This thesis studies physical and stochastic aspects of microorganisms. From the point of view of $\textit{physics}$, the studies in this thesis are motivated by the goal of gaining biological insight using the machinery of physics and mathematics. From the point of view of $\textit{biology}$, the studies in this thesis focus primarily on choanoflagellates, eukaryotes that are the closest living unicellular relatives of animals. This choice of model organism was motivated by the important biological question of the origin of multicellularity. Why was it that single-celled organisms evolved to become multicellular? In particular, we study closely the species $\textit{Salpingoeca rosetta}$, which has the ability to form colonies that resemble true multicellular organisms. A large part of this thesis deals with the random walks of microorganisms. We study these active random walks both for single cells and those composed of individual organisms adhered together. The latter colonial random walkers are typified by choanoflagellates. We develop quantitative theories and use these to extract physical parameters. The increasing ocean oxygen levels in the Precambrian era are thought to be an important factor in the emergence of complex multicellular, animal life. As a first step, we address this situation by studying the response of $\textit{S. rosetta}$ to oxygen gradients. We find that $\textit{S. rosetta}$ displays positive aerotaxis. Analysis of the spatial population distributions provides evidence for logarithmic sensing of oxygen, which enhances sensing in low oxygen neighbourhoods. Analysis of search strategy models on the experimental colony trajectories finds that choanoflagellate aerotaxis is consistent with stochastic navigation, the statistics of which are captured using an effective continuous version of classical run-and-tumble chemotaxis. We compare this continuous run-to-tumble with the run-and-tumble seen in bacteria by formulating a general model for persistent run-and-tumble. We find that although an optimal persistence does exist for a given tumble frequency, in the full parameter space there is a continuum of optimal solutions. We develop this model further by introducing finite tumble times. Efficient uptake of prey and nutrients from the environment is an important component in the fitness of all microorganisms, and its dependence on size may reveal clues to the origins of evolutionary transitions to multicellularity. We examine these issues in depth for choanoflagellates, finding that in the absence of other requirements and in a homogeneously nutritious environment, the optimal strategy to maximise filter feeding is to swim fast which favours swimming unicells. In contrast, in large external flows, a sessile form becomes advantageous. Effects of prey diffusion are discussed and are also found to be advantageous for the swimming unicell. Finally, we consider the switching between synchronous and anti-synchronous beating of flagella in the green alga $\textit{Chlamydomonas}$, a phenomenon that results in run-and-tumble behaviour in eukaryotes. We develop a theoretical model to describe this beating and use it to argue that the synchrony itself is obtained intracellularly, whereas the flagella shapes are most likely strongly influenced by hydrodynamic interactions.

Lipid molecules form thin biological membranes that envelop all living cells, and behave as two-dimensional liquid sheets immersed in bulk water. The interactions of such biomembranes with their environment lay the foundation of a plethora of biological processes rooted in the mesoscopic domain - length scales of 1-1000 nm and time scales of 1-1000 ns. Research in this intermediate regime has for a long time been out of reach for conventional experiments, but breakthroughs in computer simulation methods and scattering experimental techniques have made it possible to directly probe static and dynamic properties of biomembranes on these scales. Biomembranes are soft, with a relatively low energy cost of bending, and are thereby influenced by random, thermal fluctuations of individual molecules. Molecular dynamics simulations show how in-plane (density fluctuations) and out-of-plane (undulations) motions are intertwined in the bilayer in the mesoscopic domain. By novel methods, the fluctuation spectra of lipid bilayers can be calculated withdirect Fourier analysis. The interpretation of the fluctuation spectra reveals a picture where density fluctuations and undulations are most pronounced on different length scales, but coalesce in the mesoscopic regime. This analysis has significant consequences for comparison of simulation data to experiments. These new methods merge the molecular fluctuations on small wavelengths, with continuum fluctuations of the elastic membrane sheet on large wavelengths, allowing electron density profiles (EDP) and area per lipid to be extracted from simulations with high accuracy. Molecular dynamics simulations also provide insight on the small-wavelength dynamics of lipid membranes. Rapidly decaying density fluctuations can be described as propagating sound waves in the framework of linearized hydrodynamics, but there is a slow, dispersive, contribution that needs to be described by a stretched exponential over a broad range of length- and time scales - recent experiments suggest that this behavior can prevail even on micrometer length scales. The origin of this behavior is discussed in the context of fluctuations of the bilayer interface and the molecular structure of the bilayer itself. Connections to recent neutron scattering experiments are highlighted. / QC 20111014 / Modelling of biological membranes

