Reactive transport models are essential tools for predicting contaminant fate and transport in the subsurface and for designing effective remediation strategies. Sound understanding of subsurface mixing in heterogeneous porous media is the key for the realistic modeling of reactive transport. This dissertation aims to investigate the extent of mixing and improve upscaling effective macroscopic models for mixing-controlled reactive transport in connected heterogeneous formations, which usually exhibit strongly anomalous transport behavior. In this research, a novel approach is developed for an accurate geostatistical characterization of connected heterogeneous formations transformed from Gaussian random fields. Numerical experiments are conducted in such heterogeneous fields with different connectivity to investigate the performance of macroscopic mean transport models for simulating mixing-controlled reactive transport. Results show that good characterization of anomalous transport of a conservative tracer does not necessarily mean that the models may characterize mixing well and that, consequently, it is questionable that the models capable of characterizing anomalous transport behavior of a conservative tracer are appropriate for simulating mixing-controlled reactive transport. In connected heterogeneous fields with large hydraulic conductivity variances, macroscopic mean models ignoring concentration variations yield good prediction, while in fields with intermediate conductivity variances, the models must consider both the mean concentration and concentration variations, which are very difficult to evaluate both theoretically and experimentally. An innovative and practical approach is developed by combining mean conservative and reactive breakthrough curves for estimating concentration variations, which can be subsequently used by variance transport models for prediction. Furthermore, a new macroscopic framework based on the dual-permeability conceptualization is developed for describing both mean and concentration variation for mixing-controlled reactive transport. The developed approach and models are validated by numerical and laboratory visualization experiments. In particular, the new dual-permeability model demonstrates significant improvement for simulating mixing-controlled reactive transport in heterogeneous media with intermediate conductivity variances. Overall, results, approaches and models from this dissertation advance the understanding of subsurface mixing in anomalous transport and significantly improve the predictive ability for modeling mixing-controlled reactive transport in connected heterogeneous media.

During the last century, the number of car users has increased as an effect of the increasing population growth. To manage the environmental and infrastructural challenges that comes with a more congested traffic network, traffic planning has become of higher importance to analyze the current traffic state and to predict future capacity challenges and effects of investments. These analysis and evaluations are commonly performed in different traffic analysis tools, where updated and realistic traffic demand needs to be provided to ensure reasonable results. In this thesis, a macroscopic model of Norrköping municipality constructed in the traffic demand modelling software Visum and a daily Origin-Destination(OD)-matrix is considered. The goal of this thesis is to produce a method that modify the current daily demand matrix into hourly demand matrices, called hourly target matrices, that represents a typical weekday. The goal is also to implement and evaluate the OD-estimation algorithm Simultaneous Perturbation Stochastic Approximation (SPSA) to obtain updated and valid demand matrices for the network model of Norrköping. The method of dividing the daily demand matrix into hourly target matrices is based on the paper by Spiess %26 Suter (1990). The method makes use of the available daily trip purpose matrices combined with hourly link flow observations from 96 links in a multiple linear regression model to obtain 24 hourly demand matrices. The resulting matrices are compared with the link flow observations and has different levels of R^2-fit, the maximum fit is 85.79 % and the minimum fit is 55.89 %. The average R^2-value is 72 %. The OD-estimation based on SPSA is performed on the AM and PM peak hours. The algorithm is implemented in Python scripts that are called from Visum where the traffic assignments is calculated. The result is an increase in R^2-value since the link flow difference between estimated and observed link flow is decreased. In total, the estimated link flows are improved by 7.4 % in the AM peak hour and 15.6 % in the PM peak hour. The total absolute change in OD-demand is 3 871 trips for AM peak hour and 6 452 trips for the PM peak hour. The estimated OD-matrices are evaluated by qualitatively visualizing the difference in heat maps and in the quantitative measure structural similarity index. The result is no major structural change from the hourly target matrices which verifies that the information used when the target matrices is produced still is considered. The total demand increased in both hours, with 505 respectively 2 431 trips and flows in some OD-pairs has a very high percental change. This was restricted by adding a penalty term to the SPSA-algorithm on the PM peak hour. The result of penalized SPSA is a much less increase of total demand as well as less percental change of the OD-flows. Though, this to a cost of not decreasing the link flow difference in the same magnitude.

