In this thesis we study the physics of colloidal dispersions in active and passive liquid crystals by computer simulations. Liquid crystals are materials that exhibit long-range orientational order, with characteristics intermediate between the ones of simple, isotropic fluids and the ones of crystalline solids. Active fluids are suspensions of particles that continuously stir their ambient fluid. Like liquid crystals, active fluids undergo phase transitions to orientationally ordered phases. The framework that we apply here to describe them extends hydrodynamic equations for liquid crystals to the active case, in which their constituent particles exert local stresses on the simple fluid in which they are embedded. Studying systems of colloids embedded in these materials can be done with multiple aims. Here we use colloids as probe particles to investigate the rheological properties of active nematics. To do so we apply a constant force to a spherical particle embedded therein and define an effective viscosity, which we determine by measuring the velocity in steady state. We find an important dependence of the effective viscosity on the size of the particle, and a regime characterised by a steady state of negative drag. We also consider collective properties for systems of many colloids and analyse how they are affected by activity. We find that spontaneous flow can either hinder or favour colloidal aggregation, depending mainly on whether a fixed orientation of the liquid crystal is imposed close to the colloidal surface. This remains true independently of the initial condition chosen for the liquid crystal, which only affects the transition to spontaneous flow.

Les microorganismes présentent des comportements collectifs qui émergent des interactions qui se produisent à l’échelle individuelle. Dans le cas des suspensions concentrées (fraction volumique > 50%) les effets stériques deviennent dominants. C’est le cas du sperme de bélier sur lequel cette étude a principalement porté. Nous avons étudié certains aspects hydrodynamiques liés à la rhéologie du sperme et à la rhéotaxie. Nous montrons un comportement rhéo-fluidifiant en loi de puissance du liquide séminal reproductible d’un in- dividu à l’autre. Nous avons aussi mis en évidence qu’un contrôle chimique peut fortement affecter le comportement rhéotactique des spermatozoı̈des chez l’ovin et chez l’homme. Nous avons par ailleurs étudié la dynamique collective de la semence confinée dans des chambres d’épaisseur contrôlée en apportant des éclaircissements sur l’origine et la caractérisation du comportement turbulent observé. Nos résultats montrent que certaines caractéristiques de la turbulence bidimensionnelle se manifestent (loi de puissance du spectre d’énergie des vitesses, loi de séparation des traceurs passifs) que nous interprétons comme résultant d’une stratification laminée de l’écoulement par les interactions stériques à forte concentration. Enfin, nous avons développé et breveté un système micro-fluidique dans lequel une mise en rotation spontanée de la semence apparaı̂t. Nous avons analysé ce phénomène et l’avons relié à une transition de phase d’orientation cohérente avec une modélisation de type Self-Organized-Hydrodynamics. De plus nos résultats montrent une bonne corrélation entre la vitesse de rotation et la note de mobilité massale, donnant des perspectives d’applications pour la prédiction de la fertilité à ce dispositif. / Microorganisms exhibit collective behaviors that emerge from interactions occurring at the individual scale. In the case of high concentrated suspensions (volume fraction > 50%) steric effects become dominant. This is the case of ram semen on which this study focused. We first studied some hydrodynamic aspects related to the semen rheology and rheotaxis. We show a reproducible seminal plasma power law shear-thinning behavior from one subject to another. We have also highlighted that a chemical control can strongly affect the rheotactic behavior of sperms in the ovine and humans. We also studied the collective dynamics of the semen in chambers of control depth by providing clarification on the origin and characterization of the observed turbulent behavior. Our results show that some characteristics of two-dimensional turbulence occur (power law of the velocity energy spectrum, the pair-particles separation law ) that we interpret as the result of a stratification laminated flow induced by steric interactions at high concentration. Finally, we have developed and patented a micro-fluidic system in which a spontaneous spin-up appears. We analyzed this phenomenon and we connect it to a coherent orientation phase transition with a Self-Organized-Hydrodynamics modeling. In addition, our results show a good correlation between the speed and scoring of mass mobility, giving opportunities for application of the prediction of fertility for this device.

No description available.

