Magma-crust interaction in magma reservoirs and conduits is a crucial process during magma evolution and ascent. This interaction is recorded by crustal xenoliths that frequently show partial melting, inflation and disintegration textures. Frothy xenoliths are widespread in volcanic deposits from all types of geological settings and indicate crustal gas liberation. To unravel the observed phenomena of frothy xenolith formation we experimentally simulated the behaviour of crustal lithologies in volcanic conduits. We subjected various sedimentary lithologies to elevated temperature (maximum 916 °C) and pressure (maximum 160 MPa) in closed-system autoclaves. Experimental conditions were held constant between 24h and 5 days. Controlled decompression to atmospheric pressure then simulated xenolith ascent. Pressure release was a function of temperature decline in our setup. Temperature lapse rate proceeded exponentially; the mean rate during the first 30 minutes was 17.8 ˚C/min and the mean decompression rate during the same interval was 3.0 MPa/min, eventually reaching room temperature after approximately 5.5 hours of slow cooling. The experimental products have been analysed for internal textures by synchrotron X-ray μ-CT at a resolution of 3.4 – 9 microns/pixel. This method permits visualisation and quantification of vesicle volumes, -networks and-connectivity in 3D without destroying the sample. Experimental products closely reproduced textures of natural frothy xenoliths in 3D and define anevolutionary sequence from partial melting to gas exsolution and bubble nucleation that eventually leads to the development of three-dimensional bubble networks. Experimental P-T-t conditions and especially rock lithology proved decisive for degassing behaviour and ensuing bubble nucleation during decompression. Progressive bubble nucleation leads to subsequent bubble coalescence to form interconnected bubble networks. This, in turn, enables efficient gas liberation and release. Our results attest to significant potential of even very common crustal rock types to release volatiles and develop interconnected bubble networks upon heating and decompression in magmatic systems. Crustal volatile input from xenoliths affects magma rheology and may drive magmas to sudden explosive eruptions. Our experiments offer insight into the mechanism of how such crustal volatile liberation is accomplished.

Made available in DSpace on 2014-12-17T14:07:19Z (GMT). No. of bitstreams: 1 EduardoRDN_TESE.pdf: 2710171 bytes, checksum: 09b5f50c7446d0f076dc4edac8718d45 (MD5) Previous issue date: 2014-02-10 / The gas migration during the cementing of wells is one of the main problems of oil wells engineering. Its occurrence can cause severe problems since shortly to loss of control of the well after cementation. Recently, 20/04/2010 In an accident of major proportions in the Gulf of Mexico, among other factors, faulty cementing operation provided the gas migration, causing the accident, in which 11 people died and 17 were injured occurred. Besides the serious consequences that can be caused by gas migration, remediation of the problem, which is made by injecting cement in damaged areas, usually involves additional costs and is not always effective. Therefore, preventing gas migration to be preferred. Some methods are used to prevent the migration of the pressurized gas as the annular space, application of pressure pulses, reducing the height of the cement column compressible cement pastes of low permeability, pastes and to control free filtered water, and binders of thixotropic cement expandable and flexible. Thus, the cement pastes used to prevent gas migration must meet the maximum these methods. Thus, this study aimed to formulate a cement paste to prevent gas migration, using the expanded vermiculite, and evaluate the behavior of the folder trials necessary for use in oil wells. Free water content, rheological properties, compressive strength, loss of liquid phase sedimentation of solids, specific weight, thickening time and gas migration: The following tests were performed. The results show that meets the specifications paste formulated for use in oil wells and the use of expanded vermiculite contribute to the absorption of free water, thixotropy and low density. The absorption of free water is proven to result in zero percentage test free water content, thixotropy is observed with the high value of the initial gel strength (Gi) in testing rheological properties and low density is proven in test weight specific / A migra??o de g?s durante a cimenta??o de po?os ? um dos principais problemas da engenharia de po?os de petr?leo. Sua ocorr?ncia pode causar desde problemas pouco severos at? a perda de controle do po?o ap?s a cimenta??o. Recentemente, Em 20/04/2010 ocorreu um acidente de grandes propor??es no Golfo do M?xico, que dentre v?rios fatores, a falha na opera??o de cimenta??o proporcionou a migra??o de g?s, causando o acidente, onde 11 pessoas morreram e 17 ficaram feridas. Al?m das s?rias consequ?ncias que podem ser causadas pela migra??o de g?s, a remedia??o do problema, que ? feita pela inje??o de cimento nas zonas danificadas, geralmente envolve custos adicionais e nem sempre ? efetiva. Por isso, a preven??o da migra??o de g?s deve ser preferida. Alguns m?todos s?o utilizados para evitar a migra??o de g?s como a pressuriza??o do espa?o anular, aplica??o de pulsos de press?o, redu??o da altura da coluna de cimento, cimento compress?vel, pastas de baixa permeabilidade, pastas com controle de filtrado e ?gua livre, e pastas de cimento tixotr?picas, expans?veis