Earthquakes are amongst the most destructive of natural phenomena and have been the subject of significant research effort over many decades, to predict the onset of seismic events. Electromagnetic emissions detected prior to earthquakes provide a potential data source for seismic predictions and research suggests that specific pre-seismic electromagnetic activity can be directly related to specific earthquakes although it is still an open issue as to the precise links between these electromagnetic emissions and subsequent earthquakes. In this research, findings of the long memory or the self-organization of several pre-earthquake MHz electromagnetic time-series provide significant outcomes regarding the earthquake prediction. It is also recognised that enhanced radon gas emission has an equally long history as being associated with seismic activity. In general, several anomalous soil radon emissions have been observed prior to earthquakes and this has been recorded all over the world. The abnormal soil radon exhalation from the interior of the earth has been associated with earthquakes and is considered as an important field of research. The research reported in this thesis compared and contrasted the merits of combining electromagnetic emission data and radon exhalation data as precursors of earthquakes with the aim of enhancing earthquake prediction methodology. The findings from the long-memory analysis of radon disturbances in the soil indicated a very significant issue: the radon disturbances in the soil prior to earthquakes exhibit similar behaviour as the MHz RF disturbances of general failure. So, the radon precursors and the MHz electromagnetic correspond to the same pre-earthquake phase. Geological explanations were proposed in view of the asperity model. Persistent and anti-persistent MHz anomalies were due to the micro-cracking of the heterogeneous medium of the earth's crust which may have led the system's evolution towards the global failure. Fractal methods have been used on historical data, to investigate MHz electromagnetic time-series spectra on emissions preceding major earthquakes over the period 2007 to 2014 and the characteristics of enhanced radon emissions have been studied over the period 2008 to 2015 for seismic events occurring in the Aegean Region. It has been found that both the electromagnetic emissions and the radon exhalation data exhibit similar fractal behaviour and are associated with impending seismic activity. Hence both phenomena are relevant to earthquake predictions and should both be employed in any systematic approach to this problem as the varying geological and geographic conditions under which earthquakes can occur, might preclude one or other data from being measurable. According to the several techniques applied in this thesis, all should be employed in sequential steps, albeit the power-law spectral fractal analysis is the most significant to trace long-memory patterns of 1/f processes as those of the processes of earthquakes.

Social behaviour is shaped by complex relationships between evolutionary and ecological processes interacting at different scales. Benefits gained from social associations can range from predator dilution to collective sensing, but little is known about how these can be influenced by social structure and phenotypic composition. In this thesis, I investigated how individual decision-making affects phenotypic social structure, and how this mediates social behaviour through emergent properties of collective group behaviour. First, using mixed-species flocks as a model system, I showed individual tits (Paridae, chapter 2) and thornbills (Acanthizae, chapter 3) varied significantly in their social positions. Within-species variation in network position was as large as between-species variation, sug- gesting that prescribing functional roles at the species level may not sufficiently account for potential differences in fitness operating at the individual level. Rather, this suggested that structure may be driven by phenotypic traits, underpinning network structure (chapter 4). Next, I used an extensive data set of foraging records to explore factors determining the composition, of flocks of great tits (Parus major, chapter 5). For example, assortment by dispersal phenotype (immigration status) was the result of spatial disaggregation, and I showed that this may facilitate social selection for breeding territories (chapter 6). Finally, I investigated how decision-making shaped mixed-species social structure. I found that tits used a common strategy for managing pressures of predation and starvation by shifting from exploration to exploitation at different times of the day (chapter 7). I then found that a very simple interaction rule successfully replicated mixed-species group structure (chapter 8). Strikingly, the same rule was applied to both conspecifics and het- erospecifics, potentially playing an important role in the maintenance of flock structure. Through experimental manipulation of ecological conditions, I found that heightened per- ceived predation resulted in stronger social attraction overall, whereas increased competition led to a reduction in attraction to conspecifics (chapter 9). Simulations suggested this could be one potential mechanism underpinning fission-fusion dynamics in these species. Together, the results in this thesis form a framework linking social behaviour to individ- ual fitness where natural selection is shaped by the social environment. This approach may prove useful for testing whether following common social rules reduces variance in benefits accrued by individuals, and how within-species variation in social behaviour can impact emergent properties of groups.

