Multi-component induction resistivity and sonic measurements acquired in high-angle wells can be strongly influenced by shoulder-bed effects, anisotropy resulting from sand-shale laminations, and presence of mud-filtrate invasion. Understanding the corresponding biasing effects aids in the interpretation of resistivity and sonic measurements and subsequently leads to more accurate and reliable formation evaluation. This dissertation describes numerical simulation studies examining the effects on multi-component induction and sonic measurements in a variety of complex formation models. Subsequently, a joint inversion scheme is presented that combines resistivity and sonic measurements to estimate in situ petrophysical and elastic properties in the presence of mud-filtrate invasion. To facilitate the simulation study of multi-component induction logs, I develop a new finite-difference algorithm for the numerical simulation of frequency-domain electromagnetic borehole measurements. The algorithm~uses a coupled scalar-vector potential formulation for arbitrary three-dimensional inhomogeneous and electrically anisotropic media. Simulations show that shoulder-bed anisotropy: enhances shoulder-bed effects across sand layers; and impacts invasion sensitivities to significantly alter the assessment of invasion in terms of invaded- and virgin-zone resistivities, radial length, and front shape. For the simulation study of sonic logs, I develop a three-dimensional, finite-difference time-domain algorithm that models elastic wave propagation in a fluid-filled borehole. Simulations show that presence of anisotropy not only alters the degree of dispersion observed in flexural and Stoneley waves, but also alters their responses to invasion. In addition, presence of a dipping shoulder bed can significantly distort flexural dispersion, making it difficult to identify the low frequency asymptote corresponding to formation shear wave velocity. Lastly, I consider a radial one-dimensional model in the development of a joint resistivity and sonic inversion algorithm. This scheme simultaneously inverts array-induction apparent conductivities and sonic flexural and Stoneley dispersions for the rock's elastic moduli and water saturation in the presence of mud-filtrate invasion. Inversions are performed on numerically simulated data for a variety of models reflecting soft and hard rock formations with presence of water- and oil-based mud-filtrate invasion. Results show the estimated invasion profiles display excellent agreement with the true models, and the elastic moduli are estimated to within a few percent of the true values. / text

Originally developed in the 1970s for the optimal control of systems governed by partial differential equations, the adjoint method has found several successful applications, e.g., in meteorology with large-scale 3D or 4D atmospheric data assimilation schemes, for carbon cycle data assimilation in biogeochemistry and climate research, or in oceanographic modelling with efficient adjoint codes of ocean general circulation models. Despite the variety of applications in these research fields, adjoint methods have only very recently drawn attention from the ocean acoustics community. In ocean acoustic tomography and geoacoustic inversion, where the inverse problem is to recover unknown acoustic properties of the water column and the seabed from acoustic transmission data, the solution approaches are typically based on travel time inversion or standard matched-field processing in combination with metaheuristics for global optimization. In order to complement the adjoint schemes already in use in meteorology and oceanography with an ocean acoustic component, this thesis is concerned with the development of the adjoint of a full-field acoustic propagation model for shallow water environments. In view of the increasing importance of global ocean observing systems such as the European Seas Observatory Network, the Arctic Ocean Observing System and Maritime Rapid Environmental Assessment (MREA) systems for defence and security applications, the adjoint of an ocean acoustic propagation model can become an integral part of a coupled oceanographic and acoustic data assimilation scheme in the future. Given the acoustic pressure field measured on a vertical hydrophone array and a modelled replica field that is calculated for a specific parametrization of the environment, the developed adjoint model backpropagates the mismatch (residual) between the measured and predicted field from the receiver array towards the source. The backpropagated error field is then converted into an estimate of the exact gradient of the objective function with respect to any of the relevant physical parameters of the environment including the sound speed structure in the water column and densities, compressional/shear sound speeds, and attenuations of the sediment layers and the sub-bottom halfspace. The resulting environmental gradients can be used in combination with gradient descent methods such as conjugate gradient, or Newton-type optimization methods tolocate the error surface minimum via a series of iterations. This is particularly attractive for monitoring slowly varying environments, where the gradient information can be used to track the environmental parameters continuously over time and space. In shallow water environments, where an accurate treatment of the acoustic interaction with the bottom is of outmost importance for a correct prediction of the sound field, and field data are often recorded on non-fully populated arrays, there is an inherent need for observation over a broad range of frequencies. For this purpose, the adjoint-based approach is generalized for a joint optimization across multiple frequencies and special attention is devoted to regularization methods that incorporate additional information about the desired solution in order to stabilize the optimization process. Starting with an analytical formulation of the multiple-frequency adjoint approach for parabolic-type approximations, the adjoint method is progressively tailored in the course of the thesis towards a realistic wide-angle parabolic equation propagation model and the treatment of fully nonlocal impedance boundary conditions. A semi-automatic adjoint generation via modular graph approach enables the direct inversion of both the geoacoustic parameters embedded in the discrete nonlocal boundary condition and the acoustic properties of the water column. Several case studies based on environmental data obtained in Mediterranean shallow waters are used in the thesis to assess the capabilities of adjoint-based acoustic inversion for different experimental configurations, particularly taking into account sparse array geometries and partial depth coverage of the water column. The numerical implementation of the approach is found to be robust, provided that the initial guesses are not too far from the desired solution, and accurate, and converges in a small number of iterations. During the multi-frequency optimization process, the evolution of the control parameters displays a parameter hierarchy which clearly relates to the relative sensitivity of the acoustic pressure field to the physical parameters. The actual validation of the adjoint-generated environmental gradients for acoustic monitoring of a shallow water environment is based on acoustic and oceanographic data from the Yellow Shark '94 and the MREA '07 sea trials, conducted in the Tyrrhenian Sea, south of the island of Elba. Starting from an initial guess of the environmental control parameters, either obtained through acoustic inversion with global search or supported by archival in-situ data, the adjoint method provides an efficient means to adjust local changes with a couple of iterations and monitor the environmental properties over a series of inversions. In this thesis the adjoint-based approach is used, e.g., to fine-tune up to eight bottom geoacoustic parameters of a shallow-water environment and to track the time-varying sound speed profile in the water column. In the same way the approach can be extended to track the spatial water column and bottom structure using a mobile network of sparse arrays. Work is currently being focused on the inclusion of the adjoint approach into hybrid optimization schemes or ensemble predictions, as an essential building block in a combined ocean acoustic data assimilation framework and the subsequent validation of the acoustic monitoring capabilities with long-term experimental data in shallow water environments.

