Дисертації з теми "Computational morphogenesi"

For many years, shell structures have had an important role in architecture and engineering. After the industrial revolution and shifting from masonry construction to steel and concrete, the social, economical and environmental role in masonry construction has been underestimated. Targeting to use the digital tools, this thesis is proposing a method to re-design vaults and domes at the present time, respecting the current architectural requirements. Reviewing the brief background of masonry construction and looking over the recent researches, two workshops have been processed in Politecnico di Torino. Both workshops were concentrated on designing and constructing free-form masonry shells by help of digital tools and computational methods. Regarding the results of these practical experiments, a tool has been created developed, which helps the masonry shell designers to model the brick patterning automatically on a curved surface. This research is exploiting the process of developing this method by means of digital tools. The bricklaying is simulated inside the 3D virtual environment by integrating the scripting language, Python, and commercial CAD software, Rhinoceros. Not ignoring the role of the designers in the decision-making procedures, this tool is implemented as an interactive method between the designers and the digital tools.

Self-organizing patterns arise in a variety of ways in nature, the complex patterning observed on animal coats is such an example. It is already known that the mechanisms responsible for pattern formation starts at the developmental stage of an embryo. However, the actual process determining cell fate has been, and still is, unknown. The mathematical interest for pattern formation emerged from the theories formulated by the mathematician and computer scientist Alan Turing in 1952. He attempted to explain the mechanisms behind morphogenesis and how the process of spatial cell differentiation from homogeneous cells lead to organisms with different complexities and shapes. Turing formulated a mathematical theory and proposed a reaction-diffusion system where morphogens, a postulated chemically active substance, moderated the whole mechanism. He concluded that this process was stable as long as diffusion was neglected; otherwise this would lead to a diffusion-driven instability, which is the fundamental part of pattern formation. The mathematical theory describing this process consists of solving partial differential equations and Turing considered deterministic reaction-diffusion systems.   This thesis will start with introducing the reader to the problem and then gradually build up the mathematical theory needed to get an understanding of the stochastic reaction-diffusion systems that is the focus of the thesis. This study will to a large extent simulate stochastic systems using numerical computations and in order to be computationally feasible a compartment-based model will be used. Noise is an inherent part of such systems, so the study will also discuss the effects of noise and morphogen kinetics on different geometries with boundaries of different complexities from one-dimensional cases up to three-dimensions.

Scientific discoveries of the 20th century had a profound impact not only on the study of the natural sciences but disciplines worldwide. The studies were rooted in understanding the complex process of organisation, development and evolution in natural systems before attempting to emulate the behaviours in artificial systems, leading to the emergence of new disciplines such as systems theory, complexity science, genetics, developmental and evolutionary biology. The discoveries had a profound impact in understanding the nature of cities as they develop over time. Once considered top-down models in equilibrium, the dynamic qualities of cities could be explained through the study of dynamic complex systems, exhibiting non-deterministic characteristics that over time emerge as organised structures. These characteristics are not exclusive to cities alone; they are inherent to all complex systems. The understanding of cities as complex systems has stimulated a body of research through mathematical and scientific modelling in understanding the behaviour of cities over time. The studies have been strongly focused on the analytical performance of city morphologies and less on the relational qualities of how systems interact to produce functioning spatial configurations. With the rapid rate of urbanisation and the emergence of new cities around the world, the approach to the design of cities remains rooted in static, top-down models. The implications of such models have led to high energy consumption, lack of integration and poor performance. It is a contradiction to consider cities as complex systems but design them as simple systems. The thesis explores principles of complex systems through the study of biological morphogenesis (the formation and development of organisms over time) for their implementation in formalising a design model for the formation, development and evolution of cities. The central contribution of the thesis lies in the computational modelling of cities in three main areas. The first is the co-evolution of networks and block systems towards the generation of differentiated spatial morphologies. Network systems are generated by coupling multi-agent systems and branching systems from the mathematics of natural systems, and the block systems are generated through procedural subdivision and volumetric modelling. The process involves substantial computational coding and the integration of knowledge from outside disciplines including biology, genetics, complexity theory and mathematics. The second is the development of a unified computational model combining morphological, topological and analytical modelling. The integration of the models is contingent on the writing of classes including graph theory, centrality measures and environmental calculations - all classes were written in C#. The third area is the evolutionary modelling of urban systems. The process utilised the open-source evolutionary solver Octopus in evolving solutions. The advantage lay in the populace-based nature of the model in generating differentiated phenotypes - or geometries - as a response to multiple-objectives. The model has been designed to enable the integration of systems of different types. Analytical data can be used as input to influence the model on the types of decisions it can make. The model has also been designed to enable the exploration of multiple design objectives at varying spatial and time scales. A significant part of the design model takes advantage of open source software including the open source language C#. The software have been extensively modified by hard coding. The model is mutable so that others may add new classes and procedures in the future.