e flex?veis. Deste modo, as pastas de cimento utilizadas para evitar migra??o de g?s devem atender ao m?ximo estes m?todos. Assim, este trabalho teve como objetivo formular uma pasta de cimento para evitar a migra??o de g?s, utilizando a vermiculita expandida, e avaliar o comportamento da pasta em ensaios necess?rios ? utiliza??o em po?os petrol?feros. Foram realizados os seguintes ensaios: teor de ?gua livre, propriedades reol?gicas, resist?ncia a compress?o, perda da fase liquida, sedimenta??o dos s?lidos, peso especifico, tempo de espessamento e migra??o de g?s. Os resultados mostram que a pasta formulada atende as especifica??es para utiliza??o em po?os de petrol?feros e que a utiliza??o da vermiculita expandida contribuiu para a absor??o da ?gua livre, tixotropia e baixa densidade. A absor??o da ?gua livre ? comprovada com o resultado de porcentagem zero no ensaio de teor de ?gua livre, a tixotropia ? verificada com o alto valor da for?a gel inicial (Gi) no ensaio de propriedades reol?gicas e a baixa densidade ? comprovada no ensaio de peso especifico

Bentonite is regarded as an ideal geomaterial for the engineering barrier system of a deep geological repository (DGR) where nuclear wastes are disposed, as it has several desirable properties for sealing the nuclear wastes, including low permeability, low diffusion coefficient, high adsorption capacity and proper swelling ability. Nevertheless, gas migration in saturated bentonite may undermine the sealing ability of the geomaterial. Previous experimental studies showed that the gas migration process is accompanied by complex hydromechanical (HM) behaviors, such as gas breakthrough phenomenon, development of preferential pathways, build-up of water pressure and total stress, nearly saturated state after gas injection test, localized consolidation, water exchange between clay matrix and developed fractures and self-sealing process. These experimentally observed behaviors should be properly modelled for conducting a reliable performance assessment for the geomaterial over the lifespan of DGR. In this thesis, two different coupled HM frameworks, i.e., one based on double porosity (DP) concept, referred to as coupled HM-DP framework, and the other on phase field (PF) method, referred to as coupled HM-PF framework, are proposed to simulate the gas migration process in saturated bentonite. For the coupled HM-DP framework, the saturated bentonite is assumed as a superposition of a MAcro-Continuum (MAC) and a MIcro-Continuum (MIC). Two-phase flow is only allowed in the MAC, whereas the MIC is impermeable to both water and gas. Nevertheless, the water can transfer between the MIC and the MAC under the water pressure gap. The first coupled HM model in this framework is based on a double effective stress concept. Mechanical behaviors of the MAC and the MIC are respectively governed by Bishop-type effective stress and Terzaghi’s effective stress. The model can well simulate the evolutions of both gas pressure and gas outflow rate, the water exchange between clay matrix and developed pathways, the high degree of saturation and the consolidation of clay matrix. To account for the development of preferential pathways, the damaging effect has been introduced in the framework. In this improved model, Bishop-type effective stress for the MAC is replaced by the independent stress state variables, i.e., net normal stress and suction, since using the net normal stress is beneficial to simulating tensile failure under high gas pressure. Numerical results showed that the damage-enhanced model can well describe the effect of the development of preferential pathways on the build-up of water pressure and total stress. In addition, the proposed hysteretic models for intrinsic and relative permeabilities make the coupled HM framework more flexible to reproduce the experimental results. To explicitly simulate the development of preferential pathways, a coupled HM-PF framework is developed by using Coussy’s thermodynamic theory and the microforce balance law. The coupled HM-PF framework is implemented in the standard Finite Element Method (FEM). To avoid the pore pressure oscillation and enhance the computational efficiency, a stabilized mixed finite element, in which linear shape functions are selected for interpolating all primary variables, is adopted to discretize the whole domain. In the developed framework, swelling pressure (initial stress) is accounted for by introducing a modified strain tensor that is the sum of the strain tensor due to deformation and the strain tensor calculated from the initial stress. The numerical results showed that the developed coupled HM-PF framework can capture some important behaviors, such as the discrete pathways, localized gas flow, built-up of water pressure and total stress under constant volume condition and nearly saturated state in clay matrix. A spatially autocorrelated random field is introduced into the framework to describe the heterogeneous distribution of HM properties in bentonite. The heterogeneity is beneficial to simulating the fracture branching and the complex fracture trajectory. Numerical results showed that some factors, such as Gaussian random field, coefficient of variation, boundary condition and injection rate, have significant influences on the fracture trajectory. At the end of the thesis, the obtained numerical results are synthesized and analyzed. Based on the analysis, the pros and cons of the developed numerical models are discussed. Corresponding to the limitations, some recommendations are proposed for future studies.

