Self-propelled particles are a class of far-from-equilibrium systems which present many complex, emergent features that are not obvious from the microscopic dynamics. Simulations of well-chosen instances of such systems are a powerful yet tractable method of investigating many real-world phenomena. The frequently non-time-reversible interactions of many cases of self-propelled particles with surfaces means that the environment has an impact on large-scale behaviour in a way that would not be true for particles close to thermal equilibrium. This work investigates several examples of such systems, and compares them with experimental results for comparable systems: firstly, the spatial distribution of smooth-swimming mutants of Eschericia Coli within water-in-oil emulsion is investigated, and its dependence on inter-bacterial interactions and the size of water droplets. The nature of bacterial collisions is inferred through data analysis and simulation. Secondly, pattern formation by chemotactic run-and-tumble bacteria due to secretion of a chemoattractant by the bacteria themselves, demonstrating a range of approaches to control the formation of biofilms by bacteria. Finally the dependence of the bulk transport properties of chemotactic self-propelled particles in porous environments, on their detailed dynamics, is probed: how they interact with obstacles, their form of chemotactic response, their ability to actively enhance their rotational noise, and their method of sensing chemical gradients.

In this Thesis I present simulation- and theory-based studies of pattern formation and growth in collections of micro-organisms, in particular bacterial colonies. The aim of these studies is to introduce simple models of the 'micro-scale' behaviour of bacterial cells in order to study the emergent behaviour of large collections of them. To do this, computer simulations and theoretical techniques from statistical physics, and in particular non-equilibrium statistical physics, were used, as the systems under study are far from thermodynamic equilibrium, in common with most biological systems. Since the elements making up these sytems - the micro-organisms - are active, constantly transducing energy from their environment in order to move and grow, they can be viewed as `active matter' systems. First, I describe my work on a generalization of an archetypal model of active matter - the Vicsek model of flocking behaviour - in which the speed of motion of active particles depends on the local density of particles. Such an interaction had previously been shown to be responsible for some forms of pattern formation in bacterial colonies grown on agar plates in the laboratory. Simulations and theory demonstrated a variety of pattern formation in this system, and these results may be relevant to explaining behaviour observed in experiments done on collections of molecular motors and actin fibres. I then go on to describe work on modelling pattern formation and growth in bacterial biofilms - dense colonies of cells growing on top of solid surfaces. I introduce a simple simulation model for the growth of non-motile cells on a flat surface, whereby they move only by growing and pushing on each other as they grow. Such colonies have previously been observed experimentally to demonstrate a transition from round to 'branched' colonies, with a pattern similar to diffusion-limited aggregation. From these simulations and analytical modelling, a theory of the growth of such colonies is developed which is quite different from previous theories. For example, I find that the colony cannot grow at a constant speed if the cells are not compressible. Finally, I present some results on genetic drift and evolution in growing bacterial colonies. Genetic drift is greatly enhanced in colonies which are expanding in space, as only a few individuals at the edge of the population are able to pass on their genes onto their progeny. The individual-based simulations of biofilms described above are used to analyse which factors - such as the shape of the colony, the thickness of the growing layer of cells, and the interactions between the cells - affect the rate of genetic drift and the probability of fixation of beneficial mutations. This has implications, for example, for the evolution of antibiotic resistance in such colonies.

The growth of bacterial colonies is a very ubiquitous phenomenon occurring in nature and observed in the laboratories. However, there is a limited knowledge on how at the microscopic level these colonies develop and the individual cells spatially organize. In this thesis, we experimentally investigate the physics of growing microcolonies at the level of the individual Escherichia coli (E. coli ) cells, focussing on the order-disorder evolution and the understanding of it in the context of active matter. Bacterial cells are indeed constantly transducing energy from the environment to move and grow, therefore they behave as active microscopic units, defining an inherently far from equilibrium system. In Part I, we present a brief summary of passive liquid crystals that provide us with some basic concepts and tools for investigating the bacterial microcolony evolution. Then an overview of the biology of E. coli cell is given, both as part of multicellular structures (biofilm) and as individuals. Active matter is then discussed along with some examples of active nematics. This first part ends with the materials and methods used in the experiments and analysis. In Part II, we provide our experimental results on the study of growing bacterial microcolonies as active nematics. We describe the way a bacterial microcolony evolves from the first mother cell into a layer of hundreds of cells, and we study the global and local orientational order. We find that a transition from an anisotropic to an isotropic phase occurs as the colony increases and that instabilities and topological defects develop, in analogy to the case of an active nematic. We also compare the real system with simulated ones by investigating (i ) the case of equilibrated configurations with respect to experimental nonequilibrium ones, and (ii ) long-time behaviour of nonequilibrium analogues. In Part III, we discuss the buckling of bacterial microcolonies, that is, the transition from a 2D layer of cells to a 3D structure. We investigate the link between the buckling event and the presence of topological defects in the nematic map of the bacterial microcolony, finding that the buckling sites tend to be closer to topological defects with a negative charge. Later, we present some results of buckling in microcolonies composed of mutants lacking some appendages that play a role in the motion in and attachment to the surrounding environment, finding that buckling occurs at earlier times in the case of these mutants than the wild type. The aim of this work is to show that a growing bacterial microcolony is an interesting model of active matter to experiment on, and that the investigation tools developed for the study of liquid crystals can be useful for describing the evolution of these living systems in mechanistic terms, and for improving the current understanding of nonequilibrium phenomena.

