Prédire l’évolution de la perméabilité avec la fissuration constitue un objectif primordial afin d’évaluer les conséquences d’un chargement mécanique sur la durabilité et l’étanchéité des structures. À l’issu de ce travail, un modèle d’évolution du tenseur de perméabilité est proposé. Ce modèle, qui est intégré dans le cadre de la poromécanique et de la théorie de l’endommagement,permet de prédire l’évolution anisotrope du tenseur de perméabilité en fonction de la fissuration. L’originalité de ce travail réside dans la prise en compte des ouvertures de fissure et des tailles anisotropes de l’élément fini durant la construction du tenseur de perméabilité. Ceci permet au débit total d’être indépendant du choix du maillage. Ce modèle est ensuite utilisé pour simuler le débit de fuite dans un tirant en béton armé ainsi que le creusement et la consolidation poroviscoplastique d’une galerie souterraine destinée au stockage profond de déchets radioactifs. Pour cette dernière application, la prise en compte de l’anisotropie induite par la fissuration sur le tenseur de Biot est considérée via une loi issue de l’homogénéisation. Les résultats fournis par ce modèle sont confrontés aux mesures expérimentales in situ. / Cracking in structures significantly affects their durability, water transfer and ultimately their safety. This structural disorder provides a preferential path for the penetration of fluids and contributes significantly to the deterioration of structures. This work provides a macroscopic model intended to predict the change of permeability with respect to cracking. The proposed development is implemented within an orthotropic damage model. It assumes an initially isotropic permeability tensor which becomes anisotropic with damage. The objectivity of the hydraulic response with respect to the finite element mesh is ensured by considering the crack localization problem when building the permeability tensor. The model was used to simulate the flow rate through a reinforced concrete element subjected to tensile loading, as well as to simulate the excavation and the poro-visco-plastic consolidation of an underground gallery designed to store radioactive waste. For the latter application, the induced anisotropy of Biot’s tensor was taken into account using the results provided by the homogenization theory. The simulation results were compared with experimental measurements.

The adult mammary gland is comprised of a bi-layered epithelium of luminal and myoepithelial cells surrounded by an adipocyte-rich fat pad, a highly collagenous extra-cellular matrix (ECM) and a number of other stromal and endothelial cell types. Mammary stem cells (MaSCs) reside within the epithelium and these are capable of repopulating a mammary fat pad that is devoid of epithelium, upon transplantation. It was sought to recapitulate this process of MaSCs repopulating a fat pad using a synthetic fat pad, engineered from a collagen scaffold invested with adipocytes, to provide an in vitro 3D model. Fluorescently tagged murine Axin2-expressing cells were obtained from transgenic mice and seeded into these scaffolds and cultured, mimicking the process of fat pad repopulation. Immunohistochemical analysis demonstrated that Axin2+ myoepithelial cells were rarely capable of forming bi-layered structures that expressed correct myoepithelial localisation and resemblance to a luminal morphology. Breast tumours surrounded by anisotropic (directional) collagen fibres running perpendicular to the tumour boundary are more aggressive and associated with poor patient prognosis. To recapitulate this anisotropic collagen phenotype in vitro, an ice-templating technique was used to modify the structure of the collagen scaffolds producing both non-directional (isotropic) and anisotropic internal architectures. Tumour cells from various breast cancer cell lines were seeded into both isotropic and anisotropic scaffolds to investigate whether this approach could distinguish cell type-specific migratory ability and whether anisotropy affected migration efficiency. Following analysis by confocal microscopy and ImageJ, anisotropic scaffolds were observed to enhance the migratory potential of MDA-MB-231 breast cancer cells. These results highlight the importance of collagen alignment and provide a reproducible method to quantitatively measure cell migration in 3D for cells derived from different breast cancer subtypes. Building on these data, the protocol was adapted to permit the direct investigation of tumour biopsy material. Given the heterogeneity of breast tumours, it was considered important to maintain tumour architecture and stromal components. Thus, murine mammary tumour fragments from two different