No description available.

This thesis employs perspectives inspired by General Systems Theory to address issues in philosophy, including moral philosophy and philosophy of mind. I present an overview of a range of ideas from the study of physical systems that may be used to provide a firm physicalist foundation to explorations of some common questions in philosophy. I divide these topics into three categories: the Physical Category, the Relevance Category and the Signal Elements Category. I interpret concepts from General Systems Theory, including information and entropy, in a way that I believe facilitates their incorporation into philosophical discussion. I also explain various points arising from General Systems Theory, such as order and disorder, stability, complexity, and self-organisation, and show how ideas from these areas can be applied to certain philosophical problems. I explain relevance in terms of stability, in order to link these scientific perspectives to questions in moral philosophy. I suggest a possible physical foundation for a theory of morality, which takes the form of a variety of Utilitarianism, intended to balance the competing needs of open systems to manage entropy. Such a theory of morality must be capable of dealing with limitations arising from the physicality of information; I propose game theory as a solution to this problem. This thesis also covers issues connected to the above points regarding the nature of consciousness and communication. In particular, I examine the role of linguistic associations in consciousness; and some related features of language and other non-linear representational schemes.

“much of what we know about leadership is today redundant because it is literally designed for a different operating model, a different context, a different time” (Pascale, Sternin, & Sternin, p. 4). This thesis describes a project that was designed with a focus on exploring ways to enhance leadership capacity in non-government organisations operating in Christchurch, New Zealand. It included 20 CEOs, directors and managers from organisations that cover a range of settings, including education, recreation, and residential and community therapeutic support; all working with adolescents. The project involved the creation of a peer-supported professional learning community that operated for 14 months; the design and facilitation of which was informed by the Appreciative Inquiry principles of positive focus and collaboration. At the completion of the research project in February 2010, the leaders decided to continue their collective processes as a self-managing and sustaining professional network that has grown and in 2014 is still flourishing under the title LYNGO (Leaders of Youth focussed NGOs). Two compelling findings emerged from this research project. The first of these relates to efficacy of a complexity thinking framework to inform the actions of these leaders. The leaders in this project described the complexity thinking framework as the most relevant, resonant and dynamic approach that they encountered throughout the research project. As such this thesis explores this complexity thinking informed leadership in detail as the leaders participating in this project believed it offers an opportune alternative to more traditional forms of positional leadership and organisational approaches. This exploration is more than simply a rationale for complexity thinking but an iterative in-depth exploration of ‘complexity leadership in action’ which in Chapter 6 elaborates on detailed leadership tools and frameworks for creating the conditions for self-organisation and emergence. The second compelling finding relates to efficacy of Appreciative Inquiry as an emergent research and development process for leadership learning. In particular the adoption of two key principles; positive focus and inclusivity were beneficial in guiding the responsive leadership learning process that resulted in a professional learning community that exhibited high engagement and sustainability. Additionally, the findings suggest that complexity thinking not only acts as a contemporary framework for adaptive leadership of organisations as stated above; but that complexity thinking has much to offer as a framework for understanding leadership development processes through the application of Appreciative Inquiry (AI)-based principles. A consideration of the components associated with complexity thinking has promise for innovation and creativity in the development of leaders and also in the creation of networks of learning. This thesis concludes by suggesting that leaders focus on creating hybrid organisations, ones which leverage the strengths (and minimise the limitations) of self-organising complexity-informed organisational processes, while at the same time retaining many of the strengths of more traditional organisational management structures. This approach is applied anecdotally to the place where this study was situated: the post-earthquake recovery of Christchurch, New Zealand.

