This thesis presents an investigation of reactive transport of species in porous media, with the aim to understand better and predict the fate of radionuclide in engineered and natural barriers of future deep geological disposal facilities for nuclear waste. The work involves developments of several pore-scale models for simulating reactive transport by coupling convective, adsorptive and diffusive processes. Pore network models (PNM) are amongst the appealing approaches that provide a suitable description for dealing with mutable pore space structures. Such models have been used to describe conservative as well as reactive transport in saturated and unsaturated porous media. In the present thesis, pore network models based on a regular tessellation of truncated octahedral cells are proposed and developed to simulate mass transport in porous media with incomplete pore space information due to limitation of existing characterisation techniques. Bentonite and Opalinus Clay are selected to illustrate the methodology. The micro- and meso-structure of these clays and their effects on the transport behaviour are investigated. The research shows that the clays are anisotropic and heterogeneous with fast diffusion parallel to the bedding plane and slow diffusion perpendicular to the bedding plane. In addition, different types of species have different accessible porosity and macroscopic diffusion coefficients. The anisotropy and heterogeneity of clays are achieved by different length scales and percentage of pores in different directions in the pore network models. The transport behaviour of various species, including sorption and anion exclusion, is simulated and analyzed. The effect of sorption is simulated via changing the pore radii by a coarse grained mathematical formula or by a formula directly in each pore. The results are in good agreement with experimentally measured macroscopic (bulk) diffusivities for the materials studied, including anisotropic diffusion coefficients. This lends strong support to the physical realism of the proposed models. The developed methodology can be used for any micro and meso-porous material with known distribution of pore sizes. It can be extended to other pore space changing mechanisms, in addition to sorption, to derive mechanism-based evolution laws for the transport parameters of porous media.

Cette thèse porte sur la conception, la modélisation et le prototypage de nanorobots pour des applications en nanomédecine, en biologie et en nanosystèmes. Principalement deux approches ont été proposées. La première approche implique la modélisation multi-échelle (la mécanique quantique, dynamique moléculaire, mécanique continue) couplée aux techniques de réalité virtuelle. La plateforme ainsi développée a permis en premier lieu, la caractérisation biomécanique de différents composants nanorobotiques : nanoressorts à base de protéines et de nanomoteurs moléculaires (ADN, nanotube de carbone, protéines). Le développement de la plateforme a permis ensuite d’assembler d’une manière interactive (retour visuel et retour de force) des structures nanorobotiques, d’optimiser leur structure et de caractériser leur comportement dynamique. Dans la seconde approche, une méthodologie originale de co-prototypage à été développée. Le co-prototypage permet en effet de coupler les expérimentations et les simulations afin d’avoir un modèle réaliste. Ceci permet de mettre à jour les paramètres de simulation et de réajuster le processus de fabrication après optimisation. D’autre part, les simulations permettent d’observer des phénomènes à l’échelle nanométrique qui sont jusque là inaccessibles par expérimentation. Durant ce travail de thèse, j’ai développé des nouvelles structures nanorobotiques : des nanomachines à base d’ADN, un bio-nanoactionneur linéaire ainsi qu’une nanomachine rotative à base de nanotubes de carbone. Quelques uns de ces prototypes ont été fabriqués, optimisés et validés expérimentalement. / Nanorobots represent a nanoscale devices where proteins such as DNA, carbon nanotubes could act as motors, mechanical joints, transmission elements, or sensors. When these different components were assembled together they can form nanorobots with multi-degree-of-freedom, able to apply forces and manipulate objects in the nanoscale world. In this work, we investigated the design, assembly, simulation, and prototyping of biological and artificial molecular structures with the goal of implementing their internal nanoscale movements within nanorobotic systems in an optimized manner. The thesis focuses, mainly on two approaches. The first one involves multiscale modeling tools (quantum mechanics, molecular dynamics, continuum mechanics) coupled to virtual reality advanced techniques. In order to design and evaluate the characteristics of molecular robots, we proposed interactive nanophysics-based simulation which permits manipulation of molecules, proteins and engineered materials in molecular dynamics simulations with real-time force feedback and graphical display. The second approach uses a novel co-prototyping methodology. The optimization of engineered nanorobotic device is coupled to experimental measurements and force field modeling algorithms.

