Les milieux biologiques et alimentaires sont généralement des mélanges contenant un nombre élevé de constituants (eau, solvants organiques, solides dissous, gaz dissous, espèces ioniques, macromolécules). La prédiction des propriétés d’équilibre de tels milieux requiert l’utilisation d’un modèle thermodynamique entièrement prédictif. Ce modèle doit également permettre d’assurer la cohérence entre des données expérimentales et garantir la robustesse de la représentation simultanée des équilibres physiques (liquide-vapeur, solubilité, etc.) et chimiques (dissociation, oxydo-réduction, complexation, etc.). Le potentiel chimique est une donnée indispensable pour modéliser ces équilibres. Sa connaissance dépend de la prédiction de deux variables : l’enthalpie libre de formation dans un état de référence choisi, et le coefficient d’activité qui dépend aussi de l’état de référence choisi. Le modèle COSMO-RS est un excellent modèle de prédiction des coefficients d’activité très largement utilisé dans le domaine du génie chimique où on s’intéresse essentiellement à des molécules neutres. Ce travail de thèse a permis d’étendre les performances du modèle COSMO-RS au traitement des milieux biologiques et alimentaires dans lesquels on trouve systématiquement des électrolytes en solution (en plus des molécules neutres). Un nouvel outil utilisant les récentes avancées de la mécanique quantique a été développé pour prédire les propriétés de formation à l’état gaz. En combinant des concepts de la thermodynamique, de la mécanique quantique, de l’électrostatique, et de la physique statistique, il a été démontré qu’il est possible d’utiliser le modèle COSMO-RS pour faire la transition entre l’état gaz et la phase condensée. Partant de là, ce travail démontre qu’il est maintenant possible de traiter simultanément les équilibres physiques et chimiques et donc de prédire les propriétés physico-chimiques (aW, pH, Eh) dans les milieux biologiques et alimentaires par le modèle COSMO-RS. / Food and biological systems are generally multicomponent mixtures (including water, organic solvents, dissolved solids, dissolved gases, ionic species, macromolecules). The prediction of the equilibrium properties of such environments requires the use of a fully predictive thermodynamic model. This model must be able to ensure the consistency between experimental data and to ensure the robustness of the simultaneous representation of physical equilibria (liquid-vapour, solubility, etc.) and chemical equilibria (dissociation, redox, complexation, etc.). The chemical potential is an essential property for modelling such equilibria. Its determination depends on two variables: the Gibbs free energy of formation in a chosen reference state, and the prediction of the activity coefficient which also depends on the chosen reference state. The COSMO-RS model is an excellent model for predicting activity coefficients that is widely used in chemical engineering where the studied molecules are generally neutral. This PhD study enabled to extend the performance of the COSMO-RS model toward the treatment of food and biological systems where there are systematically electrolytes in solution (in addition to neutral molecules). A new tool based on the recent advances of quantum mechanics has been developed in order to predict gas phase formation properties. By combining concepts of thermodynamics, quantum physics, electrostatics and statistical physics, it has been demonstrated that it is possible to use the COSMO-RS model to ensure the transition between the gas phase and the condensed phase. In this context, this work demonstrates that it is possible to treat simultaneously physical and chemical equilibria and thus to predict physico-chemical properties (aW, pH, Eh) in food and biological systems using the COSMO-RS model.