Durant ces dernières années, nous avons assisté à une forte émergence de nouvelles technologies et environnements informatiques tels que le cloud computing, l'informatique ubiquitaire ou les réseaux de capteurs. Ces environnements ont permis d'élaborer de nouveaux types d'applications avec une forte valeur ajoutée pour les usagés. Néanmoins, ils ont aussi soulevés de nombreux défis liés notamment à la conception, au déploiement et à la gestion de cycle de vie des applications. Ceci est dû à la nature même de ces environnements distribués, caractérisés par une grande flexibilité, un dynamisme accru et une forte hétérogénéité des ressources. L'objectif principal de cette thèse est de fournir une solution générique, réutilisable et extensible pour l'auto-gestion de ces applications. Nous nous sommes concentrés sur la fourniture d'un support logiciel permettant de gérer à l'exécution les architectures et leur cycle de vie, notamment pour les applications à base de composants s'exécutant dans des environnements dynamiques, distributes et à grande échelle. De façon à atteindre cet objectif, nous proposons une solution synergique – le framework Cube – combinant des techniques issues de domaines de recherche adjacents tels que l'auto-organisation, la satisfaction de contraintes, l'auto-adaptation et la reflexion fondée sur les modèles architecturaux. Dans notre solution, un ensemble de gestionnaires autonomiques décentralisés s'auto-organise de façon à construire et gérer une application cible en s'appuyant sur une description partagée des buts de l'application. Cette description formelle, appelé Archetype, prend la forme d'un graphe orienté exprimant les différents éléments de l'architecture et un ensemble de contraintes. Un prototype du framework Cube a été implanté dans le domaine particulier de la médiation. Des expériences ont été conduites dans le cadre de deux projets de recherché nationaux: Self-XL et Medical. Les résultats obtenus démontrent la validité de notre approche pour créer, réparer et adapter des applications à base de composants s'exécutant dans des environnements distribués, dynamiques et hétérogènes. / In recent years, the world has witnessed the rapid emergence of several novel technologies and computing environments, including cloud computing, ubiquitous computing and sensor networks. These environments have been rapidly capitalised upon for building new types of applications, and bringing added-value to users. At the same time, the resulting applications have been raising a number of new significant challenges, mainly related to system design, deployment and life-cycle management during runtime. Such challenges stem from the very nature of these novel environments, characterized by large scales, high distribution, resource heterogeneity and increased dynamism. The main objective of this thesis is to provide a generic, reusable and extensible self-management solution for these types of applications, in order to help alleviate this stringent problem. We are particularly interested in providing support for the runtime management of system architecture and life-cycle, focusing on applications that are component-based and that run in highly dynamic, distributed and large-scale environments. In order to achieve this goal, we propose a synergistic solution – the Cube framework – that combines techniques from several adjacent research domains, including self-organization, constraint satisfaction, self-adaptation and self-reflection based on architectural models. In this solution, a set of decentralised Autonomic Managers self-organize dynamically, in order to build and administer a target application, by following a shared description of administrative goals. This formal description, called Archetype, contains a graph-oriented specification of the application elements to manage and of various constraints associated with these elements. A prototype of the Cube framework has been implemented for the particular application domain of data-mediation. Experiments have been carried-out in the context of two national research projects: Self-XL and Medical. Obtained results indicate the viability of the proposed solution for creating, repairing and adapting component-based applications running in distributed volatile and evolving environments.