This thesis has been concerned with a few problems in systems driven at the scale of particles. The problems dealt with here can be extended and elaborated upon in a variety of ways. In 2 we examine the dynamics of a fluid membrane in contact with a fluid containing active particles. In particular, we show that such a membrane generically enters a statistical steady state with wave-like dispersion. While the numerical results are satisfying, a one-step coarse-graining calculation, in line with [66,93], will, we expect, yield a pair of coupled stochastic differential equations (probably KPZ like at least in one dimension) with wave-like dispersion. This calculation in of interest from a theoretical point-of-view. Further, the numerical exploration of the full set of equations is also left for future work, but can be relevant to many biological systems. In 3 we show that an active fluid confined in an annular channel starts to rotate spontaneously. Further, we predict the existence of banded concentration profile. Such profiles have not yet been observed in experiments. Further, it will be interesting to study what happens to our conclusions if we include the effect of treadmilling in our calculation. In 4 we describe a solid driven by active particles. Specifically, we only concern ourselves with the polar elastomeric phase of the material. However, the questions regarding the transition into that phase are interesting and have not been explored. How exactly does a polarisation transition happen in an active polar elastomer? Is it the same as in an active nematic elastomer? What is the nature of the gelation transition in an active polar fluid? What is the dynamics of nematic defects in an elastomer? Can the presence of the elastomer prevent defect separation? We are at present trying to answer these questions. In 5 we examine the dynamics of an active fluid confined in a channel. It will be interesting to test the prediction about fluctuations in a confined active system, which we show will be normal, in experiments on highly confined actomyosin systems. In 6 we write down the coupled equations of a conformation tensor and the apolar order parameter. This is a generic framework for studying viscoelastic active fluids. A fuller study of the effect of increasing the cross-linker density in such system remains to be done, both theoretically and experimentally. In general, we have shown in the thesis that the understanding of active systems can provide a mechanistic explanation of various biological observations. However, at times the comparison between theory and biological experiments become complicated due to the inherently complicated nature of the experimental systems. Thus, for a more rigorous experimental test of the theory, it is necessary to construct cleaner reconstituted systems with possibly as few as three components. Efforts in this direction have recently borne fruit [129]. However, a complete theoretical understanding of the rich behaviour evinced in these systems is as yet lacking. We expect that the conformation tensor theory we developed in chapter 6 will provide an explanation for the anomalous rheological behaviour observed in these systems. Even in the theoretical front, lot of questions remain to be answered. The dry polar active system, described by the Toner-Tu equations have been shown to undergo a transition to a state with LRO. However, though mean-field theory predicts a second order transition [151, 152, 156], detailed numerical analysis suggests that it is actually first-order with pre-transitional solitonic bands. This has been recently examined by Chate et al. [26] who mapped it to a dynamical system, but a complete theory is still lacking. Apolar systems present another set of challenges. First, the concentration coupling with the order parameter should create similar pre-transitional effects at the order-disorder transition for this system also. This has been studied to a certain extent [133]. However, the more interesting question concerns the role of defects in apolar systems and whether they allow for the possibility of even QLRO in two dimensions. The +1/2 nematic defect has a polarity, and can thus move balistically [51, 108, 115, 149] in a dry system. However, the −1/2 defect has a three-fold symmetry [27] and its motion is thus purely diffusive. Now consider a pair of +1/2 and −1/2 defect pair that can form due to noise in the system (since it does not violate charge conservation). Depending on the configuration and the kind of activity, this defect pair can unbind at zero temperature. Unbound defects would imply that the order is short-ranged. However, it appears from detailed simulations of an agent based Vicsek-like model of active nematics, that there exists a QLRO nematic in two dimensions [111]! How does an active nematic escape being destroyed by defect unbinding? Does concentration have a major role to play? If so, does making the concentration a non-conserved, and thus fast, variable by, for example, including evaporation-deposition rules in the model studied by Chate et al. [28] destroy the QLRO? Also, does the hydrodynamic theory for Malthusian (i.e. one in which the concentration relaxes fast to a steady value) nematics show only short-ranged order, while the one in which mass is conserved show QLRO? These questions are being studied at present by simulating both the agent-based model due to Chate with evaporation-deposition and the dynamical equation for the active nematic order-parameter. These studies should clarify the role of concentration in assisting apolar order. It must be borne in mind, however, that numerical simulations of active models are more difficult than their passive counterparts due to the larger number of parameters present in the problem. In passive systems Onsager symmetry relations constrain some parameters. However, the absence of an equivalent rule for systems far away from equilibrium implies that the spatial symmetry allowed couplings will all have independent kinetic coefficients. This increases the size of the parameter space in many problems. Also, many techniques like Monte Carlo have to be carefully modified to suit such systems. A new and exciting area of research from the point of view of statistical mechanics of active systems is an examination of collective behaviour of run-and-tumble particles pioneered by Tailleur and Cates [25]. This has led to fruitful active generalisations of models of dynamic critical phenomena like model B and model H. Also, it has led to an exploration of rules for selecting a state in a region of phase coexistence – an out of equilibrium generalisation of the Maxwell construction. Another interesting avenue is building up active matter equations from microscopics. This has been done for Vicsek model by Thomas Ihle [64,65], for a simple generalisation of Vicsek-type model for both polar and apolar alignment interactions by Bertin et al. and Chate et al. [15, 16, 107], and for a model of hard rods by Marchetti et al. [10, 11]. The issues of closure still remain to be fully resolved however in deriving the macroscopic equations. A particularly exciting new system that has been recently studied extensively is a collection of chemotactic Janus particles [127]. The far-field interaction in this case does not promote polar order but state with proliferation of asters. The coarse-grained hydrodynamic equations have been derived in this case starting from a microscopic picture of colloids coated axisymetrically with a catalyst in an inhomogeneous concentration of reactants by Saha et al. [127]. Another theoretical issue that plagues the derivation of hydrodynamic equations is that of noise. So far most theories have modelled the noise as Gaussian and white, akin to equilibrium systems, but with unknown strength. However, it is likely that the noise also depends on activity, thus requiring a microscopic picture treating the active forces as stochastic quantities. It is known that multiplicative character of the noise induces interesting features at least in the case of active nematics [104]. Thus, a lot of questions need to be answered if theories of active matter have to graduate from merely offering qualitative explanations of biological experiments to becoming the prototypical theory of systems in which energy input and dissipation both occur at a scale smaller than the coarse-graining volume.

