Mathematical modeling of biological systems is a powerful tool to systematically investigate the functions of biological processes and their relationship with the environment. To obtain accurate and biologically interpretable predictions, a modeling framework has to be devised whose assumptions best approximate the examined scenario and which copes with the trade-off of complexity of the underlying mathematical description: with attention to detail or high coverage. Correspondingly, the system can be examined in detail on a smaller scale or in a simplified manner on a larger scale. In this thesis, the role of photosynthesis and its related biochemical processes in the context of plant metabolism was dissected by employing modeling approaches ranging from kinetic to stoichiometric models. The Calvin-Benson cycle, as primary pathway of carbon fixation in C3 plants, is the initial step for producing starch and sucrose, necessary for plant growth. Based on an integrative analysis for model ranking applied on the largest compendium of (kinetic) models for the Calvin-Benson cycle, those suitable for development of metabolic engineering strategies were identified. Driven by the question why starch rather than sucrose is the predominant transitory carbon storage in higher plants, the metabolic costs for their synthesis were examined. The incorporation of the maintenance costs for the involved enzymes provided a model-based support for the preference of starch as transitory carbon storage, by only exploiting the stoichiometry of synthesis pathways. Many photosynthetic organisms have to cope with processes which compete with carbon fixation, such as photorespiration whose impact on plant metabolism is still controversial. A systematic model-oriented review provided a detailed assessment for the role of this pathway in inhibiting the rate of carbon fixation, bridging carbon and nitrogen metabolism, shaping the C1 metabolism, and influencing redox signal transduction. The demand of understanding photosynthesis in its metabolic context calls for the examination of the related processes of the primary carbon metabolism. To this end, the Arabidopsis core model was assembled via a bottom-up approach. This large-scale model can be used to simulate photoautotrophic biomass production, as an indicator for plant growth, under so-called optimal, carbon-limiting and nitrogen-limiting growth conditions. Finally, the introduced model was employed to investigate the effects of the environment, in particular, nitrogen, carbon and energy sources, on the metabolic behavior. This resulted in a purely stoichiometry-based explanation for the experimental evidence for preferred simultaneous acquisition of nitrogen in both forms, as nitrate and ammonium, for optimal growth in various plant species. The findings presented in this thesis provide new insights into plant system's behavior, further support existing opinions for which mounting experimental evidences arise, and posit novel hypotheses for further directed large-scale experiments. / Mathematische Modellierung biologischer Systeme eröffnet die Möglichkeit systematisch die Funktionsweise biologischer Prozesse und ihrer Wechselwirkungen mit der Umgebung zu untersuchen. Um präzise und biologisch relevante Vorhersagen treffen zu können, muss eine Modellierungsstrategie konzipiert werden, deren Annahmen das untersuchte Szenario bestmöglichst widerspiegelt und die dem Trade-off der Komplexität der zugrunde liegenden mathematischen Beschreibung gerecht wird: Detailtreue gegenüber Größe. Dementsprechend kann das System detailliert, in kleinerem Umfang oder in vereinfachter Darstellung im größeren Maßstab untersucht werden. In dieser Arbeit wird mittels verschiedener Modellierungsansätze, wie kinetischen und stöchiometrischen Modellen, die Rolle der Photosynthese und damit zusammenhängender biochemischer Prozesse im Rahmen des Pflanzenstoffwechsels analysiert. Der Calvin-Benson-Zyklus, als primärer Stoffwechselweg der Kohlenstofffixierung in C3-Pflanzen, ist der erste Schritt der Stärke- und Saccharoseproduktion, welche maßgeblich für das Wachstum von Pflanzen sind. Basierend auf einer integrativen Analyse zur Modellklassifizierung wurden aus der größten bekannten Sammlung von (kinetischen) Modellen des Calvin-Benson-Zyklus diejenigen ermittelt, die für die Entwicklung von Metabolic-Engineering-Strategien geeignet sind. Angeregt von der Fragestellung