Considerado a alternativa mais pesquisada para substituir o diesel, o biodiesel, oriundo da transesterificação, é cotado como a mais promissora opção de combustível obtido de fontes renováveis para o lugar dos ameaçados combustíveis de origem fóssil. A reação de transesterificação para produção do biodiesel pode ocorrer de forma catalítica, a mais utilizada atualmente, e não-catalítica, por meio de fluidos supercríticos. A grande diversidade de matérias-primas que pode ser usada na obtenção do biodiesel supercrítico é apenas um dos atrativos para sua produção, porém uma produção em larga escala esbarraria nos altos custos operacionais do processo. Devido ao potencial revelado nos processos supercríticos, o estudo do comportamento de fases dentro de um reator se mostra relevante ao domínio do processo, visto que pesquisas indicam que é possível balancear os custos de uma produção de biodiesel em condições supercríticas com os custos de uma produção de biodiesel com uso de catalisadores. Na termodinâmica, a modelagem é um método prático e rápido de se estimar o comportamento do equilíbrio líquido-vapor (ELV) do sistema e reduzir gastos com excessivos experimentos, através de um modelo termodinâmico apropriado. Para isso, os modelos testados foram obtidos pela equação de estado (EdE) de Peng-Robinson com as regras de misturas de van der Waals com um (vdW1) e dois (vdW2) parâmetros de interação binária em sistemas formados por componentes presentes na produção do biodiesel. Utilizando a abordagem phi-phi e o método de BOLHA P, sistemas binários em condições próximas ao ponto crítico e em condições supercríticas, encontrados na literatura, foram modelados. A modelagem termodinâmica foi realizada após a aplicação de um teste de consistência termodinâmica, uma vez que foram encontradas diferenças nas propriedades críticas de um mesmo composto em diferentes referências. A adequação dos modelos termodinâmicos variou de acordo com as condições do processo, o que fará necessária uma análise específica da situação de acordo com o caso em que estiver sendo empregada. Na simulação termodinâmica, as redes neurais artificiais foram utilizadas para o ajuste computacional dos dados experimentais, produzindo os melhores resultados com a introdução dos descritores moleculares, junto às variáveis independentes do processo (temperatura e composição na fase líquida), na primeira camada de neurônios nas diversas configurações analisadas dentre as arquiteturas utilizadas, demonstrando ser uma ferramenta interessante para o estudo do equilíbrio de fases. / Considered the most researched alternative to replace the diesel fuel, the biodiesel, from transesterification, is rated as the most promising fuel option from renewable sources for the place of threatened fossil fuels. The transesterification reaction for biodiesel production can occur catalytically, commonly used, and non-catalytic, through supercritical fluids. The diversity of raw materials that can be used to obtain supercritical biodiesel is only one of the attractions for its production, but a large-scale production would encounter obstacles in the high operating costs of the process. Due to the potential revealed in the supercritical processes, the study of phase behavior in a reactor is relevant for domaining the process, since researches indicates that it is possible to balance the costs of producing biodiesel in supercritical conditions with the costs of a production of biodiesel using catalysts. In thermodynamics, modeling is a quick and practical method of estimating the vapor-liquid equilibria (VLE) behavior of the system and reducing expenses with excessive experiments, using an appropriated thermodynamic model. For this, the models tested were obtained by the Peng-Robinson equation of state (EoS) with the mixture rules of van der Waals with one (vdW1) and two (vdW2) binary interaction parameters in systems formed by components present in the production of biodiesel. Using the phi-phi approach and the BOL P method, binary systems in conditions near to the critical point and under supercritical conditions, found in the literature, were modeled. The thermodynamic modeling was performed after the application of a thermodynamic consistency test, since differences were found in the critical properties of the same compound in different references. The suitability of the thermodynamic models varied according to the process conditions, which will require a specific analysis of the situation according to the case in which it is being used. In the thermodynamic simulation, the artificial neural networks were used for the computational adjustment of the experimental data, producing the best results when the molecular descriptors were used with the independent variables of the process (temperature and composition of the liquid phase) in the first layer of nodes in the different configurations analyzed among the architectures used, proving to be a tool of interest for the study of phase equilibria.

The current thesis presents work on the structure and dynamics of oligosaccharides and polysaccharides as well as the free energetics of carbohydrate-protein interactions. By applying various computational tools such as molecular dynamics simulation, our in-house fast sugar structure prediction software, replica exchange molecular dynamics, homology modeling, umbrella sampling, steered molecular dynamics as well as the thermodynamic integration formalism, we have been able to study the role of water on the surface of homopolysaccharides as well as complex oligosachharides, we have been able to produce a prediction of the bound structure of triantennary oligosaccride on the asialoglycoprotein receptor, we have been able to estimate the free energy of binding of ManΑ1→2Man to the HIV-1 inactivating protein, Cyanovirin-N as well as the relative binding free energies of mutants of Cyanovirin-N to the same ligand.

