A fundamental understanding of the kinetics and mechanisms of the catalytic reaction steps involved in the process of converting a fuel into hydrogen rich stream suitable for a fuel cell, as well as the electro-catalytic reactions within a fuel cell, is not only conceptually appealing, but could provide a sound basis for the design and development of efficient fuel processor/fuel cell systems. With the quantum chemical calculations on kinetics of elementary catalytic reaction steps becoming rather commonplace, and with increasing information now available in terms of electronic structures, vibration spectra, and kinetic data (activation energy and pre-exponential factors), the stage is set for development of a comprehensive approach. Toward this end, we have developed a framework that can utilize this basic information to develop a comprehensive understanding of catalytic and electrocatalytic reaction networks. The approach is based on the development of Reaction Route (RR) Graphs, which not only represent the reaction pathways pictorially, but are quantitative networks consistent with the Kirchhoff's laws of flow networks, allowing a detailed quantitative analysis by exploiting the analogy with electrical circuits. The result is an unambiguous portrayal of the reaction scheme that lays bare the dominant pathways. Further, the rate-limiting steps are identified rationally with ease, based on comparison of step resistances, as are the dominant pathways via flux analysis. In fact, explicit steady-state overall reaction (OR) rate expression can also be derived in an Ohm's law form, i.e. OR rate = OR motive force/OR resistance of an equivalent electric circuit, which derives directly from the RR graph of its mechanism. This approach is utilized for a detailed analysis of the catalytic and electro-catalytic reaction systems involved in reformer/fuel cell systems. The catalytic reaction systems considered include methanol decomposition, water gas shift, ammonia decomposition, and methane steam reforming, which have been studied mechanistically and kinetically. A detailed analysis of the electro-catalytic reactions in connection to the anode and cathode of fuel cells, i.e. hydrogen electrode reaction and the oxygen reduction reaction, has also been accomplished. These reaction systems have not so far been investigated at this level of detail. The basic underlying principles of the RR graphs and the topological analysis for these reaction systems are discussed.

Dans ce travail de thèse, l'efficacité de la voie intrapulmonaire et les paramètres biopharmaceutiques influençant la diffusion pulmonaire après nébulisation d'antibiotiques ont été évalués. La présence et l'impact de certaines pompes d'efflux dans un modèle in vitro de cellules primaires épithéliales pulmonaires de rat ont été testés. Trois fluoroquinolones et la colistine ont été utilisées comme molécules de référence. La combinaison des molécules testées a permis d'obtenir une vue d'ensemble des caractéristiques de diffusion intrapulmonaire des antibiotiques. L'étude in vivo avec les fluoroquinolones a démontré que les concentrations pulmonaires de ces molécules sont plus importantes que dans le plasma, probablement dû à la présence des transporteurs comme la glycoprotéine-P. La présence de ces transporteurs a été confirmée dans le modèle de cellules pulmonaires de rats. L'étude in vivo avec la colistine a montré qu'une lente diffusion pourrait conférer un avantage à la nébulisation par rapport à l'administration intraveineuse. En conclusion, l'administration par nébulisation des molécules, qui traversent les tissus lentement (colistine), pourrait être avantageuse, alors que pour d'autres, qui traversent vite la barrière (fluoroquinolones), la voie nébulisée pourrait ne pas présenter des avantages par rapport à la voie intraveineuse. De plus, les résultats ont démontré qu'une faible perméabilité à travers le poumon (colistine) pourrait donner un avantage à la nébulisation des antibiotiques, tandis qu'une affinité pour des transporteurs (fluoroquinolones) semble présenter un intérêt aussi bien dans le cadre d'une nébulisation que d'une administration intraveineuse. / The aim of this study was to investigate the efficiency of intrapulmonary administration and the biopharmaceutical parameters regulating the pulmonary diffusion following nebulization. We examined whether certain efflux pumps were present in an in vitro model of rat lung cells and whether these efflux pumps could be beneficial by increasing lung concentrations in vivo. Fluoroquinolones and colistin were the molecules used as reference. These different molecules allowed an overview of the intrapulmonary diffusion characteristics of antibiotics. The in vivo study with fluoroquinolones showed that their lung concentrations are higher than in plasma, probably due to glycoprotein-P. The presence of this efflux pump was confirmed in the model with rat lung cells. The in vivo study with colistin showed that a slow diffusion may confer an advantage for nebulization over intravenous administration. In conclusion, the nebulization molecules passing slowly (colistin) across the tissues may be advantageous, whereas for others, with a fast passage across the barrier (fluoroquinolones), the pulmonary route may not provide an advantage over the intravenous administration. Moreover, the results showed that a slow permeability across the lung (colistin) may confer an advantage for the antibiotic nebulization, while affinity by transporters (fluoroquinolones) is beneficial for both nebulization and intravenous administration.