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.
Includes bibliographical references (leaves 57-58).
This thesis presents a programming-language viewpoint for morphogenesis, the process of shape formation during embryological development. We model morphogenesis as a self-organizing, self-repairing amorphous computation and describe how we can program large-scale shape formation by giving local instructions to cell-like objects. Our goal is to simulate systems that display properties, like robustness, regeneration, and evolvability, that are present in biological systems but ordinarily not present in computer systems. Consistent with the theory of facilitated variation from evolutionary biology, we find that many of these properties can be introduced and conserved by a hierarchical organization of growth specification.
by Arnab Bhattacharyya.
M.Eng.

Kyoto University (京都大学)
0048
新制・課程博士
博士(工学)
甲第17557号
工博第3716号
新制||工||1566(附属図書館)
30323
京都大学大学院工学研究科マイクロエンジニアリング専攻
(主査)教授 安達 泰治, 教授 楠見 明弘, 准教授 井上 康博, 教授 琵琶 志朗
学位規則第4条第1項該当

Evolvable hardware (EHW) uses simulated evolution to generate an electronic circuit with specific characteristics, and is generally implemented on Field Programmable Gate Arrays (FPGAs). EHW has proven to be successful at producing small novel circuits for applications such as robot control and image processing, however, traditional approaches, in which the FPGA configuration is directly encoded on the chromosome, have not scaled well with increases in problem and FPGA architecture complexity. One of the methods proposed to overcome this is the incorporation of a growth process, known as morphogenesis, into the evolutionary process. However, existing approaches have tended to abstract away the underlying architectural details, either to present a simpler virtual FPGA architecture, or a biochemical model that hides the relationship between the cellular state and the underlying hardware. By abstracting away the underlying architectural details, EHW has moved away from one of its key strengths, that being to allow evolution to discover novel solutions free of designer bias. Also, by separating the biological model from the target FPGA architecture, too many assumptions and arbitrary decisions need to be made, which are liable to lead to the growth process failing to produce the desired results. In this thesis a new approach to applying morphogenesis to gate-level FPGA- based EHW is presented, whereby circuit growth is closely tied to the underlying gate-level architecture, with circuit growth being driven largely by the state of gate-level resources of the FPGA. An investigation into the applicability of biological processes, structures and mechanisms to morphogenetic EHW (MGEHW) is conducted, and the resulting design elaborated. The developed MGEHW system is applied to solving a signal routing problem with irregular and severe constraints on routing resources. It is shown that the morphogenetic approach outperforms a traditional EHW approach using a direct encoding, and importantly, is able to scale to larger, more complex, signal routing problems without any significant increase in the number of generations required to find an optimal solution. With the success of the MGEHW system in solving primarily structural prob- lems, it is then applied to solving a combinatorial function problem, specifically a one-bit full adder, with a more complete set of FPGA resources. The results of these experiments, together with the previous experiments, has provided valuable information that when analysed has enabled the identification of the critical factors that determine the likelihood of an EHW problem being solvable. In particular this has highlighted the importance of effective fitness feedback for guiding evolution towards its desired goal. Results indicate that the gate-level morphogenetic approach is promising. The research presented here is far from complete; many avenues for future research have opened. The MGEHW system that has been developed allows further research in this area to be explored experimentally. Some of the most fruitful directions for future research are described.

