Cystic fibrosis (CF) is the most common lethal genetic disease in the white population. It is due to mutations in the gene coding for the cystic fibrosis transmembrane conductance regulator (CFTR), a protein that functions mainly as a cAMP-activated chloride channel. The disease impairs ion and water transport in epithelia-lined organs such as airways, digestive tract, reproductive epithelium and sweat glands. At present the only therapy is symptomatic and development of curative treatment depends on uncovering the links between the defective CFTR and the disease, as well as on improving end-point measurements. A method has been established for studying ion transport in an easily accessible cell type (nasal epithelial cells) from normal and cystic fibrosis patients by X-ray microanalysis. This method represents a rather simple and direct way of measuring simultaneously several chemical elements of biological interest. Studies of chloride transport by means of a fluorescent indicator (MQAE) in nasal epithelial cells from CF patients showed that the phenotype cannot exclusively be explained by the CFTR activity in patients with severe genotype. A common Portuguese CFTR mutation (A561E) causes protein mislocalization in the endoplasmic reticulum similar to the most common CF mutation (ΔF508) and thus it should be possible to treat it with the same pharmacological strategies. Chronic treatment of CF airway epithelial cells with nanomolar concentrations of colchicine increased the chloride efflux via chloride channels other than CFTR, strengthening the notion that colchicine could be beneficial to CF patients. Successful in vitro transfection of CF airway epithelial cells with cationic vectors was possible with short incubation times. Heparin added at the end of the transfection incubation time could help to maintain the viability of the cells, without interfering with the transfection efficiency. It seems possible that heparin could be an adjuvant for non-viral mediated gene therapy.

Concrete is a popular construction material for bridges, due to its high durability and energy efficiency. An important concern for concrete bridges is the possible occurrence of chloride- induced corrosion in prestressing strands and reinforcing bars, which may substantially impact the service life of such structures. Chloride- induced corrosion is a complicated electrochemical process which is affected by heat transfer, moisture flow and transport of chemical species through the concrete pore network. Reliable and robust analytical tools are required to allow multi-physics simulations of steel corrosion. This study has developed a nonlinear finite element analysis program, called VT-MultiPhys, to enable multi-physics simulations, including analyses of chloride-induced corrosion. The program includes constitutive laws, element formulations and global solution schemes to allow the analysis of steady-state (static) and time-dependent (dynamic) problems, involving multiple, coupled processes such as mechanical deformation, heat transfer, mass flow and chemical reactions combined with advective/diffusive transport of the various species. Special analysis schemes, based on the streamline-upwind Petrov-Galerkin (SUPG) method, have also been implemented to address the spatial instabilities which characterize analyses of advection-dominated transport. The finite element modeling scheme, constitutive laws and boundary conditions for analysis of chloride-induced corrosion are described in detail. The constitutive laws can be combined with inelastic material models to capture the damage (e.g., cracking) due to chloride-induced corrosion. A set of verification analyses is presented, to demonstrate the capabilities of VT-MultiPhys to conduct different types of simulations and reproduce the closed-form analytical solutions of simple cases. Validation analyses for heat conduction, moisture flow and chloride transport, using data from experimental tests in the literature, are also presented. / Master of Science / The deterioration of concrete structures and infrastructures due to the chloride-induced corrosion in prestressing strands and reinforcing bars may substantially impact the service life of such structures. Chloride-induced corrosion is a complicated electrochemical process which is initiated and proceeds due to the chloride attacks at the surfaces of concrete structures and ends in the volume expansion, cracking and spalling of concrete. Due to the lack of comprehensive modeling tool, which can simultaneously comprise the influential factors in chloride-induced corrosion, the realistic estimation of the service life of reinforced concrete structures is still challenging. Reliable and robust analytical tools are required to allow multi-physics simulations of steel corrosion. This study has developed a comprehensive finite element analysis program, called VT-MultiPhys, for calculating and monitoring the contribution of chloride ions to chloride-induced corrosion during service life of concrete structures. The present analysis program enables modeling of the coupled physical process including heat transfer, moisture flow and transport of chemical species through the concrete pore network. Also, by modeling the influence of flexural cracks on chloride transport in concrete, the analysis program is able to predict the rate of steel corrosion in cracked concrete structures. A set of verification analyses is presented, to demonstrate the capabilities of VT-MultiPhys to conduct different types of simulations of heat conduction, moisture flow and chloride transport and the comparison is found to be satisfactory. The element formulations and solution algorithms in VT-MultiPhys also allow the investigation of other long-term deterioration mechanisms, such as carbonation-induced corrosion, alkali-silika reaction (ASR) and sulfate attack. The present contribution will hopefully enable and facilitate future research in these topics, through the formulation and implementation of proper constitutive laws and chemical reaction equations.