Předkládaná diplomová práce se zabývá stavbou živých živočišných buněk a jejich odezvou na mechanické zatěžování. Zobecněným zaměřením práce je popis mechanického chování buňky nejenom ve fyziologickém, ale i v patologickém stavu. Výchozím předpokladem pro úspěšné řešení zadané úlohy je vysoce interdisciplinární přístup kombinující výpočtové přístupy mechaniky těles (v~tomto případě metodu konečných prvků) s lékařským výzkumem. Nejdůležitějším bodem při tvorbě výpočtového modelu, pomocí něhož je možné aproximovat chování živé buňky při zatížení, je zejména identifikace mechanicky významných komponent a~jejich materiálových parametrů. V tomto případě jsou jako mechanicky význačné identifikovány spojité součásti jádro, membrána a cytoplazma, které jsou nově propojeny s prvky diskrétními (mitochondriální sítí) v hybridním modelu, jehož platnost je ověřena pomocí experimentálních dat. Tento model slouží jako podklad k vyhodnocení míry vlivu mitochondrií na celkovou tuhost buňky.

The master’s thesis deals with the computational modelling of the mechanical testing of isolated smooth muscle cells. The main aims are to create computational model of a cell, to simulate single-axis tensile test and to modify the model so that the model reflects real mechanical response. The model of the cell includes cytoplasm, nucleus, cell membrane and cytoskeleton which is modelled as a tensegrite structure. On this model the tensile test was simulated in case of the cell with cytoskeleton and the cell with distributed the cytoskeleton. Force-elongation curves, which were obtained from this simulation, were compared with experimental data which were taken from literature. Tensile properties were measured on freshly isolated cells from rat thoracic aorta, cultured cells, and cells treated with cytochalasin D to disrupt their actin filaments. It was found that the cytoskeleton influence on the cell load in computational model was smaller than in the real cell. Therefore the model was modified by changing material propreties and geometry so that the model of the cell corresponded with the different types of experimentally measured cells.

Nowadays, PEM fuel cell systems for passenger cars are always realized as hybrid systems. If the architecture of a hybrid system is given, then the dimensioning of the fuel cell and battery subsystems is crucial in terms of costs, dynamics, and driving behavior in general. In order to analyze these dependencies correctly, the ZBT fuel cell model was integrated into a fuel cell system and a full vehicle simulation. The subject of the investigation is the interaction of different drive cycles, which in part are very different, with differently dimensioned sub models for the fuel cell system and the battery. The ZBT fuel cell model is integrated into the simulation environment AVL CRUISE™ M for the fuel cell system and the vehicle. An analysis is presented that compares the different drive cycles and system dimensions and provides specific recommendations for different use cases.