Saccharothrix algeriensis est une bactérie filamenteuse capable de produire différentes molécules de la famille des dithiolopyrrolones présentant des activités antibiotiques et anticancéreuses. Ce travail porte sur l’analyse macroscopique et la modélisation du comportement dynamique de cette bactérie en vue de concevoir et d’optimiser un procédé de bioproduction de thiolutine. Les expériences menées en fermenteur de deux litres ont permis de décrire le comportement macroscopique de Sa. algeriensis. Sur substrat mixte (extrait de levure et glucose), la bactérie présente une croissance diauxique. La production de thiolutine, découplée de la croissance, est provoquée par l’épuisement du substrat préférentiel (extrait de levure). L’analyse des bilans carbone, azote et rédox nous a conduit à considérer deux phénomènes physico-chimiques qui n’étaient pas pris en compte dans le modèle proposé par Strub (2008) : l’entrainement de l’ammonium dans la phase gazeuse et l’adsorption des ions ammonium et des acides aminés sur la biomasse. Les données réconciliées sur la base des bilans élémentaires sont utilisées comme support pour la construction d’un modèle stœchio-cinétique. Différentes approches de modélisation des cinétiques et de représentation des bascules métaboliques ont été testées afin de retenir un schéma stœchio-cinétique apparent cohérent avec les données réconciliées. Cette étape de discrimination a été réalisée à l’aide de la toolbox ExOptim, développée en partenariat avec AgroParisTech. Cet outil, alliant une méthode d’optimisation robuste tout en limitant les temps de calcul, permet de prendre en compte les erreurs de mesure dès la mesure initiale et de reparamétrer indépendamment les paramètres du modèle et les données expérimentales. Les cinétiques réactionnelles sont représentées de manière satisfaisante par l’association du modèle de Monod et la loi logistique. Les seize paramètres du modèle sont identifiés sur sept expériences indépendantes. Le modèle finalement obtenu est ensuite testé sur cinq nouvelles expériences aux conditions initiales différentes. Ce modèle permet de prédire raisonnablement les cinétiques de croissance et de production de thiolutine. Toutefois, son utilisation reste limitée à des conditions initiales proches de celles de cette étude. / Saccharothrix algeriensis is a filamentous bacterium that produces several dithiolopyrrolone compounds with antibiotic and antitumor properties. This study focuses on the macroscopic analysis and modelling of the dynamic behaviour of this bacterium, in order to design and optimize the bioproduction process of thiolutin. Experiments were conducted in a two-litres bioreactor to characterise the macroscopic behaviour of Sa. algeriensis. On a medium containing several substrates (yeast extract and glucose), the bacterium shows a diauxic growth. Thiolutin production, which appears to be dissociated from growth, is triggered by the preferential substrate (yeast extract) depletion. The analysis of the carbon, nitrogen and redox balances led us to consider two physicochemical phenomena, which were not taken into consideration in the model proposed by Strub (2008): ammonium stripping in gaseous phase and adsorption of ammonium ions and amino acids on biomass. The data, reconciled on the basis of elementary balances, were used for the construction of a stoichio-kinetic model. Different modelling of kinetic and metabolic switches were tested in order to select a stoichio-kinetic model consistent with the reconciled data. This discrimination step was carried out using the ExOptim toolbox, developed in partnership with AgroParisTech. This toolbox combines a robust optimisation method and a reduced computation time. The experimental biases are taken into account from the first measurement and model parameters and experimental data reconditioned independently. The reaction kinetics are well represented by association of the Monod model and logistic laws. The sixteen model parameters were estimated from seven experiments. Finally, the model was validated by five additional experiments using different initial conditions. The kinetics of growth and thiolutin production are reasonably well predicted. However, the model is limited to initial conditions close to those of this study.

