Les réseaux bidimensionnels de nanofils (NFs) d’oxyde de zinc (ZnO) aléatoirement orientés, ou nanonets (pour « nanowire networks »), constituent des nanostructures innovantes et prometteuses pour de nombreuses applications. L’objectif de cette thèse est de développer des nanonets de ZnO en vue d’applications à la détection de molécules biologiques ou gazeuses, en particulier de l’ADN, ceci selon une procédure bas coût et industrialisable. Dans ce but, il est essentiel de bien maitriser les différentes étapes d’élaboration qui sont : (i) le dépôt de couches minces de germination de ZnO sur des substrats de silicium par voie sol-gel, (ii) la croissance de NFs de ZnO sur ces couches de germination par synthèse hydrothermale, et (iii) l’assemblage par filtration sous vide de ces NFs en nanonets de ZnO. Des études approfondies de chacun de ces procédés ont donc été menées. Ces travaux ont permis d’élaborer des couches minces, des NFs et des nanonets de ZnO reproductibles et homogènes dont les propriétés morphologiques sont précisément contrôlées sur une large gamme. Deux protocoles de biofonctionnalisation des nanonets avec de l’ADN ont ensuite été développés et ont abouti à des résultats encourageants mais restant à optimiser. Les nanonets ont également été intégrés au sein de dispositifs fonctionnels et les premières caractérisations électriques ont fourni des résultats prometteurs. A terme, ce travail ouvre la voie à l’intégration collective de NFs de ZnO qui permettrait la réalisation d’une nouvelle génération de capteurs (de biomolécules, de gaz…) à la fois portables, rapides et très sensibles. / Two-dimensional randomly oriented zinc oxide (ZnO) nanowire (NW) networks, or nanonets, represent innovative and promising nanostructures for numerous applications. The objective of this thesis is to develop ZnO nanonets for the detection of biological or gaseous molecules, in particular DNA, by using a low cost and scalable procedure. To this end, it is essential to control the different elaboration steps which are: (i) the deposition of ZnO seed layer films on silicon substrates by sol-gel approach, (ii) the growth of ZnO NWs on these seed layer films by hydrothermal synthesis, and (iii) the assembly of these NWs into ZnO nanonets by vacuum filtration. In-depth studies of each of these processes were thus carried out. This work enabled to elaborate reproducible and homogenous ZnO thin films, NWs and nanonets whose morphological properties are precisely controlled over a wide range. Two DNA biofunctionnalization protocols were then developed for the nanonets and led to encouraging results which need however to be further optimized. The nanonets were also integrated into functional devices and the first electrical characterizations provided promising results. In the longer term, this work opens the way to the collective integration of ZnO NWs which would enable the development of a new generation of portable, fast and ultra-sensitive (bio- or gas-) sensors.

Determining the mechanical properties of living cells accurately and repeatably is critical to understanding developmental, disease, and repair biology. The cellular environment is composed of fibrous proteins of a mix of diameters organized in random and aligned configurations. In the past two decades, several methods, including modified atomic force microscopy (AFM) and micro-pipette aspiration have been developed to measure cellular viscoelastic properties at single-cell resolution. We inquired if the fibrous environment affected cellular mechanobiology. Using our non-electrospinning Spinneret based Tunable Engineered Parameters (STEP) fiber manufacturing platform, we developed fused nanonets to measure single-cell forces and viscoelasticity. Using computer-controlled probes, we stretched single cells attached to two-fiber and three-fiber systems precisely and recorded the relaxation response of cells. The viscoelastic properties were determined by fitting the data to the standard linear viscoelastic solid model (SLS), which includes a spring (k0) in parallel with a spring (km)-damper (cm) series. In cases in which cells are seeded on two fibers, we tested hMSCs and BJ-5TA cells, and the viscoelastic components measurements k0, km, and cm are 26.16 ± 3.38 nN/µm, 5.81 ± 0.81 nN/µm, and 41.15 ± 5.97 nN-s/µm, respectively for hMSCs, while the k0, km, and cm, measurements of BJ-5TA cells are 20.02 ± 2.89 nN/µm, 4.62 ± 0.75 nN/µm, and 45.46 ± 6.00 nN-s/µm respectively. Transitioning to the three-fiber system resulted in an overall increase in native contractility of the cells while allowing us to understand how the viscoelastic response was distributed with an increasing number of fibers. Viscoelastic experiments were done twice. First, we pulled on the outermost fiber similar to the two-fiber case. The cell was then allowed to rest for two hours, sufficient time to regain its pre-stretching contractility. The cell was then excited by pulling on the middle fiber. The experimental results of cell seeding on three fibers proved that the viscoelastic property measurements depend on the excitation position. Overall, we present new knowledge on the cellular