Adsorption processes are utilized in both medicine and industry. It is important to have an understanding of adsorption processes to better predict the outcomes and discern potential difficulties. The primary objective of this research is to further the understanding of the nature and extent of the adsorption process in solution, which is a function of the chemical composition of the adsorbates, adsorbents, and solvent. This was accomplished by employing experimental studies as well as thermodynamic calculations and molecular dynamic simulations. Four activated carbons were used as the model adsorbents in this study. And, barbital, phenobarbital and primidone were used to elucidate the structural features of the adsorbates that were most responsible for the interaction with activated carbons. A Two-Mechanism Langmuir-Like Equation (TMLLE) was proposed to describe the independent presence of two adsorption mechanisms: non-site-specific adsorption and site-specific adsorption. The analyses of data generated by both previous investigators and current studies, suggest that the TMLLE allows an accurate analysis of the adsorption process. Based on the parameters in the TMLLE, the Modified Crisp Model and the van’t Hoff Model were employed to determine the Gibbs free energy changes for both site-specific adsorption and non-site-specific adsorption. Comparing the Gibbs free energy changes calculated by the Modified Crisp Model and the van’t Hoff Model (site-specific adsorption case), it is concluded that 5 water molecules are displaced by a phenobarbital molecule on the surface of activated carbons. And, for non-site-specific adsorption, it is concluded that 12 water molecules are displaced by a phenobarbital molecule on the nonpolar (hydrocarbon) part of the activated carbon surface. The adsorption of phenobarbital from solution by activated carbons has been simulated by employing Molecular Dynamic (MD) Modeling. The predicted differential Gibbs free energy values for site-specific adsorption at pH 2-9 were consistent with the thermodynamic calculations. And, the present MD simulations provide a good basis for the further understanding and quantitatively assessment of the adsorption driven by hydrophobic bonding. The conclusions reached in the current studies are expected to be applicable to a wide range of similar adsorption processes.

L’auto-assemblage moléculaire au niveau des surfaces est un exemple majeur de l'auto-organisation de la matière avec des applications technologiques d’intérêt. La capacité́ de prédire la structure de la monocouche auto-assemblée (SAM) formée à l'équilibre est d'une importance fondamentale. Dans cette thèse, je présente une théorie aux premiers principes pour l’interprétation de l’auto-assemblage 2D basée sur la modélisation et la thermodynamique statistique. La méthode mise au point permet d'accéder à la stabilité́ thermodynamique de la SAM et à sa dépendance à l'égard de la concentration. Cela permet d'étudier les équilibres concurrentiels au niveau des surfaces et de rationaliser le polymorphisme en 2D. De plus, cette théorie prédit l'existence d'une concentration critique de monomères au-dessus de laquelle l’auto-assemblage 2D est favorisé. Celle-ci est utilisée pour définir une échelle absolue définissant la propension à l’auto-assemblage en 2D. Enfin, quatre applications technologiques sont discutées, exposant les possibilités de la méthode développée. / Molecular self-assembly at surfaces is a prominent example of self-organization of matter with outstanding technological applications. The ability to predict the structure of the self-assembled monolayer (SAM) formed at equilibrium is of great fundamental and technological importance. In this dissertation I present a self-consistent theory for a first-principle interpretation of 2D self-assembly based on modeling and statistical thermodynamics. The developed framework provides access to the thermodynamic stability of the SAM and to its concentration dependence. This allows to study competitive equilibria at surfaces and to rationalize the 2D polymorphism evidenced by scanning probe techniques. The theory predicts the existence of a critical concentration of monomers, which is used to set an absolute scale for the 2D self-assembly propensity. Last, four technological applications are discussed, showing the potentials of the developed framework.