Evolvable hardware (EHW) uses simulated evolution to generate an electronic circuit with specific characteristics, and is generally implemented on Field Programmable Gate Arrays (FPGAs). EHW has proven to be successful at producing small novel circuits for applications such as robot control and image processing, however, traditional approaches, in which the FPGA configuration is directly encoded on the chromosome, have not scaled well with increases in problem and FPGA architecture complexity. One of the methods proposed to overcome this is the incorporation of a growth process, known as morphogenesis, into the evolutionary process. However, existing approaches have tended to abstract away the underlying architectural details, either to present a simpler virtual FPGA architecture, or a biochemical model that hides the relationship between the cellular state and the underlying hardware. By abstracting away the underlying architectural details, EHW has moved away from one of its key strengths, that being to allow evolution to discover novel solutions free of designer bias. Also, by separating the biological model from the target FPGA architecture, too many assumptions and arbitrary decisions need to be made, which are liable to lead to the growth process failing to produce the desired results. In this thesis a new approach to applying morphogenesis to gate-level FPGA- based EHW is presented, whereby circuit growth is closely tied to the underlying gate-level architecture, with circuit growth being driven largely by the state of gate-level resources of the FPGA. An investigation into the applicability of biological processes, structures and mechanisms to morphogenetic EHW (MGEHW) is conducted, and the resulting design elaborated. The developed MGEHW system is applied to solving a signal routing problem with irregular and severe constraints on routing resources. It is shown that the morphogenetic approach outperforms a traditional EHW approach using a direct encoding, and importantly, is able to scale to larger, more complex, signal routing problems without any significant increase in the number of generations required to find an optimal solution. With the success of the MGEHW system in solving primarily structural prob- lems, it is then applied to solving a combinatorial function problem, specifically a one-bit full adder, with a more complete set of FPGA resources. The results of these experiments, together with the previous experiments, has provided valuable information that when analysed has enabled the identification of the critical factors that determine the likelihood of an EHW problem being solvable. In particular this has highlighted the importance of effective fitness feedback for guiding evolution towards its desired goal. Results indicate that the gate-level morphogenetic approach is promising. The research presented here is far from complete; many avenues for future research have opened. The MGEHW system that has been developed allows further research in this area to be explored experimentally. Some of the most fruitful directions for future research are described.

Optimisation of the experimental technique (BrdU-IddU double-staining) and development of new computational tools have allowed, for the first time, a comprehensive spatio-temporal map of quantitative cell cycle times in the early vertebrate limb. A key question of limb morphogenesis is how genes create the digit pattern. An example of such a gene is Sox9, which is an early marker of chondrogenesis and is, therefore, assumed to follow a pattern similar to early stages of digit patterning. Classical chondrogenic experiments, suggest digital regions are patterned by the intermediate formation of a “digital arch” from which the digits arise in a posterior to anterior order. In contrast, a through analysis of a large number of Sox9 in situs revealed digital regions 1, 2 and 3 branch from a region reminiscent of the tibia (anterior zeugopod) and digital regions 4 and 5 branch from a fibula-like region (posterior zeugopod). Moreover, the Sox9 pattern first arises in digital regions 2, 3 and 4, followed by digital regions 5 and 1. The Sox9 in situ analysis was achieved using newly developed software for the 3D analysis of optical projection tomographic (OPT) images at a very high spatial resolution. These studies have highlighted the importance of integrating practical and computational tools in order to close the gaps in our knowledge and understanding of limb development, and developmental processes as a whole. The computational tools generated for the proliferation studies are valuable in offering a thorough means of analysis of cell cycle times and the new OPT software will be invaluable for the study of both weak and strong gene expression patterns in whole embryos. In the future, the proliferation data and 3D Sox9 in situ data can be incorporated into simulation software, the results of which should shed light upon the interactive effects of different factors upon the process of limb morphogenesis.

Systems biology takes a holistic approach to biological questions as it applies mathematical modeling to link and understand the interaction of components in complex biological systems. Multiscale modeling is the only method that can fully accomplish this aim. Mutliscale models consider processes at different levels that are coupled within the modeling framework. A first requirement in creating such models is a clear understanding of processes that operate at each level. This research focuses on modeling aspects of biological development as a complex process that occurs at many scales. Two of these scales were considered in this work: cellular differentiation, the process of in which less specialized cells acquired specialized properties of mature cell types, and morphogenesis, the process in which an organism develops its shape and tissue architecture. In development, cellular differentiation typically is required for morphogenesis. Therefore, cellular differentiation is at a lower scale than morphogenesis in the overall process of development. In this work, cellular differentiation and morphogenesis were modeled in a variety of biological contexts, with the ultimate goal of linking these different scales of developmental events into a unified model of development. Three aspects of cellular differentiation were investigated, all united by the theme of how the dynamics of gene regulatory networks (GRNs) control differentiation. Two of the projects of this dissertation studied the effect of noise and robustness in switching between cell types during differentiation, and a third deals with the evaluation of hypothetical GRNs that allow the differentiation of specific cell types. All these projects view cell types as highdimensional attractors in the GRNs and use random Boolean networks as the modeling framework for studying network dynamics. Morphogenesis was studied using the emergence of three-dimensional structures in biofilms as a relatively simple model. Many strains of bacteria form complex structures during growth as colonies on a solid medium. The morphogenesis of these structures was modeled using an agent-based framework and the outcomes were validated using structures of biofilm colonies reported in the literature.

