal-poor silicic magma that feed them to assemble in the shallow crust are still poorly understood. Of particular interest is the timescales over which these reservoirs exist prior to eruption. Long storage times—up to 105 y—have previously been estimated using the repose times between eruptions and radiometric dating of crystals found within the eruptive products. However, more recent work modelling diffusion within single crystals has been used to argue that the reservoirs that feed even the largest eruptions are assembled over much shorter periods—101–102 y. In order to address this question, I studied the >10km3, 22-ka, dacitic Cape Riva eruption of Santorini, Greece. Over the 18 ky preceding the Cape Riva eruption a series of dacitic lava dome and coulées were erupted, and these lavas are interspersed with occasional dacitic pumice fall deposits (the Therasia dome complex). These dacites have similar major element contents to the dacite that was erupted during the Cape Riva eruption, and have previously been described as “precursory leaks” from the growing Cape Riva magma reservoir. However, the Cape Riva magma is depleted in incompatible elements (such as K, Zr, La, Ce) relative to the Therasia magma, as are the plagioclase crystals in the respective magmas. This difference cannot be explained using shallow processes such as fractional crystallisation or crustal assimilation, which suggests that the Cape Riva and Therasia magmas are separate batches. Furthermore, there is evidence that the Therasia dacites were not fed from a long-lived, melt-dominated reservoir. There are non-systematic variations in melt composition, plagioclase rim compositions, and plagioclase textures throughout the sequence. In addition, high-temperature residence times of plagioclase and orthopyroxene crystals from the Therasia dacites estimated using diffusion chronometry are 101–102 y. This is short compared to the average time between eruptions (1,500 y), which suggests the crystals in each lava grew only shortly before eruption. The different incompatible element contents of the Cape Riva and Therasia magmas and plagioclase crystals suggest that a new batch of incompatible-depleted silicic magma arrived in the shallow volcanic plumbing system shortly before the Cape Riva eruption. This influx must have taken place after the last Therasia eruption, which 40Ar/39Ar dates show occurred less than 2,800±1,400 years before the Cape Riva eruption. The rims of the plagioclase crystals found in the Cape Riva dacite are in equilibrium with a rhyodacite, with a similar composition to the Cape Riva glass. However, the major and trace element zoning patterns of the crystals record variations in the melt composition during their growth. The compositions at the centre of most crystals are the same as the rims; however, these crystals are often partially resorbed and overgrown by more calcic plagioclase. The plagioclase then grades normally back to rim compositions. This cycle is repeated up to three times. The tight relationships between the anorthite, Sr and Ti contents of the different zones suggests that the composition of the plagioclase crystals correlates with the composition of the melt from which theygrew. The different plagioclase compositions correspond to dacitic and rhyodacitic melt compositions. The orthopyroxene crystals reveal a similar sequence, although they only record one cycle. These zoning patterns are interpreted to document the assembly of the Cape Riva reservoir in the shallow crust through the amalgamation of multiple batches of compositionally diverse magma. Models of magnesium diffusion in plagioclase and Fe–Mg interdiffusion in orthopyroxene suggest that this amalgamation took place within 101–102 y of the Cape Riva eruption

Arctic rivers transport 31-42 Tg organic carbon (OC) each year to the Arctic Ocean, which is equal to 10% of the global riverine OC discharge. Since the Arctic Ocean only holds approximately 1% of the global ocean volume, the influence of terrestrially derived organic carbon (OCter) in the Arctic Ocean is relatively high. Despite the global importance of this region the behavior of the, by far largest fraction of the OCter, the dissolved organic carbon (DOC) in Arctic and sub-arctic estuaries is still a matter of debate. This thesis describes data originating from field cruises in Arctic and sub-arctic estuaries and coastal areas with the aim to improve the understanding of the fate of OCter in these areas, with specific focus on DOC. All presented studies indicate that DOCter and terrestrially derived particulate organic carbon (POCter) are subjected to substantial degradation in high-latitude estuaries, as shown by the non-conservative behavior of DOC in the East Siberian Arctic Shelf Seas (ESAS) (paper I) and the even more rapid degradation of POC in the same region (paper II). The removals of OCter in Arctic shelf seas were further supported by multiple isotope studies (paper III and IV), which showed that a use of 13C/12C in both OC and DIC, together with 34S/32S is a powerful tool to describe the sources and fate of OCter in estuaries and coastal seas. High-latitude estuaries play a key role in the coupling between terrestrial and marine carbon pools. In contrast to the general perception, this thesis shows that they are not only transportation areas for DOCter from rivers to the ocean, but are also active sites for transformation, degradation and sedimentation of DOCter, as well as for POCter. In a rapidly changing climate, the importance of these areas for the coupling between inorganic and organic carbon pools cannot be underestimated.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: In press. Paper 2: Submitted. Paper 4: Manuscript.

Le développement des technologies de communication et de l’information nécessite des composants semi-conducteurs ultrarapides et à faible niveau de bruit. Les transistors bipolaires à hétérojonction (TBH) sont des dispositifs qui visent des applications à hautes fréquences et qui peuvent satisfaire ces conditions. L’objet de cette thèse est l’étude expérimentale et la modélisation du bruit haute fréquence des TBH Si/SiGe:C (technologie STMicroelectronics) et InP/InGaAs (III-V Lab Alcatel-Thales).Accompagné d’un état de l’art des performances dynamiques des différentes technologies de TBH, le chapitre I rappelle brièvement le fonctionnement et la caractérisation des TBH en régime statique et dynamique. La première partie du chapitre II donne la description des deux types de TBH, avec l’analyse des performances dynamiques et statiques en fonction des variations technologiques de ceux-ci (composition de la base du TBH SiGe:C, réduction des dimensions latérales du TBH InGaAs). Avec l’aide d’une modélisation hydrodynamique, la seconde partie montre l’avantage d’une composition en germanium de 15-25% dans la base du TBH SiGe pour atteindre les meilleurs performances dynamiques. Le chapitre III synthétise des analyses statiques et dynamiques réalisées à basse température permettant de déterminer le poids relatif des temps de transit et des temps de charge dans la limitation des performances des TBH. L’analyse expérimentale et la modélisation analytique du bruit haute fréquence des deux types de TBH sont présentées en chapitre IV. La modélisation permet de mettre en évidence l’influence de la défocalisation du courant, de l’auto-échauffement, de la nature de l’hétérojonction base-émetteur sur le bruit haute fréquence. Une estimation des performances en bruit à basse température des deux types de TBH est obtenues avec les modèles électriques
In order to fulfil the roadmap for the development of telecommunication and information technologies (TIC), low noise level and very fast semiconductor devices are required. Heterojunction bipolar transistor has demonstrated excellent high frequency performances and becomes a candidate to address TIC roadmap. This work deals with experimental analysis and high frequency noise modelling of Si/SiGe:C HBT (STMicroelectronics tech.) and InP/InGaAs HBT (III-V Lab Alcatel-Thales).Chapter I introduces the basic concepts of HBTs operation and the characterization at high-frequency. This chapter summarizes the high frequency performances of many state-of-the-art HBT technologies. The first part of chapter II describes the two HBT sets, with paying attention on the impact of the base composition (SiGe:C) or the lateral reduction of the device (InGaAs) on static and dynamic performances. Based on TCAD modelling, the second part shows that a 15-25% germanium composition profile in the base is able to reach highest dynamic performances. Chapter III summarizes the static and dynamic results at low temperature, giving a separation of the intrinsic transit times and charging times involved into the performance limitation. Chapter IV presents noise measurements and the derivation of high frequency noise analytical models. These models highlight the impact of the current crowding and the self-heating effects, and the influence of the base-emitter heterojunction on the high frequency noise. According to these models the high frequency noise performances are estimated at low temperature for both HBT technologies

