[pt] O presente trabalho visa dois objetivos. 0 primeiro, didático, é de apresentar algumas versões da Termodinâmica dos Meios Contínuos, elucidando suas semelhanças e diferenças várias formas da segunda lei são apresentadas, questionando-se em alguns casos as suas supostas generalidades. O segundo objetivo, de pesquisa, desenvolve na versão de Serrin os conceitos de Estabilidade Termodinâmica e Exergia, aplicando-os no estudo dos ciclos de Carnot e de Rankine. Através do conceito de função de acumulação introduz-se uma nova maneira de se determinar a eficiência dos referidos ciclos. Ainda na versão de Serrin, aplica-se a teoria de processos de transição no estudo do efeito Joule-Thomson. Os fluidos de trabalho são um gás ideal, caracterizado pela convexidade do seu espaço de estados, e um fluido de Van der Halls, que não possui a mesma característica. Finalmente, no contexto da Termodinâmica de Processos Irreversíveis é feita uma comparação entre as soluções de problemas de condução de calor em meios rígidos e elásticos lineares isotrópicos. / [en] The present work has two purposes. The first one is didactic. It intend to present many versions of the Continuun Thermodynamics discussing their resemblances and diferences. Many forms of the second law are presented and in some cases their supposed generalities are questioned. The second purpose lies on the basic research. It is carried out applying the Serrin s version the concepts of Thermodynamic Stability and Availability in the studied of the Carnot s and Rankine s cycles. By meaning of the accumulation function concept a newform to determine the efficience of the above cycles is introduced. On the other hand in the Serrin s version the theory of transition processes can be applied in the study of the Joule-Thomson effect. The working fluids are an ideal gas which is characterized by the convexity of it s state space and the Van der Waals fluid which is not provided of such characteristic. Finally in the context of the Irreversible Thermodynamics is made a comparison between the solutions of heat conduction problems in rigid and linear isotropic elastic continuum.

La thermodynamique a été développée au XIXe siècle pour décrire la physique des moteurs et autres machines thermiques macroscopiques. Depuis lors, le progrès des nanotechnologies a rendu nécessaire d'étendre ces lois, initialement pensées pour des systèmes classiques, aux systèmes obéissant à la mécanique quantique. Durant cette thèse, j'ai mis en place un formalisme pour étudier la thermodynamique stochastique des systèmes quantiques, dans lequel la mesure quantique occupe une place centrale: à l'instar du bain thermique de la thermodynamique statistique classique, la mesure est ici la source première d'aléatoire dans la dynamique. Dans un premier temps, j'ai étudié la mesure projective comme une transformation thermodynamique à part entière. J'ai montré que la mesure cause un changement incontrôlé de l'énergie du système quantique étudié, que j'ai appelé chaleur quantique, ainsi qu'une production d'entropie. Comme application de ces concepts, j'ai proposé un moteur qui extrait du travail à partir des fluctuations quantiques induites par la mesure. Ensuite, j'ai étudié les mesures généralisées, ce qui a permis de décrire des systèmes quantiques ouverts. J'ai défini les notions de travail, de chaleur, et de production d'entropie pour une réalisation unique d'une transformation thermodynamique, et retrouvé que ces quantités obéissent à des théorèmes de fluctuation. Ce formalisme m'a permis d'analyser le comportement thermodynamique de la situation canonique de l'optique quantique : un atome à deux niveaux en couplé à un laser et au vide électromagnétique. Enfin, j'ai étudié une plate-forme prometteuse pour tester la thermodynamique d'un Qubit : un système hybride optomécanique.Le formalisme développé dans cette thèse peut être d'un grand intérêt pour la communauté de thermodynamique quantique car il permet de caractériser les performances des machines thermiques quantiques et de les comparer à leurs analogues classiques. En outre, en caractérisant la mesure quantique comme un processus thermodynamique, il ouvre la voie à de nouveaux types de machines thermiques, exploitant d'une manière inédite les spécificités du monde quantique. / Thermodynamics was developed in the XIXth century to provide a physical description to engines and other macroscopic thermal machines. Since then, progress in nanotechnologies urged to extend these formalism, initially designed for classical systems, to the quantum world. During this thesis, I have built a formalism to study the stochastic thermodynamics of quantum systems, in which quantum measurement plays a central role : like the thermal reservoir of standard stochastic thermodynamics, it is the primary source of randomness in the system's dynamics. I first studied projective measurement as a thermodynamic process. I evidenced that measurement is responsible for an uncontroled variation of the system's energy that I called quantum heat, and also a production of entropy. As a proof of concept, I proposed an engine extracting work from the measurement-induced quantum fluctuations. Then, I extended this formalism to generalized measurements, which allowed to describe open quantum systems (i.e. in contact with reservoirs). I defined work, heat and entropy production for single realizations of thermodynamic protocols, and retrieved that these quantities obey fluctuation theorems. I applied this formalism to the canonical situation of quantum optics, i.e. a Qubit coupled to a laser and a the vacuum. Finally, I studied a promising platform to test Qubit's thermodynamics: a hybrid optomechanical system.The formalism developed in this thesis could be of interest for the quantum thermodynamics community as it enables to characterize quantum heat engines and compare their performances to their classical analogs. Furthermore, as it sets quantum measurement as a thermodynamic process, it pave the ways to a new kind of thermodynamic machines, exploiting the specificities of quantum realm in an unprecedented way.