This thesis focuses on computational design techniques that incorporate structural considerations in the early stages of the architectural design process. Since structural behavior is most affected by geometric form and problems are mainly associated with the complexity of their design process in the early conceptual design. This research conceptual structure is based on complex interactions between architectural forms and the functionality of the design. Starting from the complex problems that arise from non-standard architecture, free form, and other specific constructive aspects. This highlights the most important consequences of free form and the complexity of design evolution and uses them to develop a typology of design complexity and explores the contribution of how computational technologies and design strategies enable us to address complexity with the help of advancements. For a better understanding of computational complexity and mechanisms that take part in conceptual design processing, and a thorough search for structural efficiency to solve a more complex issue than reality and achieve an original solution through direct search method of optimization using mathematic–mechanical modeling operations with the aid of computer models/simulations. These models address how complex systems are formed, how they evolve, and how they can break down. The interdisciplinary scientific approach is concerned with theoretical studies of real-world engineering design to understand the relationship between architectures (topologies) and dynamics and to evaluate structural systems with physical and geometrical nonlinearities with which to explain how the concept of architectonic is continuously transformed within contingent, complex, and dynamic structural design practices as buildings materialize.

Die Entstehung unterschiedlicher Zellformen ist eine zentrale Frage der Biologie und von besonderer Bedeutung für ein umfassendes Verständnis des Modellorganismus Saccharomyces cerevisiae. Form und Integrität dieser Hefen werden durch die Eigenschaften ihrer Zellwand bestimmt. Die mechanischen Prozesse in der Zellwand während der Morphogenese von Hefen sind jedoch wenig verstanden. Zwei Arten der Morphogenese, Knospung und Paarung, wurden hier untersucht, um gemeinsame Prinzipien und Unterschiede hinsichtlich ihrer Zellwandmechanik zu finden. Dabei wurden AFM-basierte Techniken sowie theoretische Modelle verwendet, um räumliche und zeitliche Unterschiede in den mechanischen Eigenschaften zu beurteilen. Im ersten Teil wird ein biophysikalisches Modell der Knospung vorgestellt, das auf einem Unterschied der mechanischen Zellwandeigenschaften von Mutter und Knospe beruht und die Volumenentwicklung einzelner Zellen beschreiben kann. Da Messungen keinen ausreichenden Unterschied in der Zellwandelastizität zwischen beiden Kompartimenten zeigten, wird deren Viskoplastizität als Unterscheidungsmerkmal vorgeschlagen. Eine Kalibrierung des Modells an Einzelzellmessungen lieferte neben Schätzungen dieser Zellwandviskoplastizität auch die anderer wichtiger Wachstumsparameter. Im zweiten Teil werden nanorheologische Messungen genutzt, um zu zeigen, dass die Zellwand hauptsächlich elastisch ist und ein strukturelles Dämpfungsverhalten aufweist. Dabei wird diskutiert, die Zellwand analog zu einem „soft glassy“ Material zu beschreiben. Im letzten Teil wird die Notwendigkeit eines spezifischen Elastizitätsmusters der Zellwand für das gerichtete Wachstum während der Paarungsmorphogenese beschrieben, welches weicheres Material am Schaft sowie steiferes Material am Apex einschließt. Zusammenfassend zeigt diese Arbeit, dass räumlich und zeitlich veränderliche viskoelastisch-plastische Zellwandeigenschaften die Morphogenese von S. cerevisiae bestimmen.
Morphogenesis is a central field in biology and of particular importance for a comprehensive understanding of the model organism Saccharomyces cerevisiae. Shape and integrity of yeast cells are determined by its cell wall. However, mechanical processes underlying yeast morphogenesis and are poorly understood. Two modes of yeast morphogenesis, budding and mating, have been studied to find common principles and differences in cell wall mechanics. AFM-based techniques as well as computational models were used to assess spatial and temporal differences in the mechanical properties. In the first part, a biophysical model for the expansion during budding is presented that bases on a difference in the mechanical cell wall properties of mother and bud and accurately describes the volume dynamics of single cells. Since measurements revealed no difference in the cell wall elasticity between both compartments, visco-plastic properties are proposed as distinguishing feature. Fitting the model to single-cell volume trajectories, provided estimations for the visco-plasticity of the cell wall and other key growth parameters. In the second part, nano-rheology measurements were used to confirm that the cell wall is mainly elastic and demonstrate that it shows structural damping behavior. Furthermore, the possibility to describe the cell wall analogous to a “soft glassy” material is discussed. In the last part, the necessity of a specific elasticity pattern of the cell wall for directed growth during yeast mating morphogenesis is shown, including softer material at the shaft and stiffer material at the apex. By showing that spatially and temporally varying viscoelastic-plastic cell wall properties govern the morphogenesis of S. cerevisiae, this work contributes to deciphering molecular mechanisms underlying the growth of yeast and other walled cells.