This dissertation study describes the development of novel heteroepitaxial growth of 3C-SiC layers by chemical vapor deposition (CVD). It was hypothesized that chloride addition to the "traditional" propane-silane-hydrogen precursors system will enhance the deposition growth rate and improve the material quality via reduced defect density. Thermodynamic equilibrium calculations were performed to obtain a criterion for which chloride specie to select for experimentation. This included the chlorocarbons, chlorosilanes, and hydrogen chloride (HCl) chloride containing groups. This study revealed no difference in the most dominant species present in the equilibrium composition mixture between the groups considered. Therefore, HCl was the chloride specie selected to test the hypothesis. CVD computerized fluid dynamic simulations were developed to predict the velocity, temperature and concentration profiles along the reactor. These simulations were performed using COMSOL Multiphysics and results are presented. The development of a high-temperature (1300 °C -1390°C) 3C-SiC growth process resulted in deposition rates up to ~38 µm/h. This is the highest value reported in the literature to date for 3C-SiC heteroepitaxy. XRD FWHM values obtained varied from 220 to 1160 arcsec depending of the process growth rate or film thickness. These values are superior or comparable to those reported in the literature. It was concluded from this study that at high deposition temperatures HCl addition to the precursor chemistry had the most significant impact on the epitaxial layer growth rate. Low-temperature (1000-1250°C) 3C-SiC growth experiments evidenced that the highest deposition rate that could be attained was ~2.5 µm/h. The best quality layer achieved in this study had a FWHM of 278 arcsec; which is comparable to values reported in the literature and to films grown at higher deposition temperatures in this study. It was concluded from this work that at lower deposition temperatures the HCl addition was more beneficial for the film quality by enhancing the surface. Surface roughness values for films grown with HCl additive were 10 times lower than for films grown without HCl. Characterization of the epitaxial layers was carried out via Nomarski optical microscopy, FTIR, SEM, AFM, XRD and XPS.

La thèse s’inscrit dans le cadre d’un projet de recherche visant à élaborer une anode permettant le dégagement d’oxygène en milieu de cryolithe fondue à 960°C et dont l’utilisation supprimerait les émissions de dioxyde de carbone du procédé de production d’aluminium Hall-Héroult. Le type d’anode envisagée est un composite Cermet (CERamique – METal), généralement constitué d’une phase métallique à base de nickel, cuivre et fer et d’une ou plusieurs phase(s) oxyde(s) conductrice(s) du type NixFe3-xO4 et Ni1-xFexO. Deux types de cermet, biphasé et triphasé, ont été étudiés dans le cadre de ce projet. L’objectif principal a été de comprendre les mécanismes de dégradation de telles anodes durant les électrolyses. Les cermets ont été testés sous une densité de courant de 0,80 A/cm² pour différentes durées, puis analysés par microscopie optique et microscopie électronique à balayage couplée à une analyse dispersive en énergie. Les premières électrolyses, effectuées dans un électrolyte synthétique, sans aluminium métallique et sous atmosphère argon ont révélé à la fois une dégradation chimique et électrochimique. L’étude de la dégradation chimique a été réalisée grâce à des immersions dans l’électrolyte sans polarisation. Les résultats ont mis en évidence une dissolution de la phase spinelle, liée à un phénomène de substitution entre les ions Al3+ de l’électrolyte et Fe3+ du spinelle, entrainant la formation d’un aluminate du type NixFe3-x-yAlyO4. Lorsque x = 0 et y proche de 2, la phase spinelle est dissoute alors que lorsque x est proche de 1, la phase spinelle est stabilisée et sa dissolution ralentie. Les électrolyses menées jusqu’à la fin de vie des matériaux ont révélé l'attaque préférentielle de la phase métallique pour former des composés fluorés et oxydes. Grâce aux caractérisations micrographiques et aux calculs thermodynamiques (logiciel FactSage 7.1), un mécanisme de dégradation global des anodes a été proposé. La compréhension des mécanismes de dégradation chimique et électrochimique des matériaux a permis de proposer des voies d'amélioration concernant à la fois le matériau d'anode et la chimie du bain cryolithique. / The thesis is a part of a research project which develop an anode permitting the release of oxygen in molten cryolite medium at 960°C, in order to eliminate carbon dioxide emissions from the aluminium production process called Hall-Héroult process. The type of anode envisaged is a Cermet composite (CERamic - METal), generally consisting of a metallic phase based on nickel, copper and iron and one or more conductor oxide phase(s) such as NixFe3-xO4 and Ni1-xFexO type. Two types of cermet, two-phase and three-phase, have been studied in this project. The main objective was to understand the degradation mechanisms of such anodes during electrolysis. The cermets were tested at a current density of 0.80 A/cm² for different durations and analyzed by optical microscopy and scanning electron microscopy coupled with dispersive energy analysis. The first electrolyses, carried out in a synthetic electrolyte, without metallic aluminum and under argon atmosphere revealed both chemical and electrochemical degradations. Study of chemical degradation was carried out thanks to immersions in the electrolyte without polarization. The results showed a dissolution of the spinel phase, linked to a substitution phenomenon between the Al3+ ions from the electrolyte and Fe3+ from spinel, resulting in the formation of a NixFe3-x-yAlyO4 aluminate type. When x = 0 and y close to 2, the spinel phase is dissolved whereas when x is close to 1, the spinel phase is stabilized and its dissolution slowed down. Electrolyses conducted to the end of life of the materials revealed the preferential attack of the metal phase to form fluorinated compounds and oxides. Thanks to micrographic characterizations and thermodynamic calculations (FactSage 7.1 software), a global degradation mechanism of the anodes has been proposed. The understanding of the chemical and electrochemical degradation mechanisms of the materials made it possible to propose ways of improvement concerning both the anode material and the cryolithic bath chemistry.

