Auto-organisation | EPFL Graph Search

L'auto-organisation ou autoorganisation est un phénomène par lequel un système s'organise lui-même. Les systèmes physiques, biologiques ou écologiques, sociaux, ont tendance à s'organiser d'eux-mêmes. Il s'agit soit de l'organisation initiale du système lors de son émergence spontanée, soit lorsque le système existe déjà de l'apparition d'une organisation plus ou complexe. L'auto-organisation agit ainsi à l'encontre de l'entropie (on parle alors de néguentropie), qui est une mesure de désordre. L'auto-organisation se produit par des internes et externes au système, au sein de son et avec lui. Elle consomme de l'énergie qui sert ainsi à établir et maintenir le système auto-organisé. L'auto-organisation s'oppose aux cas où un système est organisé ou réorganisé de force de l'extérieur, c'est-à-dire à la violence, aux actes de pouvoir : cela rejoint aussi le contraste entre autonomie et hétéronomie. Typiquement, un système auto-organisé a des propriétés émergentes. Passé un seuil crit

Exploiting Marginal Stability in Slow-Fast Quasilinear Dynamical Systems

Alessia Ferraro

The accurate investigation of many geophysical phenomena via direct numerical simulations is computationally not possible nowadays due to the huge range of spatial and temporal scales to be resolved. Therefore advances in this field rely on the development of new theoretical tools and numerical algorithms. In this work we investigate a new mathematical formalism that exploits the property of quasi-linear systems to self-tune towards marginally stable states. The inspiration for this study comes from the asymptotic analysis of strongly stratified flows, performed by Chini et al.. The application of multi-scale analysis to this problem, justified by the presence of scale separation, yields to a simplified quasi-linear model. In this reduced description small-scale instabilities evolve linearly about a large-scale hydrostatic field (whose evolution is fully non-linear) and modify it via a feedback term. From the only assumption of scale separation, two extremely interesting features of this model arise. First the presence of the coupling term between the two dynamics and second the quasi-linearity of the dynamics. The first aspect, generally not present in the hydrostatic approximation, can capture the non-local energy transfer between the small and the large scales, which is key for the quantification of the mixing efficiency in the deep ocean. The second aspect, namely the quasi-linearity, is suggestive of the self-organisation of the dynamics about marginally-stable states. This results in a coupled evolution where the fast dynamics adapts (is slaved) to the mean field, maintaining the marginal stability of the latter. The low-dimensional evolution that arises, enables the integration of the reduced system on temporal scales comparable to the characteristic time scale of the slow dynamics, making this novel approach highly suited to the investigation of the stratified flow problem.Building upon the results obtained by Chini et al. in the present work we extend this methodology addressing three different aspects of the reduced model.As a first case we investigate the twofold nature of the fluctuation feedback, which is not sign-definite and might lead to intense bursting events where the fluctuations exhibit positive growth rates on a fast time scale. In this scenario the scale separation is temporarily lost and the two dynamics have to be co-evolved until a new marginally stable manifold can be approached. Here we propose three different co-evolution techniques and test their efficacy on a one-dimensional model problem.The second aspect we address is the presence of a finite scale separation between the two dynamics. We develop an algorithm that carefully identifies the validity regions of the quasi-linear reduction and determines the relevance of the fluctuation feedback w.r.t. the characteristic time scale of the slow dynamics and the growth rate of the fluctuations.As a third case we derive an efficient extension of the original methodology to two-dimensional model problems, deriving an evolution equation for the wavenumber of the fastest growing mode, which then get slaved to the mean dynamics.Eventually the methodologies derived in the context of the two model problems are applied and discussed for the strongly stratified flow problem.