Ce travail présente un modèle théorique de morphogenèse animale, sous la forme d’un système complexe émergeant de nombreux comportements, processus internes, expressions et interactions cellulaires. Son implémentation repose sur un automate cellulaire orienté système multi-agents avec un couplage énergico-génétique entre les dynamiques cellulaires et les ressources.Notre objectif est de proposer des outils permettant l’étude numérique du développement de tissus cellulaires à travers une approche hybride (discrète/continue et qualitative/quantitative) pour modéliser les aspects génétiques, énergétiques et comportementaux des cellules. La modélisation de ces aspects s’inspire des principes de la théorie de la viabilité et des données expérimentales sur les premiers stades de division de l’embryon du poisson-zèbre.La théorie de la viabilité appliquée à la morphogenèse pose cependant de nouveaux défis en informatique pour pouvoir implémenter des algorithmes dédiés aux dynamiques morphologiques. Le choix de données biologiques pertinentes à considérer dans le modèle à proposer, la conception d’un modèle basé sur une théorie nouvelle, l’implémentation d’algorithmes adaptés reposant sur des processeurs puissants et le choix d’expérimentations pour éprouver nos propositions sont les enjeux fondamentaux de ces travaux. Les hypothèses que nous proposons sont discutées au moyen d’expérimentations in silico qui ont porté principalement sur l’atteignabilité et la capturabilité de formes de tissus ; sur la viabilité de l’évolution d’un tissu pour un horizon de temps ; sur la mise en évidence de nouvelles propriétés de tissus et la simulation de mécanismes tissulaires essentiels pour leur contrôlabilité face à des perturbations ; sur de nouvelles méthodes de caractérisation de tissus pathologiques, etc. De telles propositions doivent venir en appoint aux expérimentations in vitro et in vivo et permettre à terme de mieux comprendre les mécanismes régissant le développement de tissus. Plus particulièrement, nous avons mis en évidence lors du calcul de noyaux de viabilité les relations de causalité ascendante reliant la maintenance des cellules en fonction des ressources énergétiques disponibles et la viabilité du tissu en croissance. La dynamique de chaque cellule est associée à sa constitution énergétique et génétique. Le modèle est paramétré à travers une interface permettant de prendre en compte le nombre de coeurs à solliciter pour la simulation afin d’exploiter la puissance de calcul offerte par les matériels multi-coeurs
This work presents a theoretical model of animal morphogenesis, as a complex system from which emerge cellular behaviors, internal processes, interactions and expressions. Its implementation is based on a cellular automaton oriented multi-agent system with an energico-genetic coupling between the cellular dynamics and resources. Our main purpose is to provide tools for the numerical study of tissue development through a hybrid approach (discrete/continuous and qualitative/quantitative) that models genetic, behavioral and energetic aspects of cells. The modeling of these aspects is based on the principles of viability theory and on experimental data on the early stages of the zebrafish embryo division. The viability theory applied to the morphogenesis, however, raises new challenges in computer science to implement algorithms dedicated to morphological dynamics. The choice of relevant biological data to be considered in the model to propose, the design of a model based on a new theory, the implementation of suitable algorithms based on powerful processors and the choice of experiments to test our proposals are fundamental issues of this work. The assumptions we offer are discussed using in silico experiments that focused on the reachability and catchability of tissue forms ; on the viability of the evolution of a tissue for a time horizon ; on the discovery of new tissue properties and simulation of tissue mechanisms that are fondamental for their controllability face to disruptions ; on new pathological tissue characterization methods, etc. Such proposals must come extra to support experiments in vitro and in vivo and eventually allow a better understanding of the mechanisms governing the development of tissues.In particular, we have highlighted through the computing of viability kernels the bottom causal relationship between the maintenance of cells according to available energy resources and the viability of the tissue in growth. The model is set through an interface that takes into account the number of cores to solicit for simulation in order to exploit the computing power offered by multicore hardware

