The atomic force microscope (AFM) provides a powerful instrument for investigating and manipulating biological samples down to the subnanometer scale. In contrast to other microscopy methods, AFM does not require labeling, staining, nor fixation of samples and allows the specimen to be fully hydrated in buffer solution during the experiments. Moreover, AFM clearly compares in resolution to other techniques. In general, the AFM can be operated in an imaging or a force spectroscopy mode. In the present work, advantage was taken of this versatility to investigate single biomolecules and biomolecular assemblies. A novel approach to investigate the visco-elastic behavior of biomolecules under force was established, using dextran as an example. While a molecule tethered between a solid support and the cantilever tip was stretched at a constant velocity, the thermally driven oscillation of the cantilever was recorded. Analysis of the cantilever Brownian noise provided information about the visco-elastic properties of dextran that corresponded well to parameters obtained by alternative methods. However, the approach presented here was easier to implement and less time-consuming than previously used methods. A computer controlled force-clamp system was set up, circumventing the need for custom built analogue electronics. A commercial PicoForce AFM was extended by two computers which hosted data acquisition hardware. While the first computer recorded data, the second computer drove the AFM bypassing the manufacturer's microscope control software. To do so, a software-based proportional-integral-differential (PID) controller was implemented on the second computer. It allowed the force applied to a molecule to be held constant over time. After tuning of the PID controller, response times obtained using that force-clamp setup were comparable to those of the recently reported analogue systems. The performance of the setup was demonstrated by force-clamp unfolding of a pentameric Ig25 construct and the membrane protein NhaA. In the latter case, short-lived unfolding intermediates that were populated for less than 10 ms, could be revealed. Conventional single-molecule dynamic force spectroscopy was used to unfold the serine:threonine antiporter SteT from Bacillus subtilis, an integral membrane protein. Unfolding force patterns revealed the unfolding barriers stabilizing structural segments of SteT. Ligand binding did not induce new unfolding barriers suggesting that weak interactions with multiple structural segments were involved. In contrast, ligand binding caused changes in the energy landscape of all structural segments, thus turning the protein from a brittle, rigid into a more stable, structurally flexible conformation. Functionally, rigidity in the ligand-free state was thought to facilitate specific ligand binding, while flexibility and increased stability were required for conformational changes associated with substrate translocation. These results support the working model for transmembrane transport proteins that provide alternate access of the binding site to either face of the membrane. Finally, high-resolution imaging was exploited to visualize the extracellular surface of Cx26 gap junction hemichannels (connexons). AFM topographs reveal pH-dependent structural changes of the extracellular connexon surface in presence of HEPES, an aminosulfonate compound. At low pH (< 6.5), connexons showed a narrow and shallow channel entrance, which represented the closed pore. Increasing pH values resulted in a gradual opening of the pore, which was reflected by increasing channel entrance widths and depths. At pH > 7.6 the pore was fully opened and the pore diameter and depth did not increase further. Importantly, coinciding with pore gating a slight rotation of the subunits was observed. In the absence of aminosulfonate compounds, such as HEPES, acidification did not affect pore diameters and depths, retaining the open state. Thus, the intracellular concentration of taurine, a naturally abundant aminosulfonate compound, might be used to tune gap junction sensitivity at low pH.

