This dissertation aims to investigate systems in which several optical and mechanical degrees of freedom are coupled through optomechanical interactions. Multimode optomechanics creates the prospect of integrated functional devices and it allows us to explore new types of optomechanical interactions which account for collective dynamics and optically mediated mechanical interactions. Owing to the development of fabrication techniques for micro- and nano-sized mechanical elements, macroscopic mechanical oscillators can be cooled to the deep quantum regime via optomechanical interaction. Based on the possibility to control the motion of mechanical oscillators at the quantum level, we design several schemes involving mechanical systems of macroscopic length and mass scales and we explore the nonlinear dynamics of mechanical oscillators. The first scheme includes a quantum cantilever coupled to a classical tuning fork via magnetic dipole-dipole interaction and also coupled to a single optical field mode via optomechanical interaction. We investigate the generation of nonclassical squeezed states in the quantum cantilever and their detection by transferring them to the optical field. The second scheme involves a quantum membrane coupled to two optical modes via optomechanical interaction. We explore dynamic stabilization of an unstable position of a quantum mechanical oscillator via modulation of the optical fields. We then develop a general formalism to fully describe cavity mediated mechanical interactions. We explore a rather general configuration in which multiple mechanical oscillators interact with a single cavity field mode. We specifically consider the situation in which the cavity dissipation is the dominant source of damping so that the cavity field follows the dynamics of the mechanical modes. In particular, we study two limiting regimes with specific applications: the weak-coupling regime and single-photon strong-coupling regime. In the weak-coupling regime, we build a protocol for quantum state transfer between mechanical modes. In the single-photon coupling regime, we investigate the nonlinear nature of the mechanical system which generates bistability and bifurcation in the classical analysis and we also explore how these features manifest themselves in interference, entanglement, and correlation in the quantum theory.

Many physiological and pathological processes, such as wound healing and tissue remodeling, are heavily influenced by continuous mechanical cell-cell and cell-ECM communication. Abnormalities that may compromise the biomechanical communication between the cells and the ECM can have significant repercussions on these physiological and pathological processes. The state of the mechanical environment and the reciprocal communication of mechanical signals between the ECM and the cell during wound healing and aged dermal tissue regeneration may be key in controlling the quality of the structure and physical properties of regenerated tissue. This dissertation encompasses a series of studies developed for characterizing the effects of mechanical cues on altering and controlling tissue remodeling, and regeneration in the context of controlling scar formation during wound healing, and the maintenance and regeneration of the dermal extracellular matrix (ECM) during aging. In order to achieve this goal, in vitro models that contained some features of the provisional ECM, and the ECM of the dermis were developed and subjected to an array of quantifiable mechanical cues. Wound models were studied with different mechanical boundary conditions, and found to exhibit differences in initial short-term structural remodeling that lead to significant differences in the long-term synthesis of collagen after four weeks in culture. Dermal models seeded with fibroblasts from individuals of different ages were treated with a hyaluronic acid (HA)-based dermal filler. Changes in the mechanical environment of the dermal models caused by swelling of the hydrophilc HA, resulted in changes in the expression of mechanosensitive, and ECM remodeling genes, essential for the maintenance and regeneration of dermal tissue. Taken together, these data provide new insights on the role of mechanical signals in directing tissue remodeling.

La construction du cerveau et de ses connexions pendant le développement reste une question ouverte dans la communauté scientifique. Des efforts fructueux ont été faits pour élucider les mécanismes de la croissance axonale, tels que la guidance axonale et les molécules de guidage. Cependant, des preuves récentes suggèrent que d'autres acteurs seraient impliqués dans la croissance des neurones in vivo. Notamment, les axones se développent dans des environnements mécaniquement contraints. Ainsi, pour bien comprendre ce processus dynamique, il faut prendre en compte les mécanismes collectifs et les interactions mécaniques au sein des populations axonales. Néanmoins, les techniques pour mesurer directement cela à partir de cerveaux vivants sont aujourd'hui insuffisantes ou lourdes à mettre en œuvre. Cette thèse résulte d'une collaboration multidisciplinaire, pour faire la lumière sur le développement axonal in vivo et les morphologies complexes des axones adultes. Notre travail a été inspiré et validé à partir d'images d'axones y individuels chez la drosophile, de type sauvage et modifiés génétiquement, que nous avons segmentés et normalisés. Nous avons d'abord proposé un cadre mathématique pour l'étude morphologique et la classification des groupes axonaux. A partir de cette analyse, nous avons émis l'hypothèse que la croissance axonale dérive d'un processus stochastique et que la variabilité et la complexité des arbres axonaux résultent de sa nature intrinsèque, ainsi que des stratégies d'élongation développées pour surmonter les contraintes mécaniques du cerveau en développement. Nous avons conçu un modèle mathématique de la croissance d'un axone isolé fondé sur des chaînes de Markov gaussiennes avec deux paramètres, représentant la rigidité axonale et l'attraction du champ cible. Nous avons estimé les paramètres de ce modèle à partir de données réelles et simulé la croissance des axones à l'échelle de populations et avec des contraintes spatiales pour tester notre hypothèse. Nous avons abordé des thèmes de mathématiques appliquées ainsi que de la biologie, et dévoilé des effets inexplorés de la croissance collective sur le développement axonal in vivo. / How the brain wires up during development remains an open question in the scientific community across disciplines. Fruitful efforts have been made to elucidate the mechanisms of axonal growth, such as pathfinding and guiding molecules. However, recent evidence suggests other actors to be involved in neuron growth in vivo. Notably, axons develop in populations and embedded in mechanically constrained environments. Thus, to fully understand this dynamic process, one must take into account collective mechanisms and mechanical interactions within the axonal populations. However, techniques to directly measure this from living brains are today lacking or heavy to implement. This thesis emerges from a multidisciplinary collaboration, to shed light on axonal development in vivo and how adult complex axonal morphologies are attained. Our work is inspired and validated from images of single wild type and mutated Drosophila y axons, which we have segmented and normalized. We first proposed a mathematical framework for the morphological study and classification of axonal groups. From this analysis we hypothesized that axon growth derives from a stochastic process, and that the variability and complexity of axonal trees result from its intrinsic nature, as well as from elongation strategies developed to overcome the mechanical constraints of the developing brain. We designed a mathematical model of single axon growth based on Gaussian Markov Chains with two parameters, accounting for axon rigidity and attraction to the target field. We estimated the model parameters from data, and simulated the growing axons embedded in spatially constraint populations to test our hypothesis. We dealt with themes from applied mathematics as well as from biology, and unveiled unexplored effects of collective growth on axonal development in vivo.