Au XVIIe siècle, Dijon, capitale de la province, est le lieu où résident les membres des organes politiques, administratifs et financiers. La ville connaît alors un remarquable essor de la construction privée. Les bâtisseurs sont principalement les officiers des cours souveraines, parlementaires ou conseillers à la chambre des comptes, qui satisfont leur besoin de représentation sociale en commandant des demeures dignes de leur rang : l’hôtel est bien l’illustration de ceux qui détiennent le pouvoir, le lieu à la fois d’une démonstration sociale, architecturale et artistique.Cette étude, première synthèse sur les hôtels particuliers dijonnais de 1610 à 1715, est abordée selon trois axes de réflexion : les commanditaires, les architectes et leurs réalisations. L’analyse architecturale des hôtels, qui laisse une large part à la distribution, permet une étude comparative avec Paris et les autres grandes villes parlementaires du royaume
In the seventeenth century, Dijon, capital of the province, was the place where proposed members of the political, administrative and financial bodies chose to live. The city therefore experienced a remarkable boom in the construction of private residences. The builders were mainly officers of the sovereign courts, members of parliament or advisors to the Board of Auditors who wanted to satisfy their need for social representation by ordering houses worthy of their rank : the private mansion was the illustration of people of power, place both a demonstration of social standing, architectural and artistic.This study, the first synthesis of the private mansions of Dijon from 1610 to 1715, is approached according to three lines of thought: the commissioners, the architects and their constructions. The architectural analysis of mansions which leaves a large part to the distribution, allows the comparison with Paris and other major cities of the parliamentary kingdom

This thesis focuses on solute transport upscaling. Upscaling of solute transport is usually required to obtain computationally efficient numerical models in many field applications such as, remediation of aquifers, environmental risk to groundwater resources or the design of underground repositories of nuclear waste. The non-Fickian behavior observed in the field, and manifested by peaked concentration profiles with pronounced tailing, has questioned the use of the classical advection-dispersion equation to simulate solute transport at field scale using numerical models with discretizations that cannot capture the field heterogeneity. In this context, we have investigated the use of the advection-dispersion equation with mass transfer as a tool for upscaling solute transport in a general numerical modeling framework. Solute transport by groundwater is very much affected by the presence of high and low water velocity zones, where the contaminant can be channelized or stagnant. These contrasting water velocity zones disappear in the upscaled model as soon as the scale of discretization is larger that the size of these zones. We propose, for the modeling solute transport at large scales, a phenomenological model based on the concept of memory functions, which are used to represent the unresolved processes taking place within each homogenized block in the numerical models. We propose a new method to estimate equivalent blocks, for which transport and mass transfer parameters have to be provided. The new upscaling technique consists in replacing each heterogeneous block by a homogeneous one in which the parameters associated to a memory functions are used to represent the unresolved mass exchange between highly mobile and less mobile zones occurring within the block. Flow upscaling is based on the Simple Laplacian with skin, whereas transport upscaling is based in the estimation of macrodispersion and mass transfer parameters as a result of the interpretation of the r
Llerar Meza, G. (2009). Upscaling nonreactive solute transport [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/5848
Palancia

On-time delivery of supplies to industry is essential because delays can disrupt production schedules. The aim of the proposed application is to predict transit times for outbound logistics thereby allowing suppliers to plan for timely mitigation of risks during shipment planning. The predictive model consists of a classifier that is trained for each specific source-destination pair using historical shipment, weather, and social media data. The model estimates the transit times for future shipments using Support Vector Machine (SVM). These estimates were validated using four case study routes of varying distances in the United States. A predictive model is trained for each route. The results show that the contribution of each input feature to the predictive ability of the model varies for each route. The mean average error (MAE) values of the model vary for each route due to the availability of testing and training historical shipment data as well as the availability of weather and social media data. In addition, it was found that the inclusion of the historical traffic data provided by INRIX™ improves the accuracy of the model. Sample INRIX™ data was available for one of the routes. One of the main limitations of the proposed approach is the availability of historical shipment data and the quality of social media data. However, if the data is available, the proposed methodology can be applied to any supplier with high volume shipments in order to develop a predictive model for outbound transit time delays over any land route.

Indiana University-Purdue University Indianapolis (IUPUI)
On-time delivery of supplies to industry is essential because delays can disrupt production schedules. The aim of the proposed application is to predict transit times for outbound logistics thereby allowing suppliers to plan for timely mitigation of risks during shipment planning. The predictive model consists of a classifier that is trained for each specific source-destination pair using historical shipment, weather, and social media data. The model estimates the transit times for future shipments using Support Vector Machine (SVM). These estimates were validated using four case study routes of varying distances in the United States. A predictive model is trained for each route. The results show that the contribution of each input feature to the predictive ability of the model varies for each route. The mean average error (MAE) values of the model vary for each route due to the availability of testing and training historical shipment data as well as the availability of weather and social media data. In addition, it was found that the inclusion of the historical traffic data provided by INRIXTM improves the accuracy of the model. Sample INRIXTM data was available for one of the routes. One of the main limitations of the proposed approach is the availability of historical shipment data and the quality of social media data. However, if the data is available, the proposed methodology can be applied to any supplier with high volume shipments in order to develop a predictive model for outbound transit time delays over any land route.