La mécanique statistique des systèmes auto-gravitants constitue un des plus fascinants et mystérieux champs de recherche. À cause de la nature à longue-portée de la force gravitationnelle, la notion usuelle d'équilibre statistique est modifiée, faisant de cette étude un problème hors-équilibre. Par conséquent, ces systèmes exhibent certaines propriétés particulières comme, par exemple, l'existence de transitions de phase associées à un effondrement gravitationnel. Le travail présenté dans cette thèse a comme but une description détaillée des transitions de phase dans un cadre général relativiste en considérant, en particulier, le cas des fermions auto-gravitants. La thèse est conceptuellement divisée en trois parties, selon le niveau de dégénérescence du système. D'abord, nous focalisons notre attention sur le cas des fermions dégénérés (T = 0), en étudiant en détail l'équilibre gravitationnel. Ensuite, en considérant la limite de haute température (T >> 1), nous montrons l'existence de deux types d'effondrement gravitationnel dans les séries d'équilibre. Enfin, nous explorons le cas général, en illustrant la présence des transitions de phase gravitationnelles, soit dans l'ensemble micro-canonique soit dans l'ensemble canonique. / The statistical mechanics of self-gravitating systems constitutes one of the most fascinating and puzzling fields of research. Due to the long-range nature of the gravitational force, the usual notion of statistical equilibrium is modified, making of this study an out-of-equilibrium problem. As a consequence, these systems exhibit some peculiar features such as the occurrence of phase transitions associated with a gravitational collapse. The work presented in this thesis aims at providing a detailed description of the phase transitions in a general relativistic framework by considering, in particular, the case of self-gravitating fermions. The thesis is conceptually divided in three parts, according to the degeneracy level of the system. We firstly focus our attention on the case of degenerate fermions (T = 0), by studying in detail the gravitational equilibrium. Successively, considering the high temperature limit (T >> 1), we show the existence of two kinds of gravitational collapse in the series of equilibria. Finally, we explore the general case, by illustrating the occurrence of the gravitational phase transitions, in both microcanonical and canonical ensembles.

This thesis is devoted to the theoretical study of slow thermodynamic processes in non-equilibrium stochastic systems. Its main result is a physically and mathematically consistent construction of relevant thermodynamic quantities in the quasistatic limit for a large class of non-equilibrium models. As an application of general methods a natural non-equilibrium generalization of heat capacity is introduced and its properties are analyzed in detail, including an anomalous far-from-equilibrium behavior. The developed methods are further applied to the related problem of time-scale separation where they enable to describe the effective dynamics of both slow and fast degrees of freedom in a more precise way. Powered by TCPDF (www.tcpdf.org)