The main contribution of the present work is the proposition of a framework for analysis of active suspensions using the Caenorhabditis elegans nematode as the living model. To do so, five different perspectives are used: kinematics, macro-reological, numerical, theoretical and micro-reological. First, a theoretical and experimental analysis of the kinematic motion of the nematodes suspended in a biological fluid is presented. Two different populations are examined: starving and well fed nematodes. We show that the relationship between the length of an individual nematode and the wavelength of its movement is linear and can be adjusted by a theoretical prediction proposed in this work. A deep discussion on propulsive mechanics based on a scale analysis that identifies three major forces acting on an individual nematode is made. In addition, we investigated the shear viscosity of Caenorhabditis elegans suspensions. The oscillatory shear experiments revealed an anomalous viscosity behavior with the variation of the volumetric fraction of suspension, ?. The effective viscosity of the suspension decreased with increasing nematode volumetric fraction at low concentrations. Based on the experimental data, a phenomenological equation for the effective viscosity of the suspension as a function of the volumetric fraction of particles is proposed. The collective behavior of the nematodes is also observed in linear regime through the difference of normal stresses. Finally, step strain tests are conducted to obtain the relaxation times. The presence of a negative active stress due to the nematoid driving behavior persists for a period of time, leading to a negative undershoot and an oscillatory behavior in the relaxation function. In order to propose a rheological model, simplifications are made in the model and immersed boundary method simulations are conducted in a flexible filament, varying the type of movement that it performs. It is observed that the presence of asymmetries in its undulating movement generates drastic changes on its kinematic responses. A rheological model as a function of filament orientation is proposed and validated with experimental data in linear regime. After validation of the proposed constitutive equation, the model is observed under the nonlinear regime of oscillatory shear, in which the rheological characterizations are made based on existing frameworks using Lissajous-Bowditch curves and Pipkin diagrams. Finally, a protocol for analysis of suspensions in a microrheometer is presented. Particles are added and tracked as unidirectional oscillatory shear (pulsatile flow) is applied. The velocity and shear rate profiles are obtained, as well as the rheological signals equivalent to the strain rate and stress. Signal analysis tools are used and an artificial intelligence system is proposed to remove the component added to the signal by unidirectional shear, aiming to reconstruct the signal with null temporal average and allowing the application of well known rheological theories, such as the decomposition of stresses in coefficients of Chebyshev, for the calculation of viscommetric quantities of compliances and fluidities. The major contribution of the study concerns the observation, characterization, modeling and simulation of a microsized animal that moves in different fashion, depending on the environment, and the surrounding fluid. The rheological properties analyzed, simuations performed and model proposed can be used for both production of artifitial microorganisms and control of living organisms. Moreover, this combination of analyses and techniques can be used to study any type of passive and active suspension providing new and conclusive results regarding the rheological characterization and the physical behavior of the particles. / A principal contribuição do presente trabalho é a proposição de um framework de análise de suspensões ativas utilizando como modelo vivo o nematoide Caenorhabditis elegans. Para tanto, cinco perspectivas diferentes são utilizadas: cinemática, macrorreológica, numérica, teórica e microrreológica. Primeiramente, uma análise teórica e experimental do movimento cinemático das partículas ativas suspensas em um fluido biológico é apresentada. Duas populações diferentes são examinadas: na ausência de alimento e com nematoides bem alimentados. Mostramos que a relação entre o comprimento de um nematoide individual e o comprimento de onda de seu movimento é linear e pode ser ajustada por uma previsão teórica proposta neste trabalho. Uma profunda discussão sobre a mecânica de propulsão com base em uma análise de escala que identifica três forças principais que atuam em um nematoide individual é feita. Além disso, investigamos a viscosidade de cisalhamento das suspensões de Caenorhabditis elegans. Os experimentos em cisalhamento oscilatório revelaram um comportamento anômalo da viscosidade com a variação da fração volumétrica de suspensão, ?. A viscosidade efetiva da suspensão diminuiu com o aumento da fração volumétrica do nematoide para pequenas concentrações. Baseando-se nos dados experimentais, uma equação fenomenológica para a viscosidade efetiva da suspensão em função da fração volumétrica de partículas é proposta. O comportamento coletivo dos nematoides é também observado, em regime linear, pela diferença de tensões normais. Finalmente, o teste de step strain é conduzido para obter os tempos de relaxação. A presença de uma tensão ativa negativa devido ao comportamento impulsor do nematoide persiste por um certo período, levando a um undershoot negativo e a um comportamento oscilatório na função de relaxação. A fim de propor um modelo reológico, simplificações são efetuadas no modelo e simulações usando o método de fronteira imersa são conduzidas em um filamento flexível, variando o tipo de movimento que este realiza. Observa-se que a presença de assimetrias em