Dissertations / Theses on the topic 'Non-equilibrium structures'

This thesis is focused on achieving materials with non-equilibrium structures fabricated by high-energy laser sintering. The chosen precursor materials have rigid and inert structures like high-melting point ceramics or metals. It was necessary to use real-time monitoring of temperature and spectrum profiles for selecting the optimal laser parameters for the laser sintering process. This monitoring was done by an off-axial setup that also controls the surface morphologies during the laser irradiation process. The laser focal spot receives very high temperatures and subsequent extreme cooling rates within a short time period. New non-equilibrium structures will emerge ruled by kinetics, huge temperature gradients or stresses and freeze by quenching in solid state. These material structures were found to form at different length scales from nano- to macro-level, frequently by a hierarchical ordering. This opens a method to engineer materials with both hierarchical and non-equilibrium structures by a single operation in both metal and ceramics by laser sintering. In the Co-Cr-Mo alloy system, structures on three levels of lengths were observed, namely i) nano-level structures dominated by the grain boundary segregation; ii) micron-level structures characterized by the interlocked clusters of columns; and iii) macro-level structures defined by the selected laser scan patterns. The non-equilibrium structures of the Co-Cr-Mo alloy are related to mechanical, corrosion and bio-compatibility properties. In ZrO2 ceramics, the final product had a non-equilibrium nano- and micron-sized structure created by uneven absorption of laser energy and rupture. The structure inside the micron-sized grains is formed through ordered coalescence of nano-crystals. Properties of the laser sintered materials were established and related to the observed structures. The materials properties might be tailored by controlling the structures in different levels and potential applications of the new materials will be given.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Accepted. Paper 3: Accepted. Paper 4: Submitted. Paper 5: Manuscript.

Ferroelectric materials have received lots of attention thanks to their intriguing properties such as the piezoelectric and pyroelectric effects, as well as the large dielectric constants and the spontaneous polarization which can potentially be used for information storage. In particular, perovskite crystal has a very simple unit cell structure yet a very rich phase transition diagram, which makes it one of the most intensively studied ferroelectric materials. In this dissertation, we use effective Hamiltonian, a first-principles-based computational technique to study the finite-temperature properties of ferroelectric perovskites. We studied temperature-graded (BaxSr1-x )TiO3 (BST) bulk alloys as well as the dynamics of nanodomain walls (nanowalls) in Pb(ZrxTi1-x )O3 (PZT) ultra-thin films under the driving force of an AC field. Our computations suggest that, for the temperature-graded BST, the polarization responds to the temperature gradient (TG), with the "up" and "down" offset observed in polarization components along the direction of TG, in agreement with the findings from experiments. For the nanowalls in PZT, the dynamics can be described by the damped-harmonic-oscillator model, and we observed a size-driven transition from resonance to relaxational dynamics at a critical thickness of 7.2 nm. The transition originates from the change in the effective mass of a nanowall as a film thickness increases. Some of the findings may find potential applications in various devices, such as thermal sensors, energy converters, or novel memory units.

Thin film and surface science is an active field with important technological applications as illustrated by the transistor and by the recording head. This thesis relates thin film and surface science experiments applied to quasicrystalline materials, ferromagnetic alloys and electron tomography. These systems have strong potentials for technological applications. Epitaxial deposition is a powerful tool to create structures which are non-stable in the bulk state. For a better understanding of the quasicrystals' physical properties, one wants to grow quasicrystalline thin films of reduced chemical complexity. Single elements don't form quasicrystalline thin films beyond a monolayer. This thesis reports the successful growth of binary AlNi quasicrystal thin films in the multilayer regime. This thesis reports also detailed analysis of annealing and phase transition related structures on different surface orientations of d-AlNiCo. The equilibrium structure of MnSb is of the NiAs type but other structures with theoretical 100% polarisation can be stabilised by epitaxy. The surface magnetism of the MnSb thin film with equilibrium bulk structure grown on GaAs(111) has been imaged by spin-polarised low-energy electron microscopy revealing the spin direction mapping of magnetic domains at the surface of MnSb. Atomic resolution is routinely obtained with the current generation of transmission electron microscopes. For three-dimensional atomic resolution, the problem is to obtain suitable samples. In this thesis, we report the development of instruments and a methodology to fabricate atomically flat terraces with nanometre dimension at the tip of etched tungsten wires and the MBE growth of Au clusters on these terraces.