Decades have passed since the realisation that a protein’s amino acid sequence can contain all the information required to form a complex three-dimensional fold. Until recently, these encoded structures were thought to be crucial determinants of protein function. Much effort was directed to fully understand the mechanisms behind how and why proteins fold, with natively unfolded proteins thought to be experimental artefacts. Today, the field of natively unfolded – or so-called intrinsically disordered – proteins, is rapidly developing. Protein disorder content has been positively correlated with organismal complexity, with over thirty percent of eukaryotic proteins predicted to contain disordered regions. However, the biophysical consequences of disorder are yet to be fully determined. With the aim of addressing some of the outstanding questions, the work described in this thesis focuses on the relevance of structure within disordered proteins. Whilst populating a variety of conformations in isolation, a subset of disordered proteins can fold upon binding to a partner macromolecule. This folded state may be present within the ensemble of conformations sampled by the unbound protein, opening the question of what comes first: folding or binding? Protein engineering techniques were employed to alter the level of residual ‘bound-like’ structure within the free conformational ensemble, and the consequences on coupled folding and binding reactions were investigated. Resultant changes in the rate of association are easily imaginable; yet, this work demonstrates that the majority of the observed changes in binding affinity were due to alterations in the rate of dissociation, thus altering the lifetime of the bound complex. Promiscuous binding is a touted advantage of being disordered. If many disordered proteins, each with their own conformational ensemble, can bind and fold to the same partner, then where is the folding component encoded? Does the partner protein template the folding reaction? Or, is the folding information contained within the disordered protein sequence? Utilising phi-value analysis on the BCL-2 family of proteins, residues in the disordered sequence were probed to ascertain which form contacts at the transition state of the reaction. Comparison with phi-value analyses of alternative pairs – sharing either the ordered or disordered protein – provides insight into the encoding of these interactions. In the context of a bimolecular reaction, the amino acid sequence of the disordered protein was shown to determine the interactions within the transition state. Thus, analogous to the discovery from decades’ past, it is the sequence of the protein that folds which encodes its pathway, even when binding is a prerequisite.

We explore the direct and inverse problem of thermodynamics in the context of rule-based modelling. The direct problem can be concisely stated as obtaining a set of rewriting rules and their rates from the description of the energy landscape such that their asymptotic behaviour when t → ∞ coincide. To tackle this problem, we describe an energy function as a finite set of connected patterns P and an energy cost function e which associates real values to each of these energy patterns. We use a finite set of reversible graph rewriting rules G to define the qualitative dynamics by showing which transformations are possible. Given G and P, we construct a finite set of rules Gp which i) has the same qualitative transition system as G and ii) when equipped with rates according to e, defines a continuous-time Markov chain that has detailed balance with respect to the invariant probability distribution determined by the energy function. The construction relies on a technique for rule refinement described in earlier work and allows us to represent thermodynamically consistent models of biochemical interaction networks in a concise manner. The inverse problem, on the other hand, is to i) check whether a rule-based model has an energy function that describes its asymptotic behaviour and if so ii) obtain the energy function from the graph rewriting rules and their rates. Although this problem is known to be undecidable in the general case, we find two suitable subsets of Kappa, our rule-based modelling framework of choice, were this question can be answer positively and the form of their energy functions described analytically.

Actuellement le prix de l'énergie augmente continuellement. Ainsi, un des grands défis de la société est de limiter au maximum la consommation énergétique. La mise en oeuvre de matériaux pour l’énergie et le développement de leurs propriétés est au coeur de cette problématique.Dans cette optique, ce travail est dédié à l’évaluation d’un nouveau procédé de fabrication thermomagnétique dans le but de développer de nouvelles microstructures et/ou des propriétés améliorées inaccessibles par des traitements thermomécaniques classiques. L’objectif principal est d'étudier l'effet du champ magnétique sur deux principaux alliages, Fe-Co et Fe-Ni en vue d'améliorer leurs propriétés magnétiques douces.Dans les alliages Fe-Co, les températures de transformation de la ferrite vers l’austénite, mesurées jusqu’à16T, sont augmentées par l'application d'un champ magnétique intense. Ce décalage est modélisé en fonction du champ, en se basant sur une analyse thermodynamique. Dans les deux alliages, la phase ferritique eststabilisée par le champ intense à plus haute température ce qui permet le développement d’une microstructure àgros grains. Les propriétés magnétiques douces sont également améliorées par l'application d'un champ magnétique à la fois dans l’alliage Fe-Co27% et dans Fe-Co49%V2% en induisant respectivement le développement d’une texture Goss dans le premier alliage et une forte anisotropie induite dans le second.Dans les alliages Fe - Ni contenant 80% l'utilisation d’un champ magnétique intense pendant le traitement thermique (jusqu'à 7 T) permet d’améliorer le développement de l'anisotropie induite, permettant de« coucher » la forme du cycle d'hystérésis. Le comportement magnétique dynamique du matériau est ainsiamélioré par le champ magnétique.Ces résultats significatifs soutiennent l'idée que l'introduction du champ magnétique dans les techniques defabrication des matériaux conventionnels est une piste prometteuse pour améliorer d’avantage leurs propriétésfonctionnelles. / Energy is becoming increasingly expensive and a major challenge for the society is to minimize energyconsumption. One of the issues of this challenge focuses on the industrial processing of energy related materialand the development of their properties.The overall objective of this work is to evaluate thermo-magnetic processing as a new technology with thegoal of developing novel microstructures and/or improved properties unattainable through conventionalthermo-mechanical processing. This main target is addressed with the study of the effect of magnetic field ontwo main alloys, Fe-Co and Fe-Ni in view of improving their functional soft magnetic properties.In FeCo alloys the non – equilibrium ferrite to austenite phase transformation measured up to 16T is foundto be increased by the application of a high magnetic field. Its evolution with the field intensity is explainedusing a thermodynamic analysis. In both grades, the ferrite phase is found to be stabilized at higher temperaturetogether with a coarse grains microstructure during recrystallization and growth in high field. Soft magneticproperties are also improved by the application of a magnetic field both in the Fe-Co27% and Fe-Co49%-V2%alloys by a field induced Goss texture enhancement and an extended field induced anisotropy respectively.In the Fe – 80%Ni composition the use of high magnetic field during processing (up to 7T) is found toimprove the magnetic induced anisotropy and to tailor the hysteresis loop shape. The dynamic magneticbehavior is greatly improved by high field annealing.These significant results support the idea that introducing the magnetic field application into conventionalmaterials processing is a promising way to improve material properties.