La prise de décision collective est un des mécanismes usités par les espèces sociales lors d’événements de collectes de nourriture, d’optimisation de chemins, de mouvements collectifs, de fuites face à un prédateur ou bien même de sélections d’habitat. Les zebrafish (Danio rerio), animaux grégaires de référence en biologie, n’ont jamais été étudiés dans des contextes de choix collectifs binaires et ils nous semblait légitime d’analyser leurs comportements décisionnels. L’objectif de cette thèse est de répondre aux attentes du projet ASSISI|bf de création d’un système expérimental modulable capable d’accueillir robots comme poissons, de mise au point d’une société mixte adaptative auto-organisée, et de caractérisation des comportements individuels et collectifs des zebrafish implémentables dans les robots. Nos observations montrent que la prise collective de décision et la cohésion des groupes en environnement ouvert, et présentant deux points de repère identiques, sont des processus dynamiques qui varient selon la souche de Danio rerio (AB ou TL) et sont liées à la densité des populations. Constamment en mouvement, les poissons oscillent entre les deux points de repère identiques installés dans leur environnement. La souche AB est toujours plus attirée par ces hétérogénéités et est beaucoup moins cohésive que la souche TL. En environnement contraint, de type deux chambres reliées par un couloir, nous réitérons le même type d’expérience chez la souche la plus à même de prendre des décisions collectivement (AB) et en faisant varier la densité des groupes de 1 à 20 individus. Il ressort que les Danio rerio de type AB restent essentiellement en groupe mais que l’augmentation de leur densité tend à les diviser. Nous remarquons aussi que la densité influe partiellement sur la topologie du groupe : il existe, lors des sorties collectives, une corrélation entre l’ordre de sortie des zebrafish (les suiveurs) et l’ordre de distance de chaque individu par rapport à l’initiateur desdites sorties. Cette corrélation est d’autant plus forte quand les suiveurs sont soit très proches, soit les plus éloignés de l’initiateur. Le dispositif expérimental précédent nous permet d’autre part de nous concentrer sur la notion de leadership chez des groupes de 2 à 10 Danio rerio AB. Nous mettons en évidence que chaque poisson initie au moins une fois un départ collectif, le nombre d’initiations effectives est proportionnel au nombre de tentatives d’initiations, que tous les poissons présentent le même taux de succès d’initiation après une tentative et qu’il existe une corrélation positive entre initiations et vitesse moyenne de nage.Une analyse poussée des mouvements collectifs nous fait constater que les zebrafish se déplacent essentiellement en groupe et transitent sans interruption ni périodicité entre les chambres. Nous sommes actuellement en train d’améliorer cette étude en apportant de nouveaux points de comparaison afin de vérifier si la non-périodicité des transitions entre les chambres est liée à la densité des groupes testés. Enfin, nous nous inspirons du précédent système expérimental – les deux chambres reliées par un couloir – pour créer une version actualisée d’un labyrinthe en Y. Ce labyrinthe en Y est dit perpétuel car il combine tout le savoir faire que nous avons développé dans l’élaboration des précédents systèmes expérimentaux : une faible habituation des zebrafish pour leur milieu, une réduction des interactions entre l’expérimentateur et les animaux et la possibilité pour les poissons de circuler dans un labyrinthe à symétrie centrale, sans zone de départ ni zone de fin formalisées (typiques des labyrinthes en Y) / The collective decision-making is one of the mecanisms used by social species during foraging, path optimisation, collective movements, predator avoidance or habitat selection. Zebrafish (Danio rerio), gregarious animal models in biology, have never been studied in the context of collective binary choices. We found logical to analyse their decision behaviours. The goal of this thesis is to meet the expectations of the ASSISI|bf project of creation of an andjustable experimental setup able to sustain robots and fish, of development of an adaptive and self-organised mixed society and of the caracterisation of individual and collective behaviours of the zebrafish, implementable in the robots. We show that the collective decision making and the cohesion of groups of zebrafish in an open environment, composed of two identical landmarks, are dynamical