Selon l’hypothèse d’idéalité de Flory, les chaînes de polymères flexibles à l’état fondu se présentent sous la forme de marches aléatoires à trois dimensions, aussi appelées pelotes gaussiennes. Cette hypothèse suppose que toute information relative à la conformation locale subit une décroissance exponentielle le long de la chaîne principale et, par conséquent, n’a aucune influence sur la conformation à grande échelle. De plus, il est avancé que l’écrantage du volume exclu par les chaînes voisines compense tout effet de gonflement. Des expériences de diffusion neutronique (DN) effectuées il y a une trentaine d’années confirment que les polymères adoptent bien des configurations gaussiennes. S’ensuit l’un des piliers de la théorie des polymères : En solution ”suffisamment dense” tout polymère flexible peut être décrit comme une marche aléatoire à trois dimensions, indépendamment de sa structure chimique, et ce, après un rééchelonnage adéquat. Les progrès réalisés dans les domaines des techniques de simulation et de la puissance informatique ont rendu possible l’étude de chaînes très longues. Ceci a permis d’observer de plus près la structure des chaînes de polymère à l’état fondu et révélé une déviation par rapport à la chaîne idéale. Jusqu’à présent, la déviation par rapport à la structure gaussienne a uniquement été étudiée dans le cas de modèles à gros grains, par simulation et calcul analytique. La présente thèse cherche à vérifier si ces déviations peuvent également être mesurées à l’aide de simulations atomistiques réalistes et d’expériences de DN modernes. / The Flory ideality hypothesis states that flexible polymer chains in a melt assume the shape of three-dimensional random walks leading to so called Gaussian coils. The basis of this hypothesis is that any local conformational information decays exponentially along the chain backbone and thus has no influence on the long range conformation. Additionally it is argued that the excluded volume shielding of neigbor chains cancels out any swelling effects. Neutron scattering (NS) experiments dating back 30 years confirm the postulated Gaussian coil shape of polymers. This leads to a pillar of polymer theory: Any flexible polymer can be described as a three-dimensional random walk. Advances in simulation technics and computing power have opened the door to the possibility of studing very long chains. This allowed for a closer look at the chain structure of polymer melts and revealed deviations from ideality. This deviation is very slight and thus great care must be taken to distinguish it from noise. So far the deviation from the Gaussian coil structure was only studied for coarse-grained models. The scope of this thesis is to explore if these deviations are also measurable in atomistically realistic simulations and modern day NS experiments.

Cette thèse concerne l’analyse et le développement de schémas d’intégration numérique de la Dynamique des Particules Dissipatives. Une présentation et une analyse de convergence faible de schémas existants est présentée, suivie d’une présentation et d’une analyse similaire de deux nouveaux schémas d’intégration facilement parallélisables. Une analyse des propriétés de conservation d’énergie de tous ces schémas est effectuée suivie d’une étude comparative de leurs biais sur l’estimation des valeurs moyennes d’observables physiques pour des systèmes à l’équilibre. Les schémas sont ensuite testés sur des systèmes choqués de fluides DPDE, où l’on montre que nos deux nouveaux schémas apportent une amélioration dans la précision de la description du comportement de tels systèmes par rapport aux schémas facilement parallélisables existants.Finalement, nous présentons une tentative d’accélération d’un schéma d’intégration de référence s’appliquant aux simulations séquentielles de la DPDE / This thesis is about the development and analysis of numerical schemes forthe integration of the Dissipative Particle Dynamics with Energy conservation. A presentation and a weak convergence analysis of existing schemes is performed, as well as the introduction and a similar analysis of two new straightforwardly parallelizable schemes. The energy preservation properties of all these schemes are studied followed by a comparative study of their biases on the estimation of the average values of physical observables on equilibrium simulations. The schemes are then tested on shock simulations of DPDE fluids, where we show that our schemes bring an improvement on the accuracy of the description of the behavior of such systems compared to existing straightforwardly parallelizable schemes. Finally, we present an attempt at accelerating a reference DPDE integration scheme on sequential simulations