Solar power tower technology can achieve higher temperatures than the most common commercial technology using parabolic troughs. In order to take advantage of higher temperatures, new power cycles are needed for generating power at higher efficiencies. Supercritical carbon dioxide (S-CO2) power cycle is one of the alternatives that have been proposed for the future concentrated solar power (CSP) plants due to its high efficiency. On the other hand, carbon dioxide can also be a replacement for current heat transfer fluids (HTFs), i.e. oil, molten salt, and steam. The main disadvantages of the current HTFs are maximum operating temperature limit, required freeze protection units, and complex control systems. However, the main challenge about utilizing s-CO2 as the HTF is to design a receiver that can operate at high operating pressure (about 20 MPa) while maintaining excellent thermal performance. The existing tubular and windowed receivers are not suitable for this application; therefore, an innovative design is required to provide appropriate performance as well as mechanical strength. This research investigates the application of s-CO2 in solar power tower plants. First, a computationally efficient method is developed for designing the heliostat field in a solar power tower plant. Then, an innovative numerical approach is introduced to distribute the heat flux uniformly on the receiver surface. Next, different power cycles utilizing s-CO2 as the working fluid are analyzed. It is shown that including an appropriate bottoming cycle can further increase the power cycle efficiency. In the next step, a thermal receiver is designed based on compact heat exchanger (CHE) technology utilizing s-CO2 as the HTF. Finally, a 3MWth cavity receiver is designed using the CHE receivers as individual panels receiving solar flux from the heliostat field. Convective and radiative heat transfer models are employed to calculate bulk fluid and surface temperatures. The receiver efficiency is obtained as 80%, which can be further improved by optimizing the geometry of the cavity.

Cette thèse de doctorat s’inscrit dans le cadre de l’étude in silico des relations qui lient la séquence d’une protéine à sa structure, sa stabilité et sa fonction. Elle a pour objectif de permettre à terme la conception rationnelle de protéines modifiées qui restent actives dans des conditions physico chimiques non physiologiques. Nous nous sommes plus particulièrement penchés sur la stabilité thermique des protéines, qui est définie par leur température de fusion Tm au delà de laquelle leur structure n’est thermodynamiquement plus stable. Notre travail s’articule en trois grandes parties : la recherche de facteurs favorisant la thermostabilité des protéines parmi des familles de protéines homologues, la mise sur pied d’une base de données de protéines de structure et de Tm déterminées expérimentalement, de laquelle sont dérivés des potentiels statistiques dépendant de la température, et enfin la mise au point de deux outils bioinformatiques visant à prédire d’une part la Tm d’une protéine à partir de la Tm de protéines homologues et d’autre part les changements de thermostabilité d’une protéine (Tm) engendrés par l’introduction d’une mutation ponctuelle. La première partie a pour objectif l’identification des facteurs de séquence et de structure (e.g. fréquence de ponts salins, d’interactions cation-{pi}) responsables des différentes stabilités thermiques de protéines homologues au sein de huit familles (chapitre 2). La spécificité de chaque famille ne nous a pas permis de généraliser l’impact de ces différents facteurs sur la stabilité thermique des protéines. Cependant, cette approche nous a permis de constater la multitude de stratégies différentes suivies par les protéines pour atteindre une plus grande thermostabilité. La deuxième partie concerne le développement d’une approche originale pour évaluer l’influence de la température sur la contribution de différents types d’interactions à l’énergie libre de repliement des protéines (chapitres 3 et 4). Cette approche repose sur la dérivation de potentiels statistiques à partir d’ensembles de protéines de thermostabilité moyenne distincte. Nous avons d’une part collecté le plus grand nombre possible de protéines de structure et de Tm déterminées expérimentalement, et d’autre part développé des potentiels tenant compte de l’adaptation des protéines aux températures extrêmes au cours de leur évolution. Cette méthode originale a mis en évidence la dépendance en la température d’interactions protéiques tels les ponts salins, les interactions cation-{pi}, certains empilements