Made available in DSpace on 2014-12-17T14:09:15Z (GMT). No. of bitstreams: 1 GustavoHVPP_TESE.pdf: 1614621 bytes, checksum: 41665985b97dd379d0430f1b97b534b6 (MD5) Previous issue date: 2012-12-17 / Many challenges have been presented in petroleum industry. One of them is the preventing of fluids influx during drilling and cementing. Gas migration can occur as result of pressure imbalance inside the well when well pressure becomes lower than gas zone pressure and in cementing operation this occurs during cement slurry transition period (solid to fluid). In this work it was developed a methodology to evaluate gas migration during drilling and cementing operations. It was considered gel strength concept and through experimental tests determined gas migration initial time. A mechanistic model was developed to obtain equation that evaluates bubble displacement through the fluid while it gels. Being a time-dependant behavior, dynamic rheological measurements were made to evaluate viscosity along the time. For drilling fluids analyzed it was verified that it is desirable fast and non-progressive gelation in order to reduce gas migration without affect operational window (difference between pore and fracture pressure). For cement slurries analyzed, the most appropriate is that remains fluid for more time below critical gel strength, maintaining hydrostatic pressure above gas zone pressure, and after that gels quickly, reducing gas migration. The model developed simulates previously operational conditions and allow changes in operational and fluids design to obtain a safer condition for well construction / Muitos desafios t?m sido apresentados na constru??o de po?os, dentre eles o de evitar o influxo de fluidos durante a perfura??o e cimenta??o. A migra??o de g?s ? resultante do desequil?brio de press?es dentro do po?o, quando a press?o do po?o se torna menor que a da zona contendo o g?s, e na cimenta??o isso ocorre durante o per?odo de transi??o da pasta (de fluido para s?lido). Nesse trabalho foi desenvolvida uma metodologia para avaliar a criticidade da migra??o de g?s durante a perfura??o e opera??es de cimenta??o de po?os. Foi considerado o conceito de for?a gel e atrav?s de ensaios experimentais, determinado o tempo inicial da migra??o de g?s. Foi desenvolvido um modelo mecanicista para obter a equa??o que avalia o deslocamento da bolha atrav?s dos fluidos enquanto eles gelificam. Por ser um comportamento dependente do tempo, foram feitos ensaios reol?gicos din?micos de viscosidade em fun??o do tempo. Para os fluidos de perfura??o analisados verificou-se que ? desej?vel que possuam uma gelifica??o r?pida e n?o progressiva de forma a reduzir a migra??o de g?s sem comprometer a janela operacional (diferen?a entre press?o de poros e fratura). Para as pastas analisadas verificou-se que a mais adequada ? a que se mant?m fluida por mais tempo abaixo do valor do gel cr?tico, mantendo a press?o hidrost?tica acima da press?o da zona de g?s, e ao atingir esse valor, gelifique rapidamente, reduzindo a migra??o de g?s. O modelo permite simular previamente as condi??es operacionais e propor mudan?as no projeto da opera??o e dos fluidos de forma a obter a condi??o mais segura para a constru??o do po?o

Bei der Suche nach einem geologischen Tiefenlager für radioaktive Abfälle müssen alle Risiken für die Integrität des Endlagers und die Sicherheit der umgebenden Biosphäre berücksichtigt werden. Nach der Einlagerung radioaktiver Abfälle kommt es durch verschiedene chemische und physikalische Prozesse innerhalb des Endlagers zur Gasbildung. Die kontinuierliche Gasbildung kann den Gasdruck im verschlossenen Endlager erheblich erhöhen. Das Multibarrierensystem des Endlagers, das häufig aus tonhaltigen Materialien besteht, verhindert, dass sich das Gas verflüchtigt. Die Auswirkungen eines hohen Gasdrucks und die damit verbundenen mechanischen Verformungen können sich negativ auf das Barrieresystem des Endlagers auswirken. Ein genaues Verständnis und die Reproduzierbarkeit der gekoppelten Prozesse ist daher unerlässlich.