Deteriorating water quality in the face of a rising demand for agricultural products triggered interest in the groundwater resources of the Najd dessert, an arid region of southern Oman. Groundwater in this area usually is abstracted from one of the largest aquifers on the Arabian Peninsula, the Umm Er Radhuma aquifer. Increased discharge stands in contrast to limited precipitation: the monsoon is an annual event but it is regionally limited; cyclones infrequently occur within the range of three to seven years. Both are possible sources for groundwater recharge in the Najd. With these preconditions in mind, the present study investigates recharge to the Najd groundwaters as part of an active flow system and evaluates the mean residence time in the deep groundwaters. The tools of choice are a groundwater flow model combined with environmental isotope tracer data. The two-dimensional flow model replicates the characteristics of the aquifer system from the potential recharge area in the south (Dhofar Mountains) to the discharge area in the north (Sabkha Umm as Sammim). The south-to-north gradients and the observed artesian heads in the confined aquifer are reproduced. Simulation results indicate that changes between wet and dry periods caused transient responses in heads and head gradients lasting for several thousand years. Based on the used parameters the model calibration indicated, that a recharge rate of around 4 mm a−1 is sufficient to reproduce current groundwater levels. Since rising groundwater levels were documented after cyclone Keila in November 2011, modern recharge evidently occurs. 36-Cl concentrations and dissolved-helium concentrations indicate that the deep groundwaters in the central Najd are up to 550,000 years old. Thus, radiocarbon values indicating groundwater residence times for the central Najd up to 20,000 years and the northern Najd up to 35,000 years underestimate the groundwater residence times and seem to have been strongly affected by mixing during sampling. Decreasing 36-Cl and increasing 4-He concentrations confirm the expected trend in the direction of groundwater flow and prove to be more robust tracers for age dating of Najd groundwaters. Backward pathline tracking was used to simulate the groundwater ages. The tracking results show that a total porosity value between 15 and 20 % is consistent with the range of the observed chlorine-36 and heliumbased ages. The results and parameters obtained in the present study provide the basis for future 3D-groundwater models designed to evaluate the water resources available to the Najd’s agricultural complex. In addition, the developed 2D-model allows for studies of paleoclimate scenarios and their influence on the groundwater regime.
Ein steigender Bedarf nach landwirtschaftlichen Produkten - und damit Wasser - bei gleichzeitiger Abnahme des verfügbaren Wassers in Qualität und Menge in den bisherigen Anbaugebieten, führt zu einer intensiven Nutzung der Grundwasserressourcen der ariden Najd-Region in der Provinz Dhofar, im Süden des Sultanats Oman. Als Quelle dienen die Grundwasservorräte des Umm Er Radhuma-Aquifers, einer der Hauptaquifere auf der arabischen Halbinsel. Der steigenden Nutzung stehen mit dem jährlichen Monsoon, der regional limitiert ist, und unrgelmässigen, zwischen 3 und 7 Jahren auftretenden Unwettern (Zyklonniederschlag) nur begrenzte Niederschlagsmengen als Quellen für eine mögliche Zufuhr von Wasser (Grundwasserneubildung) zum Aquifersystem gegenüber. Der Ansatz der vorliegenden Arbeit besteht darin, mit Hilfe eines Grundwassermodells und der Einbeziehung von Umweltisotopen das tiefe und zur Nutzung geförderte Grundwasser in der Najd-Region als Teil eines aktiven Fließsystemes zu untersuchen und mittlere Verweilzeiten des Grundwassers abzuleiten. Ein 2D-Grundwassermodell entlang einer Fließlinie vom Dhofar Gebirge im Süden zur Sabkha Umm as Sammim im Nordosten wurde entwickelt. Das Modell reproduziert den Süd-Nord-Gradienten als auch den aufwärts gerichteten Gradienten mit höheren Grundwasserständen in den tiefen Grundwasserleitern. Die Simulationen zeigen, dass der Wechsel von ariden und humiden Phasen (wenig bzw. viel Grundwasserneubildung) zu Veränderungen der Grundwasseroberfläche führt die mehrere tausend Jahre anhalten können. Das kalibrierte Grundwassermodel zeigt, dass mit einer Neubildungsrate von 4 mm a−1 die natürlichen Grundwasserverhältnisse im Najd abgebildet werden können. Dass eine moderne Grundwasserneubildung stattfindet, konnte mittels Loggermessungen anhand steigender Grundwasserstände im tiefen Aquifersystem nach dem Extremunwetter im November 2011 (Zyklon Keila) eindeutig nachgewiesen werden. Die Analyse der 36Cl- und 4He-Konzentrationen zeigt, dass die tiefen Grundwasser im zentralen Najdgebiet bis 550 000 Jahren alt sein können. Das bedeutet allerdings, dass die über 14C Daten berechneten Grundwasseralter mit ca. 20 000 Jahren für das zentrale Najdgebiet und bis zu 35 000 Jahren für den nördlichen Najd, die Grundwasseralter deutlich unterschätzen. Die abnehmenden 36Cl und ansteigenden 4He Konzentrationen zeigen den erwarteten Trend in Grundwasserfließrichtung und können als aussagefähige Tracer für die Bewertung der Verweilzeiten und Alter des fossilen Grundwassers der Najd-Region angesehen werden. Mit Hilfe des Partickeltrackings wurden die Grundwasseralter, basierend auf den Isotopentracern, im Grundwassermodel simuliert. Die Porosität wurde dabei für das Aquifesystem mit Werten zwischen 15 und 20 % bestimmt. Die generierten Parameter und das gewonnene Systemverständnis sind eine wichtige Basis für zukünftige 3D-Modellstudien welche die Verfügbarkeit der Wasserresourcen im Najd untersuchen werden. Weitere Anwendungen für das in dieser Studie aufgebaute 2D-Modell sind Untersuchungen zum Paläoklima und dessen Einfluss auf das Grundwassersystem.

Surface transient storage (STS) in stream ecosystems serve an important function in retaining nutrients and refugia for aquatic communities. Unfortunately, they can retain contaminants as well. Therefore, it is of importance to determine the residence time distribution (RTD). A RTD of a particular STS zone encompasses the time it takes for the first pulse of water to leave the STS zone, and for the mean residence time of water in that zone, among other things. The RTD of STS is also useful to subtract from the RTD of the total transient storage in streams in order to determine the hyporheic transient storage (HTS) of streams, which is difficult to measure. Currently, there is no definitive method of determining the RTD of STS. They have been determined with tracer injection alone, though this is time consuming and subject to interference from HTS. A relationship between STS physical characteristics and a RTD would be desirable, as this would characterize the time of entrainment of STS based upon a few easily measured physical parameters. This exists for groyne fields and flumes, which both have artificial STS. However, direct application of these equations to natural STS leads to errors due to simplistic geometries. The focus of this study determines RTDs in lateral STS, which is adjacent to the main channel of a stream and a significant proportion of STS, and its relationship to physically measurable parameters of lateral STS. Twenty sites throughout Oregon were each injected with NaCl to determine four residence timescales: Langmuir time (��[subscript L]), negative inverse slope of the normalized concentration curve of the primary gyre (��[subscript 1]), negative inverse slope of the normalized concentration curve of the entire STS zone (��[subscript 2]), and the mean residence time (��[subscript STS]). The RTDs of these sites were then compared to the length, width, and depth of each lateral STS zone, as well as the velocity of the adjacent main channel. This data also was used to calculate dimensionless parameters submergence, a measure of bed roughness, and k, a measure of exchange that relates ��STS to lateral STS and associated parameters. ��[subscript 1] was found to be identical to ��[subscript STS], and ��[subscript 2] could not be defined. ��[subscript STS] was found to be approximately 1.35 times ��[subscript L], the ratio of which (��[subscript L]/��[subscript STS]) is positively correlated with lateral STS submergence. ��[subscript L] and ��[subscript STS] are positively correlated with lateral STS parameters, and inversely correlated with main channel velocity. The value of k from this study was comparable to the value of k from other studies in flumes, and so there is a relationship between RTDs and lateral STS parameters.
Graduation date: 2013