Neste trabalho apresentamos uma análise de possíveis processos de tunelamento em sistemas unidimensionais através do estudo do potencial de barreira dupla com região intermediária confinante, conseguimos verificar a existência de um processo de tunelamento que ocorre através da ocupação virtual da região intermediária. Uma modelagem deste fenômeno é proposta baseando-se em uma teoria perturbativa realizada em termos de estados \"quase-localizados\" da partícula. Além da descrição qualitativa do fenômeno, determinamos as condições físicas para que este processo de tunelamento, também chamado de cotunelamento ou tunelamento de ordem superior, ocorra. Como resultado, recuperamos com boa aproximação o coeficiente de transmissão exato do sistema escolhido. Por fim, um outro resultado obtido durante o desenvolvimento deste trabalho foi uma prova conclusiva da convergência do método de diferenças finitas FDTD aplicada à equação de Schrödinger. Esta prova, diferente das demais encontradas na literatura, conseguiu demonstrar de maneira conclusiva a inclusão do limite superior para o passo temporal, de maneira a assegurar a convergência das soluções numéricas, algo até então testado numericamente, mas sem uma prova rigorosa da sua validade. / In this work, we present a study about tunnelling processes occurring in one-dimensional systems. Choosing a double well potential with a confining region as a case study, we verified that there is a tunnelling process which is due to virtual occupation of the confining region. Using perturbative theory of quasi-localized states to describe the particles dynamics, we provide a qualitative description of the phenomenon of tunnelling through virtual occupation, and we are capable of determining the conditions for which such a tunneling (also known as cotunnelling or high-order tunneling) should be present. With this analysis we could calculate with good approximation the particle transmission coefficient through the barrier. Finally, we also provide a rigorous proof of the convergence conditions for the numerical calculation of the Schrödinger equation using the finite difference method.

Le réalisme d'une application traitant de l'animation comportementale de foules est fondé d'une part sur le rendu graphique des scènes produites par l'application, mais aussi sur le réalisme du comportement lui-même. C'est ce dernier point qui est notre objet d'étude. Le réalisme du comportement d'une foule est avant tout global (réalisme macroscopique) : elle doit avoir des propriétés statistiques (densité, dispersion, vitesse moyenne,…) proches de celles d'une foule réelle. Il est aussi local (réalisme microscopique), c'est-à-dire que les agents ou groupes d'agents doivent idéalement avoir des comportements proches de ceux des humains ou groupes humains pris pour référence, tout au moins dans le domaine d'application restreint considéré. L'objet de cette thèse est de proposer un modèle générique pour effectuer des simulations comportementales de foules, pour pouvoir satisfaire simultanément les deux types de réalisme macroscopique et microscopique et rendre compte de la plupart des types de foules (foules homogènes, groupes, collection d'agents). Pour ce faire, nous avons dégagé quelques principes simples et peu coûteux en ressources. Nous introduirons la notion de contexte (global, localisé, et propagateur). Les contextes globaux et localisés appliqués à un groupe d'agents tendent à leur donner un même comportement et constituent ainsi un moyen de contrôle global de ces acteurs (réalisme macroscopique). Le contexte propagateur donne un moyen de propagation d'informations entre les agents de la foule (communication). Les agents eux-mêmes sont dotés de tendances qui, en les différenciant dans un même contexte, leur donne une variété de comportements qui concourt au réalisme microscopique. / The realism of crowd behavioral animation is based on one hand on a rendering of graphic scenes generated by the application, and on the other hand on the realism of the behavior. This is last point which is our object of study. The realism of crowds' behavior is essentially global (macroscopic realism). It must respect the required statistical characteristics of the crowd (density, dispersal, speed…) similar to those of a real crowd. The realism is also local (microscopic realism), i.e. agents should ideally behave like humans or human groups taken as reference, at least in the focus of the considered application. The aim of our research is to propose a generic model to perform crowd behavior simulation in order to simultaneously satisfy the criterion of macroscopic and microscopic realism and that may be used to build various crowd behavioral simulations (homogeneous crowds, groups, collections of agents). To do this, we identified some simple principles and inexpensive resources; we introduce the notion of context (global, localized, and propagator). Global contexts applied to a group of agents, it tends to give them the same behavior and thus constitutes a means for global control of those agents (macroscopic realism). Propagator contexts allow the propagation of information among agents (communication). Agents are themselves equipped with tendencies that differentiate them within the context, and give them a variety of behaviors that contributes to microscopic realism.