L’objectif de cette thèse a consisté en l’étude des apports d’une architecture radar MIMO pour la détection d’êtres humains à l’intérieur des bâtiments. Pour ce faire, il a tout d’abord été mis en évidence sur un point théorique la supériorité d’une architecture radar MIMO comparée au SIMO, en terme de robustesse et de pouvoir discriminant de cibles rapprochées. Ensuite, les effets de la traversée du mur sur le signal radar furent décrits et une caractérisation quantitative de la transmission à travers un mur fut réalisée sur mesures expérimentales. Différents simulateurs de scénarii de détection à travers les murs ont été produits : un simulateur réaliste FDTD ainsi qu’un simulateur «comportemental» simplifié.La méthode de détection et de localisation retenue est l’imagerie radar.Ainsi, différents algorithmes d’imagerie radar pour une architecture MIMO furent développés. Des traitements incohérents (migration, multilatération),cohérents (filtrage adapté) et haute résolution (MVDR, MUSIC Time Reversal) furent détaillés. Enfin des considérations techniques (bilan de liaison, temps d’observation de la scène) ont été discutées et deux architectures radar MIMO ultra-large bande furent proposées. Une architecture radar MIMO avec 2GHz de bande et un multiplexage temporel pour l’adressage des antennes d’émission a été réalisée par le personnel du laboratoire. Des mesures expérimentales ont conduites permettant de réaliser la détection à travers les murs à l’aide du dispositif réalisé. / This thesis focused on the study of the contributions of MIMO radar systemfor human beings detection inside buildings. First, on a theoretical point, it was highlighted the superiority of MIMO systems compared with the SIMO, in term of robustness and discrimination abilities of close targets. Then, through the wall propagation effects were described and a quantitative characterization of the transmission through a wall wasrealised based on experimental measures. Various simulators of scenarios of detection through walls were produced : a full-wave FDTD simulator and a simplified «behavioral» one. The method of detection and localisation is the radar imaging. So, differents algorithms of radar imaging for MIMO system were developed. Among them, incoherent processings (migration,multi-lateration), coherent (matched filtering) and high resolution(MVDR, MUSIC Time Reversal) were detailed. Finally, technical considerations(link budget, observation time of the scene) were discussed and two ultrawide band MIMO radar architectures were proposed. A experimental bench of MIMO radar with 2GHz bandwidth and a temporal multiplexing was realized in the laboratory. Experimental measures allow to realize the detection through walls with the realized MIMO radar.

The atomic force microscope (AFM) provides a powerful instrument for investigating and manipulating biological samples down to the subnanometer scale. In contrast to other microscopy methods, AFM does not require labeling, staining, nor fixation of samples and allows the specimen to be fully hydrated in buffer solution during the experiments. Moreover, AFM clearly compares in resolution to other techniques. In general, the AFM can be operated in an imaging or a force spectroscopy mode. In the present work, advantage was taken of this versatility to investigate single biomolecules and biomolecular assemblies. A novel approach to investigate the visco-elastic behavior of biomolecules under force was established, using dextran as an example. While a molecule tethered between a solid support and the cantilever tip was stretched at a constant velocity, the thermally driven oscillation of the cantilever was recorded. Analysis of the cantilever Brownian noise provided information about the visco-elastic properties of dextran that corresponded well to parameters obtained by alternative methods. However, the approach presented here was easier to implement and less time-consuming than previously used methods. A computer controlled force-clamp system was set up, circumventing the need for custom built analogue electronics. A commercial PicoForce AFM was extended by two computers which hosted data acquisition hardware. While the first computer recorded data, the second computer drove the AFM bypassing the manufacturer's microscope control software. To do so, a software-based proportional-integral-differential (PID) controller was implemented on the second computer. It allowed the force applied to a molecule to be held constant over time. After tuning of the PID controller, response times obtained using that force-clamp setup were comparable to those of the recently reported analogue systems. The performance of the setup was demonstrated by force-clamp unfolding of a pentameric Ig25 construct and the membrane protein NhaA. In the latter case, short-lived unfolding intermediates that were populated for less than 10 ms, could be revealed. Conventional single-molecule dynamic force spectroscopy was used to unfold the serine:threonine antiporter SteT from Bacillus subtilis, an integral membrane protein. Unfolding force patterns revealed the unfolding barriers stabilizing structural segments of SteT. Ligand binding did not induce new unfolding barriers suggesting that weak interactions with multiple structural segments were involved. In contrast, ligand binding caused changes in the energy landscape of all structural segments, thus turning the protein from a brittle, rigid into a more stable, structurally flexible conformation. Functionally, rigidity in the ligand-free state was thought to facilitate specific ligand binding, while flexibility and increased stability were required for conformational changes associated with substrate translocation. These results support the working model for transmembrane transport proteins that provide alternate access of the binding site to either face of the membrane. Finally, high-resolution imaging was exploited to visualize the extracellular surface of Cx26 gap junction hemichannels (connexons). AFM topographs reveal pH-dependent structural changes of the extracellular connexon surface in presence of HEPES, an aminosulfonate compound. At low pH (< 6.5), connexons showed a narrow and shallow channel entrance, which represented the closed pore. Increasing pH values resulted in a gradual opening of the pore, which was reflected by increasing channel entrance widths and depths. At pH > 7.6 the pore was fully opened and the pore diameter and depth did not increase further. Importantly, coinciding with pore gating a slight rotation of the subunits was observed. In the absence of aminosulfonate compounds, such as HEPES, acidification did not affect pore diameters and depths, retaining the open state. Thus, the intracellular concentration of taurine, a naturally abundant aminosulfonate compound, might be used to tune gap junction sensitivity at low pH.