established mammary cancer models were utilised and cultured in anisotropic collagen scaffolds in the presence or absence of adipocytes to allow an investigation of their influence on tumour cell migration. Further experiments included addition of various therapeutic drugs followed by immunofluorescence microscopy coupled with an optical clearing technique. These data demonstrated the utility of the model in determining both the rate and capacity of tumour cells to migrate through the engineered stroma while shedding light also on the mode of migration. Moreover, the response of different mammary tumour types to chemotherapeutic drugs could be could be readily quantified. To humanize the fat pad for subsequent human tissue analysis, human mesenchymal stem cells (MSC) were obtained from reduction mammoplasties and immortalised, before differentiating them into adipocytes within anisotropic collagen scaffolds. Human breast cancer cells were fluorescently tagged for tracking using lentiviral methods and were seeded into scaffolds invested with differentiated MSCs. Both cell types were successfully co-cultured for 7 days and imaged using multiphoton methods.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / In this work a study of the exchange interaction between ferromagnetic (NiFe) and antiferromagnetic (IrMn) layers was done through structural, magnetic and electric characterization. NiFe/IrMn/Ta films were grown with different number of repetitions of this basic structure aiming to evaluate possible changes on the magnetic anisotropies presented by the samples. It was implanted in the Laboratório de Magnetismo e Materiais Magnéticos a system in order to measure the Anisotropic Magnetorresistance (AMR) as function of the applied field angle. The AMR consists in a change of the eletric resistance of a ferromagnetic material as function of the angle between the electric current and the magnetization of the material and, by this way, sensible to changes in the anisotropy presented by the samples. It is presented a simple model to calculate the AMR as function of the angle field and, by comparing with the experimental curves, to obtain the magnetic parameters who describe the system. In the model the equilibrium direction of the magnetization is obtained from the minimization of the free magnetic energy, which is given by the Zeeman, uniaxial, unidirectional and manetostatic energies. The AMR curves present an assymetry around 180 degrees when measured at fields below the bias one. According to the fittings, it was found that such assymetry can be due by a misalignment between the anisotropy axis (uniaxial and unidirectional) or by a misalignment between the measuring current and the easy magnetic axis of the samples. It was not observed, as expected, an expressive increase of the anisotropy dispersion of the uniaxial anisotropy with the increase of the number of trilayers. The same was observed with the bias and coercive fields. / Neste trabalho, o estudo da interação de troca entre as camadas ferromagnética (NiFe) e antiferromagnética (IrMn) em multicamadas foi realizado através da caracterização estrutural, magnética e de transporte elétrico. Foram crescidos filmes de NiFe/IrMn/Ta com diferentes números de repetições dessa estrutura básica com o objetivo de avaliar as possíveis modificações nas anisotropias apresentadas pelas amostras. Foi implantado no Laboratório de Magnetismo e Materiais Magnéticos (LMMM) um sistema para medidas de Magnetorresistência Anisotrópica (AMR) em função do ângulo de aplicação do campo. A AMR consiste na variação da resistência elétrica e a magnetização do material e, portanto, sensível as modificações de anisotropia nas amostras. É apresentado um modelo simples para calcular as curvas de AMR em função do ângulo do campo e, na comparação com as curvas experimentais obter os parâmetros magnéticos que descrevem o sistema. No modelo, a direção de equilíbrio da magnetização é obtida a partir da minimização da energia livre magnética, que por sua vez é dada pela soma da energia Zeeman, uniaxial, unidirecional e magnetostática. As curvas de AMR apresentam uma assimetria em torno de 180 graus quando medidas em valores de campo menores que o campo de Bias. De acordo com os ajustes, foi verificado que esta assimetria pode ser causada tanto por um desalinhamento entre os eixos de anisotropias (uniaxial ou unidirecional) como por um desalinhamento entre o eixo da corrente de medição e o eixo de fácil magnetização da amostra. Não foi observado, conforme esperado, um aumento expressivo na dispersão da anisotropia uniaxial com o aumento do número de repetições das tricamadas. O mesmo ocorrendo com os valores dos campos de Bias e coercivo.