Modéliser le mouvement des foules humaines est essentiel pour des situations aussi diverses que la prévention de risque dans les lieux publics, la planification d’évènements ou la création d’animations visuelles réalistes. Cependant, la difficulté de mener des expériences quantitatives limite notre compréhension de la dynamique des piétons, et le manque de mesures de référence rend impossible une comparaison poussée des modèles existants. Cette thèse tente d’augmenter notre compréhension des foules humaines par deux approches distinctes. Dans un premier temps, nous avons conduit une étude numérique et théorique pour étudier formation de lignes au sein de flux bidirectionnels d'agents motiles. Nous avons montré qu’une transition de phase critique du second ordre séparait un état mélangé d’un état constitué de lignes géantes le long desquelles se déplacent les agents visants une même direction. Cette séparation est caractéristique des systèmes actifs. Une approche hydrodynamique nous a ensuite permis de prouver que les phases mélangées sont aussi algébriquement corrélées dans la direction longitudinale. Nous avons expliqué et montré que ces fortes corrélations sont génériques de tous systèmes de flux bidirectionnels, qu’ils soient constitués de particules forcées ou de particules actives. Dans un second temps, nous avons mené une campagne expérimentale de grande envergure afin d’établir une expérience de référence des foules humaines. Nous avons pour cela choisi un système modèle, la zone d’attente de marathons. Dans ces foules de dizaines de milliers d’individus, nous avons quantitativement établi que les fluctuations de vitesse se propagent sur de grandes échelles, alors que les variations d’orientation s’évanouissent en quelques secondes. Grâce à ces mesures, nous avons construit une théorie prédictive hydrodynamique des foules polarisées. / Modelling crowd motion is central to situations as diverse as risk prevention in mass events and visual effects rendering in the motion picture industry. The difficulty to perform quantitative measurements in model experiments, and the lack of reference experimental system, have however strongly limited our ability to model and control pedestrian flows. The aim of this thesis is to strengthen our understanding of human crowds, following two distinct approaches.First, we designed a numerical model to study the lane formation process among bidirectional flows of motile particles. We first evidenced the existence of two distinct phases: one fully laned and one homogeneously mixed, separated by a critical phase transition, unique to active systems. We then showed with a hydrodynamic approach that the mixed phase is algebraically correlated in the direction of the flow. We elucidated the origin of these strong correlations and proved that they were a universal feature of any system of oppositely moving particles, active of passive.Second, we conducted a substantial experimental campaign to establish a model experiment of human crowds. For that purpose we performed systematic measurements on crowds composed of tens of thousands of road-race participants in start corrals, a geometrically simple setup. We established that speed information propagates through polarized crowds over system spanning scales, while orientational information is lost in a few seconds. Building on these observations, we laid out a hydrodynamic theory of polarized crowds and demonstrated its predictive power.

