Although aluminides with the B2 crystal structures have good properties for high temperature applications, the strong ordered bonds that make them durable at high temperature also make them too brittle at room temperature for industrial fabrication. In order to better understand this lack of ductility, molecular statics simulations of planar fault defects and dislocation core structures were conducted in a series of B2 aluminides with increasing ordering energy (FeAl, NiAl, CoAl). The simulation results in NiAl were compared with in-situ straining observations of dislocation motion. The dislocations simulated were of (100) and (111) types. The simulations results obtained indicate a strong influence of the planar fault energies on the mobility of the dislocations. As the cohesive energy increases from FeAl to CoAl, antiphase boundary and unstable stacking fault energies increase resulting in more constricted dislocation core spreadings. This constriction of the cores decreases the mobility of dislocation with planar core structures and increases the mobility of dislocations with non-planar cores. The (100) screw dislocations were found with planar cores in {110} planes for FeAl, NiAl and CoAl. For very high APB values, the cores were very compact, as predicted by the Peierls- Nabarro model. As the APB energies decrease, increasingly two dimensional spreading of the cores was observed and ultimately dislocation dissociation into partials. As a result of the deviation of the stable planar fault energy from the APB fault, the partials were not exact 1/2(111) but deviate to the point corresponding to the actual minima of the γ-surfaces for these compounds. Alloying NiAl with Fe was found to promote the dissociation of the (100) dislocation. The in-situ straining of a single crystal of NiAl only revealed the motion of (100) dislocations. Both in-situ observations and atomistic simulations agreed on the zig-zag shape of the (100) dislocation with an average screw orientation. In this configuration, the mobility of the dislocation is severely reduced. / Ph. D.

Designing materials for fusion applications is a very challenging problem, requiring detailed understanding of the behaviour of materials under the kinds of extreme conditions expected in a fusion environment. During the lifetime of fusion-reactor components, materials will be subjected to high levels of neutron irradiation, but must still perform effectively at high operating temperatures and under significant loading conditions. Body-centred cubic (bcc) transition metals are some of the most promising candidates for structural materials in fusion because of their relatively high density, which allows for effective neutron-shielding with the minimum volume and mass of material. In this work we perform atomistic simulations on two of the most important of these, Fe and W. In this thesis we describe atomic-scale simulations of defects found in bcc systems. In part I we consider the vacancy and interstitial loop defects that are produced and accumulated as a result of irradiation-induced displacement cascades. We show that vacancy dislocation loops have a critical size below which they are highly unstable relative to planar void defects, and thus offer an explanation as to why they are so rarely seen in TEM observations of irradiated bcc metals. Additionally, we compare the diffusion rates of these vacancy loops to their interstitial counterparts and find that, while interstitial loops are more mobile, the difference in mobility is not as significant as might have been expected. In part II we study screw dislocations, which, as the rate limiting carriers of plastic deformation, are significantly responsible for the strength of materials. We present results from large-scale finite temperature molecular dynamics simulations of screw dislocations under stress and observe the thermally-activated kink-pair formation regime at low stress, which appears to be superseded by a frictional regime at higher stresses. The mobility functions fitted to the results are vital components in simulations of dislocation networks and other large-scale phenomena. Lastly, we develop a multi-string Frenkel-Kontorova model that allows us to study the core structure of screw dislocations. Subtle changes in the form of the interaction laws used in this model demonstrate the difference between the non-degenerate and degenerate core structures. We provide simple criteria to guarantee the correct structure when developing interatomic potentials for bcc metals.