viscoelasticity of cells attached to ECM-mimicking fibers. / Master of Science / Investigating living cell mechanical properties including the viscoelastic properties of single living cell is critical to understanding developmental, disease, and repair biology. With the advancement of micrometer scale technologies, researchers are able to excite individual living cells. Current methods are mostly based on perturbing cells attached to flat 2D surfaces with limited physiological relevance. Since the native environment of cells is fibrous in nature, we inquired if cellular viscoelasticity could be measured of cells attached to suspended fibers. Using our non-electrospinning Spinneret based Tunable Engineered Parameters (STEP) fiber manufacturing platform, we developed fused nanonets to measure single-cell forces and viscoelasticity. Our suspended, aligned nanonet provides a unique way for us to pull on individual living cells using computercontrolled probes. By controlling the aligned fiber spacing, we are able to determine how many fibers the cells were seeded on. We first measured the viscoelastic properties of human mesenchymal stem cells(hMSCs) and human fibroblast BJ-5TA cells seeded on two fibers. The standard linear solid (SLS) model, which includes a spring in parallel with a spring-damper series, was used to quantitatively analyze the viscoelastic properties of cells. By giving the excitation on one fiber and measuring the cell forces on the other fiber, we calculated the corresponding spring constants and damping coefficients of the model. Then we investigated the viscoelastic properties of hMSCs seeded on three fibers by giving the excitation on the outermost fiber and then the middle fiber. Between the two excitations, the cell was allowed to relax for two hours and regain contractility. Our results confirm that the viscoelastic properties measurements depend on the excitation position. Overall, we present a new fiber-based force measurement system capable of determining the viscoelastic response of cells repeatably.

Un « Nanonet », acronyme pour « NANOstructured NETwork », est défini comme un réseau de nanostructures unidimensionnelles à fort facteur de forme et aléatoirement orientées sur un substrat. Dans ce travail de thèse, une étude approfondie de nanonets à base de nanofils de silicium est présentée en vue d'une intégration dans des capteurs d'ADN. Une méthode de fabrication simple de ces réseaux a tout été d'abord développée afin d'obtenir des nanonets homogènes et reproductibles. La surface des nanofils a ensuite été fonctionnalisée afin de permettre la détection de l'hybridation de l'ADN par fluorescence. Les capteurs ainsi réalisés présentent une excellente sélectivité et une meilleure limite de sensibilité que des substrats plans. Les propriétés électriques des nanonets de silicium ont également été étudiées ce qui a mené à la description des mécanismes de conduction de ces réseaux. Ainsi, il a été démontré que le comportement électrique de ces structures est dominé par les nombreuses jonctions nanofil-nanofil et suit la théorie de la percolation électrique. De plus, une procédure d'optimisation de ces jonctions a finalement permis de stabiliser les propriétés électriques des nanonets de silicium.Ces réseaux possèdent donc des propriétés remarquables provenant des constituants individuels, les nanofils, qui présentent une surface spécifique élevée, mais également de leur structure en réseaux aléatoires offrant la possibilité de les manipuler simplement et à bas coût à l'échelle macroscopique. Ces travaux ouvrent la voie à l'intégration des nanonets de silicium dans des capteurs d'ADN reposant sur la détection électrique. / A "nanonet", acronym for "NANOstructured NETwork", is defined as a network of one-dimensional nanostructures with high aspect ratio and randomly oriented on a substrate. In this work, a comprehensive study of nanonets based on silicon nanowires is presented for integration into DNA sensors. First, a simple method for the network fabrication has been developed in order to obtain homogeneous and reproducible nanonets. Then, the nanowire surface has been functionalized, so that the DNA hybridization detection is possible by fluorescence. The elaborated sensors exhibit excellent selectivity and a better sensitivity limit than planar substrates. The electrical properties of the silicon nanonets have also been investigated which resulted in the description of the conduction mechanisms of these networks. It has been shown that the electrical behaviour of such structures is ruled by the numerous nanowire-nanowire junctions and follows the electrical percolation theory. Moreover, an optimization procedure of these junctions has allowed stabilizing the electrical properties of silicon nanonets.Therefore, these networks have attractive characteristics which arise from the individual components, the nanowires with a high specific surface, but also from the structural properties of the network itself which can be simply manipulated, at a low cost, on macroscopic scales. This work paves the way for the integration of silicon nanonets into DNA sensors based on electrical detection.