seu movimento ondulatório gera drásticas mudanças em suas respostas cinemáticas. Um modelo reológico em função da orientação do filamento é proposto e validado com os dados experimentais em regime linear. Após a validação da equação constitutiva proposta, o modelo é observado sob o regime não-linear do cisalhamento oscilatório, no qual as caracterizações reológicas são feitas com base nos frameworks existentes, utilizando curvas de Lissajous-Bowditch e diagramas de Pipkin. Por fim, é apresentado um protocolo de análise de suspensões em um microrreômetro. Partículas são adicionadas e rastreadas à medida que um cisalhamento unidirecional (escoamento pulsátil) é aplicado. Os perfis de velocidade e taxa de cisalhamento são obtidos, assim como os sinais reológicos equivalentes à taxa de deformação e tensão. Ferramentas de análise de sinais são utilizadas e um sistema de inteligência artificial é proposto para remoção da componente constante do sinal adicionada pelo cisalhamento unidirecional, visando reconstruir o sinal com média temporal nula e possibilitando a aplicação de teorias reológicas já conhecidas, como a decomposição de tensões em coeficientes de Chebyshev para o cálculo das quantidades viscométricas de conformidade e fluidez. A principal contribuição do estudo diz respeito à observação, caracterização, modelagem e simulação de um animal microscópico que se movimenta de maneira diferente dependendo do ambiente e do fluido circundante. As propriedades reológicas analisadas, as simulações realizadas e o modelo proposto podem ser utilizados tanto para a produção de microorganismos artificiais quanto para o controle de organismos vivos. Além disso, essa combinação de análises e técnicas pode ser usada para estudo de qualquer tipo de suspensão ativa e passiva, fornecendo resultados novos e conclusivos em relação à caracterização reológica e ao comportamento físico das partículas.

Biological matter is driven far from thermodynamic equilibrium by active processes on the molecular scale. These processes are usually driven by the chemical reaction of a fuel and generate spontaneous movements and mechanical stresses in the system, even in the absence of external forces or torques. Moreover these active stresses effectively fluidify the material. The cell cytoskeleton, suspensions of swimming microorganisms or tissues are prominent examples of active fluids. Active processes in biological systems often exhibit chiral asymmetries. Examples are the chirality of cytoskeletal filaments which interact with motor proteins, the chirality of the beat of cilia and flagella as well as the helical trajectories of many biological micro-swimmers. Moreover, large scale chiral flows have been observed in the cell cortex of C. elegans and Xenopus embryos. Active force generation induces force and torque dipoles in the material. If all forces are internal the total force and torque vanish as required by the conservation of momentum and angular momentum. The density of force dipoles is an active stress in the material. In addition, active chiral processes allow for the existence of active torque dipoles which enter the conservation of angular momentum and generate an active antisymmetric stress and active angular momentum fluxes. We developed a generic description of active fluids that takes into account active chiral processes and explicitly keeps track of spin and orbital angular momentum densities. We derived constitutive equations for an active chiral fluid based on identifying the entropy production rate from the rate of change of the free energy and linearly expanding thermodynamic fluxes in terms of thermodynamic forces. We identified four elementary chiral motors that correspond to localized distributions of chiral force and torque dipoles that differ by their symmetry and produce different chiral fluid flows and intrinsic rotation fields. We employ our theory to analyze different active chiral processes. We first show that chiral flows can occur spontaneously in an active fluid even in the absence of chiral processes. For this we investigate the Taylor-Couette motor, that is an active fluid confined between two concentric cylinders. For sufficiently high active stresses the fluid generates spontaneous rotations of the two cylinders with respect to each other thus breaking the chiral symmetry of the system spontaneously. We then investigate cases where active chiral processes on the molecular scale break the chiral symmetry of the whole system. We show that chiral flows occur in films of chiral motors and derive a generic theory for thin films of active fluids. We discuss our results in the context of carpets of beating cilia or E. coli swimming close to a surface. Finally, we discuss chiral flows that are observed in the cellular cortex of the nematode C. elegans at the one cell stage. Two distinct chiral flow events are observed. The first chiral flow event (i) is a screw like chiral rotation of the two cell halves with respect to each other and occurs around 15min after fertilization. This event coincides with the establishment of cortical cell polarity. The second chiral flow event (ii) is a chiral rotation of the entire cell cortex around the anterior posterior axis of the whole cell and occurs around 30min after fertilization. Measuring densities of molecular motors during episode (i) we fit the flow patterns observed using only two fit parameters: the hydrodynamic length and cortical chirality. The flows during (ii) can be understood assuming an increase of the hydrodynamic length. We hypothesize that the cell actively regulates the cortical viscosity and the friction of the cortex with the eggshell and cytosol. We show that active chiral processes in soft biological matter give rise to interesting new physics and are essential to understand the material properties of many biological systems, such as the cell cortex.