碩士
國立陽明大學
生物醫學影像暨放射科學系
102
Background and Objective: Chronic liver disease and cirrhosis result in about 35,000 deaths each year in the United States. Cirrhosis is the ninth leading cause of death in the United States and is responsible for 1.2% of all US deaths. MRI has been reported to be an excellent imaging modality because of its high tissue contrast and use of tissue-specific contrast agents. Gadoxetic acid (Gd-EOB-DTPA) is a more recently developed liver specific MR imaging contrast agent. The excretion of Gd-EOB-DTPA might be related to the liver disease and liver function. The pur¬pose of this study was to determine transit times for excretion of Gd-EOB-DTPA in the hepatobiliary system in patients with liver cirrhosis1. Material and Methods: Institutional Review Board of our hospital approved the study; in-formed consent was waived. We retrospectively included consecutive patients with liver cirrho¬sis who underwent contrast-enhanced abdominal MR examination after injection of 10 mL Gd-EOB-DTPA at 1.5-T MR from December 2009 to March 2012. Finally, the 47 patients were en-rolled in this study. The Gd-EOB-DTPA-enhanced MRI included arterial phase (18~20sec, arterial phase, AP), por¬tal venous phase (50~55 sec, portal venous phase, PP), venous phase (85~90s, venous phase, VP) and three delayed phases (180s, 20mins and 30mins after the injection of contrast agent). The images were evaluated for the presence of contrast agent in the intra-hepatic bile ducts (IHD), the common bile duct (CBD), the gallbladder and the duodenum in AP, PP, VP and three delay phases. Results: The optimal time of arterial phase was from 15 s after injection, and the optimal time for portal venous imaging was from 40 s after injection. Meanwhile, the optimal time to observe changes was 20 min after contrast initiation of Gd-EOB-DTPA in 39 patients (39/47, 83 %) at the IHD and 37 patients (37/47, 78.5%) at the CBD. Gallbladder reflux was visible in 26 (26/47, 43%), duodenal excretion in 17 patients (17/47, 36%), respectively. After 30 min of contrast injection, Gd-EOB-DTPA could still be detected in 6 patients (6/47, 13 %) at the IHD and 7 patients (7/47, 15 %) at the CBD, and gallbladder reflux was visible in 10 (10/47, 21%), duodenal excretion in 20 patients (26/47, 55%), respectively.(Fig 2 and Fig 3) GB was not visible in 9 patients, 4 out of these 9 patients received cholecystectomy. Conclusion: The results of our study shows that in patients with liver cirrhosis, the excretion of Gd-EOB-DTPA can be observed. Our results also demonstrated that the bilirubin level and the severity of cirrhosis (according to the Child Pugh scores had certain effect on excretion of Gd-EOB-DTPA into biliary tree.

The Pseudo Random Arterial Modulation (PRAM) is a non-invasive MRI based method to measure blood flow. It does not require any contrast agent but rather uses water protons in the body as the contrast. PRAM is based on a pseudo random sequence of inversions and non-inversions of the arterial blood using radio frequency (RF) pulses at a labeling plane inferior to the imaging plane. A series of images are taken at the imaging plane and flow reconstructed from the transit time measurements. PRAM does not require separate control and label acquisition as is common in Arterial Spin Labeling (ASL) but rather measures the distribution of transit times to a voxel within one integrated scan. Adiabatic inversion or non-inversion pre-pulses (PRAM pulses) are performed prior to a gradient echo imaging. The PRAM method has been tested on a flow phantom and the results were in confirmation with the theoretical flow and velocity measurements. Subsequently the PRAM method was tested on a human leg and the results were comparable with the Ultrasound measurements. The final testing phase was performed on a human brain and the results were compared with the phased contrast MRA. We have demonstrated here that that the PRAM technique can measure the velocity profile and the transit time accurately and efficiently on any organ such as human brain.