processes that vary in function of the strain of Danio rerio (AB or TL) and are related to the density of the populations. Always on the move, the fish oscillate between the two landmarks. The AB zebrafish are more attracted by the landmarks and are less cohesive than the TL zebrafish. In a contrained environment, two rooms connected by a corridor, we do the same type of experiments with only AB zebrafish and vary the density of the groups from 1 to 20 individuals. AB zebrafish swim together. The increase of the density of the groups make them split. We noticed that the density of the groups has an effect on the topology of the groups : during collective departures from a room to the other one, there is a correlation between the rank of exit of the zebrafish (followers) and the rank of the distances of each individual from the initiator of the exits. This correlation is higher when the followers are either the closest or the farest from the initiator.Using the previous experimental setup, we focused also on the topics related to leadership for groups of 2 to 10 individuals. We show that each fish intiate at least once a collective departure and that the number of initiations is proportional to the number of initiation attempts. Also, we found that all the fish have the same success rate in the initiations after an initiation attempt and that there is a positive correlation between the intiations and the average speed. A deeper analysis of the collective movements shows that the zebrafish swim in group and transit without any interruption or even without periodicity between the rooms. We are currently improving this study and will bring new points of comparison to check if the non-periodicity of the transitions could be related to the density of the groups. Finally, we developed a new version of the Y-maze based on the previous observations.This perpetual Y-maze shows many usefull features for the study of the behaviour : a low habituation rate, a reduction of the interactions between the animals and the experimentators, and allows the fish to move in a Y-maze without starting nor ending zones as in typical Y-maze

L’environnement naturel des levures est constitué d’une communauté de cellules. Les chercheurs, cependant, préfèrent étudier les levures dans des environnements plus simples et homogènes, comme des cultures en cellule unique ou en population, s’affranchissant ainsi de la complexité de la croissance spatiotemporelle, la différentiation, l’auto-organisation, ainsi que la façon dont ces caractéristiques sont formées et s’entrelacent à travers l’évolution et l’écologie. Nous avons mis en place un dispositif microfluidique multicouches permettant la croissance de colonie de levures dans des environnements dynamiques, spatialement structurés, contrôlés, partant d’une monocouche de levures à une colonie multicouches. La croissance des colonies, dans son ensemble comme à des positions spécifiques, est le résultat de la formation d’un gradient de nutriment au sein de celles-ci - gradient qui trouve son origine dans le différent taux de diffusion des nutriments, des taux d’absorption de ceux-ci par les cellules, ainsi que de leurs concentrations initiales. Lorsqu’un nutriment en quantité limitante (par exemple le glucose ou un acide aminé) est épuisé, à une distance spécifique de la source de nutriments, les cellules au sein de la colonie cessent de croitre. Nous avons été en mesure de moduler cette distance spécifique en variant la concentration initiale de nutriments ainsi que le taux d’absorption des cellules. Les motifs d’expression de gènes de la colonie nous ont donné des informations sur la formation de micro environnements spécifiques ainsi que sur le développement subséquent, la différentiation et l’auto-organisation. Nous avons quantifié les motifs d’expression de sept gènes de transport du glucose (HXT1-7), chacun exprimé spécifiquement suivant la concentration de glucose, ce qui nous a permis de reconstituer la formation de gradients de glucose au sein d’une colonie. En étudiant des gènes spécifiques de la fermentation et de la respiration, nous avons pu observer la différentiation en deux sous-populations. Nous avons de plus cartographié l’expression de gènes impliqués dans différentes parties du métabolisme des glucides, suivi et quantifié la dynamique spatio-temporelle de croissance et d’expression génétique et finalement modélisé la croissance de la colonie ainsi que la formation du gradient de nutriment. Pour la première fois, nous avons