Le transport des micro-organismes, comme par exemple les bactéries, par un fluide se retrouve au centre de thématiques de recherche dans des domaines aussi variés que de la biologie, l’écologie, l’ingénierie et la médecine.Ce manuscrit résume mon étude expérimentale du couplage entre le mouvement microscopique de la nage des bactéries et le mouvement advectif de l’écoulement.La première partie du manuscrit porte sur la rhéologie des suspensions d’E. coli sous faible taux de cisaillement. Pour cette condition, j’ai montré que les perturbations hydrodynamiques induites par la nage réduisent fortement la viscosité. Cet effet peut-être si important pour qu’il soit suffisant pour compenser entièrement la perte visqueuse due au cisaillement.La seconde partie traite des expériences d’écoulement réalisées dans un canal capillaire. Pour cette géométrie, j’ai examiné le couplage pour des écoulements caractérisés par un plus fort taux de cisaillement. Le suivi des trajectoires et le dénombrement des bactéries m’ont permis de mettre en évidence l’existence d’une composante de vitesse normal à la direction de l’écoulement. Cette dernière montre que les bactéries suivent des trajectoires hélicoïdales qui s’enroulent autour du centre du capillaire d’une façon antihoraires. Cette nouvelle composante est corrélée à la migration préférentielle des bactéries dans une couche de localisation proche de la paroi du canal.Les couplages rhéotactiques bactéries/fluide que j’ai étudiés doivent avoir des conséquences potentielles sur le transport en géométries plus complexes qui mériteraient une étude particulière. / The question of transfer and spreading of living microorganisms, such as motile bacteria, is of interest in biology and ecology, but also in engineering and medicine.The way in which the background flow affects the behavior of these bacteria and how it impacts the bacterial transport through complex systems and on the macroscopic properties of the fluid remains unclear and little studied.In this thesis, I present an experimental investigation of the coupling between the local bacteria-driven motion and the fluid advection.In a first part, I investigate the rheological response of E. coli suspensions when subjected to weak flows (low shear rates). I show that, in particular conditions, the microscopic perturbations caused by the bacteria highly impact on the macroscopic viscosity of the suspension, leading to a striking viscosity decrease and eventually overcoming the dissipative effects due to viscous loss. I also identify the relevant time scales defining this viscosity decrease.In a second part, I perform experiments in a capillary channel and analyze the coupling for stronger flows (higher shear rates), at which bacteria were found not to impact on the macroscopic viscosity. Instead, by analyzing the bacterial trajectories under flow, I evidence a breakage of the symmetry of this trajectories which, characterized by a preferential migration, causes the localization of the bacteria in a layer that extends over a significant distance from the surface, and thus potentially influencing the bacterial transport in complex systems

During development, higher organisms grow from a single fertilized egg cell to the adult animal. The many processes that lead to the eventual shape of the developed organism are subsumed as morphogenesis, which notably involves the growth of tissues by repeated rounds of cell division. Whereas coordinated tissue growth is a prerequisite for animal development, excessive cell division in adult animals is the key ingredient to cancer. In this thesis, we investigate the collective organization of cells by cell division and cell death. The multicellular dynamics of growing tissues is influenced by mechanical conditions and can give rise to cell rearrangements and movements. We develop a continuum description of tissue dynamics, which describes the stress distribution and the cell flow field on large scales. Cell division and apoptosis introduce stress sources that, in general, are anisotropic. By combining cell number balance with dynamic equations for the stress source, we show that the tissue effectively behaves as a viscoelastic fluid with a relaxation time set by the rates of division and apoptosis. If the tissue is confined in a fixed volume, it reaches a homeostatic state in which division and apoptosis balance. In this state, cells undergo a diffusive random motion driven by the stochasticity of division and apoptosis. We calculate the effective diffusion coefficient as a function of the tissue parameters and compare our results concerning both diffusion and viscosity to simulations of multicellular systems. Introducing a second material component that accounts for the extracellular fluid, we show that a finite permeability of the tissue gives rise to additional mechanical effects. In the limit of long times, the mechanical response of the tissue to external perturbations is confined to a region of which the size depends on the ratio of tissue viscosity and cell-fluid friction. The two-component description furthermore allows to clearly distinguish the different contributions to the isotropic