Made available in DSpace on 2016-05-02T13:55:31Z (GMT). No. of bitstreams: 1 IsildoMartinsAparecidoJunior-dissertacao.pdf: 959439 bytes, checksum: 413a8601a4a37e97458ac607cb21ebf0 (MD5) Previous issue date: 2010-12-15 / The objective was to evaluate the improvement of the radiographic technique for the early detection of dyschondroplastic lesions in the tibia of broiler chickens in the city of Formiga, MG, Brazil. The experiment was conducted on the premises of UNIFOR/ MG, in the city of Formiga, and UNIFENAS, in the city of Alfenas. Four hundred and twenty one-day-old male chicks of the Cobb lineage were used. With 20 days of age, all the birds were radiographed and an alpha-numeric ring was placed in the lower right leg. Fourth-two chicks were previously selected on the basis of scores received by the bone mineral density and thickness of the lesions, and confined as long as 40 days. On day 40, after being radiographic again to determine new scores, the birds were killed for the removal of the right tibia for the microscopic and histological evaluation of the growth plate. Nonparametric statistical analyses were used with the chi-square test at the 5% significance level. It was possible to verify that the techniques using x-rays correlate with the macroscopic and histological examinations, and that no significant differences were found between the techniques (P>0.05). This study indicates that the use of x-rays for identifying dyschondroplasia in broiler chickens do not require the use of bone mineral density to diagnose dyschondroplastic lesions. / Objetivou-se avaliar o aperfeiçoamento da técnica radiográfica na detecção precoce de lesões discondroplásicas em tíbias de frangos de corte no município de Formiga - MG. O experimento foi realizado nas instalações da UNIFOR/MG em Formiga e UNIFENAS/Alfenas. Foram utilizados 420 pintinhos de um dia de idade, machos, da linhagem Cobb. Com 20 dias de idade todas as aves foram radiografadas, adicionando-se uma anilha alfa numérica no membro inferior direito. Quarenta e duas aves previamente selecionadas em função dos escores recebidos pela densidade mineral óssea e espessura da lesão foram confinadas até 40 dias. Com 40 dias as aves foram radiografadas novamente e determinados novos escores. Em seguida, estas foram abatidas e delas retirou-se a tíbia direita para avaliação macroscópica e histológica da placa de crescimento. Foi possível verificar que as técnicas utilizando a radiografia têm correlação com exames macroscópico e histológico e que não houve diferença significativa entre as técnicas (P>0,05). Portanto indica-se o uso do exame radiográfico para a identificação de discondroplasia em frangos de corte, não se necessitando do uso da densidade mineral óssea para diagnosticar lesões discondisplásicas. A estatística utilizada para a análise dos resultados foi a não paramétrica, utilizando-se o teste de qui-quadrado ao nível de 5% de significância.

Cette thèse porte sur la modélisation, l’analyse et l’analyse numérique des équations aux dérivées partielles non-linéaires et non-locales avec des applications au trafic routier. Le trafic routier peut être modélisé à des différentes échelles. En particulier, on peut considérer l’échelle microscopique qui décrit la dynamique de chaque véhicule individuellement et l’échelle macroscopique qui voit le trafic comme un fluide et qui décrit le trafic en utilisant des quantités macroscopiques comme la densité des véhicules et la vitesse moyenne. Dans cette thèse, en utilisant la théorie des solutions de viscosité, on fait le passage entre les modèles microscopiques et les modèles macroscopiques. L’intérêt de ce passage est que les modèles microscopiques sont plus intuitifs et faciles à manipuler pour simuler des situations particulières (bifurcations, feux tricolores,...) mais ils ne sont pas adaptés à des grosses simulations (pour simuler le trafic dans toute une ville par exemple). Au contraire, les modèles macroscopiques sont moins évidents à modifier (pour simuler une situation particulière) mais ils peuvent être utilisés pour des simulations à grande échelle. L’idée est donc de trouver le modèle macroscopique équivalent à un modèle microscopique qui décrit un scénario précis (une jonction, une bifurcation, des différents types de conducteurs, une zone scolaire,...). La première partie de cette thèse contient un résultat d’homogénéisation et d’homogénéisation numérique pour un modèle microscopique avec différents types de conducteurs. Dans une seconde partie, on obtient des résultats d’homogénéisation et d’homogénéisation numérique pour des modèles microscopiques con- tenant une perturbation locale (ralentisseur, zone scolaire,...). Finalement, on présente un résultat d’homogénéisation dans le cadre d’une bifurcation. / This work deals with the modelling, analysis and numerical analysis of non- linear and non-local partial differential equations and their application to traffic flow. Traffic can be simulated at different scales. Mainly, we have the microscopic scale which describes the dynamics of each of the vehicles individually and the macroscopic scale which describes the traffic as a fluid using macroscopic quantities such as the density of vehicles and the average speed. In this PhD thesis, using the theory of viscosity solutions, we derive macroscopic models from microscopic models. The interest of these results is that microscopic models are very intuitive and easy to manipulate to describe a particular situation (bifurcation, a traffic light,...), however, they are not adapted for big simulations (to simulate the traffic in an entire city for example). Conversely, macroscopic models are less easy to modify (to simulate a particular situation) but they can be used for big simulations. The idea is then to find the macroscopic model equivalent to a microscopic model describing a particular scenario (a junction, a bifurcation, different types of drivers, a school zone,...). The first part of this work contains an homogenization result and a numerical homogenization result for a microscopic model with different types of drivers. The second part contains an homogenization and numerical homogenization result for microscopic models with a local perturbation (a moderator, a school zone,...). Finally, we present an homogenization result for a bifurcation.