La membrane cellulaire est principalement une bicouche phospholipidique constituant une barrière qui régule les échanges entre la cellule et son environnement. Son intérieur hydrophobe empêche le passage d’espèces hydrophiles, chargées, de grande masse moléculaire et polaires, qui sont généralement transportées par des protéines à travers la bicouche. Dans certains cas de systèmes défectueux (e.g. les canalopathies), l’équilibre des concentrations en ions à l’intérieur et à l’extérieur des cellules est perturbé et les cellules sont compromises. C’est pourquoi le développement de transporteurs transmembranaires synthétiques est nécessaire. De nombreux travaux ont été faits dans le développement de transporteurs synthétiques d’anions (particulièrement du chlorure). Dans cette thèse, nous présentons nos travaux sur un nouveau transporteur d’anion appelé axe parapluie, capable de changer de conformation dépendamment de la polarité de son environnement. Dans un premier temps, nous avons conçu le design, puis synthétisé ces axes parapluie qui montrent une importante activité en tant que transporteur de chlorures. Ces composés réunissent deux concepts : - Le parapluie, constitué d’acides biliaires amphiphiles (une face hydrophile, une face hydrophobe). La flexibilité des articulations combinée à la grande surface des acides choliques permettent d’empêcher les interactions défavorables entre les parties hydrophiles et hydrophobes, ce qui facilite l’insertion dans la bicouche. - Un site ammonium secondaire en tant que site de reconnaissance, capable de former des ponts hydrogène avec des ions chlorure. De plus, l’axe peut complexer une roue de type éther couronne pour former un pseudo-rotaxane ou rotaxane parapluie ce qui résulte en l’inhibition partielle de leurs propriétés de transport. Ceci nous mène au second objectif de cette thèse, le développement d’un nouveau moyen de transport pour les médicaments cycliques. Certains macrocycles polaires et biologiquement actifs tels que les nactines ont besoin d’atteindre leur objectif à l’intérieur de la cellule pour jouer leur rôle. La membrane cellulaire est alors un obstacle. Nous avons imaginé tirer profit de notre axe parapluie pour transporter un médicament cyclique (en tant que roue d’un rotaxane parapluie). Les assemblages des rotaxanes parapluie furent accomplis par la méthode de clipage. Le comportement de l’axe et du rotaxane parapluie fut étudié par RMN et fluorimétrie. Le mouvement du parapluie passant d’une conformation fermée à exposée dépendamment du milieu fut observé pour le rotaxane parapluie. Il en fut de même pour les interactions entre le rotaxane parapluie et des vésicules constituées de phospholipides. Finalement, la capacité du rotaxane parapluie à franchir la bicouche lipidique pour transporter la roue à l’intérieur de la vésicule fut démontrée à l’aide de liposomes contenant de la α-chymotrypsine. Cette dernière pu cliver certains liens amide de l’axe parapluie afin de relarguer la roue. / The cell membrane is a phospholipid bilayer barrier that controls the exchanges between the cell and its environment. Its hydrophobic core prevents the entrance of hydrophilic, charged or large polar species that are transported through the bilayer by proteins. In some dysfunctional systems e.g. channelopathies), the balance of ion concentrations between the interior and exterior of the cell is no longer insured and the cell’s health is compromised. That is why the synthesis of synthetic transmembrane transporters is needed. There have been many synthetic anion carriers (especially chloride) developed in this area using different strategies. In this thesis we present our work on a new anion transporter, an umbrella thread. First, we designed and synthesized umbrella threads that showed significant chloride transport activity. These compounds combine two concepts: - the umbrella moiety, made from facial amphiphilic bile acids. The flexibility and large surface of the cholic acids can shield disfavored interactions between hydrophilic and hydrophobic elements that should ease their insertion into the bilayer. - a secondary ammonium recognition site on the thread that can form hydrogen bonds with chloride ions. Furthermore, the thread moiety is able to complex a crown-ether like wheel to form an umbrella pseudo-rotaxane or rotaxane that showed partially inhibited properties for chloride transport. This leads us to the second goal of this thesis, i.e. the development of a new vehicle for drug delivery. Some biologically active polar macrocycles (e.g. nactins) need to reach their target inside the cell to be efficient. The cell membrane also represents an obstacle here. In our work, we imagined using an umbrella thread as the vehicle for the cyclic drug as the wheel of the umbrella rotaxane). The umbrella rotaxanes were successfully assembled by the clipping method. The behavior of both the umbrella thread and umbrella rotaxane was extensively studied by NMR and fluorimetry. The umbrella motion from a shield conformation to an exposed one depending on the environment was observed for the rotaxane. Interactions between the umbrella rotaxane and phospholipid vesicles were also noticed. Finally, its ability to cross the lipid bilayer to deliver the wheel inside the vesicle was shown with α-chymotrypsin-filled liposome assays. This enzyme was able to cleave amide bonds on the umbrella thread to release the wheel.