\textbf{Molecular Determinants of Drug-Target Residence Times of Bacterial Enoyl-ACP Reductases.} Whereas optimization processes of early drug discovery campaigns are often affinity-driven, the drug-target residence time $t_R$ should also be considered due to an often strong correlation with \textit{in vivo} efficacy of compounds. However, rational optimization of $t_R$ is not straightforward and generally hampered by the lack of structural information about the transition states of ligand association and dissociation. The enoyl-ACP reductase FabI of the fatty acid synthesis (FAS) type II is an important drug-target in antibiotic research. InhA is the FabI enzyme of \textit{Mycobacterium tuberculosis}, which is known to be inhibited by various compound classes. Slow-onset inhibition of InhA is assumed to be associated with the ordering of the most flexible protein region, the substrate binding loop (SBL). Diphenylethers are one class of InhA inhibitors that can promote such SBL ordering, resulting in long drug-target residence times. Although these inhibitors are energetically and kinetically well characterized, it is still unclear how the structural features of a ligand affect $t_R$. Using classical molecular dynamics (MD) simulations, recurring conformational families of InhA protein-ligand complexes were detected and structural determinants of drug-target residence time of diphenyl\-ethers with different kinetic profiles were described. This information was used to deduce guidelines for efficacy improvement of InhA inhibitors, including 5'-substitution on the diphenylether B-ring. The validity of this suggestion was then analyzed by means of MD simulations. Moreover, Steered MD (SMD) simulations were employed to analyze ligand dissociation of diphenylethers from the FabI enzyme of \textit{Staphylococcus aureus}. This approach resulted in a very accurate and quantitative linear regression model of the experimental $ln(t_R)$ of these inhibitors as a function of the calculated maximum free energy change of induced ligand extraction. This model can be used to predict the residence times of new potential inhibitors from crystal structures or valid docking poses. Since correct structural characterization of the intermediate enzyme-inhibitor state (EI) and the final state (EI*) of two-step slow-onset inhibition is crucial for rational residence time optimization, the current view of the EI and EI* states of InhA was revisited by means of crystal structure analysis, MD and SMD simulations. Overall, the analyses affirmed that the EI* state is a conformation resembling the 2X23 crystal structure (with slow-onset inhibitor \textbf{PT70}), whereas a twist of residues Ile202 and Val203 with a further opened helix $\alpha 6$ corresponds to the EI state. Furthermore, MD simulations emphasized the influence of close contacts to symmetry mates in the SBL region on SBL stability, underlined by the observation that an MD simulation of \textbf{PT155} chain A with chain B' of a symmetry mate in close proximity of the SBL region showed significantly more stable loops, than a simulation of the tetrameric assembly. Closing Part I, SMD simulations were employed which allow the delimitation of slow-onset InhA inhibitors from rapid reversible ligands. \textbf{Prediction of \textit{Mycobacterium tuberculosis} Cell Wall Permeability.} The cell wall of \textit{M. tuberculosis} hampers antimycobacterial drug design due to its unique composition, providing intrinsic antibiotic resistance against lipophilic and hydrophilic compounds. To assess the druggability space of this pathogen, a large-scale data mining endeavor was conducted, based on multivariate statistical analysis of differences in the physico-chemical composition of a normally distributed drug-like chemical space and a database of antimycobacterial--and thus very likely permeable--compounds. The approach resulted in the logistic regression model MycPermCheck, which is able to predict the permeability probability of small organic molecules based on their physico-chemical properties. Evaluation of MycPermCheck suggests a high predictive power. The model was implemented as a freely accessible online service and as a local stand-alone command-line version. Methodologies and findings from both parts of this thesis were combined to conduct a virtual screening for antimycobacterial substances. MycPermCheck was employed to screen the chemical permeability space of \textit{M. tuberculosis} from the entire ZINC12 drug-like database. After subsequent filtering steps regarding ADMET properties, InhA was chosen as an exemplary target. Docking to InhA led to a principal hit compound, which was further optimized. The quality of the interaction of selected derivatives with InhA was subsequently evaluated using MD and SMD simulations in terms of protein and ligand stability, as well as maximum free energy change of induced ligand egress. The results of the presented computational experiments suggest that compounds with an indole-3-acethydrazide scaffold might constitute a novel class of InhA inhibitors, worthwhile of further investigation
\textbf{Molekulare Determinanten von Wirkstoff-Angriffsziel Verweilzeiten bakterieller Enoyl-ACP Reduktasen.} In frühen Phasen der Wirkstoffentwicklung sind Optimierungsprozesse häufig affini\-täts\-geleitet. Darüber hinaus sollte zusätzlich die Wirkstoff-Angriffsziel Verweilzeit $t_R$ berücksichtigt werden, da diese oft eine starke Korrelation zur \textit{in vivo} Wirksamkeit der Substanzen aufweist. Rationale Optimierung von $t_R$ ist jedoch auf Grund eines Mangels an struktureller Information über den Übergangszustand der Ligandbindung und Dissoziierung nicht einfach umsetzbar. Die Enoyl-ACP Reduktase FabI der Fettsäurebio\-synthese (FAS) Typ II ist ein wichtiger Angriffspunkt in der Antibiotikaforschung. InhA ist das FabI Enzym des Organismus \textit{Mycobacterium tuberculosis} und kann durch Substanzen diverser Klassen gehemmt werden. Es wird vermutet, dass Hemmung von InhA durch langsam-bindende (``slow-onset'') Inhibitoren mit der Ordnung der flexibelsten Region des Enzyms assoziiert ist, dem Substratbindungsloop (SBL). Diphenylether sind eine InhA Inhibitorenklasse, die eine solche SBL Ordnung fördern und dadurch lange Verweilzeiten im Angriffsziel aufweisen. Obwohl diese Inhibitoren energetisch und kinetisch gut charakterisiert sind, ist noch immer unklar, wie die strukturellen Eigenschaften eines Liganden $t_R$ beeinflussen. Durch die Verwendung klassischer Molekulardynamik (MD) Simulationen wurden wiederkehrende Konformationsfamilien von InhA Protein-Ligand Komplexen entdeckt und strukturelle Determinanten der Wirkstoff-Angriffsziel Verweilzeit von Diphenylethern mit verschiedenen kinetischen Profilen beschrieben. Anhand dieser Ergebnisse wurden Richtlinien zur Wirksamkeitsoptimierung von InhA Inhibitoren abgeleitet, einschließlich einer 5'-Substitution am Diphenylether B-Ring. Die Validität dieses Vorschlags wurde mittels MD Simulationen nachfolgend analysiert. Darüber hinaus wurden ``Steered MD'' (SMD) Simulationen als MD Technik für umfangreicheres Sampling verwendet um die Liganddissoziation von Diphenylethern aus dem FabI Enzym von \textit{Staphylococcus aureus} zu untersuchen. Dieser Ansatz resultierte in einem sehr akkuraten, quantitativen linearen Regressionsmodell der experimentellen Verweilzeit $ln(t_R)$ dieser Inhibitoren als Funktion der berechneten maximalen freien Energieänderung induzierter Ligandextraktion. Dieses Modell kann genutzt werden um die Verweilzeiten neuer potentieller Inhibitoren aus Kristallstrukturen oder validen Dockingposen vorherzusagen. Die korrekte strukturelle Charakterisierung des intermediären und des finalen Zustandes (EI und EI*-Zustand) eines Enzym-Inhibitor Komplexes bei einem zweistufigen Inhibitionsmechanismus durch langsam-bindende Hemmstoffe ist essentiell für rationale Verweilzeitoptimierung. Daher wurde die gegenwärtige Ansicht des EI und EI*-Zustandes von InhA mittels Kristallstrukturanalyse, MD und SMD Simulationen erneut aufgegriffen. Insgesamt bestätigten die Analysen, dass der EI*-Zustand einer Konformation ähnlich der 2X23 Kristallstruktur (mit langsam-bindenden Inhibitor \textbf{PT70}) gleicht, während eine Drehung der Reste Ile202 und Val203 mit einer weiter geöffneten Helix $\alpha 6$ dem EI-Zustand entspricht. Des Weiteren zeigten MD Simulationen den Einfluss naher Kristallkontakte zu Symmetrie-Nachbarn in der SBL Region auf die SBL Stabilität. Dies wird durch die Beobachtung hervorgehoben, dass die Ketten A und B' eines InhA-\textbf{PT155}-Komplexes und des angrenzenden Symmetrie-Nachbars, welche in engem Kontakt in der SBL Region stehen, signifikant stabilere SBLs aufweisen, als die Ketten A und B in einer Simulation des Tetramers. Zum Abschluss von Teil I wurden SMD Simulationen angewandt, auf deren Basis es möglich war, langsam-bindende InhA Inhibitoren von schnell-reversiblen (``rapid reversible'') Liganden zu unterscheiden. \textbf{Vorhersage von \textit{Mycobacterium tuberculosis} Zellwand Permeabilität.} Die Zellwand von \textit{M.~tuberculosis} erschwert die antimycobakterielle Wirkstofffindung auf Grund ihrer einzigartigen Zusammensetzung und bietet eine intrinsische Antibiotikaresistenz gegenüber lipophilen und hydrophilen Substanzen. Um den chemischen Raum wirkstoffähnlicher Moleküle gegen diesen Erreger (``Druggability Space'') einzugrenzen, wurde eine groß angelegte Dataminingstudie durchgeführt, welche auf multivariater statistischer Analyse der Unterschiede der physikochemischen Zusammensetzung eines normalverteilten wirkstoffähnlichen chemischen Raumes und einer Datenbank von antimycobakteriellen -- und somit höchstwahrscheinlich permeablen -- Substanzen beruht. Dieser Ansatz resultierte in dem logistischen Regressionsmodell MycPermCheck, welches in der Lage ist die Permeabilitätswahrscheinlichkeit kleiner organischer Moleküle anhand ihrer physikochemischen Eigenschaften vorherzusagen. Die Evaluation von MycPermCheck deutet auf eine große Vorhersagekraft hin. Das Modell wurde als frei zugänglicher online Service und als lokale Kommandozeilenversion implementiert. Methodiken und Ergebnisse aus beiden Teilen dieser Dissertation wurden kombiniert um ein virtuelles Screening nach antimycobakteriellen Substanzen durchzuführen. Myc\-PermCheck wurde verwendet um den chemischen Permeabilitätsraum von \textit{M.~tuberculosis} anhand der gesamten ZINC12 Datenbank wirkstoffähnlicher Moleküle abzuschätzen. Nach weiteren Filterschritten mit Bezug auf ADMET Eigenschaften, wurde InhA als exemplarisches Angriffsziel ausgewählt. Docking nach InhA führte schließlich zu einer Treffersubstanz, welche in darauffolgenden Schritten weiter optimiert wurde. Die Interaktionsqualität ausgewählter Derivate mit InhA wurde daraufhin mittels MD und SMD Simulationen in Bezug auf Protein und Ligand Stabilität, sowie auch der maximalen freien Energieänderung induzierter Ligandextraktion, untersucht. Die Ergebnisse der vorgestellten computerbasierten Experimente legen nahe, dass Substanzen mit einem Indol-3-Acethydrazid Gerüst eine neuartige Klasse von InhA Inhibitoren darstellen könnten. Weiterführende Untersuchungen könnten sich somit als lohnenswert erweisen