part of the mechanical stress, i.e., the fluid pressure and the stress exerted by cells. Last but not least, we study the propagation of an interface between two different cell populations within a tissue driven by differences in the mechanical control of the rates of cell division and apoptosis. Combining simple analytical limits and numerical simulations, we distinguish two different modes of propagation of the more proliferative population: a diffusive regime in which relative fluxes dominate the expansion, and a propulsive regime in which the proliferation gives rise to dominating convective flows. / Die Entwicklung höherer Organismen beginnt mit einer einzelnen befruchteten Eizelle und endet beim erwachsenen Tier. Die vielen Prozesse, die zur endgültigen Form des entwickelten Organismus führen, werden als Morphogenese zusammengefasst; diese umfasst insbesondere das Wachstum von Geweben durch wiederholte Zellteilungszyklen. Während koordiniertes Gewebewachstum eine Voraussetzung normaler Entwicklung ist, führt übermäßige, unkontrollierte Zellteilung letztlich zu Krebs. In dieser Arbeit untersuchen wir den Einfluss von Zellteilung und Zelltod auf die Organisation von Zellen in Geweben. Die Dynamik wachsender Gewebe wird durch mechanische Bedingungen beeinflusst, die u.a.~Anlass zu Zellbewegungen sein können. Wir entwickeln eine Kontinuumsbeschreibung der Gewebedynamik, die die mechanischen Spannungen und das Zellströmungsfeld auf großen Skalen beschreibt. Zellteilung und Apoptose wirken als Spannungsquellen, die in der Regel anisotrop sind. Indem wir die Erhaltungsgleichung für die Zellanzahldichte mit dynamischen Gleichungen für die Spannungsquellen kombinieren, zeigen wir, dass sich das Gewebe effektiv wie eine viskoelastische Flüssigkeit verhält, deren Relaxationszeit von Zellteilungs- und Apoptose-Raten abhängt. Wenn das Gewebe in einem gegebenen Volumen eingeschlossen ist, erreicht es einen homöostatischen Zustand, in dem Zellteilung und der Apoptose im Gleichgewicht sind. In diesem Zustand unterliegen die Zellen einer diffusiven Bewegung aufgrund der Stochastizität von Zellteilung und Apoptose. Wir berechnen den effektiven Diffusionskoeffizienten als Funktion der Gewebeparameter und vergleichen unsere Ergebnisse sowohl hinsichtlich der Diffusion und als auch der Viskosität mit numerischen Simulationen solcher vielzelliger Systeme. Die Berücksichtigung der extrazellulären Flüssigkeit als einer zweiten Materialkomponente erlaubt uns zu zeigen, dass eine endliche Permeabilität des Gewebes zusätzliche mechanische Effekte bedingt. Auf langer Zeitskalen bleibt die mechanische Reaktion des Gewebes auf externe Störungen auf einen Bereich beschränkt, dessen Größe vom Verhältnis der Gewebeviskosität zum Permeabilitätskoeffizienten abhängt. Die Zweikomponenten-Beschreibung erlaubt darüber hinaus eine klare Unterscheidung der verschiedenen Beiträge zum isotropen Teil der mechanischen Spannung, d.h., des hydrodynamischen und des von Zellen ausgeübten Drucks. Zuletzt untersuchen wir die Dynamik einer Grenzfläche zwischen zwei verschiedenen Zellpopulationen innerhalb eines Gewebes, die durch Unterschiede in der mechanischen Kontrolle der effektiven Zellteilungsraten angetrieben wird. Mithilfe der Kombination einfacher analytischer Grenzfälle und numerischer Simulationen zeigen wir, dass zwei unterschiedliche Ausbreitungsmodi unterschieden werden können: ein diffusives Regime, in dem relative Flüsse die Expansion der stärker wachsenden Zellpopulation dominieren, sowie ein Regime, in dem die Grenzfläche durch konvektive Strömungen angetrieben wird. / Les organismes supérieurs se développent à partir d\'une seule cellule fécondée jusqu\'à l\'animal adulte. Les nombreux processus qui conduisent à la forme finale de l\'organisme sont connus sous le nom de morphogenèse, qui comprend notamment la croissance des tissus par des cycles répétés de division cellulaire. Alors que la croissance coordonnée des tissus est une condition nécessaire au développement des animaux, la division cellulaire excessive chez les animaux adultes est l\'ingrédient clé du cancer. Dans cette thèse, nous étudions l\'organisation collective des cellules par division et mort cellulaire. La dynamique multicellulaire des tissus en croissance est influencée par des conditions mécaniques et peut donner lieu à des réarrangements ainsi qu\'à des mouvements cellulaires. Nous élaborons une description continue de la dynamique des tissus qui décrit la distribution des contraintes et le champ d\'écoulement des cellules sur de grandes échelles. La division cellulaire et l\'apoptose introduisent des sources de contraintes qui, en général, sont anisotropes. En combinant l\'équation de conservation du nombre de cellules avec des équations dynamiques des sources de contraintes, nous montrons que le tissu se comporte de manière effective comme un fluide viscoélastique avec un temps de relaxation fixé par les taux de division et d\'apoptose. Si le tissu est confiné dans un volume donné, il atteint un état homéostatique dans lequel division et apoptose s\'équilibrent. Dans cet état, les cellules subissent un mouvement diffusif aléatoire dû à la stochasticité