Le bois est un matériau nanocomposite complexe, fortement anisotrope et hiérarchiquement organisé. La micro-structure à l'échelle nanométrique est caractérisée par des nanofibres rigides de cellulose cristalline parallèles les unes aux autres et noyées dans un matrice plus molle et moins anisotrope. Cette matrice est composée par hémicelluloses et lignine, avec une absorption contrôlée par l'entropie et les liaisons hydrogène entre hémicelluloses, lignine, et la surface de micro-cristaux de cellulose. La matrice est hygroscopique et se gonfle avec les changements de l'humidité relative, en fournissant une source de stress interne, tandis que les fibrilles de cellulose s'enroulent en spirale autour de la lumière centrale à un angle précis, qui est appellé AMF, angle des micro-fibrilles. Les micro-fibrilles se réorganisent passivement selon les contraintes osmotique appliquées. Selon l'AMF, le positionnement et les propriétés mécaniques des fibres de bois varient considérablement: le matériau rigide se rétrécit ou il s'allonge dans le sens de la longueur lors du gonflement, en générant de cette façon une grande déformation anisotrope.Une première forme d'équation d'état comprenant entropie et termes chimiques, colloïdaux (comme la force d'hydratation) et termes mécaniques macroscopiques a été établie et permet de prédire sans paramètres l'absorption d'eau en fonction de l'humidité relative du composite de bois pas traité.Le but de la thèse est d'étendre cette équation d'état au bois traité par absorption d'électrolytes en conditions hydrotermales, en intégrant l'équation avec des termes chimiques lié à la présence d'électrolytes. Les résultats du modèle sont comparés avec les données expérimentales de sorption d'électrolytes formulés en fonction de la balance entre chaotropes et cosmotropes de l'échelle de Hofmeister. Les données expérimentales sont produit à partir des isothermes de sorption et des mécanismes moteurs pour tester la prédiction de la théorie en explorant l'effet du soluté (introduit dans le bois par mise en équilibre avec une solution utilisée comme une réservoir osmotique) sur la structure et les dimensions du matériau. / The so-called “wood material” is a complex, highly anisotropic and hierarchically organized nanocomposite. At the nanometric scale, it is characterised by stiff crystalline cellulose nanofibres parallel to each others embedded in a matrix of a much softer, less anisotropic, gel of hemicelluloses, lignin and water. This matrix is hygroscopic and the solvent uptake is controlled by molecular forces like entropy, H-bonding of polysaccharides to cellulose nano-crystals and hydration force. The swelling provides a source of internal stress for the cellulose fibrils that, winding with a spiral angle (the microfibril angle, MFA) around the central lumen, passively reorient following the osmotic stress applied to them. Depending on the MFA, wood fibres exhibit a wide range of behaviors and mechanical properties, being able to act as stiff material to bear load, or shrink or expand in the longitudinal direction upon swelling, generating in this way either large tensile or compressive stresses or large strains.For the first time, the equation of state including entropic, chemical, colloidal terms (as the hydration force) as well as the mechanical, macroscopic, term has been established and allows to predict with a parameterless analytical expression, the water absorption of untreated softwoods as a function of relative humidity changes.The aim of the thesis is to extend this first equation of state to describe wood treatments by electrolytes adsorption in hydrothermal conditions. The experimental part is performed using specific sorption devices as well as X-Ray scattering techniques. The theoretical part is developed extending the established master equation linking molecular level chemical forces, colloidal interactions and mechanics. The results of the model are tested against experimental data of electrolytes adsorption and compared with their chaotropic/cosmotropic character according to the Hofmeister series.Nowadays, several wood treatments have been developed to reduce the water uptake by wood, in order to confer higher resistance to moist to low-quality wood materials. The final aim of the project is to test the prediction of the model against these known treatments and to develop a general model to describe the behaviour of the wood under different chemical and physical environments. This way, new treatments can be conceptually designed and pre-existing treatments (as for instance the patented "woodprotect" one) improved.