The docotoral thesis titled 'Modeling the effects of Transient Stream Flow on Solute Dynamics in Stream Banks and Intra-meander Zones' investigates flow and solute dynamcis across surface water-groundwater interface under dynamic flow conditons through numerical simulations. The abstract of the thesis is as follows: Waters from various sources meet at the interface between streams and groundwater. Due to their different origins, these waters often have contrasting chemical signatures and therefore mixing of water at the interface may lead to significant changes in both surface and subsurface water quality. The riparian zone adjacent to the stream serves as transition region between groundwater and stream water, where complex water and solute mixing and transport processes occur. Predicting the direction and the magnitude of solute exchanges and the extent of transformations within the riparian zone is challenging due to the varying hydrologic and chemical conditions as well as heterogeneous morphological features which result in complex, three-dimensional flow patterns. The direction of water flow and solute transport in the riparian zone typically varies over time as a result of fluctuating stream water and groundwater levels. Particularly, increasing groundwater levels can mobilize solutes from the unsaturated zone which can be subsequently transported into the stream. Such complex, spatially and temporally varying processes are hard to capture with field observations alone and therefore modeling approaches are required to predict the system behavior as well as to understand the role of individual factors. In this thesis, we investigate the inter-connectivity of streamthe s and adjacent riparia zones in the context of water and solute exchanges both laterally for bank storage and longitudinally for hyporheic flow through meander bends. Using numerical modeling, the transient effect of stream flow events on solute transport and transformation within the initially unsaturated part of stream banks and meander bends have been simulated using a systematic set of hydrological, chemical and morphological scenarios. A two dimensional variably saturated media groundwater modeling set up was used to explore solute dynamics during bank flows. We simulated exchanges between stream and adjacent riparian zone driven by stream stage fluctuations during stream discharge events. To elucidate the effect of magnitude and duration of discharge events, we developed a number of single discharge event scenarios with systematically varying peak heights and event duration. The dominant solute layer was represented by applying high solute concentration in upper unsaturated riparian zone profile. Simulated results show that bank flows generated by high stream flow events can trigger solute mobilization in near stream riparian soils and subsequently export significant amounts of solutes into the stream. The timing and amount of solute export is linked to the shape of the discharge event. Higher peaks and increased duration significantly enhance solute export, however, peak height is found to be the dominant control for overall lateral mass export. The mobilized solutes are transported towards the stream in two stages (1) by return flow of stream water that was stored in the riparian zone during the event and (2) by vertical movement to the groundwater under gravity drainage from the unsaturated parts of the riparian zone, which lasts for significantly longer time (> 400 days) resulting in a theoretically long tailing of bank outflows and solute mass outfluxes. Our bank flow simulations demonstrate that strong stream discharge events are likely to mobilize and export significant quantity of solutes from near stream riparian zones into the stream. Furthermore, the impact of short-term stream discharge variations on solute exchange may sustain for long times after the flow event. Meanders are prominent morphological features of stream systems which exhibit unique hydrodynamics. The water surface elevation difference across the inner bank of a meander induces lateral hyporheic exchange flow through the intrameander region, leading to solute transport and reactions within intra-meander region. We examine the impact of different meander geometries on the intra-meander hyporheic flow field and solute mobilization under both steady-state and transient flow conditions. In order to explore the impact of meander morphology on intrameander flow, a number of theoretical meander shape scenarios, representing various meander evolution stages, ranging from a typical initial to advanced stage (near cut off ) meander were developed. Three dimensional steady-state numerical groundwater flow simulations including the unsaturated zone were performed for the intra-meander region for all meander scenarios. The meandering stream was implemented in the model by adjusting the top layers of the modeling domain to the streambed elevation. Residence times for the intra-meander region were computed by advective particle tracking across the inner bank of meander. Selected steady state cases were extended to transient flow simulations to evaluate the impact of stream discharge events on the temporal behavior of the water exchange and solute transport in the intra-meander region. Transient hydraulic heads obtained from the surface water model were applied as transient head boundary conditions to the streambed cells of the groundwater model. Similar to the bank storage case, a high concentration of solute (carbon source) representing the dominant solute layer in the riparian profile was added in the unsaturated zone to evaluate the effect of stream flow event on mobilization and transport from the unsaturated part of intrameander region. Additionally, potential chemical reactions of aerobic respiration by the entry of oxygen rich surface water into subsurface as well denitrification due to stream and groundwater borne nitrates were also simulated. The results indicate that intra-meander mean residence times ranging from 18 to 61 days are influenced by meander geometry, as well as the size of the intra-meander area. We found that, intra-meander hydraulic gradient is the major control of RTs. In general, larger intra-meander areas lead to longer flow paths and higher mean intra-meander residence times (MRTs), whereas increased meander sinuosity results in shorter MRTs. The vertical extent of hyporheic flow paths generally decreases with increasing sinuosity. Transient modeling of hyporheic flow through meanders reveals that large stream flow events mobilize solutes from the unsaturated portion of intra-meander region leading to consequent transport into the stream via hyporheic flow. Advective solute transport dominates during the flow event; however significant amount of carbon is also consumed by aerobic respiration and denitrification. These reactions continue after the flow events depending upon the availability of carbon source. The thesis demonstrates that bank flows and intra-meander hyporheic exchange flows trigger solute mobilization from the dominant solute source layers in the RZ. Stream flow events driven water table fluctuations in the stream bank and in the intra-meander region transport substantial amount of solutes from the unsaturated RZ into the stream and therefore have significant potential to alter stream water quality.:Declaration Abstract Zusammenfassung 1 General Introduction 1.1 Background and Motivation 1.2 Hydrology and Riparian zones 1.2.1 Transport processes driven by fluctuation in riparian water table depth 1.2.1.1 Upland control 1.2.1.2 Stream control 1.2.2 Biochemical Transformations within the Riparian Zone 1.3 Types and scales of stream-riparian exchange 1.3.1 Hyporheic Exchange 1.3.1.1 Small Scale Vertical HEF 1.3.1.2 Large Scale lateral HEF 1.3.2 Bank Storage 1.4 Methods for estimation of GW-SW exchanges 1.4.1 Field Methods 1.4.1.1 Direct measurement of water flux 1.4.1.2 Tracer based Methods 1.4.2 Modeling Methods 1.4.2.1 Transient storage models 1.4.2.2 Physically based models 1.5 Research gaps and need 1.6 Objectives of the research 1.7 Thesis Outline 2 Flow and Transport Dynamics during Bank Flows 2.1 Introduction 2.2 Methods 2.2.1 Concept and modeling setup 2.2.2 Numerical Model 2.2.3 Stream discharge events 2.2.4 Model results evaluation 2.3 Results and discussion 2.3.1 Response of water and solute exchange to stream discharge events 2.3.1.1 Water exchange time scales 2.3.1.2 Stream water solute concentration 2.3.2 Solute mobilization within the riparian zone 2.3.3 Influence of peak height and event duration on solute mass export towards the stream 2.3.4 Effects of event hydrograph shape on stream water solute concentration 2.3.5 Model limitations and future studies 2.4 Summary and Conclusions Appendix 2 3 Flow and Transport Dynamics within Intra-Meander Zone 3.1 Introduction 3.2 Methods 3.2.1 Meander Shape Scenarios 3.2.2 Surface Water Simulations 3.2.3 3D Groundwater Flow Simulations with Modeling code MIN3P 3.2.3.1 Steady Flow Simulations 3.2.3.2 Stream flow event and Solute Mobilization Set-up 3.2.4 Reactive Transport 3.3 Results and Discussion 3.3.1 Groundwater heads and flow paths in the saturated intrameander zone 3.3.1.1 Groundwater heads 3.3.1.2 Flow paths and isochrones 3.3.1.3 Vertical extent of flow paths 3.3.2 Intra-Meander Residence Time Distribution 3.3.3 Factors affecting intra-meander flow and residence times 3.3.3.1 intra-meander hydraulic gradient 3.3.3.2 Maximum penetration depth 3.3.3.3 Meander sinuosity 3.3.3.4 intra-meander area (A) 3.3.4 Influence of Discharge Event on intra-meander Flow and Solute Transport 3.3.4.1 Spatial distribution of groundwater head and solute concentration 3.3.4.2 Time scales of intra-meander groundwater heads and solute transport 3.3.4.3 Solute export during stream discharge event 3.3.5 Intra-meander reactive transport during stream discharge event 3.3.5.1 Impact of stream discharge on aerobic respiration and denitrification 3.3.5.2 DOC mass removal during stream discharge event 3.4 Summary and Conclusions Appendix 3 4 General Summary and Conclusions 4.1 Summary 4.2 Conclusions 4.2.1 Flow and Transport Dynamics in Near Stream Riparian Zone (Bank Flows) 4.2.2 Flow and Transport Dynamics within Intra-Meander Zone 4.3 Model Limitations and Future Studies Bibliography Acknowledgement