de la division et de l\'apoptose. Nous calculons le coefficient de diffusion effectif en fonction des paramètres du tissu et comparons nos résultats concernant à la fois la diffusion et la viscosité à des simulations numériques de tels systèmes multicellulaires. En introduisant un deuxième composant qui représente le liquide extracellulaire, nous montrons qu\'une perméabilité finie du tissu donne lieu à des effets mécaniques supplémentaires. Dans la limite des temps longs, la réponse mécanique du tissu à des perturbations extérieures est confinée à une région dont la taille dépend du rapport entre la viscosité tissulaire et le coefficient de frottement entre les cellules et le liquide extracellulaire. La description à deux composants permet en outre de distinguer clairement les différentes contributions à la partie isotrope de la contrainte mécanique, c\'est-à-dire la pression du fluide et la contrainte exercée par les cellules. Finalement, nous étudions la propagation d\'une interface entre deux populations de cellules différentes, due à des différences dans le contrôle mécanique des taux de division et de mort cellulaire. En combinant de simples limites analytiques et des simulations numériques, nous distinguons deux modes de propagation différents de la population cellulaire la plus proliférante : un régime diffusif dans lequel les flux relatifs dominent l\'expansion, et un régime de propulsion dans lequel la prolifération domine et entraine des flux convectifs.

La phorèse est un mécanisme physico-chimique par lequel certains colloïdes microscopiques dérivent à travers les gradients d'un champ de concentration de soluté dans un fluide. Ce mécanisme est exploité par des particules autophorétiques, ou colloïdes actifs chimiquement, pour auto-propulser. Ces particules influencent les mouvements de leurs voisines par le biais d'interactions chimiques et hydrodynamiques et sont donc étudiées pour leur comportement collectif. La modélisation de ces interactions a fait l'objet de recherches approfondies au cours des dernières années, à la fois d'un point de vue physique pour comprendre les mécanismes précis des interactions, et d'un point de vue expérimental pour expliquer les observations de la formation de structures cohérentes à grande échelle. Cependant, une modélisation exacte de ces suspensions actives est difficile en raison des interactions à grand nombre de particules. Jusqu'à présent, la plupart des modèles proposés reposent sur la superposition d'approximations de champ lointain pour les signatures chimiques et hydrodynamiques de chaque particule, qui ne sont valides que de manière asymptotique dans la limite de suspensions très diluées. Un cadre analytique systématique et unifié basé sur la méthode classique de réflexion (MoR) est développé ici pour les problèmes de Laplace et de Stokes afin d'obtenir les interactions entre particules phorétiques et les vitesses résultantes avec un ordre de précision arbitraire en terme du rapport du rayon et de la distance typique entre deux particules voisines.Un système comprenant uniquement des particules autophorétiques homogènes et isotropes chimiquement et géométriquement est ensuite considéré en détail. On sait que de telles particules isotropes ne peuvent se propulser seules; cependant, en présence d'autres particules identiques, la symétrie du champ de concentration est brisée et les particules forment spontanément des agrégats ou clusters denses. De manière remarquable, ceux-ci peuvent s'auto-propulser si leur arrangement est présente une asymétrie. Ce résultat identifie donc une nouvelle voie pour briser la symétrie du champ de concentration et ainsi générer un mouvement, qui ne repose pas sur une conception anisotrope des particules individuelles, mais sur les interactions collectives de particules actives identiques et homogènes. Un argument pour l'origine de ce comportement auto-propulsif des clusters, basé sur la MoR, est proposé. De plus, en utilisant des simulations numériques complètes combinées à un modèle théorique réduit, nous caractérisons les propriétés statistiques de l'autopropulsion. / Diffusiophoresis is a physico-chemical mechanism by which certain microscopic colloids drift through gradients of a solute concentration field in a fluid. This mechanism is exploited by autophoretic particles, which are chemically active synthetic colloids, to achieve self-propulsion. These particles influence each others' motion through chemical and hydrodynamic interactions and are hence known to exhibit collective behaviour. Modeling these interactions is a subject of intense research over the past decades, both from a physical perspective to understand the precise mechanisms of the interactions, as well as from an experimental point of view to explain the observations of formation of coherent large-scale structures. However, an exact modeling of is difficult due to multi-body interactions and surface effects. Most efforts so far rely on the superposition of far-field approximations for each particle's signature, which are only valid asymptotically in the dilute suspension limit. A systematic and unified analytical framework based on the classical