La localisation de source Distribuée Cohérente (DC) présente un défi du traitement d'antenne. Les contributions de cette thèse s’articulent principalement autour de trois aspects. Premièrement, un estimateur conjoint de l'angle, la distance, la dispersion et la forme de la source appelée JADSSE est proposé pour le cas champ proche. L’estimation d’un paramètre de forme de distribution de la dispersion permet d’éviter des erreurs de modèles sur l’a priori de la forme de la distribution. Deuxièmement, on généralise l'estimateur Decoupled DSPE en champ proche. Cette approche permet de découpler l'estimation de la Direction D’Arrivée (DDA) et de la distance de l'estimation de la dispersion. Afin de permettre l’estimation de la dispersion sans connaître a priori les formes de distribution, on propose le DADSSE qui consiste à estimer successivement la DDA, la distance et ensuite la dispersion et la forme de la distribution de la source. Troisièmement, on généralise le modèle DC avec une dispersion spatiale bidimensionnelle de la source ainsi que l’estimateur JADSSE. Deux approches sont proposées pour l’estimation de la puissance prenant en compte le modèle d’étalement des sources. Les méthodes proposées sont testées sur les données expérimentales de la soufflerie de Renault. Les résultats mettent en évidence des sources aéro-acoustiques proches et de faibles puissances. L’ensemble de ces travaux permet de fournir un outil pour une meilleure cartographie et caractérisation des sources aéro-acoustiques grâce à l’estimation de la position, l'étalement, la puissance et la forme. / Localization of Coherently Distributed (CD) source presents a challenge in the array signal processing. Our work motivates the localization of aero-acoustic source based on its spatial extension. This challenge is practically ignored in the literature of acoustic imaging field where many applications consist in mapping noisy source to reduce its contribution. The thesis presents the three following contributions. First, we propose a Joint Angle, Distance, Spread and Shape Estimator called JADSSE. The estimation of the so-called spread shape distribution parameter proposed by JADSSE avoids the modeling error due to the required a priori knowledge on the source shape when using classical estimators. Second, we expand the Decoupled DSPE to the near field. This method decouples the Direction of Arrival (DoA) and the range estimation from the spread estimation. Meanwhile, this method prevents the spread estimation for unknown shape distribution. Therefore, we propose the DADSSE to successively estimate the DOA, the range and then the spread and the shape distribution of the source. Third, we generalize the CD model and the JADSSE to consider the bi-dimensional spread of the source. Next, we propose two source power estimation approaches accounting the spatial spread of the source. The proposed methods are tested using a set of experimental data of the Renault wind tunnel application. Results show the presence of new aero-acoustic sources especially the overlapped ones with weak powers. We provide a tool to better map and characterize the aero-acoustic source by estimating the position, spread, power and shape.