Migratory cells in vivo move within a predominantly fibrous microenvironment through the action of forces. These dynamic interactions facilitate mechanosensing, critical to fundamental biological processes in pathophysiology. Naturally, the field of mechanobiology has evolved over the past several decades to decipher the role of forces in mechanotransduction using a variety of force-measurement platforms. A central challenge that has yet to be overcome in the field is connecting forces with the interplay between cell shape and ever-changing environment. Here, through design of specific fibrous architectures, a mechanobiological understanding of force feed-forward loop accounting for shape shifting of the environment and cells is developed. Using the non-electrospinning Spinneret Tunable Engineered Parameters (STEP) technique, two complementary force measurement platforms of varying physical attributes are developed to investigate how the force feed-forward loop impacts cell fate. Nanonet Force Microscopy (NFM) comprised of aligned nanonets is designed to study anisotropic cell shapes, while Crosshatch Force Microscopy (CM) comprised of orthogonal arrangement of fibers is designed to study cell bodies of broad shapes. The combination of shapes achieved on these networks recapitulate mesenchymal shapes observed in vivo, which are used to describe cell behaviors not reported before. The new findings include (i) discovery of a new biological structure, termed 3D-perpendicular lateral protrusions (3D-PLPs) which is proposed to be the missing biophysical link in the remodeling of the ECM and perpetuation of desmoplasia. Using NFM, seven discreet steps in formation of force-exerting PLPs anywhere along the cell body is documented, which allow cells to spread laterally and increase in contractility. Using a variety of fiber networks, it is shown that aligned fibers are necessary for PLP formation and suitable environments for myofibroblast activation, and (ii) a force dipole that links matrix deformability with cell contractility. Aided by machine learning, CFM automates the process of fiber feature recognition to measure forces as cells change shapes during migration and differentiate to osteogenic and adipogenic lineages. The force platforms are applied to investigate (i) the bioenergetic contributors fueling cellular migration and a surprisingly overwhelming impact of glycolytic energetic pathway over the traditionally thought mitochondrial energy production is found. However, neither pathway has substantial impact over the cellular force production, and (ii) quantitate the migratory and contractile response of enucleated cytoplasmic fragments naturally shed by cells. A peculiar contractility driven oscillatory migratory phenotype is found, capable of lasting over tens of hours, and absent in intact cells. Overall, new high spatiotemporal capabilities are developed in mechanobiology to quantitate the force-feed forward loops between cell shape and ECM in pathophysiology. / Doctor of Philosophy / Pathophysiology is the study of abnormal changes in the regular body functions of an organism that are causes or consequences of disease onset. Research in this area is mainly focused on identifying the different factors that cause and propagate the disease states such as cancer. Central to many of these processes are events such as cell migration and remodeling of their surrounding environment. The native microenvironment surrounding cells is highly complex and is composed of many classes of macromolecules, with fibrous components being one of the most important. How cells interact with these environments through application of forces and how this further regulates cellular behavior is vital to advancing our understanding of many of these pathophysiological processes. Currently, there is a lack in our understanding of how this dynamic process referred to as the "force feed-forward loop", is perpetuated. This limitation in our understanding can be attributed to the lack of an in vivo mimicking platform that captures this dynamic interaction and is capable of measuring the forces. To this end, the development of two novel single cell force measurement platforms: Nanonet Force Microscopy (NFM) and Crosshatch Force Microscopy (CFM) is presented. These platforms are fiber based systems, generated with the utilization of previously established non-electrospinning technique of Spinneret based Tunable Engineered Parameters (STEP) technique. Using NFM and CFM, forces were computed in wide range of cell shapes from anisotropic to all other spread morphologies. These platforms were applied to identify a new biological structure called perpendicular lateral protrusions and shown to have potential role in the spreading of tumor microenvironment. Furthermore, the force dynamics in physiological processes such as stem cell differentiation into fat cells or bone cells is also identified. How cellular processes such as migration and force production is fueled is also investigated and found to be not heavily reliant on the commonly understood mitochondrial activity. Finally, sub-cellular components known as cell fragments, which are devoid of nucleus, are also observed to be contractile and migratory in nature, independent of parent cell body. These platforms and findings can be further utilized to advance our current knowledge of the progression of these physiological and pathological processes and serve as diagnostic tools for the early identification of disease onset. Furthermore, based on these findings, strategies can be developed for early intervention to inhibit disease progression or devise bioengineered scaffolds for applications in tissue engineering.