O presente trabalho trata da modelagem da condução de calor transiente com geração de calor em meios heterogêneos, e tem o objetivo de desenvolver um modelo multiescala adequado a esse fenômeno. Já existem modelos multiescala na literatura relacionados ao problema proposto, e que são válidos para os seguintes casos: (a) o elemento de volume representativo tem tamanho desprezível quando comparado ao comprimento característico macroscópico (e como consequência, a microescala tem inércia térmica desprezível); ou (b) a geração de calor é homogênea na microescala. Por outro lado, o modelo proposto nesta tese, o qual é desenvolvido utilizando uma descrição variacional do problema, pode ser aplicado a elementos de volume representativos finitos e em condições em que a geração de calor é heterogênea na microescala. A discretização temporal (diferenças finitas) e as discretizações espaciais na microescala e na macroescala (método dos elementos finitos) são apresentadas em detalhes, juntamente com os algoritmos necessários para implementar a solução do problema. Nesta tese são apresentados casos numéricos simples, procurando verificar não só o modelo teórico multiescala desenvolvido, mas também a implementação feita. Para tanto, são analisados, por exemplo, (a) casos em que considera-se a microescala um material homogêneo, tornando possível a comparação da solução multiescala com a solução convencional (uma única escala) pelo método dos elementos finitos, e (b) um caso em um material heterogêneo para o qual a solução completa, isto é, modelando diretamente os constituintes no corpo macroscópico, é obtida, tornando possível a comparação com a solução multiescala. A solução na microescala para vários casos analisados nesta tese sofre grande influência da inércia térmica da microescala. Para demonstrar o potencial de aplicação do modelo multiescala, simula-se a cura de um elastômero carregado com negro de fumo. Embora a simulação demonstre que a inércia térmica não precise ser considerada para esse caso em particular, a aplicação da presente metodologia torna possível modelar a cura do elastômero diretamente sobre a microescala, uma abordagem até então não utilizada no contexto de métodos multiescala. Essa metodologia abre a possibilidade para futuros aperfeiçoamentos da modelagem do estado de cura. / This work deals with the modeling of transient heat conduction with heat generation in heterogeneous media, and its objective is to develop a proper multiscale model for this phenomenon. There already exist multiscale models in the literature related to this proposed problem, and which are valid for the following cases: (a) the representative volume element has a negligible size when compared to the characteristic macroscopic size (and, as a consequence, the microscale has a negligible thermal inertia); or (b) the heat generation is homogeneous at the microscale. On the other hand, the model proposed in this thesis, which is developed using a variational description of the problem, can be applied to finite representative volume elements and in conditions in which the heat generation is heterogeneous at the microscale. The time discretization (finite difference) and the space discretizations at both the microscale and the macroscale (finite element method) are presented in details, together with the algorithms needed for implementing the solution of the problem. In this thesis, simple numerical cases are presented, aiming to verify not only the theoretical multiscale model developed, but also its implementation. For this, it is analyzed, for instance, (a) cases in which the microscale is taken as a homogeneous material, making it possible the comparison of the multiscale solution with the conventional solution (one single scale) by the finite element method, and (b) a case in a heterogeneous material for which the full solution, that is, modeling all constituents directly on the macroscale, is obtained, making it possible the comparison with the multiscale solution. The solution at the microscale for several cases analyzed in this thesis suffers a large influence of the microscale thermal inertia. To demonstrate the application potential of the multiscale model, the cure of a carbon black loaded elastomer is simulated. Although the simulation shows that the thermal inertia does not have to be considered for this case in particular, the application of the present methodology makes it possible to model the cure of the elastomer directly at the microscale, an approach not used in multiscale methods context until now. This methodology opens the possibility for future improvements of the state of cure modeling.