Indiana University-Purdue University Indianapolis (IUPUI) / In the last few decades, forensic science has played a significant role in bringing criminals to justice. Shoe and tire track impressions found at the crime scene are important pieces of evidence since the marks and cracks on them can be uniquely tied to a person or vehicle respectively. We have designed a device that can generate a highly accurate 3-Dimensional (3D) map of an impression without disturbing the evidence. The device uses lasers to detect the changes in depth and hence it is crucial to accurately detect the position of the laser. Typically, the forensic applications require very high resolution images in order to be useful in prosecutions of criminals. Limitations of the hardware technology have led to the use of signal and image processing methods to achieve high resolution images. Super Resolution is the process of generating higher resolution images from multiple low resolution images using knowledge about the motion and the properties of the imaging geometry. This thesis presents methods for developing some of the image processing components of the 3D impression scanning device. In particular, the thesis describes the following two components: (i) methods to detect the laser stripes projected onto the impression surface in order to calculate the deformations of the laser stripes due to 3D surface shape being scanned, and (ii) methods to improve the resolution of the digitized color image of the impression by utilizing multiple overlapping low resolution images captured during the scanning process and super resolution techniques.

L'athérosclérose est une maladie vasculaire complexe qui affecte la paroi des artères (par l'épaississement) et les lumières (par la formation de plaques). La rupture d'une plaque de l'artère carotide peut également provoquer un accident vasculaire cérébral ischémique et des complications. Bien que plusieurs modalités d'imagerie médicale soient actuellement utilisées pour évaluer la stabilité d'une plaque, elles présentent des limitations telles que l'irradiation, les propriétés invasives, une faible disponibilité clinique et un coût élevé. L'échographie est une méthode d'imagerie sûre qui permet une analyse en temps réel pour l'évaluation des tissus biologiques. Il est intéressant et prometteur d’appliquer une échographie vasculaire pour le dépistage et le diagnostic précoces des plaques d’artère carotide. Cependant, les ultrasons vasculaires actuels identifient uniquement la morphologie d'une plaque en termes de luminosité d'écho ou l’impact de cette plaque sur les caractéristiques de l’écoulement sanguin, ce qui peut ne pas être suffisant pour diagnostiquer l’importance de la plaque. La technique d’élastographie vasculaire non-intrusive (« noninvasive vascular elastography (NIVE) ») a montré le potentiel de détermination de la stabilité d'une plaque. NIVE peut déterminer le champ de déformation de la paroi vasculaire en mouvement d’une artère carotide provoqué par la pulsation cardiaque naturelle. En raison des différences de module de Young entre les différents tissus des vaisseaux, différents composants d’une plaque devraient présenter différentes déformations, caractérisant ainsi la stabilité de la plaque. Actuellement, les performances et l’efficacité numérique sous-optimales limitent l’acceptation clinique de NIVE en tant que méthode rapide et efficace pour le diagnostic précoce des plaques vulnérables. Par conséquent, il est nécessaire de développer NIVE en tant qu’outil d’imagerie non invasif, rapide et économique afin de mieux caractériser la vulnérabilité liée à la plaque. La procédure à suivre pour effectuer l’analyse NIVE consiste en des étapes de formation et de post-traitement d’images. Cette thèse vise à améliorer systématiquement la précision de ces deux aspects de NIVE afin de faciliter la prédiction de la vulnérabilité de la plaque carotidienne. Le premier effort de cette thèse a été dédié à la formation d'images (Chapitre 5). L'imagerie par oscillations transversales a été introduite dans NIVE. Les performances de l’imagerie par oscillations transversales couplées à deux estimateurs de contrainte fondés sur un modèle de déformation fine, soit l’ « affine phase-based estimator (APBE) » et le « Lagrangian speckle model estimator (LSME) », ont été évaluées. Pour toutes les études de simulation et in vitro de ce travail, le LSME sans imagerie par oscillation transversale a surperformé par rapport à l'APBE avec imagerie par oscillations transversales. Néanmoins, des estimations de contrainte principales comparables ou meilleures pourraient être obtenues avec le LSME en utilisant une imagerie par oscillations transversales dans le cas de