Les phases MAX forment une famille de carbures et de nitrures nano-lamellaires de formule chimique Mn+1AXn, où M est un métal de transition des premières colonnes, A appartient aux colonnes 13-16 et X est soit C, soit N, ou une combinaison des deux éléments. Ces phases combinent les mérites des céramiques et des métaux, comme une bonne stabilité chimique, l’usinabilité, la résistance aux chocs mécaniques, de bonnes conductivités thermique et électrique, etc. Malgré tout, l’étude de leurs propriétés intrinsèques et de leurs anisotropies a été jusqu’à présent limitée par l’indisponibilité de monocristaux. Cette thèse traite de la réactivité de tels monocristaux de phases MAX. Grâce à la large taille des cristaux produits au LMGP, il a été possible d’évaluer directement l’anisotropie de la réactivité chimique et d’obtenir des données originales. Nous avons montré le rôle prépondérant joué par l’élément A pour initier des transformations chimiques menant parfois à la synthèse de matériaux originaux, et nous nous sommes concentrés sur quatre aspects différents : Tout d’abord, nous avons tenté de synthétiser des MXènes de grande taille, en profitant de la grande taille des cristaux disponibles. Un effort particulier a été porté sur la description de la réactivité chimique de phases MAX plongées dans diverses solutions d’attaque, avec un accent particulier mis sur l’utilisation de HF. En second lieu, nous avons étudié la chloruration de phases MAX : l’objectif initial était de former des MXènes, mais nous avons finalement développé une méthode pour synthétiser des carbures de chrome poreux avec des propriétés intéressantes. Troisièmement, nous avons utilisé des cristaux de grande taille pour évaluer l’anisotropie des propriétés électrochimiques. Une anisotropie significative a été trouvée, soit en mesurant le courant durant la polarisation électrochimique, soit par mesure de spectroscopie d’impédance. Divers mécanismes ont été proposés afin d’expliquer cette anisotropie des propriétés de corrosion. Enfin, nous avons montré que les résultats électrochimiques pouvaient être utilisés pour révéler indirectement la présence de défauts structurels récemment identifiés dans la littérature. De tels défauts, appelés « ripplocations », sont spécifiques aux matériaux nano-lamellaires. / MAX phases are a family of layered ternary carbides and nitrides with chemical formula Mn+1AXn, where M is an early transition element, A is an element of groups 13 to16 and X is either C, N or both. These phases combine the merits of ceramics and metals, such as chemical stability, machinability, shock resistance, good electrical and thermal conductivity, etc. However, the investigation of their intrinsic properties and anisotropies has heretofore been limited by a lack of availability of single crystals. This thesis mainly deals with the chemical reactivity of MAX phase single crystals. Owing to the large size single crystals grown at LMGP, it was possible to directly assess the anisotropy of the chemical reactivity and to obtain original data. We showed that the prominent role played by the A element for initiating chemical transformations could lead to the synthesis of original materials, and we focused on four different aspects. First, we tried to synthesize MXenes from MAX phase single crystals: The purpose was to obtain large-scale MXenes by taking advantage of the large size of the single crystals. Effort was put on describing the chemical reactivity of MAX phases dipped in different etchants, focusing on HF. Secondly, we studied the MAX phase reactivity with chlorination: the initial purpose was to obtain MXenes, but we finally developed a method for synthesizing porous chromium carbides which exhibit several interesting properties. Thirdly, we used large size single crystals in order to assess the anisotropy of the electrochemical properties. A significant anisotropy was found, either by measuring the current during electrochemical polarization or by frequency-dependent impedance measurements. Several mechanisms were proposed in order to explain this anisotropy of the corrosion properties. Eventually, we showed that the electrochemical results could be used to indirectly evidence the presence of structural defects recently identified in the literature. Such defects, called ripplocations, are specific to nano-lamellar materials.

This thesis was created to design instruction papers for the physical experiments, which will be used in the Physical practice of mechanics and thermodynamics in the new premises of the Faculty of Science of the University of the South Bohemia. The work not only documents the theoretical background and approach to measurement, but also describes how these individual experiment sets were prepared and what the problems (and solutions) for each task were.