observé la croissance, la différentiation et l’auto-organisation des colonies de S. cerevisiae avec une résolution spatio-temporelle jusqu’à maintenant inégalée / The natural environment of yeast is often a community of cells but researchers prefer to study them in simpler homogeneous environments like single cell or bulk liquid cultures, losing insight into complex spatiotemporal growth, differentiation and self-organization and how those features are intertwined and shaped through evolution and ecology. I developed a multi-layered microfluidic device that allows us to grow yeast colonies in spatially controlled dynamically structured changing environments from a monolayer of single yeast cells to a multi-layered colony. Colony growth, as a whole and at specific locations, is a result of the nutrient gradient formation within a colony through interplay of nutrient diffusion rates, nutrient uptake rates by the cells and starting nutrient concentrations. Once a limiting nutrient (e.g. glucose or amino acids) is depleted at a specific distance from the nutrients source the cells within a colony stop to grow. I was able to modulate this specific distance by changing the starting nutrient concentrations and uptake rates of cells. Colony gene expression patterns gave us information on specific micro environments formation and consequential development, differentiation and self-organization. I quantified the patterns of expression of seven glucose transporter genes (HXT1-7), each of them specifically expressed depending on the glucose concentration. This enabled us to reconstruct glucose gradients formation in a colony. I further followed the expression of fermentation and respiration specific genes and observed differentiation between two subpopulations. We also mapped other genes specific for different parts of carbohydrate metabolism, followed and quantified the spatiotemporal dynamics of growth and gene expression, and finally modelled the colony growth and nutrient gradient formation. For the first time, we were able to observe growth, differentiation and self-organization of S. cerevisiae colony with such an unprecedented spatiotemporal resolution

The goal of the research activities presented in this thesis is the design of intelligent behaviours for a complex robotic system, which is composed of a swarm of autonomous units. Inspired by the organisational skills of social insects, we are particularly interested in the study of collective behaviours based on self-organisation.<p><p>The problem of designing self-organising behaviours for a swarm of robots is tackled resorting to artificial evolution, which proceeds in a bottom-up direction by first defining the controllers at the individual level and then testing their effect at the collective level. In this way, it is possible to bypass the difficulties encountered in the decomposition of the global behaviour into individual ones, and the further encoding of the individual behaviours into the controllers' rules. In the experiments presented in this thesis, we show that this approach is viable, as it produces efficient individual controllers and robust self-organising behaviours. To the best of our knowledge, our experiments are the only example of evolved self-organising behaviours that are successfully tested on a physical robotic platform.<p><p>Besides the engineering value, the evolution of self-organising behaviours for a swarm of robots also provides a mean for the understanding of those biological processes that were a fundamental source of inspiration in the first place. In this perspective, the experiments presented in this thesis can be considered an interesting instance of a synthetic approach to the study of collective intelligence and, more in general, of Cognitive Science.<p> / Doctorat en sciences appliquées / info:eu-repo/semantics/nonPublished