\\ Experimentelle Ergebnisse deuten darauf hin, dass die Gasmigration bei hohen Gasdrücken über lokal begrenzte, preferentielle Strömungs-pfade erfolgt. In dieser Arbeit wurden verschiedene numerische Ansätze entwickelt, um diese Strömungspfade in numerischen Modellen effektiv zu reproduzieren. Ein entwickelter Ansatz nutzt mikroskalige Eigenschaften, die aus Messungen der Porengrößendichte gewonnen werden. Diese werden hochskaliert und in die Eigenschaften des porösen Mediums integriert. Darüber hinaus ist ein bimodales Porenmodell entwickelt worden, das speziell das dehnungsabhängige Wasserrückhaltevermögen beschreibt und einen verringerten Gaseintrittsdruck und erhöhten Anteil der Makroporosität simulieren kann. Die Simulationsmethoden beinhalten zusätzlich die Verwendung von dehnungsabhängigen Permeabilitätsmodellen für die implizite Darstellung der Strömungspfade. Diese Modellierungsansätze werden dann zur Simulation verschiedener Experimente angewandt, wodurch ein detaillierter Vergleich zwischen berechneten Parametern und experimentellen Ergebnissen ermöglicht wird.\\ Die mit dem Open-Source-Code OpenGeoSys durchgeführten Simulationen zeigen, dass bestimmte Merkmale der Gasmigration durch gesättigten Bentonit oder Tonstein erfolgreich reproduziert werden können. Heterogene Verteilungen der Materialeigenschaften können genutzt werden, um bevorzugte Strömungspfade und plötzliche Gasdurchbrüche zu simulieren. Eine Kombination aus dehnungsabhängigen Modifikationen der intrinsischen Permeabilität und der Wasserrückhalte-kurve ermöglicht eine verbesserte Modellierung impliziter präferentieller Pfade. Das sich daraus ergebende tiefere Verständnis der zugrundeliegenden Prozesse der Gasmigration kann das Sicherheitsanalyse für ein geologisches Tiefenlager für radioaktive Stoffe verbessern.:I Background 1 INTRODUCTION 1.1 Motivation 2 1.2 Objectives 4 1.3 Structure 5 II Theory and Numerics 2 GEOTECHNICAL CONTEXT AND FLUID TRANSPORT 2.1 Deep Geological Repository 9 2.2 Gas production in a DGR 11 2.2.1 Anaerobic metal corrosion 12 2.2.2 Water radiolysis 12 2.2.3 Biodegradation 13 2.3 Fluid transport mechanisms 13 2.3.1 Unsaturated initial conditions 13 2.3.2 Saturated initial conditions 14 2.3.2.1 Advective or diffusive transport of dissolved gas 14 2.3.2.2 Visco-capillary two-phase flow 16 2.3.2.3 Dilatancy-controlled gas flow 18 2.3.2.4 Fracture-controlled gas flow 19 3 NUMERICS AND METHODOLOGY 3.1 Balance equations 21 3.2 Mechanical models 23 3.3 Enhanced permeability functions 24 3.4 Spatial heterogeneity 27 3.5 Bimodal water retention in bentonite 29 4 APPLICATION AND MODEL DESCRIPTION 36 4.1 Application within the DECOVALEX Project 36 4.1.1 Task A – COx claystone 37 4.1.2 Task B – MX-80 Bentonite 38 4.2 Additional gas flow tests 40 III Simulations 5 RESULTS OF GAS FLOW TESTS WITH MX-80 BENTONITE 5.1 Heterogeneous Gas Entry Pressure from Measurements (Paper I) 45 5.2 Bimodal Heterogeneous Gas Entry Pressure (Paper II) 46 5.3 Strain-dependent Bimodal Water Retention Model (Paper III) 47 5.4 Strain-dependent Pore-Model with Heterogeneity 48 6 RESULTS OF GAS FLOW TESTS WITH COX CLAYSTONE (PAPER IV) 51 7 DISCUSSION 53 IV Summary 8 CONCLUSIONS AND OUTLOOK 57 A APPENDIX A 72 A.1 List of Publications 72 B APPENDIX B B.1 Paper I 75 B.2 Paper II 87 B.3 Paper III 109 B.4 Paper IV 121 / In the search for a deep geological repository for radioactive waste, all risks to the integrity of the repository and the safety of the surrounding biosphere must be considered. Following the emplacement of radioactive waste, various chemical and physical processes within the repository induce gas generation. Continuous gas generation can significantly increase the gas pressure in the sealed repository. The repository's multi-barrier system, which often consists of clayey materials such as clayrock and bentonite, prevents the gas from dissipating. The resulting high gas pressure and the associated mechanical deformations can have a negative impact on the multi-barrier system of the repository, e.g. by creating fluid pathways. A sufficiently precise understanding and reproducibility of the processes associated with gas migration through clayey materials is therefore essential for the safety analysis of a repository for radioactive waste.