Cortical bone tissue - one of the most intriguing materials found in nature - demonstrate some fascinating behaviours that have attracted great attention of many researchers from all over the world. In contrast to engineering materials, bone has its unique characters: it is a material that has both sufficient stiffness and toughness to provide physical support and protection to internal organs and yet adaptively balanced for its weight and functional requirements. Its structure and mechanical properties are of great importance to the physiological functioning of the body. Still, our understanding on the mechanical deformation processes of cortical bone tissue is rather limited. Penetration into a bone tissue is an intrinsic part of many clinical procedures, such as orthopaedic surgery, bone implant and repair operations. The success of bone-cutting surgery depends largely on precision of the operation and the extent of damage it causes to the surrounding tissues. The anisotropic behaviour of cortical bone acts as a distinctive protective mechanism and increases the difficulty during cutting process. A comprehensive understanding of deformation and damage mechanisms during the cutting process is necessary for improving the operational accuracy and postoperative recovery of patients. However, the current literature on experimental results provides limited information about processes in the vicinity of the cutting tool-bone interaction zone; while; numerical models cannot fully describe the material anisotropy and the effect of damage mechanisms of cortical bone tissue. In addition, a conventional finite-element scheme faces numerical challenges due to large deformation and highly localised distortion in the process zone. This PhD project is aimed at bridging the gap in current lack of understanding on cutting-induced deformation and fracture processes in the cortical bone tissue through experimental and numerical approaches. A number of experimental studies were accomplished to characterise the mechanical behaviour of bovine cortical bone tissue and to analyse deformation and damage mechanisms associated with the cutting process II along different bone axes in four anatomic cortices, namely, anterior, posterior, medial and lateral. These experiments included: (1) a Vickers hardness test to provide initial assessments on deformation and damage processes in the cortical bone tissue under a concentrated compressive load; (2) uniaxial tension and compression tests, performed to understand the effect of orientation and local variability of microstructure constituents on the macroscopic material properties of cortical bone; (3) fracture toughness tests, aimed at elucidating the anisotropic character of fracture toughness of cortical bone and its various fracture toughness mechanisms in relation to different orientations; (4) penetration tests, conducted to evaluate and validate mechanisms involved in bone cutting as well as orientation associated anisotropic deformation and damage processes at various different cortex positions. Information obtained in these experimental studies was used to assist the development of advanced finite-element models: (1) the effective homogenised XFEM models developed in conjunction with three-point bending test to represent a macroscopically, anisotropic elasticplastic fracture behaviour of cortical bone tissue; (2) three microstructured XFEM models to further investigate the effect of the randomly distributed microstructural constituents on the local fracture process and the variability of fracture toughness of cortical bone; (3) a novel finite-element modelling approach encompassing both conventional and SPH elements, incorporating anisotropic elastic-plastic material properties and progressive damage criteria to simulate large deformation and damage processes of cortical bone under penetration. The established models can adequately and accurately reflect large deformations and damage processes during the penetration in bone cutting. The results of this study made valuable contributions to our existing understanding of the mechanics of cortical bone tissue and most importantly to the understanding of its mechanical behaviours during the cutting process.

Doctor of Philosophy / Biochemistry and Molecular Biophysics / Phillip E. Klebba / The goal of the research included in this dissertation is to provide a more complete model of the role of TonB, an energy transducing protein that resides in the inner membrane and is an essential component of the iron transport of Escherichia coli under iron-starved conditions. Using fluorescent hybrid proteins, the anisotropy of TonB in the cytoplasmic membrane (CM) of Escherichia coli was determined. With the aim of understanding the bioenergetics of outer membrane (OM) iron transport, the dependence of TonB motion on the electrochemical gradient and the effect of CM proteins ExbB and ExbD on this phenomenon was monitored and analyzed. The native E. coli siderophore, enterobactin chelates Fe⁺³ in the environment and ferric enterobactin (FeEnt) enters the cell by energy- and TonB-dependent uptake through FepA, its OM transporter. The TonB-ExbBD complex in the CM is hypothesized to transfer energy to OM transporters such as FepA. We observed the polarization of GFPTonB hybrid proteins and used metabolic inhibitors (CCCP, azide and dinitrophenol) and chromosomal deletions of exbBD to study these questions. The results showed higher anisotropy (R) values for GFP-TonB in energy-depleted cells, and lower R-values in bacteria lacking ExbBD. Metabolic inhibitors did not change the anisotropy of GFP-TonB in ΔexbBD cells. These findings suggest that TonB undergoes constant, energized motion in the bacterial CM, and that ExbBD mediates its coupling to the electrochemical gradient. By spectroscopic analyses of extrinsic fluorophore labeled site-directed Cys residues in 7 surface loops of Escherichia coli FepA, binding and transport of ferric enterobactin (FeEnt) was characterized. Changes in fluorescence emissions reflected conformational motion of loops that altered the environment of the fluorophore, and we observed these dynamics as quenching phenomena during FeEnt binding and transport in living cells or outer membrane vesicles. Cys residues in each of the 7 surface loops (L2, L3, L4, L5, L7 L8, and L11) behaved individually and characteristically with regard to both fluorophore maleimide reactivity and conformational motion. Fluorescence measurements of FeEnt transport, by either microscopic or spectroscopic methodologies, demonstrated that ligand uptake occurs uniformly throughout the cell envelope, and susceptibility of FeEnt uptake to the proton ionophore m-chlorophenyl hydrazone (CCCP) at concentrations as low as 5 uM. The latter result recapitulates the sensitivity of inner membrane major facilitator transporters to CCCP (Kaback, 1974), providing further evidence of the electrochemical gradient as a driving force for TonB-dependent metal transport.