Shock waves create a unique environment of high pressure, high temperature and high strain-rates. It has been observed that chemical reactions that occur in this regime are exothermic and can lead to the synthesis of new materials that are not possible under other conditions. The exothermic reaction is used in the development of binary energetic materials. These materials are of significant interest to the energetic materials community because of its capability of releasing high heat content during a chemical reaction and the relative insensitivity of these types of energetic materials. Synthesis of these energetic materials, at nano grain sizes with structural reinforcements, provides an opportunity to develop a dual functional material with both strength and energetic characteristics. Shock-induced chemical reactions pose challenges in experiment and instrumentation. This thesis is addressed to the theoretical development of constitutive models of shock-induced chemical reactions in energetic composites, formulated in the framework of non-equilibrium thermodynamics and mixture theories, in a continuum scale. Transition state-based chemical reaction models are introduced and incorporated with the conservation equations that can be used to calculate and simulate the shock-induced reaction process. The energy that should be supplied to reach the transition state has been theoretically modeled by considering both the pore collapse mechanism and the plastic flow with increasing yield stress behind the shock wave. A non-equilibrium thermodynamics framework and the associated evolution equations are introduced to account for time delays that are observed in the experiments of shock-induced or assisted chemical reactions. An appropriate representation of the particle size effects is introduced by modifying the initial energy state of the reactants. Numerical results are presented for shock-induced reactions of mixtures of Al, Fe2O3 and Ni, Al with epoxy as the binder. The theoretical model, in the continuum scale, requires parameters that should be experimentally determined. The experimental characterization has many challenges in measurement and development of nano instrumentation. An alternate approach to determine these parameters is through ab-initio calculations. Thus, this thesis has initiated ab-initio molecular dynamics studies of shock-induced chemical reactions. Specifically, the case of thermal initiation of chemical reactions in aluminum and nickel is considered.

Le formalisme des fonctions de Green hors-équilibre (NEGF pour « Non-equilibrium Green’s function) a suscité au cours des dernières décennies un engouement fort pour étudier les propriétés du transport quantique des nanostructures et des nano-dispositifs dans lesquels les interactions inélastiques, comme la diffusion des électrons-phonons, jouent un rôle significatif. L'incorporation d'interactions inélastiques dans le cadre du NEGF s’effectue généralement dans l'approximation auto-cohérente de Born (SCBA pour « Self-consistent Born approximation) qui représente une approche itérative plus exigeante en ressources numériques. Nous proposons dans ce travail de thèse une méthode efficace alternative dite LOA pour (« Lowest Order Approximation. Son principal avantage est de réduire considérablement le temps de calcul et de décrire physiquement la diffusion électron-phonon. Cette approche devrait considérablement étendre l'accessibilité de l'utilisation de codes atomistiques de transport quantique pour étudier des systèmes 3D réalistes sans faire à des ressources numériques importantes
Non-equilibrium Green’s function (NEGF) formalism during recent decades has attracted numerous interests for studying quantum transport properties of nanostructures and nano-devices in which inelastic interactions like electron-phonon scattering have a significant impact. Incorporation of inelastic interactions in NEGF framework is usually performed within the self-consistent Born approximation (SCBA) which induces a numerically demanding iterative scheme. As an alternative technique, we propose an efficient method, the so-called Lowest Order Approximation (LOA) coupled with the Pade approximants. Its main advantage is to significantly reduce the computational time, and to describe the electron-phonon scattering physically. This approach should then considerably extend the accessibility of using atomistic quantum transport codes to study three-dimensional (3D) realistic systems without requiring numerous numerical resources

In the present work, we discuss two subjects related to the nonequilibrium dynamics of polymers or biological filaments adsorbed to two-dimensional substrates.

The first part is dedicated to thermally activated dynamics of polymers on structured substrates in the presence or absence of a driving force. The structured substrate is represented by double-well or periodic potentials. We consider both homogeneous and point driving forces. Point-like driving forces can be realized in single molecule manipulation by atomic force microscopy tips. Uniform driving forces can be generated by hydrodynamic flow or by electric fields for charged polymers.

In the second part, we consider collective filament motion in motility assays for motor proteins, where filaments glide over a motor-coated substrate. The model for the simulation of the filament dynamics contains interactive deformable filaments that move under the influence of forces from molecular motors and thermal noise. Motor tails are attached to the substrate and modeled as flexible polymers (entropic springs), motor heads perform a directed walk with a given force-velocity relation. We study the collective filament dynamics and pattern formation as a function of the motor and filament density, the force-velocity characteristics, the detachment rate of motor proteins and the filament interaction. In particular, the formation and statistics of filament patterns such as nematic ordering due to motor activity or clusters due to blocking effects are investigated. Our results are experimentally accessible and possible experimental realizations are discussed.
In der vorliegenden Arbeit behandeln wir zwei Probleme aus dem Gebiet der Nichtgleichgewichtsdynamik von Polymeren oder biologischen Filamenten, die an zweidimensionale Substrate adsorbieren.

Der erste Teil befasst sich mit der thermisch aktivierten Dynamik von Polymeren auf strukturierten Substraten in An- oder Abwesenheit einer treibenden Kraft. Das strukturierte Substrat wird durch Doppelmulden- oder periodische Potentiale dargestellt. Wir betrachten sowohl homogene treibende Kräfte als auch Punktkräfte. Punktkräfte können bei der Manipulation einzelner Moleküle mit die Spitze eines Rasterkraftmikroskops realisiert werden. Homogene Kräfte können durch einen hydrodynamischen Fluss oder ein elektrisches Feld im Falle geladener Polymere erzeugt werden.