<p>A first-principles theory of plasticity in metals currently does not exist. While many plasticity models make reference to rules based on heuristic arguments regarding dislocations (the fundamental mediators of plastic deformation in crystals), the scientific community still does not have a theory of dislocation dynamics which can recover even basic features of plasticity theory. Discrete dislocation dynamics, though a valuable tool for understanding fundamentals topics in dislocation plasticity, becomes unusable beyond ~1.5\% strain due to the line length multiplication inherent in deformation. As a result, it is necessary to develop continuum theories of dislocation dynamics which treat dislocation densities rather than individual dislocations. This thesis examines the foundations of one such continuum theory: line bundle continuum dislocation dynamics, which assumes that dislocations are roughly parallel at every point. First, this assumption is given definite meaning and it is shown from discrete dislocation dynamics data that to be appropriate when modelling dislocation densities on fine length scales (resolving densities on lengths less than 100 nm). Second, it is found that an additional driving force, the correlation stress, emerges from coarse-graining the line bundle dynamics. This correction to the dislocation interactions is dependent on tensorial dislocation correlation functions describing the short-range errors in the products of dislocation densities lying on two slip systems. The full set of these dislocation correlation functions are evaluated from discrete density data with the aid of a novel left-and-right handed classification of slip system interactions in FCC crystals. Lastly, a study of the correlation stress in a representative dislocation system suggests that these stresses are roughly one tenth the magnitude of the mean-field dislocation interaction stress. Taken together, this thesis bridges discrete and continuum models of dislocation dynamics and provides a foundation for future work on a first-principles theory of metal plasticity. </p>

Das Enzym Tryptophan Synthase ist ein ausgezeichnetes Beispiel einer molekularen Fabrik auf der Nanoskala mit zwei katalytischen Zentren. Der katalytische Zyklus des Moleküls beruht zudem auf zahlreichen allosterischen Wechselwirkungen sowie der Übertragung des Intermediats Indol durch einen intramolekularen Tunnel. In dieser Arbeit wird das erste kinetische Modell eines einzelnen Tryptophan Synthase Moleküls konstruiert und analysiert. Simulationen zeigen starke Korrelationen zwischen den Zuständen der Katalysezentren sowie die Ausbildung von Synchronisation. Mit stochastischer Thermodynamik wird die experimentell unzugängliche Reaktionskonstante für die Rückübertragung des Indols aus Messdaten rekonstuiert. Methoden, die den Informationsaustausch in bipartiten Markovnetzwerken charakterisieren, werden auf beliebige Markovnetzwerke verallgemeinert und auf das Modell angewendet. Der abschließende Teil befasst sich mit chemischen Reaktionsnetzwerken von Metaboliten und Enzymen. Es werden algebraische Modelle (Halbgruppen) konstruiert, welche aufeinanderfolgende und simultane katalytische Funktionen von Enzymen und von Unternetzwerken erfassen. Diese Funktionen werden genutzt, um eine natürliche Dynamikum sowie hinreichende und notwendige Bedingungen für seine Selbsterhaltung zu formulieren. Anschließend werden die algebraischen Modelle dazu genutzt, um eine Korrespondenz zwischen Halbgruppenkongruenzen und Skalenübergängen auf den Reaktionsnetzwerken herzustellen. Insbesondere wird eine Art von Kongruenzen erörtert, welche dem Ausspuren der globalen Struktur des Netzwerkes unter vollständiger Beibehaltung seiner lokalen Komponenten entspicht. Während klassische Techniken eine bestimmte lokale Komponente fixieren und sämtliche Informationen über ihre Umgebung ausspuren, sind bei dem algebraischen Verfahren alle lokalen Komponenten zugleich sichtbar und eine Verknüpfung von Funktionen aus verschiedenen Komponenten ist problemlos möglich. / The channeling enzyme tryptophan synthase provides a paradigmatic example of a chemical nanomachine with two distinct catalytic subunits. It catalyzes the biosynthesis of tryptophan, whereby the catalytic activity in a subunit is enhanced or inhibited depending on the state of the other subunit, gates control the accessibility of the