\\ Experimental evidence suggests that, under high gas pressure, gas migration predominantly occurs through localized, preferential pathways characterised by spontaneous breakthroughs. In this work, various numerical approaches have been developed to effectively reproduce these pathways in numerical models. One developed approach utilises microscale properties obtained from measurements of pore size density. These are upscaled and integrated into the properties of the porous medium. Additionally, a bimodal pore model is developed specifically to capture strain-dependent water retention, allowing the simulation of gas entry pressure reduction and macroporosity increase within preferential pathways. The simulation methods include the use of strain-dependent permeability models for the implicit representation of these pathways. These modelling approaches are then applied to replicate different experiments, allowing a detailed comparison between calculated parameters and experimental results.\\ The simulations, performed with the open-source code OpenGeoSys, show that certain features of gas migration through saturated bentonite or claystone can be successfully reproduced. Heterogeneous distributions of material properties can be used to simulate preferential pathways and sudden gas breakthroughs. A combination of permeability models as well as strain-dependent modifications of the intrinsic permeability and the water retention curve provide opportunities for improved modelling of implicit preferential pathways. The resulting deeper understanding of the underlying processes of gas migration can strengthen the safety case for a deep geological repository for radioactive materials.:I Background 1 INTRODUCTION 1.1 Motivation 2 1.2 Objectives 4 1.3 Structure 5 II Theory and Numerics 2 GEOTECHNICAL CONTEXT AND FLUID TRANSPORT 2.1 Deep Geological Repository 9 2.2 Gas production in a DGR 11 2.2.1 Anaerobic metal corrosion 12 2.2.2 Water radiolysis 12 2.2.3 Biodegradation 13 2.3 Fluid transport mechanisms 13 2.3.1 Unsaturated initial conditions 13 2.3.2 Saturated initial conditions 14 2.3.2.1 Advective or diffusive transport of dissolved gas 14 2.3.2.2 Visco-capillary two-phase flow 16 2.3.2.3 Dilatancy-controlled gas flow 18 2.3.2.4 Fracture-controlled gas flow 19 3 NUMERICS AND METHODOLOGY 3.1 Balance equations 21 3.2 Mechanical models 23 3.3 Enhanced permeability functions 24 3.4 Spatial heterogeneity 27 3.5 Bimodal water retention in bentonite 29 4 APPLICATION AND MODEL DESCRIPTION 36 4.1 Application within the DECOVALEX Project 36 4.1.1 Task A – COx claystone 37 4.1.2 Task B – MX-80 Bentonite 38 4.2 Additional gas flow tests 40 III Simulations 5 RESULTS OF GAS FLOW TESTS WITH MX-80 BENTONITE 5.1 Heterogeneous Gas Entry Pressure from Measurements (Paper I) 45 5.2 Bimodal Heterogeneous Gas Entry Pressure (Paper II) 46 5.3 Strain-dependent Bimodal Water Retention Model (Paper III) 47 5.4 Strain-dependent Pore-Model with Heterogeneity 48 6 RESULTS OF GAS FLOW TESTS WITH COX CLAYSTONE (PAPER IV) 51 7 DISCUSSION 53 IV Summary 8 CONCLUSIONS AND OUTLOOK 57 A APPENDIX A 72 A.1 List of Publications 72 B APPENDIX B B.1 Paper I 75 B.2 Paper II 87 B.3 Paper III 109 B.4 Paper IV 121