L’étude multi-échelle d’un lit fluidisé gaz-particule est réalisée afin de comprendre les raisons de la mauvaise prédiction de la combustion dans ce type de réacteur. Dans un premier temps, des simulations numériques directes à l’échelle de quelques particules montrent le couplage entre la fraction volumique de particules et la fraction massique des espèces dans l’écoulement. Ensuite, une analyse des équations flitrées en LES montre qu’un terme de corrélation fluide-particule apparaît lorsque l’on explicite le taux de réaction gaz-particules. On comprend alors que si ce couplage n’est pas pris en compte correctement dans les simulations aux grandes échelles, le résultat ne peut pas être bon. Des simulations numériques à l’échelle du réacteur sont alors réalisées avec différents maillages pour tenter de mettre en évidence les effets de sous-maille liés à ce couplage à l’échelle des petites structures solides dans l’écoulement. / The multiscale study of a reactive gas-solid fluidized bed is performed to understand the reason of the bad prediction of the combustion in such a reactor. First, Direct Numerical Simulations at the particle array lenght scale show the dependency of the species mass fraction released in the gas phase on the solid volume fraction. Then, the analysis of the filtered continuity equations for the eulerian granular model highlights that a fluid-particle coupling term appears when expliciting the heterogeneous reaction rate. Therefore, we understand the need to take this coupling into account in large scales simulations to obtain good results. Computations at the lab-scale reactor are eventually performed using different grid refinements in order to try to highlight the subgrid terms due to this coupling at the small solid structure scale.

abstract: There are many applications for polymer matrix composite materials in a variety of different industries, but designing and modeling with these materials remains a challenge due to the intricate architecture and damage modes. Multiscale modeling techniques of composite structures subjected to complex loadings are needed in order to address the scale-dependent behavior and failure. The rate dependency and nonlinearity of polymer matrix composite materials further complicates the modeling. Additionally, variability in the material constituents plays an important role in the material behavior and damage. The systematic consideration of uncertainties is as important as having the appropriate structural model, especially during model validation where the total error between physical observation and model prediction must be characterized. It is necessary to quantify the effects of uncertainties at every length scale in order to fully understand their impact on the structural response. Material variability may include variations in fiber volume fraction, fiber dimensions, fiber waviness, pure resin pockets, and void distributions. Therefore, a stochastic modeling framework with scale dependent constitutive laws and an appropriate failure theory is required to simulate the behavior and failure of polymer matrix composite structures subjected to complex loadings. Additionally, the variations in environmental conditions for aerospace applications and the effect of these conditions on the polymer matrix composite material need to be considered. The research presented in this dissertation provides the framework for stochastic multiscale modeling of composites and the characterization data needed to determine the effect of different environmental conditions on the material properties. The developed models extend sectional micromechanics techniques by incorporating 3D progressive damage theories and multiscale failure criteria. The mechanical testing of composites under various environmental conditions demonstrates the degrading effect these conditions have on the elastic and failure properties of the material. The methodologies presented in this research represent substantial progress toward understanding the failure and effect of variability for complex polymer matrix composites. / Dissertation/Thesis / Doctoral Dissertation Mechanical Engineering 2016

abstract: A hybrid molecular dynamics (MD) simulation framework is developed to emulate mechanochemical reaction of mechanophores in epoxy-based nanocomposites. Two different force fields, a classical force field and a bond order based force field are hybridized to mimic the experimental processes from specimen preparation to mechanical loading test. Ultra-violet photodimerization for mechanophore synthesis and epoxy curing for thermoset polymer generation are successfully simulated by developing a numerical covalent bond generation method using the classical force field within the framework. Mechanical loading tests to activate mechanophores are also virtually conducted by deforming the volume of a simulation unit cell. The unit cell deformation leads to covalent bond elongation and subsequent bond breakage, which is captured using the bond order based force field. The outcome of the virtual loading test is used for local work analysis, which enables a quantitative study of mechanophore activation. Through the local work analysis, the onset and evolution of mechanophore activation indicating damage initiation and propagation are estimated; ultimately, the mechanophore sensitivity to external stress is evaluated. The virtual loading