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In tissue development, wound healing and aberrant cancer progression cell–cell interactions drive mixing and segregation of cellular composites. However, the exact nature of these interactions is unsettled. Here we study the dynamics of packed, heterogeneous cellular systems using wound closure experiments. In contrast to previous cell sorting experiments, we find non-universal sorting behavior. For example, monolayer tissue composites with two distinct cell types that show low and high neighbor exchange rates (i.e., MCF-10A & MDA-MB-231) produce segregated domains of each cell type, contrary to conventional expectation that the construct should stay jammed in its initial configuration. On the other hand, tissue compounds where both cell types exhibit high neighbor exchange rates (i.e., MDA-MB-231 & MDA-MB-436) produce highly mixed arrangements despite their differences in intercellular adhesion strength. The anomalies allude to a complex multi-parameter space underlying these sorting dynamics, which remains elusive in simpler systems and theories merely focusing on bulk properties. Using cell tracking data, velocity profiles, neighborhood volatility, and computational modeling, we classify asymmetric interfacial dynamics. We indicate certain understudied facets, such as the effects of cell death & division, mechanical hindrance, active nematic behavior, and laminar & turbulent flow as their potential drivers. Our findings suggest that further analysis and an update of theoretical models, to capture the diverse range of active boundary dynamics which potentially influence self-organization, is warranted.

Cette thèse présente une étude expérimentale sur l'évaporation de gouttes reposant sur un substrat solide. Dans une première partie, nous nous sommes intéressés à la description de l'évaporation d'une goutte liquide en regardant notamment l'influence du substrat. Le problème est approché sous un angle nouveau : en contrôlant avec précision les différentes propriétés du substrat que sont sa rugosité, son énergie de surface et ses propriétés thermiques. Cette méthode a permis de découpler les différentes influences du substrat et d'étudier l'évaporation pour différentes dynamiques de ligne triple et une large gamme d'angles de contact, de conductivités thermiques et de températures de substrat. Les résultats expérimentaux sont comparés au modèle classique d'évaporation. Ce modèle considère l'évaporation comme un processus contrôlé par la diffusion de la vapeur dans l'atmosphère. L'étude révèle les domaines de validité de ce modèle et met en évidence les différents mécanismes additionnels pouvant se développer ainsi que leur contribution. L'utilisation d'une caméra infrarouge dévoile le développement d'un motif hydrodynamique complexe non-axisymétrique. L'origine de cette instabilité, ces dynamiques spatiales et temporelles sont également explorées. Dans une seconde partie, l'étude a été étendue à l'évaporation d'une goutte de suspension biologique : le sang. Le séchage de ce fluide conduit à la formation d'un motif complexe dépendant de la mouillabilité du substrat. Alors qu'une situation mouillante met en évidence un dépôt de type annulaire accompagné de fractures radiales, une situation non-mouillante révèle une forme complexe composée de fractures et de plis. / This thesis presents an experimental study on the evaporation of droplets on a solid substrate. In the first part we describe the evaporation of a liquid droplet, taking a particular interest in the influence of the substrate. The problem is approached from a new angle by ensuring that the various properties of the substrate, such as its roughness, surface energy and thermal properties, are controlled precisely. Thanks to this method it is possible to decouple the different influences of the substrate and to study evaporation in relation to various dynamics of triple lines and a wide range of contact angles, thermal conductivities and temperatures of the substrate. Experimental results are compared with the classic evaporation model, which considers evaporation as a process determined by the diffusion of vapor into the atmosphere. The study reveals the range of validity of this model and highlights the different additional mechanisms which may develop as well as their contribution. The use of an infrared camera reveals the development of a complex hydrodynamic non-axisymmetric pattern. The origin of this instability and its spatial and temporal dynamics are also explored. In the second part, the study is extended to the evaporation of a dropl of a biological suspension: human blood. As this fluid dries a complex pattern is formed which is dependent on the wettability of the substrate. Whereas a wetting situation leads to a ring-like deposit with radial cracks, a non-wetting situation reveals a complex shape composed of cracks and folds. The study focuses on the understanding of the physical mechanisms leading to these patterns and of the role of biology.