warum Kohlenstoff transitorisch vorwiegend in Form von Stärke anstatt Saccharose gespeichert wird, wurden die metabolischen Kosten beider Syntheseprozesse genauer betrachtet. Die Einbeziehung der Bereitstellungskosten der beteiligten Enzyme stützt die Tatsache, dass bevorzugt Stärke als temporärer Kohlenstoffspeicher dient. Die entprechende Untersuchung erfolgte einzig auf Grundlage der Stöchiometrie der Synthesewege. In vielen photosynthetisch-aktiven Organismen findet zudem Photorespiration statt, die der Kohlenstofffixierung entgegenwirkt. Die genaue Bedeutung der Photorespiration für den Pflanzenmetabolismus ist noch umstritten. Eine detaillierte Einschätzung der Rolle dieses Stoffwechselweges bezüglich der Inhibierung der Kohlenstofffixierungsrate, der Verknüpfung von Kohlenstoff- und Stickstoffmetabolismus, der Ausprägung des C1-Stoffwechsels sowie die Einflussnahme auf die Signaltransduktion wurde in einer modell-basierten, kritischen Analyse vorgenommen. Um die Photosynthese in ihrem metabolischen Kontext verstehen zu können, ist die Betrachtung der angrenzenden Prozesse des primären Kohlenstoffmetabolismus unverzichtbar. Hierzu wurde in einem Bottom-up Ansatz das Arabidopsis core Modell entworfen, mittels dessen die Biomasseproduktion, als Indikator für Pflanzenwachtum, unter photoautotrophen Bedingungen simuliert werden kann. Neben sogenannten optimalen Wachstumsbedingungen kann dieses großangelegte Modell auch kohlenstoff- und stickstofflimitierende Umweltbedingungen simulieren. Abschließend wurde das vorgestellte Modell zur Untersuchung von Umwelteinflüssen auf das Stoffwechselverhalten herangezogen, im speziellen verschiedene Stickstoff-, Kohlenstoff- und Energiequellen. Diese auschließlich auf der Stöchiometrie basierende Analyse bietet eine Erklärung für die bevorzugte, gleichzeitige Aufnahme von Nitrat und Ammonium, wie sie in verschiedenen Spezies für optimales Wachstum experimentell beobachtet wurde. Die Resultate dieser Arbeit liefern neue Einsichten in das Verhalten von pflanzlichen Systemen, stützen existierende Ansichten, für die zunehmend experimentelle Hinweise vorhanden sind, und postulieren neue Hypothesen für weiterführende großangelegte Experimente.

Une des voies privilégiées pour réduire la teneur en soufre dans les essences commerciales est l'hydrodésulfuration sélective (HDS) des essences issues du procédé de FCC. Une essence étant composée d'un mélange de composés soufrés (1000 ppm) et d'oléfines (20-40%pds). Il est important de comprendre leur transformation de manière à améliorer l'HDS tout en minimisant l'hydrogénation (HYD) des oléfines. Par conséquent, la transformation de plusieurs molécules modèles soufrées (2-méthylthiophène, 3-méthylthiophène et le benzothiophène) et oléfiniques (hex-1-ène, 4-méthylpent-1-ène, 3,3-diméthylbut-1-ène et 2,3-diméthylbut-2-ène) a été étudiée dans les conditions opératoires d'HDS. Par une approche expérimentale couplée à de la modélisation cinétique, nous avons établi une échelle de réactivité entre les composés soufrés d'une part et les oléfines d'autre part. Le benzothiophène est le composé le plus réactif, mais aussi celui qui est le plus inhibiteur pour la transformation des autres composés soufrés. Concernant les oléfines, l'hex-1-ène est la plus réactive par rapport aux autres oléfines ramifiées. Lorsque ces composés sont en mélange, on constate des inhibitions mutuelles plus au moins conséquentes selon la structure des composés modèles. Ces effets qui résultent de compétitions à l'adsorption entre les molécules à la surface du catalyseur ont été modélisés et quantifiés (constantes cinétique et d'adsorption) à partir d'un modèle unique en considérant le formalisme de Langmuir-Hinshelwood. / A preferred route to reduce the sulfur content on the commercial gasoline is the selective hydrodesulfurization (HDS) process of FCC gasoline. A typical gasoline is composed by a mixture of sulfur (1000 ppm) and olefins (20-40%wt) compounds. Therefore, it is important to understand their transformation in order to improve the HDS and minimizing the olefin hydrogenation (HYD). Consequently, the transformation of various sulfur (2-methylthiophene, 3-methylthiophene and benzothiophene) and olefins (hex-1-ene, 4-methylpent-1-ene, 3,3-dimethylbut-1-ene and 2,3-dimethylbut-2-ene) has been studied under HDS operating conditions.By experimental and theoretical (kinetic modeling) approaches, a reactivity scale has