Cette thèse comporte quatre fichiers vidéo. This thesis comes with four video files. / L'industrie chimique mondiale est en pleine mutation, cherchant des solutions pour rendre la synthèse organique classique plus durable. Une telle solution consiste à passer de la catalyse chimique classique à la biocatalyse. Bien que les avantages des enzymes incluent leur stéréo, régio et chimiosélectivité, cette sélectivité réduit souvent leur promiscuité. Les efforts requis pour adapter la fonction enzymatique aux réactions désirées se sont révélés d'une efficacité modérée, de sorte que des méthodes rapides et rentables sont nécessaires pour générer des biocatalyseurs qui rendront la production chimique plus efficace. Dans l’ère de la bioinformatique et des outils de calcul pour soutenir l'ingénierie des enzymes, le développement rapide de nouvelles fonctions enzymatiques devient une réalité. Cette thèse commence par un examen des développements récents sur les outils de calcul pour l’ingénierie des enzymes. Ceci est suivi par un exemple de l’ingénierie des enzymes purement expérimental ainsi que de l’évolution des protéines. Nous avons exploré l’espace mutationnel d'une enzyme primitive, la dihydrofolate réductase R67 (DHFR R67), en utilisant l’ingénierie semi-rationnelle des protéines. La conception rationnelle d’une librarie de mutants, ou «Smart library design», impliquait l’association covalente de monomères de l’homotétramère DHFR R67 en dimères afin d’augmenter la diversité de la librairie d’enzymes mutées. Le criblage par activité enzymatique a révélé un fort biais pour le maintien de la séquence native dans un des protomères tout en tolérant une variation de séquence élevée pour le deuxième. Il est plausible que les protomères natifs procurent l’activité observée, de sorte que nos efforts pour modifier le site actif de la DHFR R67 peuvent n’avoir été que modérément fructueux. Les limites des méthodes expérimentales sont ensuite abordées par le développement d’outils qui facilitent la prédiction des points chauds mutationnels, c’est-à-dire les sites privilégiés à muter afin de moduler la fonction. Le développement de ces techniques est intensif en termes de calcul, car les protéines sont de grandes molécules complexes dans un environnement à base d’eau, l’un des solvants les plus difficiles à modéliser. Nous présentons l’identification rapide des points chauds mutationnels spécifiques au substrat en utilisant l'exemple d’une enzyme cytochrome P450 industriellement pertinente, la CYP102A1. En appliquant la technique de simulation de la dynamique moléculaire par la force de polarisation adaptative, ou «ABF», nous confirmons les points chauds mutationnels connus pour l’hydroxylation des acides gras tout en identifiant de nouveaux points chauds mutationnels. Nous prédisons également la conformation du substrat naturel, l’acide palmitique, dans le site actif et nous appliquons ces connaissances pour effectuer un criblage virtuel d'autres substrats de cette enzyme. Nous effectuons ensuite des simulations de dynamique moléculaire pour traiter l’impact potentiel de la dynamique des protéines sur la catalyse enzymatique, qui est le sujet de discussions animées entre les experts du domaine. Avec la disponibilité accrue de structures cristallines dans la banque de données de protéines (PDB), il devient clair qu’une seule structure de protéine n’est pas suffisante pour élucider la fonction enzymatique. Nous le démontrons en analysant quatre structures cristallines que nous avons obtenues d’une enzyme β-lactamase, parmi lesquelles un réarrangement important des résidus clés du site actif est observable. Nous avons réalisé de longues simulations de dynamique moléculaire pour générer un ensemble de structures suggérant que les structures cristallines ne reflètent pas nécessairement la conformation de plus basse énergie. Enfin, nous étudions la nécessité de compléter de manière informatisée un hémisphère où l’expérimental n’est actuellement pas possible, à savoir la prédiction de la migration des gaz dans les enzymes. À titre d'exemple, la réactivité des enzymes cytochrome P450 dépend de la disponibilité des molécules d’oxygène envers l’hème du site actif. Par le biais de simulations de la dynamique moléculaire de type Simulation Implicite du Ligand (ILS), nous dérivons le paysage de l’énergie libre de petites molécules neutres de gaz pour cartographier les canaux potentiels empruntés par les gaz dans les cytochromes P450 : CYP102A1 et CYP102A5. La comparaison pour les gaz CO, N2 et O2 suggère que ces enzymes évoluent vers l’exclusion du CO inhibiteur. De plus, nous prédisons que les