reactive sites and the intermediate product indole is directly channeled within the protein. The first single-molecule kinetic model of the enzyme is constructed. Simulations reveal strong correlations in the states of the active centers and the emergent synchronization. Thermodynamic data is used to calculate the rate constant for the reverse indole channeling. Using the fully reversible single-molecule model, the stochastic thermodynamics of the enzyme is closely examined. The current methods describing information exchange in bipartite systems are extended to arbitrary Markov networks and applied to the kinetic model. They allow the characterization of the information exchange between the subunits resulting from allosteric cross-regulations and channeling. The final part of this work is focused on chemical reaction networks of metabolites and enzymes. Algebraic semigroup models are constructed based on a formalism that emphasizes the catalytic function of reactants within the network. A correspondence between coarse-graining procedures and semigroup congruences respecting the functional structure is established. A family of congruences that leads to a rather unusual coarse-graining is analyzed: The network is covered with local patches in a way that the local information on the network is fully retained, but the environment of each patch is not resolved. Whereas classical coarse-graining procedures would fix a particular patch and delete information about the environment, the algebraic approach keeps the structure of all local patches and allows the interaction of functions within distinct patches.

<p align="justify">In a context of restoration of historical masonry structures, it is crucial to properly estimate the residual strength and the potential structural failure modes in order to assess the safety of buildings. Due to its mesostructure and the quasi-brittle nature of its constituents, masonry presents preferential damage orientations, strongly localised failure modes and damage-induced anisotropy, which are complex to incorporate in structural computations. Furthermore, masonry structures are generally subjected to complex loading processes including both in-plane and out-of-plane loads which considerably influence the potential failure mechanisms. As a consequence, both the membrane and the flexural behaviours of masonry walls have to be taken into account for a proper estimation of the structural stability.</p><p><p align="justify">Macrosopic models used in structural computations are based on phenomenological laws including a set of parameters which characterises the average behaviour of the material. These parameters need to be identified through experimental tests, which can become costly due to the complexity of the behaviour particularly when cracks appear. The existing macroscopic models are consequently restricted to particular assumptions. Other models based on a detailed mesoscopic description are used to estimate the strength of masonry and its behaviour with failure. This is motivated by the fact that the behaviour of each constituent is a priori easier to identify than the global structural response. These mesoscopic models can however rapidly become unaffordable in terms of computational cost for the case of large-scale three-dimensional structures.</p><p><p align="justify">In order to keep the accuracy of the mesoscopic modelling with a more affordable computational effort for large-scale structures, a multi-scale framework using computational homogenisation is developed to extract the macroscopic constitutive material response from computations performed on a sample of the mesostructure, thereby allowing to bridge the gap between macroscopic and mesoscopic representations. Coarse graining methodologies for the failure of quasi-brittle heterogeneous materials have started to emerge for in-plane problems but remain largely unexplored for shell descriptions. The purpose of this study is to propose a new periodic homogenisation-based multi-scale approach for quasi-brittle thin shell failure.</p><p><p align="justify">For the numerical treatment of damage localisation at the structural scale, an embedded strong discontinuity approach is used to represent the collective behaviour of fine-scale cracks using average cohesive zones including mixed cracking modes and presenting evolving orientation related to fine-scale damage evolutions.