Im zweiten Teil betrachten wir die kollektive Bewegung von Filamenten in Motility-Assays, in denen Filamente über ein mit molekularen Motoren überzogenes Substrat gleiten. Das Modell zur Simulation der Filamentdynamik beinhaltet wechselwirkende, deformierbare Filamente, die sich unter dem Einfluss von Kräften, die durch molekulare Motoren erzeugt werden, sowie thermischem Rauschen bewegen. Die Schaftdomänen der Motoren sind am Substrat angeheftet und werden als flexible Polymere (entropische Federn) modelliert. Die Kopfregionen der Motoren vollführen eine gerichtete Schrittbewegung mit einer gegebenen Kraft-Geschwindigkeitsbeziehung. Wir untersuchen die kollektive Filamentdynamik und die Ausbildung von Mustern als Funktion der Motor- und der Filamentdichte, der Kraft-Geschwindigkeitscharakteristik, der Ablöserate der Motorproteine und der Filamentwechselwirkung. Insbesondere wird die Bildung und die Statistik der Filamentmuster, wie etwa die nematische Anordnung aufgrund der Motoraktivität oder die Clusterbildung aufgrund von Blockadeeffekten, untersucht. Unsere Ergebnisse sind experimentell zugänglich und mögliche experimentelle Realisierungen werden diskutiert.

Neben ihrer Bedeutung in industriellen Anwendungen dienen Kolloide als Modellsysteme in Experimenten und in der Theorie, um die Struktur und Dynamik von kondensierter Materie zu untersuchen. Kürzlich wurde experimentell gezeigt, dass eine kleine Anisotropie ausreicht, um die viskoelastische Antwort im Vergleich zu harten Kugeln drastisch zu ändern. Die mikroskopischen Ursachen hierfür sind bisher nicht verstanden. In dieser Arbeit werden daher Nichtgleichgewichts-Brownsche-Dynamik-Simulationen (NEBD) von harten kolloidalen Dumbbells in oszillatorischen Scherfeldern entwickelt und eingesetzt, um diese Resultate mit Verbindung zu Rheologie- und Neutronenstreuexperimenten zu erklären. Weiterhin wird die Bedeutung der Anisotropie für Struktur und Dynamik von solchen Suspensionen im Gleichgewicht mit Hilfe von "Linear-Response"-Theorie und Brownsche-Dynamik-Simulationen analysiert. Im linearen Limit zeigt die Scherviskosität bei hohen Packungsdichten einen dramatischen Anstieg jenseits eines kritischen Anisotropieparameters. Dies weist darauf hin, dass schon bei den kleinen Anisotropien kollektive Rotations-Translations-Kopplungen für langsame Zeitskalen verantwortlich sind. Weiterhin wird ein Nichtgleichgewichtsübergang mittels NEBD-Simulationen von Suspensionen harter Dumbbells im PC unter oszillatorischer Scherung ersichtlich. Es wird gezeigt, dass der kontinuierliche Übergang nur für sehr kleine Aspektverhältnisse erhalten bleibt. Oberhalb eines bestimmten Aspektverhältnisses wird der Übergang durch einen ungeordneten Zustand vermittelt. Außerdem wird ein Sliding-Layer Zustand mit kollektiver Ordnung der Teilchenausrichtung bei hohen Scheramplituden beobachtet. Somit zeigt diese Arbeit, dass die NEBD-Simulationen Phänomene in Rheologie- und Streuexperimenten erklären. Angesichts dieser Experimente wird gezeigt, dass der Orientierungsfreiheitsgrad einen starken Einfluss auf den strukturellen Übergang bei steigenden Amplituden hat.
Besides being important for industrial applications, colloidal suspensions have long served as model systems for investigating the structure and dynamics of condensed matter. Recently, it has been demonstrated experimentally that apparently a small particle anisotropy is sufficient to dramatically change the viscoelastic response under external shearing fields, of which the microscopic mechanisms are not yet sufficiently understood. In the present work, NEBD simulations of colloidal hard dumbbells in oscillatory shear fields are developed and employed to elucidate the novel findings in close connection with comprehensive rheology and SANS experiments. Furthermore, by utilising BD simulations and linear response theory, the impact of anisotropy on structure and dynamics of such suspensions in equilibrium is analysed. In the linear response limit, the shear viscosity exhibits a dramatic increase at high packing fractions beyond a critical anisotropy of the particles. This indicates that newly occurring, collective rotational-translational couplings must be made responsible for slow time scales appearing in the PC. Moreover, a non-equilibrium transition emerging at moderate aspect ratios is revealed by NEBD of plastic crystalline suspensions under oscillatory shear. This transition behaviour is systematically studied. It is demonstrated that the continuous nature of the transition is retained for very low aspect ratios only. Above a certain aspect ratio, the transition is mediated by an intermediate disordered state. Furthermore, a partially oriented sliding layer state featuring a finite collective order in the particles'' orientations is observed at high strains. Hence, this thesis demonstrates that the NEBD simulations explain novel phenomena in rheology and scattering experiments. In the light of these experiments, it is shown that the orientational degree of freedom has a vigorous impact on the structural transition under increasing oscillatory shear.