tests also provide accurate estimations of mechanical properties such as elastic, shear, bulk modulus, yield strain/strength, and Poisson’s ratio of the system. Experimental studies are performed in conjunction with the simulation work to validate the hybrid MD simulation framework. Less than 2% error in estimations of glass transition temperature (Tg) is observed with experimentally measured Tgs by use of differential scanning calorimetry. Virtual loading tests successfully reproduce the stress-strain curve capturing the effect of mechanophore inclusion on mechanical properties of epoxy polymer; comparable changes in Young’s modulus and yield strength are observed in experiments and simulations. Early damage signal detection, which is identified in experiments by observing increased intensity before the yield strain, is captured in simulations by showing that the critical strain representing the onset of the mechanophore activation occurs before the estimated yield strain. It is anticipated that the experimentally validated hybrid MD framework presented in this dissertation will provide a low-cost alternative to additional experiments that are required for optimizing material design parameters to improve damage sensing capability and mechanical properties. In addition to the study of mechanochemical reaction analysis, an atomistic model of interphase in carbon fiber reinforced composites is developed. Physical entanglement between semi-crystalline carbon fiber surface and polymer matrix is captured by introducing voids in multiple graphene layers, which allow polymer matrix to intertwine with graphene layers. The hybrid MD framework is used with some modifications to estimate interphase properties that include the effect of the physical entanglement. The results are compared with existing carbon fiber surface models that assume that carbon fiber has a crystalline structure and hence are unable to capture the physical entanglement. Results indicate that the current model shows larger stress gradients across the material interphase. These large stress gradients increase the viscoplasticity and damage effects at the interphase. The results are important for improved prediction of the nonlinear response and damage evolution in composite materials. / Dissertation/Thesis / Doctoral Dissertation Mechanical Engineering 2017

abstract: Interstitial impurity atoms can significantly alter the chemical and physical properties of the host material. Oxygen impurity in HCP titanium is known to have a considerable strengthening effect mainly through interactions with dislocations. To better understand such an effect, first the role of oxygen on various slip planes in titanium is examined using generalized stacking fault energies (GSFE) computed by the first principles calculations. It is shown that oxygen can significantly increase the energy barrier to dislocation motion on most of the studied slip planes. Then the Peierls-Nabbaro model is utilized in conjunction with the GSFE to estimate the Peierls stress ratios for different slip systems. Using such information along with a set of tension and compression experiments, the parameters of a continuum scale crystal plasticity model, namely CRSS values, are calibrated. Effect of oxygen content on the macroscopic stress-strain response is further investigated through experiments on oxygen-boosted samples at room temperature. It is demonstrated that the crystal plasticity model can very well capture the effect of oxygen content on the global response of the samples. It is also revealed that oxygen promotes the slip activity on the pyramidal planes. The effect of oxygen impurity on titanium is further investigated under high cycle fatigue loading. For that purpose, a two-step hierarchical crystal plasticity for fatigue predictions is presented. Fatigue indicator parameter is used as the main driving force in an energy-based crack nucleation model. To calculate the FIPs, high-resolution full-field crystal plasticity simulations are carried out using a spectral solver. A nucleation model is proposed and calibrated by the fatigue experimental data for notched titanium samples with different oxygen contents and under two load ratios. Overall, it is shown that the presented approach is capable of predicting the high cycle fatigue nucleation time. Moreover, qualitative predictions of microstructurally small crack growth rates are provided. The multi-scale methodology presented here can be extended to other material systems to facilitate a better understanding of the fundamental deformation mechanisms, and to effectively implement such knowledge in mesoscale-macroscale investigations. / Dissertation/Thesis / Doctoral Dissertation Mechanical Engineering 2018