EPFL2022

Towards engineering an artificial neural tube

Jisoo Park

In this thesis, I present a self-organizing neural tube organoid that is strikingly similar in morphology, cell-type composition, and patterning to the mouse embryonic neural tube. When exposed to a sequence of epiblast culture conditions and neural differentiation conditions in 3D Matrigel, single mouse embryonic stem cells develop into spontaneously elongating neuroepithelial tissues organized with key hallmarks of the neural tube. Single cell transcriptomics revealed the presence of regionalized cell types spanning the region from the midbrain to the spinal cord along the AP axis of the embryo. In long-term culture experiments for organoid maturation, I observed the emergence of neural crest cells and mature neurons. Furthermore, I developed a microfluidics-based system to promote a similar DV patterning to a neural tube. Also, maturation of neural tube organoid exhibited the emergence and migration of multipotent neural crest cells. Collectively, the accessibility and scalability of these organoids make them a unique model of the developing neural tube, allowing the study of key mechanisms involved in striking morphogenesis by self-organization, cell regionalization, neural crest development, and morphogen-triggered patterning in vivo.

EPFL2021

In vitro endoderm emergence and self-organisation in the absence of extraembryonic tissues and embryonic architecture

Stefano Davide Vianello

In humans, mice, and other mammals key internal organs such as the gut, the lungs, the pancreas, and the liver all derive from the same embryonic tissue: the endoderm. The development of all of these structures thus depends on a same set of early cells, and on the developmental instructions provided to them by the embryo. One approach to study what these instructions might be is to study the behaviour of endoderm cells when they can not rely on embryonic instructions. That is, when they are generated and made to develop outside of the embryo. The rationale behind this approach, widely embraced by the field of synthetic embryology, is that the unguided development of specific embryonic cell types can provide a window to the observation of intrinsic characteristics of these cells and of fundamental developmental principles which might not be executed or manifested within the regulated environment of the embryo. Accordingly, in the work here described I use gastruloids, synthetic models of development made by aggregation of mouse embryonic stem cells in vitro to characterise the developmental behaviour of endoderm cells, in the absence of embryonic cues and in the absence of the extraembryonic tissues that they would usually rely on in vivo. In the first chapter of this thesis, I provide an introduction, overview, and review of our current understanding of the developmental biology of mouse endoderm as this develops in the embryo. I also introduce gastruloids as stem-cell-based experimental systems to study developmental mechanisms in vitro, decoupled from the constraints of experimental work with animals and animal embryos. Chapter 2 is dedicated to the earliest steps of endoderm development in gastruloids. I show when and where these cells appear, and how they sort as the gastruloid starts to mature. I find that endoderm cells follow similar spatial and temporal developmental patterns as those they would follow if they were in the embryo. I notably find that they always remain in an epithelial state, even as other cell types undergo mesenchymal transition. In Chapter 3 I describe surprising dynamics of endoderm cells over time, and how they self-organise into complex architectures at the core of the gastruloids. The epithelial domain that forms is dynamic and plastic, and partitions the gastruloids into interfacing compartments. Importantly, I reveal a significant endodermal component to this in vitro system, usually considered to be unstructured and neural/mesodermal in character. In Chapter 4 I show how the core endoderm compartment that I see forming in gastruloids is patterned along the longitudinal axis of the aggregate, with different cellular identities at different anterior-posterior position of the domain. By comparison with published embryonic datasets, I identify endodermal identities corresponding to the full spectrum of those that make up the gut tube in the embryo. Specifically, I describe how most endodermal cells adopt an early intestinal fate, and how many acquire anterior foregut identities. The work described in this thesis presents gastruloids as promising in vitro systems for the study of endoderm biology, morphogenesis, and mature fate specification, filling a gap within the field of synthetic embryology. It also notably opens translational possibilities to the use of gastruloids to produce endodermal cell types which may be otherwise difficult to generate using conventional directed differentiation methods.

EPFL2022

In vitro endoderm emergence and self-organisation in the absence of extraembryonic tissues and embryonic architecture

Stefano Davide Vianello

EPFL2022

Exploiting Marginal Stability in Slow-Fast Quasilinear Dynamical Systems

Alessia Ferraro

EPFL2022