</p><p><p align="justify">A first originality of this research work is the definition and analysis of a criterion based on the homogenisation of a fine-scale modelling to detect localisation in a shell description and determine its evolving orientation. Secondly, an enhanced continuous-discontinuous scale transition incorporating strong embedded discontinuities driven by the damaging mesostructure is proposed for the case of in-plane loaded structures. Finally, this continuous-discontinuous homogenisation scheme is extended to a shell description in order to model the localised behaviour of out-of-plane loaded structures. These multi-scale approaches for failure are applied on typical masonry wall tests and verified against three-dimensional full fine-scale computations in which all the bricks and the joints are discretised.</p> / Doctorat en Sciences de l'ingénieur / info:eu-repo/semantics/nonPublished

Diese Arbeit beschäftigt sich mit Coarse-Graining (dt. ``Vergröberung", ``Zusammenfassung von Zuständen") für Gradientensysteme und Markov-Prozesse. Coarse-Graining ist ein etabliertes Verfahren in der Mathematik und in den Naturwissenschaften und hat das Ziel, die Komplexität eines physikalischen Systems zu reduzieren und effektive Modelle herzuleiten. Die mathematischen Probleme in dieser Arbeit stammen aus der Theorie der Systeme interagierender Teilchen. Hierbei werden zwei Ziele verfolgt: Erstens, Coarse-Graining mathematisch rigoros zu beweisen, zweitens, mathematisch äquivalente Beschreibungen für die effektiven Modelle zu formulieren. Die ersten drei Teile der Arbeit befassen sich mit dem Grenzwert schneller Reaktionen für Reaktionssysteme und Reaktions-Diffusions-Systeme. Um effektive Modelle herzuleiten, werden nicht nur die zugehörigen Reaktionsratengleichungen betrachtet, sondern auch die zugrunde liegende Gradientenstruktur. Für Gradientensysteme wurde in den letzten Jahren eine strukturelle Konvergenz, die sogenannte ``EDP-Konvergenz", entwickelt. Dieses Coarse-Graining-Verfahren wird in der vorliegenden Arbeit auf folgende Systeme mit langsamen und schnellen Reaktionen angewandt: lineare Reaktionssysteme (bzw. Markov-Prozesse auf endlichem Zustandsraum), nichtlineare Reaktionssysteme, die das Massenwirkungsgesetz erfüllen, und lineare Reaktions-Diffusions-Systeme. Für den Grenzwert schneller Reaktionen wird eine mathematisch rigorose und strukturerhaltende Vergröberung auf dem Level des Gradientensystems inform von EDP-Konvergenz bewiesen. Im vierten Teil wird der Zusammenhang zwischen Gleichungen mit Gedächtnis und Markov-Prozessen untersucht. Für Gleichungen mit Gedächtnisintegralen wird explizit ein größer Markov-Prozess konstruiert, der die Gleichung mit Gedächtnis als Teilsystem enthält. Der letzte Teil beschäftigt sich mit verschieden Diskretisierungen für den Fokker-Planck-Operator. Dazu werden numerische und analytische Eigenschaften untersucht. / This thesis deals with coarse-graining for gradient systems and Markov processes. Coarse-graining is a well-established tool in mathematical and natural sciences for reducing the complexity of a physical system and for deriving effective models. The mathematical problems in this work originate from interacting particle systems. The aim is twofold: first, providing mathematically rigorous results for physical coarse-graining, and secondly, formulating mathematically equivalent descriptions for the effective models. The first three parts of the thesis deal with fast-reaction limits for reaction systems and reaction-diffusion systems. Instead of deriving effective models by solely investigating the associated reaction-rate equation, we derive effective models using the underlying gradient structure of the evolution equation. For gradient systems a structural convergence, the so-called ``EDP-convergence", has been derived in recent years. In this thesis, this coarse-graining procedure has been applied to the following systems with slow and fast reactions: linear reaction systems (or Markov process on finite state space), nonlinear reaction systems of mass-action type, and linear reaction-diffusion systems. For the fast-reaction limit, we perform rigorous and structural coarse-graining on the level of the gradient system by proving EDP-convergence. In the fourth part, the connection between memory equations and Markov processes is investigated. Considering linear memory equations, which can be motivated from spatial homogenization, we explicitly construct a larger Markov process that includes the memory equation as a subsystem. The last part deals with different discretization schemes for the Fokker–Planck operator and investigates their analytical and numerical properties.