Die Durchführung von Experimenten und das mathematische Modellieren von zellulären Prozessen gehören in der Systembiologie untrennbar zusammen. Das gemeinsame Ziel ist die Aufklärung des Zusammenspiels intrazellulärer Prozesse wie Metabolismus, Genexpression oder Signaltransduktion. Während sich molekularbiologische Untersuchungen mit den molekularen Mechanismen einzelner isolierter Systeme beschäftigen, zielt die Systembiologie auf die Aufklärung der Zusammenhänge ganzer Prozesse und schließlich auch ganzer Zellen ab. Die Verfügbarkeit von umfangreichen Datensätzen und die steigenden Möglichkeiten im Bereich der Computersimulation haben in den letzten Jahren den Weg geebnet, um auch Ganzzellsimulationen nicht mehr unmöglich erscheinen zu lassen. Diese Arbeit stellt das erste eukaryotische Ganzzellmodell der Bäckerhefe Saccharomyces cerevisiae vor. Hefe als eukaryotischer Modellorganismus ist hierbei der perfekte Kandidat für die Erstellung eines solchen Modells. Er bietet, als wohl meist erforschter eukaryotischer Einzeller in Verbindung mit der Verfügbarkeit einer großen Menge experimenteller Daten, beste Voraussetzungen zur Erstellung eines solchen Modells. Das Projekt ist hierbei in drei Teile gegliedert: i) Die Erstellung eines modularen Ganzzellmodells das alle zellulären Funktionen wie Zellzyklus, Genexpression, Metabolismus, Transport und Wachstum abbildet. ii) Die Implementation einer spezialisierten Simulationsumgebung in Verbindung mit einer Datenbank, um die Erstellung, Simulation und Parametrisierung von Modulen zu ermöglichen. iii) Die Durchführung von Experimenten, um einen ganzheitlichen Datensatz zu erlangen, der Wachstum, Genexpression und Metabolismus abbildet. Die hier vorgestellte Arbeit liefert nicht nur ein mathematisches Modell, sondern benennt auch die Herausforderungen, die während der Arbeit an einem Ganzzellmodell auftreten und stellt mögliche Lösungsansätze vor. / In systems biology experiments and mathematical modeling are going hand in hand to gain and increase understanding of cellular processes like metabolism, gene expression, or signaling pathways. While molecular biology investigates single isolated parts and molecular mechanisms of cellular processes, systems biology aims at unraveling the whole process and ultimately whole organisms. Today the availability of comprehensive high-throughput data and computational power paved the way to increase the size of analyzed systems to reach the cellular level. This thesis presents the first whole-cell model (WCM) of a eukaryotic cell, the yeast Saccharomyces cerevisiae. This established model organism is the perfect candidate for the implementation of a holistic model based on the available experimental data and the accumulated biological knowledge. The project is split into three parts: i) The creation of a modular functional-complete whole-cell model, combining the processes cell cycle, gene expression, metabolism, transport, and growth. ii) The implementation of a specialized simulation environment and a database to support module creation, simulation, and parameterization. iii) The elicitation of experimental data by conducting an experiment to achieve a comprehensive data set for parameterization, combining growth, metabolic, proteomic, and transcriptomic data. The presented work provides not only a simple mathematical model but also addresses challenges occurring during the development of whole-cell models and names possible solutions and new methodologies required for the creation of WCMs.

No description available.

The (Battery management system)BMS has the task of ensuring that for the individual bat-tery cell parameters such as the allowed operating voltage window or the allowable temperature range are not violated. Since the battery itself is a highly distinct nonlinear electrochemical de-vice it is hard to detect its internal characteristics directly. The requirement of predicting battery packs’ present operating condition will become one of the most important task for the BMS. Therefore, special algorithms for battery monitoring are required.In this thesis, a model based battery state estimation technique using an adaptive filter tech-nology is investigated. Different battery models are studied in terms of complexity and accuracy. Following up with the introduction of different adaptive filter technology, the implementation of these methods into battery management system is decribed. Evaluations on different estimation methods are implemented from the point of view of the dynamic performance, the requirement on the computing power and the accuracy of the estimation. Real test drive data will be used as a reference to compare the result with the estimation value. Characteristics of different moni-toring methods and models are reported in this work. Finally, the trade-offs between different monitor’s performance and their computational complexity are analyzed. / BMS (eng. battery management system) har till uppgift att se till att viktiga parametrar såsom tillspännings- och temperaturintervall upprätthålls för varje individuell battericell. Då en battericells beteende är ickelinjärt är det svårt att bestämma cellens interna karakteristika direkt. Att kunna förutsäga dessa karakteristika för ett komplett batteripack kommer att en mycket viktig funktion hos framtida BMS. I detta examensarbete har en modellbaserad tillståndsestimeringsmetod med användande av adaptiv filtrering undersökts. Olika batterimodeller har studerats med avseende på komplexitet och noggrannhet. Efter introduktionen av olika metoder för adaptiv filtrering har dessa metoder implementerats i en BMS modell. Utvärdering av de olika metoderna för att åstadkomma tillståndsestimering har sedan utförts med avseende på dynamisk prestanda, krav på beräkningskraft och noggrannhet hos de resulterande estimaten. Data från uppmätta kördata från ett fordon har använts som referens för att jämföra de olika estimaten. Slutligen presenteras en jämförelse mellan de olika tillståndsestimeringsmetodernas prestanda när de appliceras på de olika batterimodellerna.