The process of a single cell evolving into a complex organism results from a series of coordinated movements of cells and tissues, especially during early embryo development. Although a wealth of morphological data characterises the shapes and movements of cells in embryos, how these movements are driven, patterned and controlled, and how this patterning is related to the mechanical properties of tissues remains unknown. Four-pole electromagnetic tweezers have been developed to probe the mechanical properties of living embryonic tissues that are undergoing active morphogenetic development. The device is capable of generating magnetic forces in the order of nano-Newtons on a grafted magnetic bead. The local passive mechanical properties of the tissues can be characterised by measuring the three-dimensional bead movement and analysing cell shape changes and cell rearrangement in response to this externally applied force. The magnetic device is used to probe the rheology in early zebrafish embryos between high stage (3.3 hpf) and the onset of gastrulation (5.3 hpf) when rapid cell cycles give way to a hollow sphere of cells. The tissue response to the applied force is modelled as linear visco- elastic. The embryo becomes stiffer and more viscous during this period of development, showing that a loose collection of cells becomes cohesive tissues. A computational model is used to explore how cells respond to local or global mechanical perturbations in two systems. First, the model simulates the movement of the bead within an embryo, and the results illustrate the generation, patterning and relaxation of the local cell stress around the bead. Second, the model reproduces the autonomous changes in mitotic cells within a stretched monolayer, and the results show that propensity of cells to divide along their long axis facilitates stress relaxation and contributes to tissue homoeostasis.

Dissertação de Mestrado Integrado em Arquitetura, com a especialização em Arquitetura apresentada na Faculdade de Arquitetura da Universidade de Lisboa para obtenção do grau de Mestre.
O presente projeto final de mestrado pretende explorar os conceitos biomórficos na arquitetura e as suas diferentes abordagens. Sempre existiram manifestos do interesse do ser humano em se aproximar da natureza, de forma consciente ou inconsciente. No decorrer da história da arquitetura, a biologia tem inspirado a forma de construir e habitar os espaços. Desde o período da Arte Nova que é possível verificar claras intenções arquitetónicas de aproximação à natureza. Biomimética, arquitetura biónica e morfogénese são alguns dos conceitos explorados no decorrer deste projeto final de mestrado, em que é imprescindível relacionar a importância do desenvolvimento do pensamento computacional com a evolução destes conceitos. Num registo prático e formalmente inspirado na natureza, o complexo de piscinas para a cidade do Barreiro ganha forma a partir do desenvolvimento de um método de morfogénese digital, configurando-se como elemento de exceção que se distingue na frente ribeirinha do Barreiro, pela sua forma orgânica invocando a fauna marinha.
ABSTRACT: This master final project intends to explore the biomorphic concepts and its different approaches in architecture. Humans have always manifested interest in resembling nature, either consciously or unconsciously. Throughout the history of architecture, biology has inspired the way of building and inhabiting spaces. Since the times of Art Nouveau, it is possible to identify clear intentions of resembling nature through architecture. Biomimetics, bionic architecture and morphogenesis are concepts that are explored along this master final project, in which it is essential to relate the importance of computational thinking progresses with the evolution of these concepts. In a practical record and formally inspired on nature, the swimming pool complex for Barreiro gains its shape through the development of a digital morphogenesis method, and it presents itself as an exception element which organic form stands out at Barreiro’s riverside area, evoking the ocean’s fauna.
N/A