<p>Seismic traveltime inversion, traveltime tomography and seismic reflection techniques have been applied for two dimensional (2D) and three dimensional (3D) data acquired in conjunction with site characterization and monitoring aspects at a carbon dioxide (CO₂) geological storage site at Ketzin, Germany (the CO₂SINK project). Conventional seismic methods that focused on investigating the CO₂ storage and caprock formations showed a poor or no image of the upper 150 m. In order to fill this information gap, an effort on imaging the shallow subsurface at a potentially risky area at the site is the principal goal of this thesis.</p><p>Beside this objective, a seismic source comparison from a 2D pilot study for acquisition parameter testing at the site found a weight drop source suitable with respect to the signal penetration, frequency content of the data and minimizing time and cost for 3D data acquisition.</p><p>For the Ketzin seismic data, the ability to obtain high-quality images is limited by the acquisition geometry, source-generated noise and time shifts due to near-surface effects producing severe distortions in the data. Moreover, these time shifts are comparable to the dominant periods of the reflections and to the size of structures to be imaged. Therefore, a combination of seismic refraction and state-of-the-art processing techniques, including careful static corrections and more accurate velocity analysis, resulted in key improvements of the images and allowed new information to be extracted. The results from these studies together with borehole information, hydrogeologic models and seismic modeling have been combined into an integrated interpretation. The boundary between the Quaternary and Tertiary unit has been mapped. The internal structure of the Quaternary sediments is likely to be complicated due to the shallow aquifer/aquitard complex, whereas the heterogeneity in the Tertiary unit is due to rock alteration associated with fault zones. Some of the major faults appear to project into the Tertiary unit. These findings are important for understanding the potentially risky anticline crest and can be used as a database for the future monitoring program at the site.</p>