La membrane cellulaire est principalement une bicouche phospholipidique constituant une barrière qui régule les échanges entre la cellule et son environnement. Son intérieur hydrophobe empêche le passage d’espèces hydrophiles, chargées, de grande masse moléculaire et polaires, qui sont généralement transportées par des protéines à travers la bicouche. Dans certains cas de systèmes défectueux (e.g. les canalopathies), l’équilibre des concentrations en ions à l’intérieur et à l’extérieur des cellules est perturbé et les cellules sont compromises. C’est pourquoi le développement de transporteurs transmembranaires synthétiques est nécessaire. De nombreux travaux ont été faits dans le développement de transporteurs synthétiques d’anions (particulièrement du chlorure). Dans cette thèse, nous présentons nos travaux sur un nouveau transporteur d’anion appelé axe parapluie, capable de changer de conformation dépendamment de la polarité de son environnement. Dans un premier temps, nous avons conçu le design, puis synthétisé ces axes parapluie qui montrent une importante activité en tant que transporteur de chlorures. Ces composés réunissent deux concepts : - Le parapluie, constitué d’acides biliaires amphiphiles (une face hydrophile, une face hydrophobe). La flexibilité des articulations combinée à la grande surface des acides choliques permettent d’empêcher les interactions défavorables entre les parties hydrophiles et hydrophobes, ce qui facilite l’insertion dans la bicouche. - Un site ammonium secondaire en tant que site de reconnaissance, capable de former des ponts hydrogène avec des ions chlorure. De plus, l’axe peut complexer une roue de type éther couronne pour former un pseudo-rotaxane ou rotaxane parapluie ce qui résulte en l’inhibition partielle de leurs propriétés de transport. Ceci nous mène au second objectif de cette thèse, le développement d’un nouveau moyen de transport pour les médicaments cycliques. Certains macrocycles polaires et biologiquement actifs tels que les nactines ont besoin d’atteindre leur objectif à l’intérieur de la cellule pour jouer leur rôle. La membrane cellulaire est alors un obstacle. Nous avons imaginé tirer profit de notre axe parapluie pour transporter un médicament cyclique (en tant que roue d’un rotaxane parapluie). Les assemblages des rotaxanes parapluie furent accomplis par la méthode de clipage. Le comportement de l’axe et du rotaxane parapluie fut étudié par RMN et fluorimétrie. Le mouvement du parapluie passant d’une conformation fermée à exposée dépendamment du milieu fut observé pour le rotaxane parapluie. Il en fut de même pour les interactions entre le rotaxane parapluie et des vésicules constituées de phospholipides. Finalement, la capacité du rotaxane parapluie à franchir la bicouche lipidique pour transporter la roue à l’intérieur de la vésicule fut démontrée à l’aide de liposomes contenant de la α-chymotrypsine. Cette dernière pu cliver certains liens amide de l’axe parapluie afin de relarguer la roue. / The cell membrane is a phospholipid bilayer barrier that controls the exchanges between the cell and its environment. Its hydrophobic core prevents the entrance of hydrophilic, charged or large polar species that are transported through the bilayer by proteins. In some dysfunctional systems e.g. channelopathies), the balance of ion concentrations between the interior and exterior of the cell is no longer insured and the cell’s health is compromised. That is why the synthesis of synthetic transmembrane transporters is needed. There have been many synthetic anion carriers (especially chloride) developed in this area using different strategies. In this thesis we present our work on a new anion transporter, an umbrella thread. First, we designed and synthesized umbrella threads that showed significant chloride transport activity. These compounds combine two concepts: - the umbrella moiety, made from facial amphiphilic bile acids. The flexibility and large surface of the cholic acids can shield disfavored interactions between hydrophilic and hydrophobic elements that should ease their insertion into the bilayer. - a secondary ammonium recognition site on the thread that can form hydrogen bonds with chloride ions. Furthermore, the thread moiety is able to complex a crown-ether like wheel to form an umbrella pseudo-rotaxane or rotaxane that showed partially inhibited properties for chloride transport. This leads us to the second goal of this thesis, i.e. the development of a new vehicle for drug delivery. Some biologically active polar macrocycles (e.g. nactins) need to reach their target inside the cell to be efficient. The cell membrane also represents an obstacle here. In our work, we imagined using an umbrella thread as the vehicle for the cyclic drug as the wheel of the umbrella rotaxane). The umbrella rotaxanes were successfully assembled by the clipping method. The behavior of both the umbrella thread and umbrella rotaxane was extensively studied by NMR and fluorimetry. The umbrella motion from a shield conformation to an exposed one depending on the environment was observed for the rotaxane. Interactions between the umbrella rotaxane and phospholipid vesicles were also noticed. Finally, its ability to cross the lipid bilayer to deliver the wheel inside the vesicle was shown with α-chymotrypsin-filled liposome assays. This enzyme was able to cleave amide bonds on the umbrella thread to release the wheel.