abstract: Among electrical properties of living tissues, the differentiation of tissues or organs provided by electrical conductivity is superior. The pathological condition of living tissues is inferred from the spatial distribution of conductivity. Magnetic Resonance Electrical Impedance Tomography (MREIT) is a relatively new non-invasive conductivity imaging technique. The majority of conductivity reconstruction algorithms are suitable for isotropic conductivity distributions. However, tissues such as cardiac muscle and white matter in the brain are highly anisotropic. Until recently, the conductivity distributions of anisotropic samples were solved using isotropic conductivity reconstruction algorithms. First and second spatial derivatives of conductivity (∇σ and ∇2σ ) are integrated to obtain the conductivity distribution. Existing algorithms estimate a scalar conductivity instead of a tensor in anisotropic samples. Accurate determination of the spatial distribution of a conductivity tensor in an anisotropic sample necessitates the development of anisotropic conductivity tensor image reconstruction techniques. Therefore, experimental studies investigating the effect of ∇2σ on degree of anisotropy is necessary. The purpose of the thesis is to compare the influence of ∇2σ on the degree of anisotropy under two different orthogonal current injection pairs. The anisotropic property of tissues such as white matter is investigated by constructing stable TX-151 gel layer phantoms with varying degrees of anisotropy. MREIT and Diffusion Magnetic Resonance Imaging (DWI) experiments were conducted to probe the conductivity and diffusion properties of phantoms. MREIT involved current injection synchronized to a spin-echo pulse sequence. Similarities and differences in the divergence of the vector field of ∇σ (∇2σ) among anisotropic samples subjected to two different current injection pairs were studied. DWI of anisotropic phantoms involved the application of diffusion-weighted magnetic field gradients with a spin-echo pulse sequence. Eigenvalues and eigenvectors of diffusion tensors were compared to characterize diffusion properties of anisotropic phantoms. The orientation of current injection electrode pair and degree of anisotropy influence the spatial distribution of ∇2σ. Anisotropy in conductivity is preserved in ∇2σ subjected to non-symmetric electric fields. Non-symmetry in electric field is observed in current injections parallel and perpendicular to the orientation of gel layers. The principal eigenvalue and eigenvector in the phantom with maximum anisotropy display diffusion anisotropy. / Dissertation/Thesis / Masters Thesis Bioengineering 2015

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / In order to determine the complex permeability of ferromagnetic samples in the GHz range, measurement techniques with transmission lines are most appropriate. These techniques use the modification of the scattering coefficients of the transmission line, induced by the sample, to obtain the permeability. In this work we have presented a shorted microstrip transmission line, suitable for the study of magnetic films as thin as 100 nm, in the 100 MHz - 5 GHz frequency range. The thin film permeability is calculated from the measurements of the reflection coefficient of a microstrip as a function of frequency and magnetic field, in the following situations: with the empty microstrip, loaded only with the substrate and loaded with the ferromagnetic film deposited on the substrate. To evaluate the developed microstrip, it was grown, by magnetron sputtering, Permalloy thin films with thickness ranging from 100 to 1000 nm. In plane magnetization measurements have shown that below a critical thickness, tcr ∼ 275 nm, the thin films present a behavior characteristic of systems with uniaxial anisotropy, this was also confirmed by the study of their dynamic properties. For this films the permeability measurement were well described by the expression called transverse permeability approximation. However, above tcr the hysteresis loops, measured in orthogonal directions, are almost identical and present the shape typical when there is an anisotropy component perpendicular to the film s plane. In these films it were observed the presence of more than just one resonance peak in the permeability spectra. / Para obter a permeabilidade complexa de amostras ferromagnéticas na faixa de GHz, técnicas de medidas com linhas de transmissão são as mais adequadas. Essas técnicas utilizam a variação dos parâmetros de espalhamento da linha, induzida pela amostra, para obtenção da permeabilidade. Nesse trabalho apresenta-se uma linha de transmissão tipo microstrip com uma porta e terminação em curto circuito, adequada para o estudo de filmes magnéticos tão finos quanto 100 nm, em frequências entre 100 MHz e 5 GHz. A permeabilidade do filme é calculada a partir de medidas do coeficiente de reflexão da microstrip em função da frequência e do campo magnético, em diferentes situações: vazia, carregada apenas com o substrato e carregada com o filme ferromagnético depositado sobre o substrato. Para avaliar a microstrip desenvolvida foram crescidos, por magnetron sputtering, filmes de Permalloy com espessuras entre 100 e 1000 nm. Curvas de magnetização medidas no plano revelaram que até uma espessura crítica, tcr ∼ 275 nm, os filmes apresentam um comportamento característico de filmes com anisotropia uniaxial, o que também foi constatado no estudo de suas propriedades dinâmicas. Para esses filmes as medidas de permeabilidade são bem descritas através de uma expressão conhecida como aproximação para a permeabilidade transversal. No entanto, a partir de tcr as curvas de histerese dos filmes, medidas em direções ortogonais, são quase idênticas e apresentam uma forma típica de quando existe uma componente da anisotropia perpendicular ao plano do filme. Nesses filmes observou-se a presença de mais de um pico de ressonância nos espectros de permeabilidade.