structures tissulaires complexes et hétérogènes. Lors de l'acquisition de signaux ultrasonores pour la formation d'images, des mouvements hors du plan perpendiculaire au plan de balayage bidimensionnel (2-D) existent. Le deuxième objectif de cette thèse était d'évaluer l'influence des mouvements hors plan sur les performances du NIVE 2-D (Chapitre 6). À cette fin, nous avons conçu un dispositif expérimental in vitro permettant de simuler des mouvements hors plan de 1 mm, 2 mm et 3 mm. Les résultats in vitro ont montré plus d'artefacts d'estimation de contrainte pour le LSME avec des amplitudes croissantes de mouvements hors du plan principal de l’image. Malgré tout, nous avons néanmoins obtenu des estimations de déformations robustes avec un mouvement hors plan de 2.0 mm (coefficients de corrélation supérieurs à 0.85). Pour un jeu de données cliniques de 18 participants présentant une sténose de l'artère carotide, nous avons proposé d'utiliser deux jeux de données d'analyses sur la même plaque carotidienne, soit des images transversales et longitudinales, afin de déduire les mouvements hors plan (qui se sont avérés de 0.25 mm à 1.04 mm). Les résultats cliniques ont montré que les estimations de déformations restaient reproductibles pour toutes les amplitudes de mouvement, puisque les coefficients de corrélation inter-images étaient supérieurs à 0.70 et que les corrélations croisées normalisées entre les images radiofréquences étaient supérieures à 0.93, ce qui a permis de démontrer une plus grande confiance lors de l'analyse de jeu de données cliniques de plaques carotides à l'aide du LSME. Enfin, en ce qui concerne le post-traitement des images, les algorithmes NIVE doivent estimer les déformations des parois des vaisseaux à partir d’images reconstituées dans le but d’identifier les tissus mous et durs. Ainsi, le dernier objectif de cette thèse était de développer un algorithme d'estimation de contrainte avec une résolution de la taille d’un pixel ainsi qu'une efficacité de calcul élevée pour l'amélioration de la précision de NIVE (Chapitre 7). Nous avons proposé un estimateur de déformation de modèle fragmenté (SMSE) avec lequel le champ de déformation dense est paramétré avec des descriptions de transformées en cosinus discret, générant ainsi des composantes de déformations affines (déformations axiales et latérales et en cisaillement) sans opération mathématique de dérivées. En comparant avec le LSME, le SMSE a réduit les erreurs d'estimation lors des tests de simulations, ainsi que pour les mesures in vitro et in vivo. De plus, la faible mise en oeuvre de la méthode SMSE réduit de 4 à 25 fois le temps de traitement par rapport à la méthode LSME pour les simulations, les études in vitro et in vivo, ce qui pourrait permettre une implémentation possible de NIVE en temps réel. / Atherosclerosis is a complex vascular disease that affects artery walls (by thickening) and lumens (by plaque formation). The rupture of a carotid artery plaque may also induce ischemic stroke and complications. Despite the use of several medical imaging modalities to evaluate the stability of a plaque, they present limitations such as irradiation, invasive property, low clinical availability and high cost. Ultrasound is a safe imaging method with a real time capability for assessment of biological tissues. It is clinically used for early screening and diagnosis of carotid artery plaques. However, current vascular ultrasound technologies only identify the morphology of a plaque in terms of echo brightness or the impact of the vessel narrowing on flow properties, which may not be sufficient for optimum diagnosis. Noninvasive vascular elastography (NIVE) has been shown of interest for determining the stability of a plaque. Specifically, NIVE can determine the strain field of the moving vessel wall of a carotid artery caused by the natural cardiac pulsation. Due to Young’s modulus differences among different vessel tissues, different components of a plaque can be detected as they present different strains thereby potentially helping in characterizing the plaque stability. Currently, sub-optimum performance and computational efficiency limit the clinical acceptance of NIVE as a fast and efficient method for the early diagnosis of vulnerable plaques. Therefore, there is a need to further develop NIVE as a non-invasive, fast and low computational cost imaging tool to better characterize the plaque vulnerability. The procedure to perform NIVE analysis consists in image formation and image post-processing steps. This thesis aimed to systematically improve the accuracy of these two aspects of NIVE to facilitate predicting carotid plaque vulnerability. The first effort of this thesis has been targeted