The Altiplano-Puna Volcanic Complex in the Central Andes is one of the youngest large silicic volcanic fields (LSVFs) in the world, erupting over 13,000 km³ of material during multiple supereruptions from 11 to 1 Ma. Understanding the timescales over which magma is stored in the crust prior to eruption is crucial to understanding the development of LSVFs such as the APVC. The residence time of a magma is defined as the time between magma formation and its eruption. While the eruption age of a volcanic system is generally well constrained through ⁴⁰Ar/³⁹Ar dating of sanidine and biotite crystals, determining the time of magma formation offers a bigger challenge. U-Pb dating of zircon—an early crystallizing, ubiquitous phase in silicic systems—is a commonly used method for determining the timing of magma formation. U-Pb zircon ages were collected for 16 ignimbrites representing the temporal and spatial distribution of the APVC. Zircon crystallization histories show significant overlap between eruptive centers of similar age separated by as much as 200 km. Ignimbrites erupted from the same multicyclic caldera show little relationship. This suggests that ignimbrites may share a deeper, regional source. Timescales of zircon crystallization for individual ignimbrites range from ~400 ka to more than 1 Ma, with little correlation with age or erupted volume. Ignimbrites with longer crystallization timescales frequently exhibit a stepped age distribution and highly variable U contents, suggesting that these ignimbrites likely formed in a very crystalline, low melt fraction environment while ignimbrites with short crystallization times and constrained U concentrations crystallized in high melt fraction systems. Zircon crystallization histories record periods of continuous zircon crystallization in the APVC that extend over 1.5-2 Ma pulses and correlate well with eruptive pulses recognized by previous studies. Overall, zircon crystallization histories of the magmas feeding ignimbrite eruptions in the APVC record long timescales of magmatic activity from a shared regional source, likely the Altiplano-Puna Magma Body currently detectable underlying the APVC.
Graduation date: 2012

abstract: In this dissertation the potential impact of some social, cultural and economic factors on Ebola Virus Disease (EVD) dynamics and control are studied. In Chapter two, the inability to detect and isolate a large fraction of EVD-infected individuals before symptoms onset is addressed. A mathematical model, calibrated with data from the 2014 West African outbreak, is used to show the dynamics of EVD control under various quarantine and isolation effectiveness regimes. It is shown that in order to make a difference it must reach a high proportion of the infected population. The effect of EVD-dead bodies has been incorporated in the quarantine effectiveness. In Chapter four, the potential impact of differential risk is assessed. A two-patch model without explicitly incorporate quarantine is used to assess the impact of mobility on communities at risk of EVD. It is shown that the overall EVD burden may lessen when mobility in this artificial high-low risk society is allowed. The cost that individuals in the low-risk patch must pay, as measured by secondary cases is highlighted. In Chapter five a model explicitly incorporating patch-specific quarantine levels is used to show that quarantine a large enough proportion of the population under effective isolation leads to a measurable reduction of secondary cases in the presence of mobility. It is shown that sharing limited resources can improve the effectiveness of EVD effective control in the two-patch high-low risk system. Identifying the conditions under which the low-risk community would be willing to accept the increases in EVD risk, needed to reduce the total number of secondary cases in a community composed of two patches with highly differentiated risks has not been addressed. In summary, this dissertation looks at EVD dynamics within an idealized highly polarized world where resources are primarily in the hands of a low-risk community – a community of lower density, higher levels of education and reasonable health services – that shares a “border” with a high-risk community that lacks minimal resources to survive an EVD outbreak.
Dissertation/Thesis
Doctoral Dissertation Applied Mathematics 2018