Un nanonet possède des propriétés remarquables qui proviennent non seulement des propriétés intrinsèques de chaque nanostructure mais aussi de leur assemblage en réseau ce qui les rend particulièrement attractifs pour de multiples applications, notamment dans les domaines de l’optique, l’électronique ou encore le biomédical. Dans ce travail de thèse, des nanonets constitués de nanofils de silicium ont été intégrés pour la première fois sous forme de transistors à effet de champ avec une grille en face arrière. La filière technologique développée est parfaitement compatible avec une production des dispositifs en masse, à bas coût et à grande échelle pour un budget thermique n’excédant pas 400°C. Des avancées technologiques majeures ont été réalisées grâce à la maîtrise du frittage des jonctions entre nanofils, de la siliciuration des contacts et de la passivation des nanofils avec de l’alumine. Les transistors à nanonets fabriqués présentent des caractéristiques électriques excellentes, stables sous air et reproductibles qui sont capables de concurrencer celles des transistors à nanofil unique. Une étude approfondie de la percolation par des mesures expérimentales et des simulations Monte-Carlo a mis en évidence que la limitation de la conduction par les jonctions entre nanofils permet d’améliorer considérablement les performances électriques. Après une intégration des dispositifs sous forme de biocapteurs, il a été montré que les transistors sont sensibles électriquement à l’hybridation de l’ADN. Bénéficiant d’un procédé de fabrication compatible avec l’industrie de la microélectronique, une intégration 3D de ces transistors à nanonet sur un circuit de lecture peut alors être envisagée ce qui ouvre la voie à des biocapteurs portables, capables de détecter l’ADN en temps réel et sans marquage. De plus, la flexibilité mécanique et la transparence optique du nanonet offrent d’autres opportunités dans le domaine de l’électronique flexible. / A nanonet exhibits remarkable properties which arises from, not only, the intrinsic properties of each nanostructure but also from their assembly into network which makes them particularly attractive for various applications, notably in the field of optics, electronics or even biomedical. During this Ph.D. work, silicon nanowire-based nanonets were integrated for the first time into field effect transistors with a back gate configuration. The developed technological process is perfectly suitable with a large-scale and massive production of these devices at low cost without exceeding a thermal budget of 400°C. Major technological breakthroughs were achieved through the control of the sintering of nanowire junctions, the contact silicidation and the nanowire passivation with alumina. The as-fabricated nanonet transistors display outstanding, air stable and reproducible electrical characteristics which can compete with single nanowire-based devices. An in-depth study of percolation using experimental measurements and Monte-Carlo simulations highlighted that the conduction limitation by nanowire junctions allow to enhance drastically the electrical performances. After device integration into biosensors, it has been shown that transistors are electrically sensitive to DNA hybridization.Beneficiating from a fabrication process compatible with the microelectronic industry, a 3D integration of these nanonet-based transistors onto a readout circuit can therefore be envisioned which opens new avenues for portable biosensors, allowing direct and label-free detection of DNA. Furthermore, mechanical flexibility and optical transparency offer other opportunities in flexible electronic field.