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Les films minces déposés sur des substrats flexibles ont été intensivement étudiés ces dernières années en raison de leur nombreuses applications en électronique flexible. Depuis peu, l'électronique flexible est étendu aux matériaux magnétiques conduisant ainsi au domaine émergeant de la magnéto-électronique flexible actuellement à l'avant garde des sujets de recherche de la spintronique. Ce travail de thèse est dédié à l'étude des propriétés magnéto-mécaniques de films minces magnétiques (Ni, NiFe, Co2FeAl, CoFeB, FeCuNbSi) sur des substrats flexibles. Les analyses structurales ont montré que les films de Ni et de CFA sont polycristallins non-texturés ; le CFB est amorphe. Par conséquent, les propriétés élastiques et magnéto-élastiques de ces films sont considérées comme étant isotropes. Une technique basée sur une utilisation conjointe d'essai mécanique, la résonance ferromagnétique (FMR) et la corrélation d'images numériques (CIN) a été développée pour étudier les propriétés magnéto-mécaniques de films minces sur substrats flexibles. A l'aide de cette méthode, il est possible de suivre l'évolution de l'anisotropie résiduelle omniprésente dans les films magnétiques sur substrats flexibles. Cette anisotropie est liée aux propriétés mécaniques contrastées lorsqu'on dépose un film mince rigide (grand module d'Young) sur un substrat flexible (petit module d'Young). L'effet du recuit sur les propriétés élastiques et magnéto-élastiques a été soigneusement étudié dans le film CFB validant ainsi l'intérêt porté à ses alliages pour des applications en spintronique. Enfin, la résonance ferromagnétique est employé en balayage en fréquence pour suivre la variation de la direction de l'aimantation en fonction des déformations induites par l'application de tension électrique sur l'actionneur piézoélectrique. Un retournement de 90° de la direction de l'aimantation dans le film Co2FeAl sur substrat flexible de Kapton® est observé. / Thin films deposited on flexible substrates have been widely studied in the last decades due to the numerous applications in flexible electronics. Recently, flexible electronics have been extended to magnetic materials leading to the so-called emerging feld of flexible magnetoelectronics which is actually at the cutting-edge of spintronics research topics.This thesis is devoted to the study magnetomechanical properties of magnetic thin films (Ni, NiFe, Co2FeAl, CoFeB, FeCuNbSi) on flexible substrates. Structural analysis have 130 Abstracts hown that the Ni and CFA films are found to be polycrystalline with no strong preferred orientations ; the CFB film is amorphous. Consequently, the elastic and magnetoelastic properties are isotropic. For the study of the magnetomechanical properties, a set-up based on a jointly use of deformation test (bending or piezoactuation), ferromagnetic resonance (FMR) and digital image correlation (DIC) have been developped. Thanks to this method, it is possible to follow the evolution of the inescapable residual anisotropy encountered in magnetic thin films on flexible substrates under deformation and to determine the effective coefficient of magnetostriction of the films (sometimes unknown).This residual anisotropy is ascribed to contrasted mechanical strength when a sti thin film is deposited on a compliant substrate. The effect of the annealing temperature on the elastic and magnetoelastic have been studied carefully in CFB validating then theinterest on such alloys for spintronics applications. Finally, we have employed FMR inits sweep frequency mode to study the effective evolution of magnetization direction as function of the voltage-induced strains. A 90-degree magnetization rotation in Co2FeAl thin film on Kapton® polyimide substrate is observed.