La plupart des systèmes non linéaires loin de l'équilibre sont sensibles aux fluctuations internes. Dans ce travail, les effets stochastiques dans des modèles génériques de réaction-diffusion sont étudiés à deux échelles différentes. Dans l'approche mésoscopique, l'évolution du système est gouvernée par une équation maîtresse résolue par des simulations de Monte Carlo cinétique. A l'échelle microscopique, des simulations de dynamique des particules sont réalisées. Ces approches stochastiques sont comparées à des équations macroscopiques, déterministes de réaction-diffusion. Dans l'introduction, les différentes échelles, les concepts concernant les systèmes non linéaires et les méthodes numériques utilisées sont présentés. La première partie du chapitre consacré aux résultats est dédiée à l'étude de la perturbation de la distribution des vitesses des particules induite par la réaction pour un système bistable et la propagation d'un front d'onde. Une équation maîtresse incluant cette perturbation est écrite et comparée à des simulations de la dynamique microscopique. La seconde partie concerne la formation de structures dans les systèmes réaction-diffusion dans le contexte de la biologie du développement. Une méthode pour simuler des structures de Turing à l'échelle microscopique est développée à partir de l'algorithme DSMC (direct simulation Monte Carlo). Ensuite, des expériences consistant à perturber la formation de la colonne vertébrale sont expliquées dans le cadre du mécanisme de Turing. Enfin, un modèle de réaction-diffusion associé à un mécanisme différent, connu sous le nom de "Clock and wavefront", est proposé pour rendre compte de la segmentation
Many nonlinear systems under non-equilibrium conditions are highly sensitive to internal fluctuations. In this dissertation, stochastic effects in some generic reaction-diffusion models are studied using two approaches of different precision. In the mesoscopic approach, evolution of the system is governed by the master equation, which can be solved numerically or used to set up kinetic Monte Carlo simulations. On the microscopic level, particle computer simulations are used. These two stochastic approaches are compared with deterministic, macroscopic reaction-diffusion equations.In the Introduction, key information about the different approaches is presented, together with basics of nonlinear systems and a presentation of numerical algorithms used.The first part of the Results chapter is devoted to studies on reaction-induced perturbation of particle velocity distributions in models of bistability and wave front propagation. A master equation including this perturbation is presented and compared with microscopic simulations.The second part of the Results deals with pattern formation in reaction-diffusion systems in the context of developmental biology. A method for simulating Turing patternsat the microscopic level using the direct simulation Monte Carlo algorithm is developed. Then, experiments consisting of perturbing segmentation of vertebrate embryo’s bodyaxis are explained using the Turing mechanism. Finally, a different possible mechanism of body axis segmentation, the “clock and wavefront” model, is formulated as a reaction-diffusion model

Molecular electronics is envisioned as a possible next step in device miniaturization. It is usually taken to mean the design and manufacturing of electronic devices and applications where organic molecules work as the fundamental functioning unit. It involves the easurement and manipulation of electronic response and transport in molecules attached to conducting leads. Organic molecules have the advantages over conventional solid state electronics of inherent small sizes, endless chemical diversity and ambient temperature low cost manufacturing.

In this thesis we investigate the switching and conducting properties of photochromic dithienylethene derivatives. Such molecules change their conformation in solution when acted upon by light. Photochromic molecules are attractive candidates for use in molecular electronics because of the switching between different states with different conducting properties. The possibility of optically controlling the conductance of the molecule attached to leads may lead to new device implementations.

The switching reaction is investigated with potential energy calculations for different values of the reaction coordinate between the closed and the open isomer. The electronic and atomic structure calculations are performed with density functional theory (DFT). It is concluded that there is a large potential energy barrier separating the open and closed isomer and that switching between open and closed forms must involve excited states.

The conducting properties of the molecule inserted between gold leads is calculated within the Non Equilibrium Green Function theory. The transmission function is calculated for the two isomers with different basis sizes for the gold contacts, as well as the electrostatic potential, for finite applied bias voltages. We conclude that a Au 6s basis give qualitatively the same result as a Au spd basis close to the Fermi level. The transmission coefficient at the Fermi energy is around 10 times larger in the closed molecule compared to the open. This will result in a large difference in conductivity. It is also found that the large difference in conductivity will remain for small applied bias voltages. The results are consistent with earlier work.

The generalized Langevin equation (GLE) has been used to describe the dynamics of particles in a stationary environment. To better understand the dynamics of polymerization, the GLE has been generalized to the irreversible generalized Langevin equation (iGLE) so as to incorporate the non-stationary response of the solvent. This non-stationary response is manifested in the friction kernel and the behavior of the projected (stochastic) force. A particular polymerizing system, such as living polymerization, is specified both through the parameters of the friction kernel and the potential of mean force (PMF). Equilibrium properties such as extent of polymerization have been obtained and are consistent with Flory-Huggin¡¯s theory. In addition, time-dependent non-equilibrium observables such as polymer length, the polymer length distribution, and polydispersity index (PDI) of living polymerization have been obtained. These have been compared to several experiments so as to validate the models, and to provide additional insight into the thermodynamic and kinetic properties of these systems. In addition to the iGLE, a stochastic model has been used to study the effect of nonequilibrium reactivity on living polymerization. This model can be used to determine whether the reaction is controlled by kinetics or diffusion. A combination of the iGLE and stochastic models may help us obtain more information about living polymerization.