The City of Cape Town is the most congested city in South Africa, with Johannesburg coming in second. Capetonians are spending 75% more time in traffic because of the congestion during peak hours, thus reducing time spent on leisure and other activities. Due to population growth, increasing car ownership and declining capacity of rail infrastructure, Cape Town's road infrastructure will continue to be under severe pressure if the status quo is maintained. Research shows that congestion levels in urban areas are key factors in determining the effectiveness and productivity of the transport system. Traffic congestion poses a threat to the economy and the environment. Increasing corridors' capacity by increasing the number of lanes does not necessarily solve the problem. Effective urban traffic management and efficient utilization of existing infrastructure are critical in creating sustainable solutions to congestion problems. To achieve this, it is important that appropriate urban-scale models and monitoring strategies are put in place. Effective traffic management and monitoring strategies require accurate characterization of the traffic state of an urban-scale network. Several approaches, including kinetic wave theory and cell transmission models or macroscopic traffic simulation models, have been proposed and developed to describe the traffic state of an urban-scale network. However, these approaches are limited and require significant amounts of computational time and effort. The application of macroscopic fundamental diagram (herein referred to as MFD) to characterize the state of an urban-scale network has thus far proven to be more effective than other approaches. MFD represents the state of urban traffic by defining the traffic throughput of an area at given traffic densities. It describes the characteristics and dynamics of urban-scale traffic conditions, allowing for improved and sustainable urban scale traffic management and monitoring strategies. Against this backdrop, the existence of MFD for the City of Cape Town (CoCT) urbanscale network is yet to be established and the implications yet to be understood, as in other parts of the world. The main aim of this research was, therefore, to empirically estimate the macroscopic fundamental diagram for the CoCT's freeway network and analyse its observed features. To achieve this, observed data of 5 minutes periods for the month of May 2019 was used to estimate the MFD. The results confirmed that when the chaotic scatter-plots of flow and density from individual fixed loop detectors were aggregated the scatter nearly disappeared and points grouped neatly to form a clearly defined free-flow state, critical state and the formation of hysteresis loops past the critical density corresponding with the network observed maximum flow. Further analysis of the MFDs showed that a single hysteresis loop always forms past the critical density during the evening peak in a weekday MFD. However, it was inconclusive during the morning peak period in weekday MFDs. Lastly, an explicit hysteresis loop seldom appears in a Saturday MFD when the peak of traffic demand is lower than on weekdays. In order to understand the dynamics of the congestion spread, the freeway network was partitioned into penetrating highways network and the ring highway network. The results showed that the maximum flows observed for the two sub-networks were significantly different (943 veh/hr/lane for the penetrating highways network and 1539 veh/hr/lane for the ring highway network). The penetrating highways network's MFD indicated the presence of congestion in the network whereas the ring highway network indicated only the free-flow state (no indication of congestion) during peak periods. The congestion seen on the penetrating highways network was found not to be sufficiently spread on those highways. On the 24th May, congestion on the penetrating highway network was observed during both the morning and evening peak periods, whereas on the 31st May congestion was observed mainly during the evening peak period, with hysteresis-like shape. These observations confirmed that congestion during peak periods is not homogenously spread across the entire network, certain areas are more congested than others, hence the observed formation of hysteresis loops and slight scatters. Lastly, the hysteresis loops observed in the penetrating highways network's MFD was further characterized in terms of their shape and size. First, the results showed that the slight scatter and hysteresis patterns observed in penetrating highways network MFD's vary in size and shape across different days. The shapes of the hysteresis loops observed during both the morning and evening peak periods, were type H2 hysteresis loops, signifying a stable recovery of the network with the average network flow remaining unchanged as average network density decreases during the recovery. Characterization of the size of the observed hysteresis loops showed that the drop of the hysteresis (an indicator of network level of instability during recovery phase) was smaller, signifying a more stable network traffic and homogenous distribution of congestion during the recovery phase.

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