Nous développons une nouvelle approche éléments finis pour des équations aux dérivées partielles elliptiques de type élasticité linéaire ou Stokes sur une surface fermée de R3. La surface considérée est décrite par le zéro d'une fonction de niveau assez régulière. Le problème se ramène à la minimisation d'une fonctionnelle énergie pour le champ de vitesse sous contraintes. Les contraintes sont de deux types : (i) la vitesse est tangentielle à la surface, (ii) la surface est inextensible. Cette deuxième contrainte équivaut à l'incompressibilité surfacique du champ de vitesse. Nous abordons ce problème de deux façons : la pénalisation et l'introduction de deux multiplicateurs de Lagrange. Cette dernière méthode a l'avantage de traiter le cas de la limite incompressible d'un écoulement en surface dont nous présentons pour la première fois l'analyse théorique et numérique. Nous montrons des estimations d'erreurs sur la solution discrète et les tests numériques confirment l'optimalité des ces estimations. Pour cela, nous proposons plusieurs approches pour le calcul numérique de la normale et la courbure de la surface. L'implémentation utilise la librairie libre d'éléments finis Rheolef. Nous présentons aussi des résultats de simulations numériques pour une application en biologie : la morphogenèse de l'embryon de la drosophile, durant laquelle des déformations tangentielles d'une monocouche de cellules avec une faible variation d'aire. Ce phénomène est connu sous le nom de l'extension de la bande germinale
We develop a novel finite element approach for linear elasticity or Stokes-type PDEs set on a closed surface of $mathbb{R}^3$. The surface we consider is described as the zero of a sufficiently smooth level-set function. The problem can be written as the minimisation of an energy function over a constrained velocity field. Constraints areof two different types: (i) the velocity field is tangential to the surface, (ii) the surface is inextensible. This second constraint is equivalent to surface incompressibility of the velocity field. We address thisproblem in two different ways: a penalty method and a mixed method involving two Lagrange multipliers. This latter method allows us to solve the limiting case of incompressible surface flow, for which we present a novel theoretical and numerical analysis. Error estimates for the discrete solution are given andnumerical tests shows the optimality of the estimates. For this purpose, several approaches for the numerical computation of the normal and curvature of the surface are proposed. The implementation relies on the Rheolef open-source finite element library. We present numerical simulations for a biological application: the morphogenesis of Drosophila embryos, duringwhich tangential flows of a cell monolayer take place with a low surface-area variation. This phenomenon is known as germ-band extension

Nous nous intéressons à la phénoménologie des villes en nous limitant à la géométrie induite par le squelette de leur réseau de rues. C'est une étude à volonté synthétique, fonctionnelle et interdisciplinaire qui vient s'ajouter aux travaux qui ont été menés à grande cadence depuis le début du XXème siècle par des urbanistes, sociologues, géographes, statisticiens, physiciens. Nous cherchons à montrer que la rue, en tant qu'alignement cohérent de segments de rues peut être considérée comme structure élémentaire de la ville. Quelle quantité d'information est donnée par la géométrie du réseau routier ? Dans quelle mesure contraint-il nos échanges ? Comment le paysage urbain actuel est-il déterminé par son évolution le long d'axes de circulation et d'éléments structurants ? Nous présentons un cadre mathématique permettant de considérer la carte d'une ville comme un continuum géométrique défi ni par la topologie d'un graphe planaire. Nous superposons à ce graphe une structure d'hypergraphe pour manipuler aisément la notion d'axes ainsi qu'une représentation multi-échelles de la ville. En dépit d'une grande diversité apparente de formes, nous montrons que le réseau de rues d'une ville se soumet à un certain nombre de lois générales qui laissent des traces sur le plan de la ville. Nous proposons des modèles de croissance et de morphogénèse de la ville, implé- mentant l'idée que l'évolution de la ville suit une logique d'extension / division structurée de l'espace et reproduisant les signatures observées sur les plans de villes réelles. La compréhension des mécanismes régulateurs de la ville nous permet de proposer des algorithmes fonctionnels dont le temps de calcul est très intéressant. Ainsi nous présentons un algorithme reconstituant les rues à partir de segments de rues ; la notion de centralité simple dont le calcul sur une carte permet une analyse hiérarchique de celle-ci, met en valeur les axes de trafic principaux et en évidence les zones mal desservies ; un algorithme permettant d'approximer rapidement le plus court chemin entre deux points aléatoires ; un algorithme prenant appui sur le Spectral Clustering pour produire des segmentations morphologiques de cartes et retravaillons l'identi cation de modèles de mosaïques aléatoires pour les substituer à un réseau urbain particulier dans la résolution par équivalents statistiques de grands problèmes d'optimisation.