Les organismes cellulaires apparaissent organisés. Les bactéries utilisent des compartiments sans membrane pour confiner les réactions chimiques dans l'espace et le temps. Il existe un paradigme général de l'auto-organisation de l'espace intracellulaire qui distingue les auto-assemblages, structures moléculaires assemblées par des mécanismes passifs de transition de phase, et les structures dissipatives, engendrés par exemple par des processus de réaction-diffusion. Si les auto-assemblages correspondent à l'évolution vers l'équilibre thermodynamique, les structures dissipatives sont des manifestations d'une dépense d'énergie hors équilibre thermodynamique. Nous illustrons ce paradigme en étudiant la ségrégation du matériel génétique chez les bactéries, en l'occurrence celle du plasmide F de Escherichia coli qui repose sur le système de partition ParABS. La ségrégation est une étape cruciale du cycle cellulaire bactérien puisqu'elle assure la transmission de l'information génétique dans les bactéries filles avant la division. Le système ParABS est constitué d'une séquence centromérique parS ; d'une protéine ParB capable de se lier à l'ADN, spécifiquement sur la séquence parS et non-spécifiquement ailleurs ; d'une protéine ATPase ParA capable de se lier à l'ADN. Les interactions entre protéines ParB sur l'ADN et l'adsorption spécifique sur la séquence parS mène à la formation d'un foyer tridimensionnel appelé complexe ParBS localisé autour de la séquence parS. Les interactions entre protéines ParA et ParB mènent au positionnement de ce complexe au centre du milieu cellulaire. Après réplication, deux complexes ParBS existent et son ségrégés par l'action des protéines ParA aux positions 1/4 et 3/4 de l'espace intracellulaire.Nous cherchons d'abord à expliquer la formation des complexes ParBS par un mécanisme passif de séparation de phase entre états de haute et basse densité en protéines ParB dans l'espace. Nous construisons deux modèles de physique statistique à l'aide d'outils empruntés à la physique des transitions de phase. Notre deuxième approche définit rigoureusement tous les éléments du système biologique constitué de l'ADN-polymère et des protéines ParB en interaction et nous permet de formuler un critère d'existence de transition de phase du premier ordre qui est vérifié par l'ADN. Nous parvenons à tracer les diagrammes de phase de cette transition. Ces deux modèles nous permettent d'argumenter que le régime thermodynamique physiologique de ce système biologique est un régime de coexistence métastable en protéines ParB sur l'ADN. La séquence parS joue le rôle d'un défaut ou d'une graine de nucléation. Nous utilisons une troisième approche pour expliciter le lien entre les distributions tridimensionnelle et sur l'ADN des protéines ParB autour de la séquence parS. Nous cherchons à expliquer les courbes de recouvrement de fluorescence issus d'expériences de photoblanchiment sur les complexes ParBS. Nous construisons une méthode de photoblanchiment in silico, c'est-à-dire que nous reproduisons ces courbes de recouvrement à partir d'une équation phénoménologique résolue numériquement. Nous développons un système d'équations qui décrivent l'évolution des protéines sur l'ADN à partir de l'approche physique statistique précédente pour produire un photoblanchiment in silico prenant en compte que les complexes ParBS sont issus d'une séparation de phase. Nous montrons qu'un pur système passif ne permet pas de faire des expériences de photoblanchiment à cause de la maturation d'Ostwald subie par les complexes. Nous corrigeons cette approche pour inclure les protéines ParA et leur cycle biochimique dans nos simulations. Nous montrons ainsi que les interactions entre les protéines ParA et ParB et l'hydrolyse de l'ATP permet la survie de plusieurs complexes ParBS grâce à un mécanisme d'inversion du murissement d'Ostwald. Cette approche fondamentale permet d'expliquer le positionnement des complexes ParBS durant la ségrégation
Cellular organisms appear organized. Bacteria use membraneless compartments to confine chemical reactions in space and time. There is a general paradigm of intracellular space self-organization that distinguishes between self-assembly, molecular structures assembled by passive phase transition mechanisms, and dissipative structures, generated for example by reaction-diffusion processes. If self-assemblies correspond to the evolution towards thermodynamic equilibrium, dissipative structures are manifestations of an out-of-equilibrium energy cost. We illustrate this paradigm by studying the segregation of bacterial genome, in this case the F-plasmid segregation of Escherichia coli, based on the ParABS partition system. Segregation is a crucial step in the bacterial cell cycle since it ensures the transmission of genetic information in daughter bacteria before division.The ParABS system consists of a parS centromeric sequence; a ParB protein which is able to bind to DNA, specifically on the parS sequence and not specifically elsewhere; and a ParA ATPase protein than can bind to DNA. Interactions between ParB proteins on DNA and specific adsorption on the parS sequence lead to the formation of a three-dimensional focus called the ParBS complex located around the parS sequence. Interactions between ParA and ParB proteins lead to the positioning of this complex at the center of the cell cytoplasm. After replication, two ParBS complexes exist and are segregated by the action of ParA proteins at positions 1/4 and 3/4 of the intracellular space.We first seek to explain the formation of ParBS complexes by a passive phase separation mechanism between high- and low-density states of ParB proteins in space. We construct two statistical physics models using tools borrowed from the physics of phase transitions. Our second approach rigorously defines all the elements of the biological system consisting of the interacting DNA-polymer and ParB proteins and allows us to formulate a first-order phase transition existence criterion that is verified by the DNA. We can draw the phase diagrams of this transition. These two models allow us to argue that the physiological thermodynamic regime of this biological system is a regime of metastable coexistence in ParB proteins on DNA. The parS sequence plays the role of a defect or nucleation seed. We use a third approach to explain the relationship between the three-dimensional and DNA distributions of ParB proteins around the parS sequence.We try to explain the fluorescence recovery curves from photobleaching experiments on ParBS complexes. We construct an in silico photobleaching method, i.e. we reproduce these recovery curves from a phenomenological equation solved numerically. We then develop a system of equations that describe the evolution of proteins on DNA from the previous statistical physical approach to produce an in silico photobleaching taking into account that ParBS complexes are the result of phase separation. We show that a pure passive system does not allow photobleaching experiments because of the Ostwald maturation undergone by the complexes. We correct this approach by including ParA proteins and their biochemical cycle in our simulations. We show that the interactions between ParA and ParB proteins and the hydrolysis of ATP allows the survival of several ParBS complexes thanks to an inversion mechanism of Ostwald's ripening. This fundamental approach explains the positioning of ParBS complexes during segregation