Tese de doutoramento em Engenharia Civil
Os estuários são sistemas hídricos que desde sempre favoreceram o desenvolvimento de aglomerados urbanos importantes, por propiciarem actividades com grande impacto sócio-económico, nomeadamente a portuária, a piscatória e as de lazer. As águas estuarinas, resultantes da confluência de águas fluviais e marinhas, com regimes hidrodinâmicos peculiares, revelam-se favoráveis à retenção de nutrientes tornando-se muito vulneráveis a factores de stress ambiental, que podem por em causa o equilíbrio destes ecossistemas aquáticos. Os processos de eutrofização podem originar florescências algais, alterando a biodiversidade e a estrutura trófica dos sistemas hídricos, provocando a depleção do oxigénio dissolvido até níveis que podem comprometer a utilização dessas águas para os seus diferentes usos. Tendo-se constatado, através da análise dos dados recolhidos na última década no estuário do rio Mondego, que as condições hidrodinâmicas influenciam decisivamente a ocorrência de episódios de proliferação intensa de macroalgas infestantes nesse sistema, procedeu-se neste trabalho ao desenvolvimento de uma metodologia hidroinformática para o estudo integrado das interacções entre o comportamento hidrodinâmico dos sistemas estuarinos e as alterações da sua qualidade ecológica, com especial interesse na mitigação dos processos de eutrofização. Após a caracterização dos processos físicos, químicos e biológicos dos ambientes estuarinos e a abordagem das capacidades dos modelos matemáticos de qualidade da água, procedeu-se a uma caracterização da área de estudo, o estuário do rio Mondego, com especial relevo para a análise dos resultados das campanhas de monitorização efectuadas para avaliar o estado trófico do seu braço sul, sujeito, nas últimas décadas a um processo de eutrofização. O ambiente hidroinformático desenvolvido (modelo MONDEST), integra vários módulos (hidrodinâmico, transporte e tempo de residência) e apresenta uma metodologia inovadora de abordagem do cálculo do tempo de residência em sistemas estuarinos, quer em termos conceptuais, quer na definição da sua variabilidade espacial, rompendo, assim, com a habitual adopção de um valor único desta grandeza para tipificar um determinado estuário. Procedeu-se neste trabalho à caracterização do comportamento hidrodinâmico do todo o sistema estuarino, de modo a avaliar as distribuições espaciais e temporais de duas grandezas - salinidade e tempo de residência - com influência directa na produção primária e, consequentemente, na vulnerabilidade do estuário do rio Mondego à eutrofização, dando um contributo para a selecção criteriosa das medidas e das práticas de gestão mais adequadas à salvaguarda do bom estado ecológico deste importante ecossistema, bem como ao desenvolvimento ambientalmente sustentável das actividades sócio-económicas predominantes no Baixo Mondego.
The south arm of Mondego estuary, located in the central western Atlantic coast of Portugal, is stressing by an eutrophication process due to massive nutrient loading from urbanised areas and diffusive runoff from intensively agricultural areas. As a consequence of nutrient enrichment, a structural change of the ecosystem has been taking place and so the opportunistic macroalgae growth was strongly stimulated allowing the occurrence of macroalgae blooms and the extinction of seagrass in more shallow areas. This situation may result in anoxic system collapse, with the development of hydrogen-sulphide conditions, lethal to rooted macrophytes such as Zostera spp. It becomes crucial to obtain information on the mechanisms that regulate the abundance of opportunistic macroalgae and its spatial and temporal distribution. Depending on the tidal amplitude, depth, current velocity, wind and wave-induced vertical turbulence, plants growing in shallow areas are suspended in the water column and transported out of the system. In the last decade a major effort has been done in integrating hydrodynamic and water quality models for estuarine environments. The analysis of available field data, obtained in this system from water column and benthos over the last twenty years, allows concluding that the occurrence of green macroalgal blooms is strongly dependent on the hydrodynamic conditions, residence time and salinity gradients. So, a hydroinformatic tool (MONDEST model) was developed and hydrodynamic modelling of Mondego estuary had been implemented in order to estimate and evidence the influence of residence time, current velocity and salinity spatial distribution on eutrophication process of Mondego estuary at different simulated scenarios and discharges characteristics. The results obtained for the spatial distribution of residence time and salinity confirm real eutrophication gradients of Mondego estuary south arm. This model (hydrodynamic, water quality and residence time calculation) constitutes a very powerful method for enhancing systems eutrophication vulnerability assessment in order to establish the best water quality management practices for the environmental sustainability of this important aquatic ecosystem.

O sistema metropolitano é um sistema de transporte ferroviário ligeiro que não se encontra com outros sistemas de transporte ou empresas, tendo assim uma linha exclusiva. Por isso, permite uma melhor regularização da oferta, tendo assim tempos de espera baixos, relativamente a outros sistemas ferroviários. Devido aos congestionamentos e tempos de espera significativos que o metro regista que podem alterar a qualidade de serviço, procedeu-se ao estudo dos mesmos no Metro de Lisboa. Devido ao planeamento da formação de uma linha circular, estudou-se os tempos de espera e congestionamentos da linha vermelha, a atual linha que faz ligação com todas as outras linhas. Para isso, escolheu-se a utilização da simulação por computador, pelas suas vantagens da potência computacional significativa, o que permite uma previsão com um rigor considerável. Com o número de entradas e saídas por estação, dia da semana, e período horário recebidos pelo metro e o intervalo temporal entre comboios, foi possível calcular o número de passageiros na plataforma e nas carruagens em cada minuto e tempo de espera de cada passageiro até entrar na carruagem por plataforma e o minuto na qual ocorreu essa entrada. Com estes dados, foi possível concluir que, tanto em congestionamentos como nos tempos de espera, existe uma diferença entre estações (tendo as estações de mudança de linha e Oriente mais congestionamento), dias da semana (principalmente entre dias úteis e fins de semana) e período horário (com a Ponta da Manhã e Tarde a ter mais procura e Noite mais tempo de espera).
Rapid Transit is a connected rail transport system that does not share its line with other transport systems or companies, having an exclusive line. It therefore allows for a better regularization of supply, thus having lower lead times compared to other rail systems. Due to overcrowding and waiting times that the subway has that may change the quality of service, it was decided to study them in Metro de Lisboa. Due to planification of a formation of a circular line, it was study the waiting times and overcrowding of the red line, the current line that have a connection with all other lines. To do so, it was chosen to do via the use of a computer simulation feature, that has advantages of high computing power and allow accurate prediction. With the number of entrances and exits per station, day of the week and time period received by Metro and time interval between trains, it was possible to calculate the number of passengers on the platform and carriages in each minute and the waiting time of each passenger until entering the carriage and the minute this entry occurred. With these data, it was concluded that, in both congestion and waiting times, there is a difference between the stations (having more overcrowding the stations that connects with all the other lines and Oriente), days of the week (mainly between working days and weekends) and time period (with morning and afternoon rush having more demand and night with longer waiting time).