Mg alloys have spurred a renewed academic and industrial interest because of their ultra-light-weight and high specific strength properties. Hexagonal close packed Mg has low deformability and a high plastic anisotropy between basal and non-basal slip systems at room temperature. Alloying with Li and other elements is believed to counter this deficiency by activating non-basal slip by reducing their nucleation stress. In this work I study how Li addition affects deformation mechanisms in Mg using atomistic simulations. In the first part, I create a reliable and transferable concentration dependent embedded atom method (CD-EAM) potential for my molecular dynamics study of deformation. This potential describes the Mg-Li phase diagram, which accurately describes the phase stability as a function of Li concentration and temperature. Also, it reproduces the heat of mixing, lattice parameters, and bulk moduli of the alloy as a function of Li concentration. Most importantly, our CD-EAM potential reproduces the variation of stacking fault energy for basal, prismatic, and pyramidal slip systems that influences the deformation mechanisms as a function of Li concentration. This success of CD-EAM Mg-Li potential in reproducing different properties, as compared to literature data, shows its reliability and transferability. Next, I use this newly created potential to study the effect of Li addition on deformation mechanisms in Mg-Li nanocrystalline (NC) alloys. Mg-Li NC alloys show basal slip, pyramidal type-I slip, tension twinning, and two-compression twinning deformation modes. Li addition reduces the plastic anisotropy between basal and non-basal slip systems by modifying the energetics of Mg-Li alloys. This causes the solid solution softening. The inverse relationship between strength and ductility therefore suggests a concomitant increase in alloy ductility. A comparison of the NC results with single crystal deformation results helps to understand the qualitative and quantitative effect of Li addition in Mg on nucleation stress and fault energies of each deformation mode. The nucleation stress and fault energies of basal dislocations and compression twins in single crystal Mg-Li alloy increase while those for pyramidal dislocations and tension twinning decrease. This variation in respective values explains the reduction in plastic anisotropy and increase in ductility for Mg-Li alloys.

As formulações baseadas na mecânica do contínuo, embora precisas até certo ponto, por vezes não podem ser utilizadas, ou não são conceitualmente corretas para o entendimento de fenômenos em escalas reduzidas. Estas limitações podem aparecer no estudo dos fenômenos tribológicos em escala nanométrica, que passam a necessitar de novos métodos experimentais, teóricos e computacionais que permitam explorar estes fenômenos com a resolução necessária. Simulações atomísticas são capazes de descrever fenômenos em pequena escala, porém, o número necessário de átomos modelados e, portanto, o custo computacional - geralmente torna-se bastante elevado. Por outro lado, os métodos de simulação associados à mecânica do contínuo são mais interessantes em relação ao custo computacional, mas não são precisos na escala atômica. A combinação entre essas duas abordagens pode, então, permitir uma compreensão mais realista dos fenômenos da tribologia. Neste trabalho, discutem-se os conceitos básicos e modelos de atrito em escala atômica e apresentam-se estudos, por meio de simulação numérica, para a análise e compreensão dos mecanismos de atrito e desgaste no contato entre materiais. O problema é abordado em diferentes escalas, e propõe-se uma abordagem conjunta entre a Mecânica do Contínuo e a Dinâmica Molecular. Para tanto, foram executadas simulações numéricas, com complexidade crescente, do contato entre superfícies, partindo-se de um primeiro modelo que simula o efeito de defeitos cristalinos no fenômeno de escorregamento puro, considerando a Dinâmica Molecular. Posteriormente, inseriu-se, nos modelos da mecânica do contínuo, considerações sobre o fenômeno de adesão. A validação dos resultados é feita pela comparação entre as duas abordagens e com a literatura. / Formulations based on continuum mechanics are generally accurate in a macroscale level, but sometimes cannot be used, or it is not conceptually correct to use for the understanding of small scale phenomena. These limitations may be observed in the study of tribological phenomena at the nanoscale, which may consequently require new experimental, theoretical and computational methods in order to analyze these phenomena with the required resolution. Atomistic simulations may describe phenomena at small scale, but the required number of atoms to be modeled, i.e. the computational cost, usually becomes very high. Moreover, simulation methods associated with continuum mechanics (such as the Finite Element Method - FEM) are more interesting in relation to computational cost, but they are not accurate for atomic scale studies. The combination of these two approaches can then enable a more realistic understanding of tribological phenomena. This work discusses the basic concepts of friction and models for friction at atomic scale. This work also presents studies, by means of numerical simulation, for the analysis of friction and wear mechanisms in the contact of materials. The problem is approached considering different scales, and basing the analysis both on Continuum Mechanics and Molecular Dynamics (MD). For both methods, numerical simulations with increasing complexity were conducted to reproduce the contact between surfaces, starting from an initial model that simulates the effect of crystalline defects during the MD analysis of pure slip. In a second stage, adhesion phenomenon were implemented through continuum mechanics models. The validation of the models and the coupling between the two approaches were conducted by comparison with literature.