abstract: With the maturity of advanced composites as feasible structural materials for various applications there is a critical need to solve the challenge of designing these material systems for optimal performance. However, determining superior design methods requires a deep understanding of the material-structure properties at various length scales. Due to the length-scale dependent behavior of advanced composites, multiscale modeling techniques may be used to describe the dominant mechanisms of damage and failure in these material systems. With polymer matrix fiber composites and nanocomposites it becomes essential to include even the atomic length scale, where the resin-hardener-nanofiller molecules interact, in the multiscale modeling framework. Additionally, sources of variability are also critical to be included in these models due to the important role of uncertainty in advance composite behavior. Such a methodology should be able to describe length scale dependent mechanisms in a computationally efficient manner for the analysis of practical composite structures. In the research presented in this dissertation, a comprehensive nano to macro multiscale framework is developed for the mechanical and multifunctional analysis of advanced composite materials and structures. An atomistically informed statistical multiscale model is developed for linear problems, to estimate and scale elastic properties of carbon fiber reinforced polymer composites (CFRPs) and carbon nanotube (CNT) enhanced CFRPs using information from molecular dynamics simulation of the resin-hardener-nanofiller nanoscale system. For modeling inelastic processes, an atomistically informed coupled damage-plasticity model is developed using the framework of continuum damage mechanics, where fundamental nanoscale covalent bond disassociation information is scaled up as a continuum scale damage identifying parameter. This damage model is coupled with a nanocomposite microstructure generation algorithm to study the sub-microscale damage mechanisms in CNT/CFRP microstructures. It is further integrated in a generalized method of cells (GMC) micromechanics model to create a low-fidelity computationally efficient nonlinear multiscale method with imperfect interfaces between the fiber and matrix, where the interface behavior is adopted from nanoscale MD simulations. This algorithm is used to understand damage mechanisms in adhesively bonded composite joints as a case study for the comprehensive nano to macroscale structural analysis of practical composites structures. At each length scale sources of variability are identified, characterized, and included in the multiscale modeling framework. / Dissertation/Thesis / Doctoral Dissertation Aerospace Engineering 2018

In this work we develop a three-scale mathematical modeling to describe electro-chemical couplings in clays using the asymptotic homogenization procedure of periodic structures. We consider the porous medium composed of kaolinite particles saturated by an electrolyte solution of water-solvent and four ionic solutes monovalents Na+, H+, Cl-, OH-At the nanoscale we develop the model of the electrical double layer wherein the electric potential and local charge distribution are ruled by the Poisson- Boltzmann problem. In addition we incorporate the protonation/deprotonation chemical reaction between the fluid and the particle surface and consequently we quantify the dependence of the surface charge density of the particles with the pH of the electrolyte solution. At the microscale, or pore-scale, the movement of the aqueous solution is governed by the Stokes problem whereas ion transport by the Nernst-Planck equation. The pore-scale governing equations are supplemented by slip boundary condition in the tangential velocity of the fluid and adsorption interface conditions arising from the averaging of the nanoscale model. We then homogenize the microscopic model to the macroscale and derive effective equations with additional closure relations for the macroscopic coefficients. The macroscopic model is discretized by the finite volume method and numerical simulations of electrokinetical remediation of a contaminated soil are performed. The numerical results illustrate the strong dependence of the remediation efficiency on the pH of the aqueous solution. / Neste trabalho desenvolvemos a modelagem matemática e computacional em três escalas (nano-micro-macro) do acoplamento eletroquímico em um meio poroso argiloso adotando técnicas de homogeneização de estruturas periódicas. Consideramos o meio poroso uma caulinita saturada por uma solução eletrolítica composta por um solvente aquoso e quatro solutos iônicos monovalentes Na+, H+, Cl-, OH-. Na escala nanoscópica adotamos a modelagem da dupla camada elétrica onde o potencial elétrico e a densidade de carga são governados pelo problema de Poisson-Boltzmann. Incorporamos ao modelo nanoscópico as reações de protonação/deprotonação entre o fluido e a superfície da partícula argilosa e quantificamos numericamente a dependência da carga superficial com o pH da solução eletrolítica. Na escala microscópica, ou escala do poro, o movimento da solução aquosa é governado pelo problema de Stokes e o transporte dos íons pelas equações de Nernst-Planck. As equações microscópicas são suplementadas por condições de contorno de deslizamento da componente tangencial do campo de velocidade e de adsorção dos íons que representam a média do modelo posto na escala nanoscópica. A partir dos modelos nanoscópico/microscópico desenvolvemos a homogeneização do problema derivando o modelo na escala de Darcy (macroscópica) com os respectivos problemas de fechamento para os coeficientes das equações efetivas postos na célula periódica. Finalmente discretizamos o modelo macroscópico utilizando o método de volumes finitos e realizamos simulações numéricas em regimes permanente e transitório do processo de descontaminação de um solo argiloso por técnicas de eletrocinética. Os resultados ilustram a forte dependência da eletroremediação com o pH da solução.