Le fonctionnement des organismes vivants requiert la production deforces à grande échelle, pour des processus biologiques aussi diversque la motilité cellulaire, le développement embryonnaire, lacicatrisation ou encore la contraction musculaire. Dans de telssystèmes, les forces générées à l'échelle moléculaire par des moteursprotéiques sont transmises par des réseaux de fibres désordonnés,menant à des tensions actives à grande échelle. Les propriétésmacroscopiques passives de ces réseaux de fibres sont biencaractérisées. En revanche, ce problème de production de stress pardes unités actives microscopiques n'est pas résolu. Cette Thèseprésente une étude approfondie, par des méthodes théoriques etnumériques, de la transmission de forces dans les réseaux élastiquesde biopolymères. Je montre que la réponse linéaire, à faible force,des réseaux est remarquablement simple : elle est déterminée par laseule la géométrie des unités actives exerçant les forces. Aucontraire, lorsque les forces actives sont suffisamment importantespour provoquer le flambage non-linéaire des fibres, ces forces sontrectifiées par le réseau, et deviennent isotropiquementcontractiles. La contraction émergente qui en résulte est amplifiéepar la transmission de forces non-linéaire à travers le réseau. Cetteamplification du stress macroscopique est renforcée par le caractèredésordonnée du réseau, mais sature lorsque la densité d'unités activesest grande. Nos prédictions sont en accord quantitatifs avec desrésultats expérimentaux sur des tissus reconstitués et des réseauxd'actomyosine in vitro, et apportent un éclairage nouveau surl'influence de l'architecture microscopique des réseaux sur structuredes stress à l'échelle de la cellule et du tissu. / Large-scale force generation is essential for biological functionssuch as cell motility, embryonic development, wound healing and musclecontraction. In these processes, forces generated at the molecularlevel by motor proteins are transmitted by disordered fiber networks,resulting in large-scale active stresses. While fiber networks arewell characterized macroscopically, this stress generation bymicroscopic active units is not well understood. In this Thesis, Ipresent a comprehensive theoretical and numerical study of forcetransmission in elastic fiber networks. I show that the linear,small-force response of the networks is remarkably simple, as themacroscopic active stress depends only on the geometry of theforce-exerting unit. In contrast, as non-linear buckling occurs aroundthese units, local active forces are rectified towards isotropiccontraction, making the local geometry of force exertion irrelevant.This emergent contractility is amplified by non-linear forcetransmission through the network. This stress amplification isreinforced by the networks' disordered nature, but saturates for highdensities of active units. Our predictions are quantitativelyconsistent with experiments on reconstituted tissues and actomyosinnetworks, and that they shed light on the role of the networkmicrostructure in shaping active stresses in cells and tissue.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第20415号 / 工博第4352号 / 新制||工||1675(附属図書館) / 京都大学大学院工学研究科化学工学専攻 / (主査)教授 山本 量一, 教授 宮原 稔, 教授 稲室 隆二 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

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OLIVEIRA, Jessé Pereira de. Transporte em um sistema binário de partículas autopropelidas. 2015. 55 f. Dissertação (Mestrado em Física) - Programa de Pós-Graduação em Física, Departamento de Física, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2015. / Submitted by Edvander Pires (edvanderpires@gmail.com) on 2015-10-28T17:59:25Z No. of bitstreams: 1 2015_dis_jpoliveira.pdf: 4553539 bytes, checksum: 34f5d2c643bcea3444dad8820e83f2a2 (MD5) / Approved for entry into archive by Edvander Pires(edvanderpires@gmail.com) on 2015-10-28T18:05:49Z (GMT) No. of bitstreams: 1 2015_dis_jpoliveira.pdf: 4553539 bytes, checksum: 34f5d2c643bcea3444dad8820e83f2a2 (MD5) / Made available in DSpace on 2015-10-28T18:05:49Z (GMT). No. of bitstreams: 1 2015_dis_jpoliveira.pdf: 4553539 bytes, checksum: 34f5d2c643bcea3444dad8820e83f2a2 (MD5) Previous issue date: 2015 / Originally introduced by T. Vicksek et al. [Phys. Rev. Lett. 75, 1226 (1995)], Self Propelled Particles (SPP) have an intrinsic constant speed which suffer variations ins its direction as results of external perturbations (another particles or system) and are used to model systems that shows agglomeration effects. The concept of SPP is applied to describe and understand dynamic effects of agglomeration in natural systems, such as living micro-organisms (bacteria, virus, etc.) and colonies of individuals which move in flocks (fishes, sheep, bees) or, artificially produced, as colloidal systems especially prepared in laboratory. The study of SPP has its relevance in several areas of knowledge, such as material engineering, medicine and sciences of nature (physics, chemistry and biology). In most of cases, the collective motion has an well-differentiated behaviour of the individual motion of the components of a given system. So, the movement of a certain individual is affected by the presence of the other elements of the system, changing its general behaviour, as direct consequences of the direct interaction between them. In this way, we see the importance of investigation and understanding of collective motion of the SPP. Especially in this dissertation, we study a binary two-dimensional system of SPP