L’adaptation des surfaces pour des fonctions prédéterminées par le choix des matériaux métalliques ou des couches minces ayant des propriétés mécaniques avancées peut potentiellement permettre de réaliser des nouvelles applications à petites échelles. Concevoir de telles applications utilisant des nouveaux matériaux nécessite en premier lieu la connaissance des propriétés mécaniques des matériaux ciblés à l’échelle microscopique et nanoscopique. Une méthode souvent appliquée pour caractériser les matériaux à petites échelles est la nanoindentation, qui peut être vue comme une mesure de dureté à l’échelle nanoscopique. Ce travail présente une contribution relative à l'interprétation des résultats de la nanoindentation, qui fait intervenir un grand nombre de phénomènes physiques couplés à l'aide de simulations numériques. A cette fin une approche interdisciplinaire, adaptée aux phénomènes apparaissant à petites échelles, et située à l’intersection entre la physique, la mécanique et la science des matériaux a été utilisée. Des modèles numériques de la nanoindentation ont été conçus à l'échelle atomique (modèle discret) et à l'échelle des milieux continus (méthode des éléments finis), pour étudier le comportement du nickel pur. Ce matériau a été choisi pour ses propriétés mécaniques avancées, sa résistance à l'usure et sa bio-compatibilité, qui peuvent permettre des applications futures intéressantes à l'échelle nanoscopique, particulièrement dans le domaine biomédical. Des méthodes avancées de mécanique du solide ont été utilisées pour prendre en compte les grandes déformations locales du matériau (par la formulation corotationelle), et pour décrire les conditions de contact qui évoluent au cours de l'analyse dans le modèle à l'échelle des milieux continus (traitement des conditions de contact unilatérales et tangentielles par une forme de Lagrangien augmenté). L’application des modèles numériques a permis de contribuer à l’identification des phénomènes qui gouvernent la nanoindentation du nickel pur. Le comportement viscoplastique du nickel pur pendant nanoindentation a été identifié dans une étude expérimentale-numérique couplée, et l'effet cumulatif de la rugosité et du frottement sur la dispersion des résultats de la nanoindentation a été montré par une étude numérique (dont les résultats sont en accord avec des tendances expérimentales). Par ailleurs, l’utilisation de l’outil numérique pour une autre application à petites échelles, la manipulation des objets par contact, a contribué à la compréhension de la variation de l’adhésion électrostatique pendant micromanipulation. La déformation plastique des aspérités de surface sur le bras de manipulateur (en nickel pur) a été identifiée comme une source potentielle d’augmentation importante de l'adhésion pendant la micromanipulation, qui peut potentiellement causer des problèmes de relâche et de précision de positionnement, observés expérimentalement. Les résultats présentés dans cette thèse montrent que des simulations numériques basées sur la physique du problème traité peuvent expliquer des tendances expérimentales et contribuer à la compréhension et l'interprétation d'essais couramment utilisé pour la caractérisation aux petites échelles. Le travail réalisé dans cette thèse s’inscrit dans un projet de recherche appelé "mini-micro-nano" (mµn), financé par la Communauté Française de Belgique dans le cadre de "l'Action de Recherche Concertée", convention 04/09-310.