O presente trabalho trata da modelagem da condução de calor transiente com geração de calor em meios heterogêneos, e tem o objetivo de desenvolver um modelo multiescala adequado a esse fenômeno. Já existem modelos multiescala na literatura relacionados ao problema proposto, e que são válidos para os seguintes casos: (a) o elemento de volume representativo tem tamanho desprezível quando comparado ao comprimento característico macroscópico (e como consequência, a microescala tem inércia térmica desprezível); ou (b) a geração de calor é homogênea na microescala. Por outro lado, o modelo proposto nesta tese, o qual é desenvolvido utilizando uma descrição variacional do problema, pode ser aplicado a elementos de volume representativos finitos e em condições em que a geração de calor é heterogênea na microescala. A discretização temporal (diferenças finitas) e as discretizações espaciais na microescala e na macroescala (método dos elementos finitos) são apresentadas em detalhes, juntamente com os algoritmos necessários para implementar a solução do problema. Nesta tese são apresentados casos numéricos simples, procurando verificar não só o modelo teórico multiescala desenvolvido, mas também a implementação feita. Para tanto, são analisados, por exemplo, (a) casos em que considera-se a microescala um material homogêneo, tornando possível a comparação da solução multiescala com a solução convencional (uma única escala) pelo método dos elementos finitos, e (b) um caso em um material heterogêneo para o qual a solução completa, isto é, modelando diretamente os constituintes no corpo macroscópico, é obtida, tornando possível a comparação com a solução multiescala. A solução na microescala para vários casos analisados nesta tese sofre grande influência da inércia térmica da microescala. Para demonstrar o potencial de aplicação do modelo multiescala, simula-se a cura de um elastômero carregado com negro de fumo. Embora a simulação demonstre que a inércia térmica não precise ser considerada para esse caso em particular, a aplicação da presente metodologia torna possível modelar a cura do elastômero diretamente sobre a microescala, uma abordagem até então não utilizada no contexto de métodos multiescala. Essa metodologia abre a possibilidade para futuros aperfeiçoamentos da modelagem do estado de cura. / This work deals with the modeling of transient heat conduction with heat generation in heterogeneous media, and its objective is to develop a proper multiscale model for this phenomenon. There already exist multiscale models in the literature related to this proposed problem, and which are valid for the following cases: (a) the representative volume element has a negligible size when compared to the characteristic macroscopic size (and, as a consequence, the microscale has a negligible thermal inertia); or (b) the heat generation is homogeneous at the microscale. On the other hand, the model proposed in this thesis, which is developed using a variational description of the problem, can be applied to finite representative volume elements and in conditions in which the heat generation is heterogeneous at the microscale. The time discretization (finite difference) and the space discretizations at both the microscale and the macroscale (finite element method) are presented in details, together with the algorithms needed for implementing the solution of the problem. In this thesis, simple numerical cases are presented, aiming to verify not only the theoretical multiscale model developed, but also its implementation. For this, it is analyzed, for instance, (a) cases in which the microscale is taken as a homogeneous material, making it possible the comparison of the multiscale solution with the conventional solution (one single scale) by the finite element method, and (b) a case in a heterogeneous material for which the full solution, that is, modeling all constituents directly on the macroscale, is obtained, making it possible the comparison with the multiscale solution. The solution at the microscale for several cases analyzed in this thesis suffers a large influence of the microscale thermal inertia. To demonstrate the application potential of the multiscale model, the cure of a carbon black loaded elastomer is simulated. Although the simulation shows that the thermal inertia does not have to be considered for this case in particular, the application of the present methodology makes it possible to model the cure of the elastomer directly at the microscale, an approach not used in multiscale methods context until now. This methodology opens the possibility for future improvements of the state of cure modeling.