Les travaux présentés dans ce mémoire visent à développer une méthode globale d'inversion des paramètres géoacoustiques par grands fonds, dans le cadre du REA (Rapid Environmental Assesment ; Evaluation Rapide de l'Environnement)) acoustique opérationnel. La méthode développée utilise du Matched Impulse Response de signaux large bande. La finalité est de renseigner les sonaristes opérationnels du domaine de la lutte anti sous-marine sur les paramètres du fond, afin qu'il puissent améliorer l'évaluation des performances de leurs senseurs acoustiques. Ces travaux doivent fournir des enseignements utiles à la conception du prototype ftitur de REA acoustique STEREO de l'EPSHOM/CMO. La validation du concept s'opère dans cette thèse après la mise en place d'une démarche globale d'inversion basée sur l'ajustement des réponses impulsionnelles mesurées en transmission et des réponses irnpulsionnelles simulées par un modèle prenant en compte les paramètres du fond. Deux étapes d'inversion sont nécessaires visant à retrouver d'une part la configuration expérimentale puis ensuite les caractéristiques de la nature du fond. La méthode d'inversion développée est appliquée de façon quasi-automatisée à un jeu de données synthétiques complexes, élaborées à partir d'un simulateur temps réel de la propagation acoustique. Les essais sur données synthétiques permettent tout d'abord de valider la faisabilité de la méthode quant à ses performances de détection d'une transition horizontale de la porosité, et quant au respect de la contrainte opérationnelle du délai d'estimation. Ils permettent de qualifier de plus l'impact de l'effet Doppler sur les performances de l'inversion. Celle-ci est ensuite testée sur un jeu de données acoustiques et environnementales réelles mis à disposition par le Centre Militaire d'Océanographie de l'EPSHOM. Ces données correspondent à la campagne de REA HERACLES qui a eu lieu par grands fonds, cas défavorable pour l'inversion en raison du faible contenu informatif des signaux. La prise en compte d'un modèle numérique de terrain dans la méthode d'inversion permet de d'inverser un milieu évolutif avec la distance et de synthétiser l'ensemble des résultats de l'inversion des données d'une campagne typique de REA. Ces travaux permettent de dégager des configurations pour lesquelles l'inversion peut fonctionner en temps réel, ce qui valorise le principe de la méthode développée et les développements réalisés.

Magnetic Resonance Elastography (MRE) is an emerging medical imaging modality that allows quantification of the mechanical properties of biological tissues in vivo. MRE typically involves time-harmonic tissue excitation followed by the displacement measurements within the tissue obtained by phase-contrast Magnetic Resonance Imaging (MRI) techniques. MRE is believed to have great potential in the detection of wide variety of pathologies, diseases and cancer formations, especially tumors. This thesis concentrates on a thorough assessment and full rheological evaluation of the Rayleigh damping (RD) material model applied to MRE. The feasibility of the RD model to accurately reconstruct viscoelastic and damping properties was assessed. The goal is to obtain accurate quantitative estimates of the mechanical properties for the in vivo healthy brain via the subzone optimization based nonlinear image reconstruction algorithm. The RD model allows reconstruction of not only stiffness distribution of the tissue, but also energy attenuation mechanisms proportionally related to both elastic and inertial effects. The latter allows calculation of the concomitant damping properties of the material. The initial hypothesis behind this research is that accurate reconstruction of the Rayleigh damping parameters may bring additional diagnostic potential with regards to differentiation of various tissue types and more accurate characterisation of certain pathological diseases based on different energy absorbing mechanisms. Therefore, the RD model offers reconstruction of three additional material properties that might be of clinical diagnostic merit and can enhance characterisation of cancer tumors within the brain. A pneumatic-based actuator was specifically developed for in vivo human brain MRE experiments. Performance of the actuator was investigated and the results showed that the actuator produces average displacement in the range of 300 µmicrons and is well suited for generation of shear waves if applied to the human head. Unique features of the the actuator are patient comfort and safety, MRI compatibility, flexible design and good displacement characteristics. In this research, a 3D finite element (FE) subzone-based non-linear reconstruction algorithm using the RD material model has been applied and rigorously assessed to investigate the performance of elastographic based reconstruction to accurately recover mechanical properties and a concomitant damping behaviour of the material. A number of experiments were performed on a variety of homogenous and heterogeneous tissue-simulating damping phantoms comprising a set of materials that mimic range of mechanical properties expected in the brain. The result showed consistent effect of a poor reconstruction accuracy of the RD parameters which suggested the nonidentifiable nature of the RD model. A structural model identifiability analysis further supported the nonidentifiabilty of the RD parameters at a single frequency. Therefore, two approaches were developed to overcome the fundamental identifiability issue. The first one involved application of multiple frequencies over a broad range. The second one was based on parametrisation techniques, where one of the damping parameters was globally defined throughout the reconstruction domain allowing reconstruction of the two remaining parameters. Based on the findings of this research, multi-frequency (MF) elastography was performed on the tissue-simulating phantoms to investigate improvement of the elastographic reconstruction accuracy. Dispersion characteristics of the materials as well as RD changes across different frequencies in various materials were also studied. Simultaneous multi-frequency inversion was undertaken where two models were evaluated: a zero-order model and a power-law model. Furthermore, parametric-based RD reconstruction was carried out to evaluate enhancement of accurate identification of the reconstructed parameters. The results showed that parametric-based RD reconstruction, compared to MF-based RD results, allowed better material characterisation on the reconstructed shear modulus image. Also, significant improvement in material differentiation on the remaining damping parameter image was also observed if the fixed damping parameter was adjusted appropriately. In application to in vivo brain imaging, six repetitive MRE examinations of the in vivo healthy brain demonstrated promising ability of the RD MRE to resolve local variations in mechanical properties of different brain tissue types. Preliminary results to date show that reconstructed real shear modulus and overall damping levels correlate well with the brain anatomical features. Quantified shear stiffness estimates for white and gray matter were found to be 3 kPa and 2.1 kPa, respectively. Due to the non-identifiability of the model at a single frequency, reconstructed RD based parameters limit any physical meaning. Therefore, MF-based and parametric-based cerebral RD elastography was also performed.