The warm dense matter regime (WDM), defined by temperatures of a few electron volts and densities comparable with solids, is a complex state of matter where multi-body particle correlations and quantum effects play an important role in determining the overall structure and equation of state. The study of WDM states represents the laboratory analogue of the astrophysical environments found in the cores of planets and in the crusts of old stars, but also has practical applications for controlled thermonuclear fusion. Time resolved X-ray diffraction is used to study the temporal evolution of a sample from solid state towards WDM, either after irradiation with an intense proton/electron beam, in carbon samples, or direct laser illumination, in thin gold nanofoils. The electron-ion equilibration time is extracted through the use of the two-temperature model and in highly excited carbon shown to be longer than previously thought, this is attributed to strong ion-ion coupling screening the interaction (coupled mode theory). Calculation of the dynamic ion-ion structure factor is performed using orbital-free density functional theory (OF-DFT) and shown to compare well with Kohn-Sham DFT in both the static and dynamic cases. Experimental verification of these results is vital and measurement of the microscopic dynamics of warm dense aluminium have been successfully demonstrated through inelastic X-ray scattering. Using the self-seeded beam at the linear coherent light source (LCLS) scattering at a small momentum exchange allowed the first direct measurement of ion acoustic waves in WDM. This data provides the basis for a direct experimental test of many dense plasma theories through direct comparison with the ion-ion dynamic structure factor.