been established between the sulfur compounds on one hand and olefins compounds on the other hand. The benzothiophene is the most reactive compound. However it is the most inhibitor compound for the transformation of others sulfur compounds. Regarding the olefins, the hex-1-ene is the most reactive compound among the others branched compounds. A mutual inhibition has been observed when those compounds are studied in mixture according with their structures. These effects result from competitive adsorption between the molecules on the catalyst surface. These results could be modeled and quantified (adsorption and kinetic constants) from a unique model considering the Langmuir-Hinshelwood formalism.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / A estimação de parâmetros cinéticos em processos químicos e cromatográficos utilizando técnicas numéricas assistidas por computadores tem conduzido para melhoria da eficiência e o favorecimento da compreensão das fenomenologias envolvidas nos mesmos. Na primeira parte deste trabalho será realizada a modelagem computacional do processo de produção de biodiesel via esterificação, sendo que, o método de otimização estocástica Random Restricted Window (R2W) será correlacionado com os dados experimentais da produção de biodiesel a partir da esterificação do ácido láurico com etanol anidro na presença do catalisador ácido nióbico (Nb2O5). Na segunda parte do mesmo será realizada a modelagem computacional do processo de cromatografia de adsorção (batch process) onde serão correlacionados os dados provenientes dos modelos cinéticos de HASHIM, CHASE e IKM2 com os dados experimentais da adsorção de amoxicilina com quitosana, e também serão correlacionados os dados experimentais da adsorção de Bovine Serum Albumin (BSA) com Streamline DEAE com os dados provenientes de uma nova aplicação do método R2W mediante a implementação de um modelo cinético reversível. Ademais, as constantes cinéticas para cada processo supracitado serão estimadas levando em consideração o valor mínimo da função resíduos quadrados. / The estimation of kinetic parameters in chemical and chromatographic processes using numerical techniques assisted by computers has led to the improved of efficiency and facilitating the understanding of phenomenologies involved in those. In the first part of this work will be carried out the computational modeling of production process of biodiesel by esterification, and that, the stochastic method of optimization Random Restricted Window (R2W) will be correlated with the experimental data of biodiesel production through the esterification of lauric acid with anhydrous ethanol in the presence of niobic acid (Nb2O5) as catalyst. In the second part of this will be carried out the computational modeling of the process of adsorption chromatographic (batch process) where will be correlated the data by the kinetic models of HASHIM, CHASE and IKM2 with the experimental data of amoxicillin adsorption with quitosan, and will also be correlated the experimental data of Bovine Serum Albumin (BSA) with Streamline DEAE with the data from a new application of R2W method through the implementation of a reversible kinetic model. Moreover, the kinetic constants for each process aforementioned will be estimated taking into account the minimum value of function of square residues.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / A estimação de parâmetros cinéticos em processos químicos e cromatográficos utilizando técnicas numéricas assistidas por computadores tem conduzido para melhoria da eficiência e o favorecimento da compreensão das fenomenologias envolvidas nos mesmos. Na primeira parte deste trabalho será realizada a modelagem computacional do processo de produção de biodiesel via esterificação, sendo que, o método de otimização estocástica Random Restricted Window (R2W) será correlacionado com os dados experimentais da produção de biodiesel a partir da esterificação do ácido láurico com etanol anidro na presença do catalisador ácido nióbico (Nb2O5). Na segunda parte do mesmo será realizada a modelagem computacional do processo de cromatografia de adsorção (batch process) onde serão correlacionados os dados provenientes dos modelos cinéticos de HASHIM, CHASE e IKM2 com os dados experimentais da adsorção de amoxicilina com quitosana, e também serão correlacionados os dados experimentais da adsorção de Bovine Serum Albumin (BSA) com Streamline