碩士
淡江大學
建築學系碩士班
101
Based on morphological computations, this study explores the productions of complex form from basic patterns during the process of time-based computations. By seeking simple rules from the domains of biology and design computation, and through recursive operations to derive complexities, the study uses the surface subdivision principle to discuss the morphological variations produced by computer generations. The latter part of the study further examines the decoration of designs of the digital era, using basic geometric transformation rules as the basis for iterative computations to produce complex and unpredictable patterns. This study is divided into two parts. The first part attempts to explore the fundamental principles of morphogenesis. Initially using points and lines as the basis for discussion, rules such as those in path trajectory, gravitational field, cellular automata and intelligent behavior algorithms are then applied for morphogenesis. The second part uses surfaces and s as the computational factors and the principle of surface subdivision to conduct fractal processing on curved surfaces and volumes. By applying different conditions at each iterative step, slight variations in rules would cause significant differences in the final patterns generated. Finally, this study uses the column form as the basis for morphological computations, to explore the possibility of morphogenesis alterations via different applications and combinations of computational rules. This study categorizes the use of digital tools into two major groups: ISO-Surface and surface subdivision. While ISO-Surface is point-based and constructs surfaces through sequential arrangements of points, surface subdivision uses surfaces as the basic forms and achieves surface transformations by selecting and moving the control points. Placement or replacement of different rules at each iterative computation is discussed in the study to produce irreversible results of morphological computations, and to derive possibilities with the same initial conditions but varying rules. Using such a conceptual design as the starting point, it anticipates to set new developments in the domain of architectural designs in the future, and to bridge the gap between virtual and practical applications of digital designs.

博士
淡江大學
土木工程學系博士班
107
Abstract: 　　The development of morphological form-finding is increasingly well-established under the influence and culture of design computation and digital fabrication derived diverse algorithmic morphology and the New Materialism of seamless information flow. Reposed deep in the complex forms, are the dialectical, methodological and discussion-centered design thinking, morphological inspiration, generating machine, tectonic system and aesthetic style. However, since the new millennium, there has been rare researches on the systematic methodology of digital morphogenesis, therefore, this study attempts to deploy digital workflow to elucidate digital form and digital fabrication, the relationship between digital diagrams and morphogenesis, while on the other hand, exploring different types of topological form-finding, and proposes a design approach of diagram-oriented morphogenesis. This study is divided into four parts: the literature review, theoretical development, design experiment and demonstration of theoretical framework. Firstly, the classification of the literature affecting the digital morphology is divided into three categories: architectural theory, natural morphology and form-finding methods. The main impetus of the theoretical discussion is to perfect the integration of the bespoke workflow with the digital diagram, while the form of natural inspiration is based on the algorithm-based design generation, and the transformation of the form-finding method focuses on deployment of discrete topology. As for theoretical development, the digital diagram is more clearly defined as the Generative Diagram, and its features covering and affecting the process of digital fabrication is meticulously analyzed, while on the other hand the approach defines the morphology-finding framework based on algorithm and topology for designing experiments. Holistically imbuing the above-mentioned literature and theoretical development, this study first analyzes the related algorithms in digital architecture, and experiments with the corresponding autonomous topology-finding methods and classifies them to elicit their typology. Finally, the algorithm of topology-finding in the design experiments is taken as the basic model, and combined with the Generative Diagram of algorithmic, behavior, performance, fabrication, and evolutionary characteristics. Empirical verification of the complex modeling of this study emerges from morphogenesis, simulation, and analysis to construction of Complex Modelling and fabrication processes. By studying the Complex Modelling process generated discrete forms, and the parametric modeling, linear design process refinement method, aggregated patterns are elucidated and proposed to integrate the digital diagram and the topology-finding of the reciprocal structure, for use as the digital morphogenesis design methodology. This study aspires to deploy this discussion to elicit the deep structure of autonomous tectonics, and aims to develop future novel paradigms in the architecture field.

Thesis (Ph. D.)--University of Notre Dame, 2005.
Thesis directed by Jesús A. Izaguirre for the Department of Computer Science and Engineering. "November 2005." Includes bibliographical references (leaves 133-139).