In this thesis work, I have used a comparative genomics approach to study a fungal model organism, Neurospora tetrasperma. My specific focus has been on genomic introgression, intron evolution, chromosomal structural rearrangements and codon usage. All of the studies are based on large-scale dataset generated by next-generation sequencing technology (NGS), combined with other techniques, such as Optical Mapping. In the introgression study, we detected large-scale introgression tracts in three N. tetrasperma lineages, and the introgression showed allele-specific and chromosomal-specific pattern. In the study of introns, we found indications of mRNA mediated intron loss and non-homologous end joining (NHEJ) mediated intron gains in N. tetrasperma. We found that selection is involved in shaping intron gains and losses, and associated with intron position, intron phase and GC content. In the study of chromosomal structural rearrangements, we found a lineage specific chromosomal inversion pattern in N. tetrasperma, which indicates that inversions are unlikely to associate with the origin of the suppressed recombination and the mating system transition in N. tetrasperma. The result suggests inversions are the consequences, rather than the causes, of suppressed recombination on the mating-type chromosome of N. tetrasperma. In the final study, analyses of codon usage indicated that the region of suppressed recombination in N. tetrasperma is subjected to genomic degeneration, and selection efficiency has been much reduced in this region.

In this thesis I address the problem of determining fracture properties of subsurface rocks from geophysical surface seismic and vertical seismic profile (VSP) data. In the first part of this thesis I perform multi-attribute analysis, including frequency content, amplitude, travel time and angle of rotation studies on field VSP data from two different carbonate fields, both containing time-lapse surveys. I compare the findings to independent data available in the region and find that the interpreted fracture orientations from the attribute analyses correlate with independent fracture studies in the area, the principal axis of major faults, or the maximum horizontal stress of the area studied. Although I show the existence of these correlations, due to the limited knowledge of the rock properties, these correlations are only qualitative. A more robust inversion of fracture properties requires more knowledge of the physical properties of the medium and forward modelling of the seismic response. A rock physics theory would be required to model the elastic response of the fractured rock; hence a more quantitative fracture characterisation is necessary. In the second part of this thesis I address this need by developing and testing a method for fracture density inversion. Linearised approximations are commonly used in azimuthal amplitude versus offset (AVO) analysis. However, these approximations perform poorly at large angles of incidence where the effect of fractures is more significant. The method proposed here uses a model based approach that does not use these approximations but calculates the exact azimuthal AVO response based on prior knowledge of the elastic constants of the medium, assumed to be known, and a range of fracture densities. A rock physics theory is used for modelling the elastic constants of the fractured rock. I then create a linearized relationship for a specific model that separates the effect due to fracture density from the modelled AVOZ responses. This separation is key to the method, as it provides both a new set of orthogonal basis functions that can be used to express the AVOZ response of field data, and a set of coefficients that are related to fracture density. In general, the inversion is based on these coefficients. The coefficient or coefficients which present the highest correlation with fracture density must be determined on a case by case basis, as they will vary depending on the contrast between the elastic constants across the boundary of interest. I develop and test the method on synthetic surface seismic data and then apply it to seismic data acquired from a laboratory-scale physical geological model. Due to the prior knowledge of the rock properties and structure of the physical geological model, I am able to corroborate that the inverted fracture density from the seismic data matches that of the physical model within the error. I compare the inversion for two different levels of uncertainty in the velocities and densities of the modelled reflection coefficients and show that the inversion results are more precise and accurate when there is less uncertainty in the rock properties of the modelled reflection coefficients. In both the synthetic and physical geological model studies I find that the inversion is optimal for a certain range of offsets/angles of incidence. This means that the optimal range for inversion must be found on a case by case basis, as it depends on the behaviour of the data. Finally, as the inversion relies on the input modelled azimuthal AVO curves, a careful choice of the input rock properties is essential for the inversion process. The inverted fracture density values will only be valid if the rock properties of the field data fall within the range of the modelled ones. This is a limitation of the method, as adequate knowledge of the rock properties is not always available.