Method of Reflections (MoR) is developed here for both Laplace and Stokes' problems to obtain the multi-body interactions and the resulting velocities of phoretic particles, up to any order of accuracy in the radius-to-distance ratio of the particles.A system comprising only of chemically- and geometrically-isotropic autophoretic particles is then considered in detail. It is known that such isotropic particles cannot self-propel in isolation; however, in the presence of other identical particles, the symmetry of the concentration field is broken and the particles spontaneously form close packed clusters. Remarkably, these clusters are observed to self-propel based on their geometric arrangement. This result thus identifies a new route to symmetry-breaking for the concentration field and to self-propulsion, that is not based on an anisotropic design, but on the collective interactions of identical and homogeneous active particles. An argument for origin of this self-propulsive behaviour of clusters is made based on MoR. Furthermore, using full numerical simulations and theoretical model for clustering, we characterize the statistical properties of self-propulsion of the system.

Biological matter is driven far from thermodynamic equilibrium by active processes on the molecular scale. These processes are usually driven by the chemical reaction of a fuel and generate spontaneous movements and mechanical stresses in the system, even in the absence of external forces or torques. Moreover these active stresses effectively fluidify the material. The cell cytoskeleton, suspensions of swimming microorganisms or tissues are prominent examples of active fluids. Active processes in biological systems often exhibit chiral asymmetries. Examples are the chirality of cytoskeletal filaments which interact with motor proteins, the chirality of the beat of cilia and flagella as well as the helical trajectories of many biological micro-swimmers. Moreover, large scale chiral flows have been observed in the cell cortex of C. elegans and Xenopus embryos. Active force generation induces force and torque dipoles in the material. If all forces are internal the total force and torque vanish as required by the conservation of momentum and angular momentum. The density of force dipoles is an active stress in the material. In addition, active chiral processes allow for the existence of active torque dipoles which enter the conservation of angular momentum and generate an active antisymmetric stress and active angular momentum fluxes. We developed a generic description of active fluids that takes into account active chiral processes and explicitly keeps track of spin and orbital angular momentum densities. We derived constitutive equations for an active chiral fluid based on identifying the entropy production rate from the rate of change of the free energy and linearly expanding thermodynamic fluxes in terms of thermodynamic forces. We identified four elementary chiral motors that correspond to localized distributions of chiral force and torque dipoles that differ by their symmetry and produce different chiral fluid flows and intrinsic rotation fields. We employ our theory to analyze different active chiral processes. We first show that chiral flows can occur spontaneously in an active fluid even in the absence of chiral processes. For this we investigate the Taylor-Couette motor, that is an active fluid confined between two concentric cylinders. For sufficiently high active stresses the fluid generates spontaneous rotations of the two cylinders with respect to each other thus breaking the chiral symmetry of the system spontaneously. We then investigate cases where active chiral processes on the molecular scale break the chiral symmetry of the whole system. We show that chiral flows occur in films of chiral motors and derive a generic theory for thin films of active fluids. We discuss our results in the context of carpets of beating cilia or E. coli swimming close to a surface. Finally, we discuss chiral flows that are observed in the cellular cortex of the nematode C. elegans at the one cell stage. Two distinct chiral flow events are observed. The first chiral flow event (i) is a screw like chiral rotation of the two cell halves with respect to each other and occurs around 15min after fertilization. This event coincides with the establishment of cortical cell polarity. The second chiral flow event (ii) is a chiral rotation of the entire cell cortex around the anterior posterior axis of the whole cell and occurs around 30min after fertilization. Measuring densities of molecular motors during episode (i) we fit the flow patterns observed using only two fit parameters: the hydrodynamic length and cortical chirality. The flows during (ii) can be understood assuming an increase of the hydrodynamic length. We hypothesize that the cell actively regulates the cortical viscosity and the friction of the cortex with the eggshell and cytosol. We show that active chiral processes in soft biological matter give rise to interesting new physics and are essential to understand the material properties of many biological systems, such as the cell cortex.