Résumé confidentiel / Confidential abstract

Les carcinomes mammaires invasifs sont des tumeurs solides, au sein desquelles le fort pouvoir de prolifération des cellules cancéreuses entraîne la formation de zones hypoxiques. Les mécanismes cellulaires d’adaptation à la diminution des apports en oxygène sont principalement déterminés par des facteurs de transcription hétérodimériques induits par l’hypoxie (HIF-1 et HIF-2, hypoxia inducible factor). Le monomère alpha de ces complexes est déstabilisé en situation de normoxie. Les récepteurs aux facteurs de croissance épidermique (EGFR) peuvent également augmenter la traduction de l’ARNm codant ces monomères indépendamment de l’oxygène. La première partie de la thèse repose sur le développement de deux clones cellulaires fluorescents stables et inductibles par l’hypoxie, à partir d’une lignée de carcinome mammaire invasif triple négatif surexprimant le récepteur EGFR (MDA- MB-231). Le modèle CA9-GFP permet de restituer l’activité transcriptionnelle des complexes HIFs et le modèle GFP-P564 traduit la stabilité de leur sous-unité alpha. La fluorescence des deux modèles cellulaires est fortement induite en situation d’hypoxie (1% O2) et en présence d’agents mimétiques de l’hypoxie (cobalt, desferrioxamine et diméthyl-oxalyl glycine). Ces modèles ont ensuite été utilisés pour évaluer l’effet de trois thérapies anti-EGFR sur les voies de réponses à l’hypoxie. Le cétuximab et le lapatinib n’ont aucun effet sur la fluorescence des cellules alors que le géfitinib diminue l’intensité du signal en situation d’hypoxie. Ces différences sont associées à un impact similaire sur la migration et la viabilité cellulaire traduisant ainsi une sensibilité différentielle à ces trois composés anti-EGFR. La deuxième partie de la thèse s’est ensuite orientée vers la quantification par RT-qPCR de 45 gènes inductibles par l’hypoxie et impliqués dans le développement du cancer du sein sur une série rétrospective portant sur 32 exérèses de carcinomes mammaires invasifs précoces. Une analyse comparative des données a été effectuée en fonction des critères anatomo-pathologiques (stade, grade, statut en récepteur HER2, rechute). Une surexpression coordonnée de l’ensemble des gènes est observée dans les tumeurs de haut grade, HER2+ et pour les sujets ayant récidivé. La comparaison des groupes « rechute » versus « non rechute » a permis de sélectionner six marqueurs de référence s’exprimant de manière significative. Elle permet en outre la réalisation d’un algorithme basique de classement des individus en fonction du risque de récidive. Celui-ci a été validé par la construction de courbes de survie (méthode de Kaplan-Meier et test du Mantel-Haenszel). L’utilisation combinée des deux modèles cellulaires fluorescents permet l’identification et la caractérisation dynamique de molécules agissant directement ou indirectement sur les réponses cellulaires à l’hypoxie tumorale. L’analyse de l’expression de gènes connus pour leur profil agressif et régulés par le microenvironnement tumoral, constitue un outil clinique d’aide au pronostic des cancers du sein. / The invasive breast cancers are solid tumors, wherein the proliferation of cells causes the formation of hypoxic zones. Cellular adaptive responses to reduced oxygen concentrations are mainly determined by heterodimeric transcription factors induced by hypoxia (HIF-1 & HIF-2, Hypoxia Inducible Factors). The alpha subunits of HIF are rapidly degraded under normoxic conditions. HIF complexes are also regulated by activation of epidermal growth-factor receptor (EGFR) signaling pathways in an oxygen-independent manner. The first part of this work was to develop stable fluorescent clones for examining responses to hypoxia from a metastatic triple-negative breast cancer cell line overexpressing EGFR (MDA-MB-231). The Ca9-GFP and GFP-P564 cell models allow to assess HIF activity and alpha subunits stability, respectively. In both models, fluorescence signals were strongly increased with hypoxia-mimicking reagents (cobalt, desferrioxamine and dimethyl-oxalyl glycine) and under hypoxia (1% O2). The impact of three EGFR inhibitors on HIF activity and stability was assessed. Cetuximab and lapatinib did not affect the signal induced by hypoxia, whereas gefitinib sharply reduced its intensity in both models. The differential effect of these three EGFR-targeted therapies on hypoxia responses was correlated with a similar impact on viability and cell migration. The second part of this work focused on the relative quantification using qPCR analysis of 45 genes involved in hypoxia responses and in the development of breast cancer, from a retrospective series of 32 tumor samples from patients with early- stage invasive breast cancer. A comparative analysis was performed according to anatomo-pathological criteria (stage, grade, HER2 status, and relapse). A coordinated overexpression of all genes was observed in high-grade and HER2+ tumors and in the group of patients that relapsed. The comparison of gene expression between "relapse" and "no relapse" groups was used to identify six reference markers. It also allowed to develop a basic algorithm to classify patients according to the risk of relapse. This algorithm was validated by constructing survival curves (Kaplan-Meier method and Mantel-Haenszel test). Combined use of two fluorescent cell models allows identification and dynamic characterization of compounds able to directly or indirectly inhibit cellular responses to tumor hypoxia. Analysis of gene expression known for their aggressive character and regulated by the tumor microenvironment is a clinical tool for assessing breast cancer prognosis.