An alternate family of “high” voltage (where the equilibrium voltage lies between 3.6 V and 4.2 V) polyanion cathode materials is reported in this thesis with the objective of improving specific energy density (Wh/kg) and developing a better understanding of polyanion electrochemistry. The electrochemical properties, synthesis and the structure of novel fluorosulfate materials crystallizing in the tavorite and the triplite type mineral structures are described. These materials display highest discharge voltages reported for any Fe2+/Fe3+ redox couple. LiFeSO4F was prepared in both the tavorite and the triplite polymorphs using inexpensive and scalable methods. Complete structural characterization was performed using X-ray and neutron based diffraction methods. A rapid synthesis of fluorosulfates can be achieved by using microwave heating. The local rapid heating created by the microwaves generates nanocrystalline LiFeSO4F tavorite with defects that induce significant microstrain. To date, this is unique to the microwave synthesis method. Phase transformation to the more stable triplite framework, facilitated by the lattice defects which include hydroxyl groups, is therefore easily triggered. The formation of nanocrystalline tavorite leads to nanocrystalline triplite, which greatly favors its electrochemical performance because of the inherently disordered nature of the triplite structure. Direct synthesis of the electrochemically active triplite type compound can be carried out either by extending the duration of the solvothermal reactions or by the partial substitution of Fe by Mn to produce LiFe1-xMnxSO4F. This study, overall, has led to a better understanding of the transformation of tavorite to the triplite phase. To examine Li and the Na ion conduction and their correlation with the electrochemical performance of 3-D, 2-D and 1-D ion conductors, atomistic scale simulations have been used to investigate tavorite type LiFeSO4F, NaFeSO4F, olivine type NaMPO4 (M= Fe, Mn, Fe0.5Mn0.5) and layered Na2FePO4F. These calculations predict high mobility of the Li-ion in the tavorite type LiFeSO4F but sluggish Na-ion transport in iso-structural NaFeSO4F. High mobility of the Na-ion is predicted for phosphate layered and olivine structures. Finally, the synthesis and structural details of NaMSO4F (M=Fe, Mn) and NH4MSO4F (M=Fe, Mn) are presented in the last chapter to show the structural diversity present in the fluorosulfate family.

In this dissertation, an innovative approach combining continuum mechanics and atomistic simulations is exposed to develop a nanomechanics theory for modeling and predicting the macroscopic behavior of nanomaterials. This nanomechanics theory exhibits the simplicity of the continuum formulation while taking into account the discrete atomic structure and interaction near surfaces/interfaces. There are four primary objectives to this dissertation. First, theory of interfaces is revisited to better understand its behavior and effects on the overall behavior of nanostructures. Second, atomistic tools are provided in order to efficiently determine the properties of free surfaces and interfaces. Interface properties are reported in this work, with comparison to both theoretical and experimental characterizations of interfaces. Specifically, we report surface elastic properties of groups 10 11 transition metals as well as properties for low-CSL grain boundaries in copper. Third, we propose a continuum framework that casts the atomic level information into continuum quantities that can be used to analyze, model and simulate macroscopic behavior of nanostructured materials. In particular, we study the effects of surface free energy on the effective modulus of nano-particles, nanowires and nano-films as well as nanostructured crystalline materials and propose a general framework valid for any shape of nanostructural elements / nano-inclusions (integral forms) that characterizes the size-dependency of the elastic properties. This approach bridges the gap between discrete systems (atomic level interactions) and continuum mechanics. Finally this continuum outline is used to understand the effects of surfaces on the overall behavior of nano-size structural elements (particles, films, fibers, etc.) and nanostructured materials. More specifically we will discuss the impact of surface relaxation, surface elasticity and non-linearity of the underlying bulk on the properties nanostructured materials.

Biological molecules are essential parts of organisms and participate in a variety of biological processes within cells. Understanding the relationship between sequence, structure, and function of biological molecules are of fundamental importance in life science and the health care industry. In this dissertation, a multi-scale approach was utilized to develop coarse-grained molecular models for protein and RNA simulations. By simplifying the atomistic representation of a biomolecular system, the coarse-grained approach enables the molecular dynamics simulations to reveal the biological processes, which occur on the time and length scales that are inaccessible to the all-atom models. For RNA, an "intermediate" coarse-grained model was proposed to provide both accuracy and efficiency for RNA 3D structure modeling and prediction. The overall potential parameters were derived based on structural statistics sampled from experimental structures. For protein, a general, transferable coarse-grain framework based on the Gay-Berne potential and electrostatic point multipole expansion was developed for polypeptide simulations. Next, an advanced atomistic model was developed to model electrostatic interaction with high resolution and incorporates electronic polarization effect that is ignored in conventional atomistic models. The last part of my thesis work involves applying all-atom molecular simulations to address important questions and problems in biophysics and structural biology. For example, the interaction between protein and miRNA, the recognition mechanism of antigen and antibody, and the structure dynamics of protein in mixed denaturants. / text