Après la découverte de la magnéto-résistance géante (GMR) par Albert Fert et Peter Grünberg, l'électronique a connu une véritable avancée avec la naissance d'une nouvelle branche appelée spintronique. Cette discipline, encore jeune, consiste à exploiter le spin des électrons dans le but notamment de stocker de l'information numérique. La plupart des dispositifs exploitant cette propriété quantique des électrons consistent en une alternance de fines couches magnétiques et non magnétiques sur un substrat semi-conducteur. L'un des outils de choix pour la caractérisation de ces structures, inventé en 1988 par Kaiser et Bell, est le microscope à émission d'électrons balistiques (BEEM). A l'origine, ce microscope, dérivé du microscope à effet tunnel (STM), était dédié à l'imagerie d'objets (nanométriques) enterrés ainsi qu'à l'étude de la barrière de potentiel (barrière Schottky) qui se forme à l'interface d'un métal et d'un semi-conducteur lors de leur mise en contact. Avec l'essor de la spintronique, le BEEM est devenu une technique de spectroscopie essentielle mais encore fondamentalement incomprise. C'est en 1996 que le premier modèle réaliste, basé sur le formalisme hors équilibre de Keldysh, a été proposé pour décrire le transport des électrons dans cette microscopie. Il permettait notamment d'expliquer certains résultats expérimentaux jusqu'alors incompris. Cependant, malgré son succès, son usage a été limité à l'étude de structures semi-infinies via un méthode de calcul appelée décimation de fonctions de Green. Dans ce contexte, nous avons étendu ce modèle au cas des films minces et des hétéro-structures du type vanne de spin : partant du même postulat que les électrons suivent la structure de bandes du matériaux dans lesquels ils se propagent, nous avons établi une formule itérative permettant le calcul des fonctions de Green du système fini par la méthode des liaisons fortes. Ce calcul des fonctions de Green a été encodé dans un programme Fortran 90, BEEM v3, afin de calculer le courant BEEM ainsi que la densité d'états de surface. En parallèle, nous avons développé une autre méthode, plus simple, qui permet de s'affranchir du formalisme hors équilibre de Keldysh. En dépit de sa naïveté, nous avons montré que cette approche permettait l'interprétation et la prédiction de certains résultats expérimentaux de manière intuitive. Cependant, pour une étude plus fine, le recours à l'approche “hors équilibre” reste inévitable, notamment pour la mise en évidence d'effets d'épaisseur, lés aux interfaces inter-plans. Nous espérons que ces deux outils puissent se révéler utiles aux expérimentateurs, et notamment pour l'équipe Surfaces et Interfaces de notre département
After the discovery of Giant Magneto-Resistance (GMR) by Albert Fert and Peter Grünberg, electronics had a breakthrough with the birth of a new branch called spintronics. This discipline, while still young, exploit the spin of electrons, for instance to store digital information. Most quantum devices exploiting this property of electrons consist of alternating magnetic and nonmagnetic thin layers on a semiconductor substrate. One of the best tools used for characterizing these structures, invented in 1988 by Kaiser and Bell, is the so-called Ballistic Electron Emission Microscope (BEEM). Originally, this microscope, derived from the scanning tunneling microscope (STM), was dedicated to the imaging of buried (nanometer-scale) objects and to the study of the potential barrier (Schottky barrier) formed at the interface of a metal and a semiconductor when placed in contact. With the development of spintronics, the BEEM became an essential spectroscopy technique but still fundamentally misunderstood. It was in 1996 that the first realistic model, based on the non-equilibrium Keldysh formalism, was proposed to describe the transport of electrons during BEEM experiments. In particular, this model allowed to explain some experimental results previously misunderstood. However, despite its success, its use was limited to the study of semi-infinite structures through a calculation method called decimation of Green functions. In this context, we have extended this model to the case of thin films and hetero-structures like spin valves: starting from the same postulate that electrons follow the band structure of materials in which they propagate, we have established an iterative formula allowing calculation of the Green functions of the finite system by tight-binding method. This calculation of Green’s functions has been encoded in a FORTRAN 90 program, BEEM v3, in order to calculate the BEEM current and the surface density of states. In parallel, we have developed a simpler method which allows to avoid passing through the non-equilibrium Keldysh formalism. Despite its simplicity, we have shown that this intuitive approach gives some physical interpretation qualitatively similar to the non-equilibrium approach. However, for a more detailed study, the use of “non-equilibrium approach” is inevitable, especially for the detection of thickness effects linked to layer interfaces. We hope these both tools should be useful to experimentalists, especially for the Surfaces and Interfaces team of our department

Les métamatériaux sont des matériaux possédant des caractéristiques exotiques qui n'existent pas dans la nature. Ils peuvent être réalisés par une structure métallique périodique dont la cellule élémentaire est assez petite devant la longueur d'onde aux fréquences d'intérêt. D'un point de vue électromagnétique, ces matériaux peuvent notamment avoir une perméabilité négative à certaines fréquences. D'autre part, un plasma à basse pression peut être modélisé comme un matériau à permittivité négative si sa densité électronique dépasse la densité critique à une fréquence spécifique. Cette thèse étudie l'intégration d'un métamatériau à perméabilité négative, le Split Ring Resonator (SRR), dans un plasma d'argon à basse pression (entre 5 et 100 mTorr). Les objectifs visent d'une part, à la réalisation d'un métamatériau reconfigurable à base du plasma comme élément contrôlable, et d'autre part, à la réalisation d'un matériau doublement négatif, connu aussi sous le nom de matériau main gauche, présentant à la fois une permittivité et une perméabilité négative. La démarche a été menée de manière expérimentale à l'aide d'une cavité métallique où une source à couplage inductive (ICP) à 13.56 MHz a été placée au-dessus de la cavité (isolée par une vitre du quartz) pour l'allumage et l'entretien du plasma. A l'intérieur de cette cavité deux antennes cornets ont été fixées pour la caractérisation microonde. Une méthode de caractérisation dédiée, spécifique à cet environnement complexe, a été développée pour caractériser électromagnétiquement la structure créée. Une sonde de Langmuir a été utilisée pour mesurer la densité électronique du plasma généré. Des simulations électromagnétiques sont faites en utilisant l'outil ANSYS Electronics Desktop(r) pour aider à comprendre les effets du plasma sur le métamatériau SRR et sa résonance
Metamaterials are materials with exotic characteristics that do not exist in nature. They can be made by a periodic metal structure whose elementary cell is quite small compared to the wavelength at the frequencies of interest. From an electromagnetic point of view, these materials can in particular have a negative permeability at certain frequencies. On the other hand, a low pressure plasma can be modeled as a material with negative permittivity if its electron density exceeds the critical density at a specific frequency. This thesis studies the integration of a negative permeability metamaterial, the Split Ring Resonator (SRR), into a low pressure argon plasma (between 5 and 100 mTorr). The objectives are, on the one hand, to produce a reconfigurable metamaterial based on plasma as a controllable element and, on the other hand, to produce a doubly negative material, also known as a left-hand material, presenting both a permittivity and a negative permeability. The approach was experimentally conducted using a metal cavity where a 13.56 MHz Inductively Coupled Source (ICP) was placed over the cavity (isolated by quartz glass) for ignition and the maintenance of the plasma. Inside this cavity two horn antennas have been fixed for the microwave characterization. A dedicated characterization method, specific to this complex environment, has been developed to electromagnetically characterize the created structure. A Langmuir probe was used to measure the electron density of the generated plasma. Electromagnetic simulations are made using the ANSYS Electronics Desktop(r) tool to help understand the effects of plasma on the SRR metamaterial and its resonance