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

De multiples plaisirs sont présents dans À la recherche du temps perdu. Ils sont importants pour les personnages en ce que, bien souvent, ils dirigent leur vie, mais aussi parce qu’ils participent à la constitution de portraits : observer les plaisirs d’un personnage permet de le peindre. L’importance du plaisir dépasse le niveau individuel pour atteindre celui du récit (diégèse et narration). Malgré une présence qui tend à l’omniprésence, le plaisir peine à être vécu au présent par des personnages qui le conjuguent plus facilement au passé ou au futur, et en ont une image très négative. C’est que les sens ne sont pas aptes à véhiculer le plaisir, et n’apportent que culpabilité, punition et déception. Il faut alors explorer d’autres voies : apparaissent artifices et perversions, qui finissent aussi par échouer à procurer un plaisir pur. Le héros proustien le trouve dans l’imaginaire, notamment la création littéraire. Paradoxalement, de l’échec du plaisir vient la fertilité créatrice. / Pleasure appears in various guise in A la Recherche du Temps Perdu. It often directs the characters’ lives or serves to define them: the objects and forms of pleasure enjoyed by the characters constitute indirect portraits of them. Pleasure is not only to be observed on an individual level, but can be analysed on the narrative level. Although it is everywhere to be found, it fails to be actually experienced by characters who more often than not reject it into the past or the future, and entertain a very negative vision of it. The senses indeed appear unable to provide pleasure, and only become sources of guilt, disappointment and retribution. Other paths to pleasure must then be discovered, but artificial paradises or perversions fail to yield real pleasure. The Proustian hero ultimately finds it in the world of imagination, especially through literary creation. Paradoxically, it is from the failure of experiencing pleasure that creative power derives.

Ce travail a pour objet l’étude génétique du personnage de Charlus dans les avant-textes de À la recherche du temps perdu : les soixante-quinze cahiers de brouillon principalement mais aussi les trois cahiers de mise au net du Côté de Guermantes et les vingt manuscrits au net de Sodome et Gomorrhe au Temps retrouvé. La quantité et la diversité des brouillons ont nécessité une approche chronologique et macrogénétique. Cette dernière a consisté à situer les avant-textes consacrés à M. de Charlus à l’intérieur du projet d’ensemble de l’œuvre, lui-même en constante évolution, afin de dégager la trajectoire du personnage dans les manuscrits, c’est-à-dire de mettre en évidence les grandes lignes de son évolution en les resituant dans chacun des chantiers successifs du projet romanesque : dans les premières esquisses de 1909, puis dans « le roman de 1912 », dans les brouillons des années 1913-1914 marqués par l’irruption d’Albertine et par l’entrée de la guerre dans le grand roman, dans ceux des années 1915-1916 enfin où l’on repère les dernières modifications de structure de l’œuvre en gestation. Le va-et-vient permanent entre genèse du personnage et genèse de l’œuvre a permis de montrer comment le personnage se modifiait en fonction de l’évolution de la structure d’ensemble mais il a également eu le mérite inverse de révéler que la structure romanesque avait à plusieurs reprises été elle-même bousculée et modifiée par le personnage de Charlus. L’interaction entre le personnage et la structure évolutive de l’œuvre a ainsi permis à la fois de dégager des facettes peu connues du baron de Charlus et de dévoiler des aspects inattendus de la genèse de À la recherche du temps perdu. / The object of this genetic study is the character Charlus in the proto texts of À la recherche du temps perdu, principally in the seventy-five workbook notebooks but also in the three revision notebooks for Le Côté de Guermantes and the twenty rough draft manuscripts from Sodome et Gomorrhe to Le Temps retrouvé. The quantity and the diversity of these notebooks required a chronological and macrogenetic approach. The latter consisted in situating the earliest texts devoted to M. de Charlus within the project of the complete work, which was itself in constant evolution. The purpose is to clarify the trajectory of the character in the manuscripts, to trace the character’s development by situating him in each of the successive constructions for the novel: first in the sketches of 1909, then in what has been called “the novel of 1912,” followed by the rough notebooks of 1913-14 in which Albertine first appears, as well as the war. The final modifications of the structure and the work–in–progress take place in 1915-16. This back and forth movement between the genesis of the character and the genesis of the work has demonstrated how the character was modified according to the evolution in the structure of the whole. Our methodology also has the inverse merit of revealing that the structure of the novel was also shaken and modified by evolutions concerning the character Charlus. The interaction between the character and the evolutive structure of the work–in–progress has allowed this study to document hidden facettes of the baron de Charlus and to reveal surprising details concerning the genesis of À la recherche du temps perdu.