canaux empruntés par les gaz sont distincts des canaux empruntés par le substrat connu et que ces canaux peuvent donc être modifiés indépendamment les uns des autres. / The chemical industry worldwide is at a turning point, seeking solutions to make classical organic synthesis more sustainable. One such solution is to shift from classical catalysis to biocatalysis. Although the advantages of enzymes include their stereo-, regio-, and chemoselectivity, their selectivity often reduces versatility. Past efforts to tailor enzymatic function towards desired reactions have met with moderate effectiveness, such that fast and cost-effective methods are in demand to generate biocatalysts that will render the production of fine and bulk chemical production more benign. In the wake of bioinformatics and computational tools to support enzyme engineering, the fast development of new enzyme functions is becoming a reality. This thesis begins with a review of recent developments on computational tools for enzyme engineering. This is followed by an example of purely experimental enzyme engineering and protein evolution. We explored the mutational space of a primitive enzyme, the R67 dihydrofolate reductase (DHFR), using semi-rational protein engineering. ‘Smart library design’ involved fusing monomers of the homotetrameric R67 DHFR into dimers, to increase the diversity in the resulting mutated enzyme libraries. Activity-based screening revealed a strong bias for maintenance of the native sequence in one protomer with tolerance for high sequence variation in the second. It is plausible that the native protomers procure the observed activity, such that our efforts to modify the enzyme active site may have been only moderately fruitful. The limitations of experimental methods are then addressed by developing tools that facilitate computational mutational hotspot prediction. Developing these techniques is computationally intensive, as proteins are large molecular objects and work in aqueous media, one of the most complex solvents to model. We present the rapid, substrate-specific identification of mutational hotspots using the example of the industrially relevant P450 cytochrome CYP102A1. Applying the adaptive biasing force (ABF) molecular dynamics simulation technique, we confirm the known mutational hotspots for fatty acid hydroxylation and identify a new one. We also predict a catalytic binding pose for the natural substrate, palmitic acid, and apply that knowledge to perform virtual screening for further substrates for this enzyme. We then perform molecular dynamics simulations to address the potential impact of protein dynamics on enzyme catalysis, which is the topic of heated discussions among experts in the field. With the availability of more crystal structures in the Protein Data Bank, it is becoming clear that a single protein structure is not sufficient to elucidate enzyme function. We demonstrate this by analyzing four crystal structures we obtained of a β-lactamase enzyme, among which a striking rearrangement of key active site residues was observed. We performed long molecular dynamics simulations to generate a structural ensemble that suggests that crystal structures do not necessarily reflect the conformation of lowest energy. Finally, we address the need to computationally complement an area where experimentation is not currently possible, namely the prediction of gas migration into enzymes. As an example, the reactivity of P450 cytochrome enzymes depends on the availability of molecular oxygen at the active-site heme. Using the Implicit Ligand Sampling (ILS) molecular dynamics simulation technique, we derive the free energy landscape of small neutral gas molecules to map potential gas channels in cytochrome P450 CYP102A1 and CYP102A5. Comparison of CO, N2 and O2 suggests that those enzymes evolved towards exclusion of the inhibiting CO. In addition, we predict that gas channels are distinct from known substrate channels and therefore can be engineered independently from one another.