Understanding complex population dynamics is critical for both basic and applied ecology. Analysis of genetic data has been promoted as a way to reconstruct recent non-equilibrium processes that influence the apportioning of genetic diversity among populations of organisms. In a structured-deme context, where individual populations exist as geographically distinct units, island biogeography theory and metapopulation genetics predict that the demographic processes of extinction, colonization, and migration will affect the magnitude and rate of genetic divergence between demes. New methods have been developed to attempt to detect the influence of non-equilibrium dynamics in structured populations. I challenged two of these methods: decomposed pairwise regression and allele frequency analyses, using simulations of genetic data from structured demes. I found that these methods suffer from a high type II error rate, or failure to reject the null hypothesis of mutation-migration-drift equilibrium for demes experiencing historical demographic events. In addition, island biogeography and metapopulation ecology predict that at equilibrium, some species in a patch will be recent colonists, as equilibrium indicates a balance between colonization of the patch and extinction from the patch. Recent colonists are unlikely to have reached population mutation-migration-drift equilibrium; hence a paradox exists between population and community level equilibrium. I used nuclear and mitochondrial genetic data from populations of two species of reptiles from the Turks and Caicos Islands, British West Indies to test for patterns of equilibrium vs. non-equilibrium. I found unexpected shallow genetic divergence in the Turks Island boa (Epicrates chrysogaster), indicating that this species likely existed as a panmictic population prior to the inundation of the Turks and Caicos Banks during the last glaciation. As the initial methods I tested using simulations proved unreliable, I used methods from phylogeography, landscape genetics, and island biogeography to detect significant non-equilibrium dynamics in the Turks and Caicos curly-tailed lizard (Leiocephalus psammodromus), finding evidence for high levels of biased gene flow. I propose that studies of genetic diversity on island archipelagos use tools from all three of these methods to evaluate empirical data in the context of equilibrium and the null hypotheses offered by island biogeography and population genetics theory. I frame the results both in the context of conservation and an understanding of equilibrium and non-equilibrium dynamics.

Co-based bulk metallic glasses (BMGs) are well known for their excellent mechanical properties with high fracture strength, hardness and elastic modulus. Since the first report of A. Inoue with co-workers in 2003 on Co43Fe20Ta5.5B31.5 BMG with fracture strength up to 5 GPa, a series of Co-based BMGs including Co-Fe-B-Si-Nb, Co-Fe-Cr-Mo-C-B-Er, Co-Ta-B systems have been developed. Co-Ta-B ternary BMGs, discovered recently, are characterized by even higher fracture strength of up to about 6 GPa. These BMGs with outstanding mechanical behavior are interesting for applications as advanced structural materials and coatings. Due to a relatively simple constitution (only three components), Co-Ta-B BMGs are very attractive for investigations of relationships between composition, structure, undercoolability, glass-forming ability, thermal and mechanical properties. However, there have been published just a few papers on Co-Ta-B BMGs focusing on the glass-forming ability in terms of the critical diameter and mechanical properties so far. In present work, a systematic study of the structure and properties of Co-Ta-B BMGs has been carried out on four intentionally chosen compositions  Co61Ta6B33, Co59Ta8B33, Co57Ta10B33 and Co53Ta10B37. Glass formation, thermal stability, crystallization kinetics upon isochronal and isothermal annealing, mechanical and magnetic properties were investigated. Co-Ta-B BMGs studied in this work are characterized by high thermal stability, ultrahigh fracture strength in compression, large Vickers hardness and high values of elastic constants. Increasing of B and Ta content is beneficial to the improvement of both thermal and mechanical properties. Based on the study of the short-range atomic order in Co57Ta10B33 BMG, Co-Ta, Co-B and B-B bonds are supposed to play an important role in the thermal and mechanical properties. A comprehensive picture on structure-composition-property relationship was established. In order to better understand the glass formation, non-equilibrium solidification of the undercooled alloys was investigated using electromagnetic levitation, high-energy X-ray diffraction and high-speed video observation. Three compositions with bulk glass-forming ability (Co61Ta8B31, Co59Ta8B33, Co55Ta8B37) were chosen to study the phase formation during non-equilibrium solidification. In addition, one ternary near-eutectic alloy Co64Ta5.5B30.5 and two binary alloys Co67B33 and Co63B37 with poor glass formation were comparably investigated using the same method. The phase formation, dendrite growth velocity and microstructure of the solidified samples were analyzed in detail as function of undercooling. The alloy composition, maximum undercooling and growth velocity were related closely with the glass-forming ability of the Co-Ta-B alloys studied.