DEAE com os dados provenientes de uma nova aplicação do método R2W mediante a implementação de um modelo cinético reversível. Ademais, as constantes cinéticas para cada processo supracitado serão estimadas levando em consideração o valor mínimo da função resíduos quadrados. / The estimation of kinetic parameters in chemical and chromatographic processes using numerical techniques assisted by computers has led to the improved of efficiency and facilitating the understanding of phenomenologies involved in those. In the first part of this work will be carried out the computational modeling of production process of biodiesel by esterification, and that, the stochastic method of optimization Random Restricted Window (R2W) will be correlated with the experimental data of biodiesel production through the esterification of lauric acid with anhydrous ethanol in the presence of niobic acid (Nb2O5) as catalyst. In the second part of this will be carried out the computational modeling of the process of adsorption chromatographic (batch process) where will be correlated the data by the kinetic models of HASHIM, CHASE and IKM2 with the experimental data of amoxicillin adsorption with quitosan, and will also be correlated the experimental data of Bovine Serum Albumin (BSA) with Streamline DEAE with the data from a new application of R2W method through the implementation of a reversible kinetic model. Moreover, the kinetic constants for each process aforementioned will be estimated taking into account the minimum value of function of square residues.

Le dioxyde de chlore se positionne actuellement comme une alternative au chlore pour la désinfection de l'eau potable. Bien que son pouvoir biocide soit aujourd'hui bien connu, il existe peu de données bibliographiques sur ses effets sur les matériaux organiques dans les réseaux d'eau intérieurs. L'utilisation du PA66 pour des clapets anti-retour est récente : son comportement à long terme est donc méconnu. L'objectif de cette étude était de progresser dans la compréhension des mécanismes d'interaction entre le dioxyde de chlore et une matrice PA66 stabilisée par un mélange de deux antioxydants et chargée de fibres de verre, mais aussi de proposer une méthode « multi-échelle » de prédiction de la durée de vie de ce matériau composite en service. Tout d'abord, une meilleure description des réactions chimiques se produisant au sein du matériau (oxydation, hydrolyse, protection du polymère par les antioxydants, attaque chimique du polymère et des antioxydants par le désinfectant) a permis d'élaborer un schéma mécanistique général de dégradation. Des équations cinétiques ont été dérivées de ce schéma mécanistique pour prédire l'évolution des modifications chimiques, en considérant une répartition hétérogène des antioxydants dans la matrice PA66 et en prenant en compte la plupart des conditions d'exposition (température de l'eau, concentration en réactifs chimiques, temps). Ensuite, le matériau vieilli a été testé en conditions d'usage grâce à des essais de pression hydrostatique pour identifier son régime de rupture. / Nowadays, chlorine dioxide is an alternative of chlorine for the disinfection of drinking water. Although its biocide ability is well known, scientific literature lacks of knowledge about its effects on organic materials in domestic water networks. The use of PA 66 for valves is quite recent: its long term behaviour is thus unknown. The aim of this study was to improve the knowledge of the interaction mechanisms between chlorine dioxide and a PA 66 matrix stabilized by blend of two antioxidants and reinforced by glass fibres, but also to propose a multi-scale method for the lifetime prediction of this composite material in service. First of all, a better description of the chemical reactions occurring within the material (oxidation, hydrolysis, polymer protection by antioxidants, chemical attack of polymer and antioxidants by disinfectant) has allowed elaborating a general degradation mechanistic scheme. Kinetic equations were derived from this mechanistic scheme for predicting the chemical changes, considering a heterogeneous distribution of antioxidants within the PA 66 matrix and taking into account most exposure conditions (water temperature, concentration in chemical reactants, time). Then, the aged material was tested in use conditions thanks to hydrostatic pressure experiments in order to identify its failure regime.