This thesis is presented in two sections. Two different multiscale models are developed in order to increase the computational speed of two well known atomistic algorithms, Molecular Dynamics (MD) and Kinetic Monte Carlo (KMC). In Section I, the MD method is introduced. Following this, a multiscale method of linking an MD simulation of heat conduction to a finite element (FE) simulation is presented. The method is simple to implement into a conventional MD code and is independent of the atomistic model employed. This bridge between the FE and MD simulations works by ensuring that energy is conserved across the FE/MD boundary. The multiscale simulation allows for the investigation of large systems which are beyond the range of MD. The method is tested extensively in the steady state and transient regimes, and is shown to agree with well with large scale MD and FE simulations. Furthermore, the method removes the artificial boundary effects due to the thermostats and hence allows exact temperatures and temperature gradients to be imposed on to an MD simulation. This allows for better study of temperature gradients on crystal defects etc. In Section II, the KMC method is introduced. A continuum model for the KMC method is presented and compared to the standard KMC model of surface diffusion. This method replaces the many discrete back and forth atom jumps performed by a standard KMC algorithm with a single flux that can evolve in time. Elastic strain is then incorporated into both algorithms and used to simulate atom deposition upon a substrate by Molecular Beam Epitaxy. Quantum dot formation due to a mismatch in the lattice spacing between a substrate and a deposited film is readily observed in both models. Furthermore, by depositing alternating layers of substrate and deposit, self-organised quantum dot super-lattices are observed in both models.

An alternate family of “high” voltage (where the equilibrium voltage lies between 3.6 V and 4.2 V) polyanion cathode materials is reported in this thesis with the objective of improving specific energy density (Wh/kg) and developing a better understanding of polyanion electrochemistry. The electrochemical properties, synthesis and the structure of novel fluorosulfate materials crystallizing in the tavorite and the triplite type mineral structures are described. These materials display highest discharge voltages reported for any Fe2+/Fe3+ redox couple. LiFeSO4F was prepared in both the tavorite and the triplite polymorphs using inexpensive and scalable methods. Complete structural characterization was performed using X-ray and neutron based diffraction methods. A rapid synthesis of fluorosulfates can be achieved by using microwave heating. The local rapid heating created by the microwaves generates nanocrystalline LiFeSO4F tavorite with defects that induce significant microstrain. To date, this is unique to the microwave synthesis method. Phase transformation to the more stable triplite framework, facilitated by the lattice defects which include hydroxyl groups, is therefore easily triggered. The formation of nanocrystalline tavorite leads to nanocrystalline triplite, which greatly favors its electrochemical performance because of the inherently disordered nature of the triplite structure. Direct synthesis of the electrochemically active triplite type compound can be carried out either by extending the duration of the solvothermal reactions or by the partial substitution of Fe by Mn to produce LiFe1-xMnxSO4F. This study, overall, has led to a better understanding of the transformation of tavorite to the triplite phase. To examine Li and the Na ion conduction and their correlation with the electrochemical performance of 3-D, 2-D and 1-D ion conductors, atomistic scale simulations have been used to investigate tavorite type LiFeSO4F, NaFeSO4F, olivine type NaMPO4 (M= Fe, Mn, Fe0.5Mn0.5) and layered Na2FePO4F. These calculations predict high mobility of the Li-ion in the tavorite type LiFeSO4F but sluggish Na-ion transport in iso-structural NaFeSO4F. High mobility of the Na-ion is predicted for phosphate layered and olivine structures. Finally, the synthesis and structural details of NaMSO4F (M=Fe, Mn) and NH4MSO4F (M=Fe, Mn) are presented in the last chapter to show the structural diversity present in the fluorosulfate family.