Microorganisms swimming in their natural habitat interact with debris and boundaries, which can modify their swimming characteristics. However, the boundary effect on swimming microorganisms have not been completely understood yet, and is one of most active areas of research. Amongst microorganisms, unicellular ciliates are the fastest swimmers and also respond to a variety of external cues. We choose Paramecium multimicronucleatum as a model system to understand the locomotion of ciliates. First, we explore the effects of boundaries on swimming modes of Paramecium multimicronu- cleatum by introducing them in 2D films and 1D channels. The geometric confinements cause the Paramecia to transition between: a directed, a meandering and a self-bending behaviors. During the self-bending mode the cell body exerts forces on the walls; which is quantified by using a beam bending analogy and measuring the elasticity of the cell body. The first inves- tigation reveals the complicated swimming patterns of Paramecium caused by boundaries. In the second study we investigate the directed swimming of Paramecium in cylindrical capillaries, which mimics the swimming of ciliates in the pores of soil. A finite-sized cell lo- comoting in extreme confinements creates a pressure gradient across its ends. By developing a modified envelop model incorporating the confinements and pressure gradient effects, we are able to predict the swimming speed of the organisms in confined channels. Finally we study how Paramecium can swim and feed efficiently by stirring the fluid around its body. We experimentally employ "-Particle Image Velocimetry to characterize flows around the freely swimming Parameicum and numerically use Boundary Element Method to quantify the effect of body shapes on the swimming and feeding process. Results show that the body shape of Paramecium (slender anterior and bulky posterior) is hydrodynamically optimized to swim as well as feed efficiently. The dissertation makes significant advances in both experimentally characterizing and the- oretically understanding the flow field and locomotion patterns of ciliates near solid bound- aries. / Ph. D.

Cette thèse est consacrée à l'étude de la dynamique et de la rhéologie des fluides complexes. Nous utilisons une méthode de simulation numérique à trois dimensions. Les systèmes que nous étudions ici sont des suspensions de micro-nageurs actifs, des suspensions de particules sphériques rigides en présence d'un champ externe auquel elles sont sensibles et de la dynamique de suspensions de particules sphériques et confinées en cisaillement. Les Micro-nageurs sont les objets microscopiques qui se propulsent dans un fluide et ils sont omniprésents dans la nature. Un exemple commun de micro-nageurs est la micro-algue textit{Chlamydomonas} . Un des buts principaux de cette thèse est de comprendre l'effet de la motilité de ces micro-organismes sur les propriétés macroscopiques globales de la suspension, telles que la viscosité effective pour expliquer les observations expérimentales. Nous avons élaboré différents modèles de suspensions de textit{Chlamydomonas} et effectué des simulations numériques utilisant la version 3D de la dynamique des particules fluides (FPD) (méthode expliquée dans cette thèse). Les résultats de nos simulations numériques ont été présentés et discutés à la lumière des observations expérimentales. Un des modèles proposés intègre tous les phénomènes observés expérimentalement et sont applicables à d'autres types de suspensions de micro-nageurs. Cette thèse consacre également un chapitre sur les effets du confinement sur la dynamique de cisaillement des suspensions diluées de particules sphériques. Nous avons constaté que dans la géométrie confinée, la vitesse angulaire des particules diminue par rapport à celle imposée par l'écoulement de cisaillement. La vitesse angulaire des particules diminue également lorsque la particule est proche d'une paroi unique et la vitesse de translation de la particule par rapport à la vitesse de la paroi diminue. Un autre objectif de cette thèse est d'étudier les suspensions à viscosité effective ajustable. Nous avons mené une étude numérique sur des suspensions de particules sphériques en présence d'un couple externe. Nous avons montré que le changement de vitesse angulaire des particules due à l'application d'un couple externe est suffisante pour modifier fortement la viscosité de la suspension. Basée sur des simulations numériques, une formule semi-empirique a été proposée pour la viscosité des suspensions de particules sphériques valables jusqu'à 40% de concentration. Nous avons également montré que la 2ème loi de Faxén peut être étendue par une expression empirique pour de grandes concentrations. / This work is dedicated to the study of dynamics and rheology of the complex fluids. We use three dimensional numerical simulations. The systems we study here are: suspensions of biological active micro-swimmers, suspensions of rigid spherical particles in presence of an external field and the dynamics of sheared confined spherical particles. Micro-swimmers are the microscopic objects that propel themselves through a fluid and they are ubiquitous in nature. A common example of micro-swimmers is the textit{Chlamydomonas} . One of the main goal of this thesis is to understand the effect of self-motility of these micro-organisms on the global macroscopic properties of the fluid, such as the effective viscosity to explain experimental observations. We elaborated different models for textit{Chlamydomonas} suspensions and conducted numerical simulations using the 3D version of the Fluid Particle Dynamics method (explained in this thesis). The results of our numerical simulations has been shown and discussed in light of the experimental observations. One of the proposed models incorporates all experimentally observed phenomena and is expendable for other types of micro-swimmer suspensions. This thesis is also dealing with the effects of confinement on the dynamics of sheared spherical particles. We found that in confined geometry, angular velocity of sheared particles decreases compared to the one imposed by the shear flow. The angular velocity of the particles decreases also when the particle are close to a single wall and the translational velocity of the particles changes so that the difference between velocity of the particle and the velocity of the wall decreases. Another objective of this work is to study suspensions with tunable effective viscosity. We conducted a numerical investigation of sheared spherical particle suspensions in presence of an external torque. We showed that the change of particle angular velocity with an external torque is sufficient to strongly change the effective viscosity of the suspension. Based on numerical simulations, a semi-empirical formula has been proposed for the effective viscosity of spherical particles suspensions valid up to 40% concentration. We also showed that a modified second Faxén law can be equivalently established for large concentrations.