hydrophobes ... Elle nous a en outre permis de mettre le doigt sur l’importance de considérer la dépendance en la température non seulement des interactions attractives mais également des interactions répulsives, ainsi que sur l’importance de décrire la résistance thermique par la Tm plutôt que la Tenv, température de l’environnement de l’organisme dont elle provient (chapitre 5). La dernière partie de cette thèse concerne l’utilisation des profils énergétiques dans un but prédictif. Tout d’abord, nous avons développé un logiciel bioinformatique pour prédire la thermostabilité d’une protéine sur la base de la thermostabilité de protéines homologues. Cet outil s’est avéré prometteur après l’avoir testé sur huit familles de protéines homologues. Nous avons également développé un deuxième outil bioinformatique pour prédire les changements de thermostabilité d’une protéine engendrés par l’introduction d’une mutation ponctuelle, en s’inspirant d’un logiciel de prédiction des changements de stabilité thermodynamique des protéines développé au sein de notre équipe de recherche. Ce deuxième algorithme de prédiction repose sur le développement d’une grande base de données de mutants caractérisés expérimentalement, d’une combinaison linéaire de potentiels pour évaluer la Tm, et d’un réseau de neurones pour identifier les coefficients de la combinaison. Les prédictions générées par notre logiciel ont été comparées à celles obtenues via la corrélation qui existe entre stabilités thermique et thermodynamique, et se sont avérées plus fiables. Les travaux décrits dans notre thèse, et en particulier le développement de potentiels statistiques dépendant de la température, constituent une nouvelle approche très prometteuse pour comprendre et prédire la thermostabilité des protéines. En outre, nos travaux de recherche ont permis de développer une méthodologie qui pourra être adaptée à l’étude et à la prédiction d’autres propriétés physico chimiques des protéines comme leur solubilité, leur stabilité vis à vis de l’acidité, de la pression, de la salinité ... lorsque suffisamment de données expérimentales seront disponibles.

With the increased interest in bainitic steels, fundamental understanding of the bainite transformationis of major importance. Unfortunately, the research on bainite has been hampered by an oldcontroversy on its formation mechanism. Over the years two quite different theories have developedclaiming to describe the bainite transformation i.e. the diffusionless and the diffusion controlledtheory. In this thesis, attention is directed towards fundamental understanding of the bainitetransformation and both experimental and theoretical approaches are used in order to reveal its truenatureIn the first part of this thesis the symmetry in the Fe-C phase diagram is studied. It is based on ametallographic mapping of microstructures using light optical microscopy and scanning electronmicroscopy in a high carbon steel. The mapping revealed symmetries both with respect to temperatureand carbon content and an acicular eutectoid with cementite as the leading phase was found andidentified as inverse bainite. By accepting that all the eutectoid microstructures forms by diffusion ofcarbon, one may explain the existence of symmetries in the Fe-C phase diagram. Additional supportof its existence is obtained from an observation of symmetries in an alloyed steel. From the performedwork it was concluded that the existence of symmetries among the eutectoid microstructures fromaustenite supports the idea that bainite forms by a diffusion controlled transformation.In the second part the growth of bainite is considered. An experimental study using laser scanningconfocal microscopy was performed and growth rates of the transformation products from austenite ina high carbon, high chromium steel was analysed. The growth rate measurements reveals the kineticrelation between Widmanstätten cementite and the acicular eutectoid previously identified as inversebainite which confirms its existence and the conclusions drawn in the first part. In addition, in-situobservations of bainite formation below Ms provide additional support for the diffusion controlledtheory for bainite formation.The final part of the work is a study of the critical conditions for the formation of acicular ferrite.Based on experimental information found in the literature a thermodynamic analysis is performed inview of the two theories. The results demonstrate that the governing process for Fe-C alloys cannot bediffusionless but both kinds of processes can formally be used for predicting Bs temperatures for Fe-Calloys. / <p>QC 20130503</p>