Polycyclic Aromatic Hydrocarbons (PAHs) are harmful by-products formed during combustion of hydrocarbons under locally fuel-rich conditions followed by incomplete combustion. PAHs act as precursors during the formation of soot. PAHs and soot are harmful for human health and legislation limits the emission of unburned hydrocarbons and soot. Consequently, other measures are necessary in order to limit the production of PAHs and soot in internal combustion engines applications, entailing a possible decrease of fuel efficiency and higher technical requirements for automotive manufactures. The combustion chemistry of PAHs is not fully understood, which prompts the need of further investigations. The chemical dynamics shown by novel pathways of PAH formation involving vinylacetylene addition to the phenyl radical opens up new horizons for the potential contribution to PAH formation through this class of reactions. In the present work novel pathways of the formation of naphthalene and phenanthrene are investigated for a laminar premixed benzene flame and a laminar ethylene diffusion flame. The purpose is to improve the prediction of the aromatic species concentration in the flames. A pathway chosen due the high potential aromatic yield is assessed through preliminary flame calculations relying on simplifying assumptions concerning reaction rates. Certain isomerisation steps of the pathway occur within a time-scale characteristic of thermal relaxation processes. Therefore, the solution of the energy grained master equation is necessary in order to calculate the phenomenological reaction rates resulting from a non-equilibrium kinetic modeling. Quantum chemical calculations are performed in order to calculate molecular properties of the species involved. These properties are subsequently processed to determine the rate constants of the sequence of multi-energy well reactions. Moreover, the chemical dynamics of the pathway is analyzed and the effect of temperature and pressure on the kinetic parameters is investigated. Despite of the potential yield demonstrated through the preliminary flame calculations, the computed rate constants show that the studied reactions are insignificant for the formation of naphthalene and phenanthrene in the studied flames. An effort is put on evaluating if the non-equilibrium kinetic modeling adopted for the calculation of the kinetic parameters is consistent with the kinetic modeling used in the flame calculations. The current work provides an efficient method to compute rate constants of multi-energy well reactions at different thermodynamic conditions, characteristic of flames and of combustion in commercial devices or in internal combustion engines. Pathways with a slightly different chemical dynamics should be tested applying the current methodology. Moreover, further studies should be aimed at overcoming possible limits of the kinetic modeling of multi-energy well reactions occurring in combustion environments.

De nos jours, en raison de l'épuisement des combustibles fossiles et des préoccupations environnementales, la transformation de la biomasse lignocellulosique devient un gros challenge pour fournir des biocarburants et des bioproduits dans un futur proche. La lignine, qui représente près de 30 %pds de la biomasse lignocellulosique, est la bioressource la plus pertinente et la plus abondante pour produire des composés aromatiques grâce à sa structure polymérique composée d’unités phénylpropane avec des liaisons éthers. Dans ce contexte, l’utilisation de la lignine en tant que précurseur de composés aromatiques suscite beaucoup d’attention de par son faible coût et sa haute disponibilité puisque co-produit dans l’industrie papetière ou les bio-raffineries. Dans la littérature, il apparaît que l'hydroconversion catalytique de la lignine constitue une méthode thermochimique intéressante pour obtenir des rendements élevés en produits liquides. Le but de ce travail était d'étudier les processus réactionnels lors de ce procédé et de développer un modèle cinétique pour l'hydroconversion catalytique de la lignine sur un catalyseur sulfure (CoMoS/Al2O3). Dans la première partie de ce travail, des mesures cinétiques ont été effectuées dans un solvant donneur d’hydrogène (tétraline) à 350 °C et 80 bar en utilisant un réacteur semi-continu, ouvert en phase gazeuse avec l’alimentation continue en H2 et équipé d’un condenseur à reflux et de pièges refroidis. Les produits récupérés ont été isolés en quatre fractions : gaz (méthane, dioxyde de carbone, hydrocarbures légers, etc.), liquide organique (phénols, aromatiques, naphtènes, etc.), résidus solubles dans le THF et insolubles dans le THF. Grâce à plusieurs outils analytiques appropriés (GPC, RMN, GCXGC, etc.), l'évolution et la composition de ces différentes fractions en fonction du temps de réaction ont été étudiés afin de comprendre les transformations lors de la conversion. Un schéma réactionnel (approche regroupée) a été établi sur la base de ces observations. La deuxième partie de ce travail a été consacrée au développement d'un modèle cinétique paramétré permettant de décrire mathématiquement chaque étape de réaction au cours de l'hydroconversion de la lignine. Premièrement, les phénomènes physiques impliqués (comportement hydrodynamique des gaz dans notre installation, équilibre vapeur-liquide des mélanges et transfert de masse liquide gaz) ont été caractérisés. Par la suite, un modèle complet de réacteur a été construit en couplant la cinétique chimique appropriée et les caractérisations physiques. En prenant les données expérimentales recueillies comme base, des paramètres cinétiques fiables (constantes de vitesse et coefficients stoechiométriques) pour chaque étape de réaction ont été obtenus au moyen d'une technique de régression non linéaire. Le modèle résultant nous permet d'avoir une compréhension approfondie du processus de conversion de la lignine / Nowadays, due to the fossil fuels depletion and environmental concerns, transformation of lignocellulosic biomass is becoming a great challenge in order to provide biofuels and biochemicals in a near future. Lignin, which accounts for nearly 30 wt% of lignocellulosic biomass, is the most relevant and abundant bio-resource to produce aromatic compounds because of its original polymeric structure composed by phenylpropane units with ether linkages. In this context, the use of lignin as a precursor of aromatic compounds attracts lots of attention thanks to its low cost and high availability in pulp industry or bio-refinery. In the literature, it appears that an interesting thermochemical method for obtaining high yields of liquid products was the catalytic hydroconversion of lignin. The aim of this work was to investigate the reaction scheme of the catalytic process and develop a kinetic model for catalytic lignin hydroconversion over a sulfided CoMoS/Al2O3. In the first part of this work, kinetic measurements were carried out in a H-donor solvent (tetralin) at 350 °C and 80 bar using a semi-continuous batch reactor, which is opened for gas phase with continuous supply of H2 and equipped with a condensing reflux followed by cooled traps. The recovered products were isolated in four fractions: gases (methane, carbon dioxide, light hydrocarbons, etc.), organic liquid (phenols, aromatics, naphthenes, etc.), THF-soluble and THF-insoluble residues. Thanks to several appropriate analytical tools (GPC, NMR, GCXGC, etc.), the evolution of these different fractions as a function of reaction time was followed in order to understand the transformations occurring during the conversion. Accordingly, a lumped reaction network was established based on the observed reaction schemes. The second part of this work was dedicated to the development of a parameterized kinetic model allowing to have a mathematical description for each reaction step involved in the lignin hydroconversion. Firstly, physical phenomena involved (the gas hydrodynamic behavior of our set-up, the vapor-liquid equilibrium of mixtures and the liquid-gas mass transfer) were characterized. Subsequently, a complete reactor model was constructed by coupling the suitable chemical kinetics and these physical characterizations. Taking the gathered experimental data as a basis, reliable kinetic parameters (rate constants and stoichiometric coefficients) for each reaction step were obtained by means of non-linear regression technique. The resulting model allows us to have an in-depth understanding of the lignin conversion process

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Yes / Cocrystals consist of two molecules bonded together in a single crystal lattice giving rise to wide applications including improving solubility of poorly soluble pharmaceuticals. Cocrystallization reaction occurs in the oily phase of liquid–liquid phase separation (LLPS) after it is mixed with coformers. Indomethacin–saccharin cocrystal formation was monitored in situ, and the kinetics of crystallization were determined. The crystallization rates show that the process can be proposed to prevent unwanted oily phase formation during LLPS. / Research Development Fund Publication Prize Award winner, Sep 2022.