on improving the image formation (Chapter 5). Transverse oscillation beamforming was introduced into NIVE. The performance of transverse oscillation imaging coupled with two model-based strain estimators, the affine phase-based estimator (APBE) and the Lagrangian speckle model estimator (LSME), were evaluated. For all simulations and in vitro studies, the LSME without transverse oscillation imaging outperformed the APBE with transverse oscillation imaging. Nonetheless, comparable or better principal strain estimates could be obtained with the LSME using transverse oscillation imaging in the case of complex and heterogeneous tissue structures. During the acquisition of ultrasound signals for image formation, out-of-plane motions which are perpendicular to the two-dimensional (2-D) scan plane are existing. The second objective of this thesis was to evaluate the influence of out-of-plane motions on the performance of 2-D NIVE (Chapter 6). For this purpose, we designed an in vitro experimental setup to simulate out-of-plane motions of 1 mm, 2 mm and 3 mm. The in vitro results showed more strain estimation artifacts for the LSME with increasing magnitudes of out-of-plane motions. Even so, robust strain estimations were nevertheless obtained with 2.0 mm out-of-plane motion (correlation coefficients higher than 0.85). For a clinical dataset of 18 participants with carotid artery stenosis, we proposed to use two datasets of scans on the same carotid plaque, one cross-sectional and the other in a longitudinal view, to deduce the out-of-plane motions (estimated to be ranging from 0.25 mm to 1.04 mm). Clinical results showed that strain estimations remained reproducible for all motion magnitudes since inter-frame correlation coefficients were higher than 0.70, and normalized cross-correlations between radiofrequency images were above 0.93, which indicated that confident motion estimations can be obtained when analyzing clinical dataset of carotid plaques using the LSME. Finally, regarding the image post-processing component of NIVE algorithms to estimate strains of vessel walls from reconstructed images with the objective of identifying soft and hard tissues, we developed a strain estimation method with a pixel-wise resolution as well as a high computation efficiency for improving NIVE (Chapter 7). We proposed a sparse model strain estimator (SMSE) for which the dense strain field is parameterized with Discrete Cosine Transform descriptions, thereby deriving affine strain components (axial and lateral strains and shears) without mathematical derivative operations. Compared with the LSME, the SMSE reduced estimation errors in simulations, in vitro and in vivo tests. Moreover, the sparse implementation of the SMSE reduced the processing time by a factor of 4 to 25 compared with the LSME based on simulations, in vitro and in vivo results, which is suggesting a possible implementation of NIVE in real time.

Indiana University-Purdue University Indianapolis (IUPUI) / In crime scene investigations it is necessary to capture images of impression evidence such as tire track or shoe impressions. Currently, such evidence is captured by taking two-dimensional (2D) color photographs or making a physical cast of the impression in order to capture the three-dimensional (3D) structure of the information. This project aims to build a digitizing device that scans the impression evidence and generates (i) a high resolution three-dimensional (3D) surface image, and (ii) a co-registered two-dimensional (2D) color image. The method is based on active structured lighting methods in order to extract 3D shape information of a surface. A prototype device was built that uses an assembly of two line laser lights and a high-definition video camera that is moved at a precisely controlled and constant speed along a mechanical actuator rail in order to scan the evidence. A prototype software was also developed which implements the image processing, calibration, and surface depth calculations. The methods developed in this project for extracting the digitized 3D surface shape and 2D color images include (i) a self-contained calibration method that eliminates the need for pre-calibration of the device; (ii) the use of two colored line laser lights projected from two different angles to eliminate problems due to occlusions; and (iii) the extraction of high resolution color image of the impression evidence with minimal distortion.The system results in sub-millimeter accuracy in the depth image and a high resolution color image that is registered with the depth image. The system is particularly suitable for high quality images of long tire track impressions without the need for stitching multiple images.