subject to the presence of rigid obstacles with anisotropic geometry (semi-circles) distributed neatly in form of a square web. Beyond the particle-particle and particleobstacle interaction, the individual movement of each SPP suffers influence of an white noise. The objective is characterize the transport of SPP trough the two-dimensional substratum in absence of an propeller external force. We present and systematic study of collective motion of SPP in function of the speed of the particles, of the noise intensity which defines the stochastic movement of SPP, of the size of the obstacles, of the SPP density e the separation between the obstacles. Due the anisotropy of the obstacles, arise an spontaneous and ordered collective motion in normal direction of the plane surface of the obstacles, characterized by an non-null mean speed for each type of SPP in absence of an external force which in affected by the system parameters. / Originalmente introduzidas por T. Vicksek et al. [Phys. Rev. Lett. 75, 1226 (1995)], part´ıculas auto-propelidas (PAP) possuem uma velocidade intr´ınseca constante que sofre varia¸c˜oes em sua dire¸c˜ao como resultados de perturba¸c˜oes externas (outras part´ıculas ou meio) e s˜ao usadas para modelar sistemas que apresentam efeitos de aglomera¸c˜ao. O conceito de PAP ´e aplicado para descrever e entender efeitos dinˆamicos de aglomera¸c˜ao em sistemas naturais, tais como microorganismos vivos (bact´erias, v´ırus, etc) e colˆonias de indiv´ıduos de que se movem em bandos (peixes, ovelhas, abelhas, etc) ou, produzidos artificialmente, como sistemas coloidais especialmente preparadas em laborat´orio. O estudo de PAP tem sua relevˆancia em diversas ´areas do conhecimento, tais como engenharia de materiais, medicina e ciˆencias da natureza (f´ısica, qu´ımica e biologia). Na maioria dos casos, o movimento coletivo tem um comportamento bastante diferenciado dos movimentos individuais dos componentes de um dado sistema. Assim, o movimento de um certo indiv´ıduo ´e influenciado pela presen¸ca dos outros constituintes do sistema, alterando o seu comportamento geral, como consequˆencia da intera¸c˜ao direta entre eles. Desta forma, vemos a importˆancia da investiga¸c˜ao e entendimento do comportamento coletivo das PAP. Nesta disserta¸c˜ao, estudamos um sistema bidimensional bin´ario de PAP na presen¸ca de obst´aculos r´ıgidos com geometria anisotr´opica (semi-c´ırculos) distribu´ıdos na forma de uma rede quadrada. Al´em das intera¸c˜oes part´ıcula-part´ıcula e part´ıcula-obst´aculo, o movimento individual de cada PAP sofre influˆencia de um ru´ıdo branco. O objetivo ´e caracterizar o transporte de PAP atrav´es do substrato bidimensional na ausˆencia de uma for¸ca externa propulsora. Apresentamos um estudo sistem´atico do movimento coletivo das PAP em fun¸c˜ao das velocidades das part´ıculas, da intensidade do ru´ıdo que define o movimento estoc´astico das PAP, do tamanho dos obst´aculos, da densidade de PAP e da separa¸c˜ao entre os obst´aculos. Devido a anisotropia dos obst´aculos, surge um movimento coletivo espontˆaneo e ordenado na dire¸c˜ao normal `a superf´ıcie plana dos obst´aculos, caracterizado por uma velocidade m´edia n˜ao-nula para cada tipo de PAP na ausˆencia de for¸ca externa e que ´e influenciado pelos parˆametros do sistema.

Thermal and viscous forces compete for dominance at the microscopic length-scales which govern the behaviour of many soft or biological systems. We study three systems of increasing complexity with the central goal of understanding the statistical or hydrodynamic nature of their mechanics. First we study experiments that have been conducted on ferromagnetic colloidal rods. At equilibrium, the magnetically pinned rod is observed to randomly flip between two orientational states, which our theoretical analysis shows is due to a competition between entropic and Hamiltonian forces. We show analytically how entropic forces can arise by considering the coupling between observed and unobserved variables of a system. Experiments in which a rod is driven out of equilibrium by a rotating field display three phases of steady-state behaviour as a function of driving frequency. Using Brownian dynamics simulations we match the lower critical frequency to the experimentally obtained values, showing that thermal fluctuations play an important role in this regime and propose a simple argument to demonstrate that hydrodynamic interactions between the substrate and rod affect the upper critical frequency. We then turn to the biophysical topic of cell locomotion in viscoelastic media. In order to study how bacterial flagella interact with similarly-sized polymers in their environment, we construct a Stokesian dynamics model of a helical filament and bead--spring polymer. Simulating their interaction first for a pinned--rotating helix, then for a swimming helix, we demonstrate that large polymers become hydrodynamically entrained by the flagellum and coil around it, causing both pinned and swimming flagella to expend more work. For the swimming helix, this results in a reduction of swimming speed on average. Finally, we consider an active nematic fluid confined to a channel and show that the inclusion of a passive colloid induces a global state of coherent flow maintained by the intrinsic activity of the system. This flow is persistent, and transports the colloid with it along the channel. By this mechanism, a passive colloid is able to spontaneously induce its own transport through an otherwise quiescent fluid.