Anders als menschengemachte Maschinen verfügen Zellen über keinen festgeschriebenen Bauplan und die Positionen einzelner Elemente sind häufig nicht genau festgelegt, da die Moleküle diffusiven Zufallsbewegungen unterworfen sind. Darüber hinaus sind einzelne Bauteile auch nicht auf eine einzelne Funktion festgelegt, sondern können parallel in verschiedene Prozesse einbezogen sein. Basierend auf Selbstorganisation und Selbstassemblierung muß die Organisation von Anordnung und Funktion einer lebenden Zelle also bereits in ihren einzelnen Komponenten inhärent enthalten sein. Die intrazelluläre Organisation wird zum großen Teil durch ein internes Biopolymergerüst reguliert, das Zytoskelett. Biopolymer-Netzwerke und –Fasern durchdringen die gesamte Zelle und sind verantworlich für mechanische Integrität und die funktionale Architektur. Unzählige essentielle biologische Prozesse hängen direkt von einem funktionierenden Zytoskelett ab. Die vorliegende Arbeit zielt auf ein besser Verständnis und den Nachbau zweier verschiedener funktionaler Module lebender Zellen anhand stark reduzierter Modellsysteme. Als zentrales Element wurde Aktin gewählt, da dieses Biopolymer eine herausragende Rolle in nahezu allen eukaryotischen Zellen spielt. Mit dem ersten Modellsystem wird der bewegliche Aktin-Polymerfilm an der Vorderkante migrierender Zellen betrachtet. Die wichtigsten Elemente dieser hochdynamischen Netzwerke sind bereits bekannt und wurden in dieser Arbeit benutzt um ein experimentelles Modellsystem zu etablieren. Vor allem aber lieferten detailierte Computersimulationen und ein mathematisches Modell neue Erkenntnisse über grundlegende Organisationsprinzipien dieser Aktinnetzwerke. Damit war es nicht nur möglich, experimentelle Daten erfolgreich zu reproduzieren, sondern das Entstehen von Substrukturen und deren Charakteristika auf proteinunabhängige, generelle Mechanismen zurückzuführen. Das zweite studierte System betrachtet die Selbstassemblierung von Aktinnetzwerken durch entropische Kräfte. Aktinfilamente aggregieren hierbei durch Kondensation multivalenter Ionen oder durch Volumenausschluss hochkonzentrierter inerter Polymere. Ein neu entwickelter Experimentalaufbau bietet die Möglichkeit in gut definierten zellähnlichen Volumina, Konvektionseinflüsse zu umgehen und Aggregationseffekte gezielt einzuschalten. Hierbei wurden neuartige, regelmäßige Netzwerkstrukturen entdeckt, die bislang nur im Zusammenhang mit molekularen Motoren bekannt waren. Es konnte ferner gezeigt werden, dass die Physik der Flüssigkristalle entscheidend zu weiteren Variationen dieser Netzwerke beiträgt. Dabei wird ersichtlich, dass entstehende Netzwerke in ihrer Architektur direkt die zuvor herrschenden Anisotropien der Filamentlösung widerspiegeln.:1 Introduction 1 2 General background 7 2.1 General concepts 7 2.1.1 Coarse-graining as hierarchical reduction 8 2.1.2 Functional modules and redundancies 10 2.1.3 Emergence 11 2.1.4 Self-organization and self-assembly 13 2.1.5 Bottom-up and top-down 13 2.2 The cytoskeleton 15 2.2.1 From actin monomers to filaments 16 2.2.2 Accessory proteins and actin networks 21 2.3 Biopolymer pattern formation 25 2.3.1 Random networks and nematic phases 25 2.3.2 Linker and motor induced networks 28 3 Lamellipodial actin network formation 33 3.1 Background: crawling cell migration 33 3.1.1 Leading edge actin structures 35 3.1.2 Lamellipodial self-organization into oriented branches? 40 3.1.3 Lamellipodial modeling 41 3.1.4 Beyond the lamellipodium: adhesion and network contraction 42 3.2 Methods: lamellar treadmilling model 45 3.2.1 Assumptions 45 3.2.2 Choice of model parameters 51 3.2.3 Computer simulation (implementation) 52 3.2.4 Mathematical modeling 56 3.3 Modeling results 63 3.3.1 Reproduction of motile cell characteristics 64 3.3.2 Self-organization into lamellipodium and lamellum 65 3.3.3 Filament severing and annealing influence network properties 70 3.3.4 Unconfined network growth 74 3.4 Feasible model extensions 76 3.4.1 Alternative nucleation mechanisms 77 3.4.2 Convergence zone through myosin-driven network contraction 80 3.5 Experimental bottom-up approach 82 3.6 Discussion: Arp2/3 induced actin networks 87 4 Actin network patterns in confined systems 91 4.1 Background: counterion condensation and depletion forces 91 4.1.1 Actin, a polyelectrolyte: counterion condensation 92 4.1.2 Actin and molecular crowding: depletion forces 95 4.2 Methods: Experimental design and data analysis 97 4.2.1 Protein purification and handling 98 4.2.2 Droplet formation 98 4.2.3 Volume monitoring and pattern analysis 100 4.3 Actin pattern formation 105 4.3.1 Counterion-induced network formation 105 4.3.2 Depletion force induced network formation 111 4.4 First modeling attempts: bundling simulation 116 4.4.1 Model concept and assumptions 116 4.5 Discussion: Counterion and depletion-based network assembly 119 5 Discussion & Outlook 125 Appendix 129 A. Variation of filament orientation 129 B. Analytical solution of the mathematical model 131 C. Pre-alignment of filaments 132 D. Protocols 134 d1. Acetone Powder Prep 134 d2. Actin prep 135 d3. Actin labling with rhodamine dye 137 Bibliography 141 Acknowledgements 157