L’objectif de notre recherche est l’exploration et l’étude de la question de l’instrumentation informatique des projets de reconstitution archéologiques en architecture monumentale dans le but de proposer de nouveaux moyens. La recherche a pour point de départ une question, à savoir : « Comment, et avec quels moyens informatiques, les projets de reconstitution architecturale pourraient-ils être menés en archéologie? ». Cette question a nécessité, en premier lieu, une étude des différentes approches de restitution qui ont été mises à contribution pour des projets de reconstitution archéologiques, et ceci, à ses différentes phases. Il s’agit de comprendre l’évolution des différentes méthodologies d’approche (épistémologiquement) que les acteurs de ce domaine ont adoptées afin de mettre à contribution les technologies d’information et de communication (TIC) dans le domaine du patrimoine bâti. Cette étude nous a permis de dégager deux principales avenues: une première qui vise exclusivement la « représentation » des résultats des projets et une seconde qui vise la modélisation de ce processus dans le but d’assister l’archéologue dans les différentes phases du projet. Nous démontrons que c’est la deuxième approche qui permet la combinaison et met à la disposition des archéologues une meilleure exploitation des possibilités que l’outil informatique peut et pourra présenter. Cette partie permet de démontrer la nature systémique et complexe de la mise à contribution des TICs dans le domaine de la restitution archéologique. La multitude des acteurs, des conditions techniques, culturelles et autres, des moyens utilisés ainsi que la variété des objectifs envisagés dans les projets de reconstitution archéologiques poussent à explorer une nouvelle approche qui tient compte de cette complexité. Pour atteindre notre objectif de recherche, la poursuite de l’étude de la nature de la démarche archéologique s’impose. Il s’agit de comprendre les liens et les interrelations qui s’établissent entre les différentes unités techniques et intellectuelles en jeu ainsi que les différents modes de réflexions présents dans les projets de reconstitution archéologique du patrimoine bâti. Cette étude met en évidence le rapport direct entre le caractère subjectif de la démarche avec la grande variabilité des approches et des raisonnements mis en œuvre. La recherche est alors exploratoire et propositionnelle pour confronter notamment le caractère systémique et complexe de l’expérience concrète et à travers les publications savantes, les éléments de la réalité connaissable. L’étude des raisonnements archéologiques à travers les publications savantes nous permet de proposer une première typologie de raisonnements étudiés. Chacune de ces typologies reflète une méthodologie d’approche basée sur une organisation d’actions qui peut être consignée dans un ensemble de modules de raisonnements. Cette recherche fait ressortir, des phénomènes et des processus observés, un modèle qui représente les interrelations et les interactions ainsi que les produits spécifiques de ces liaisons complexes. Ce modèle témoigne d’un processus récursif, par essais et erreurs, au cours duquel l’acteur « expérimente » successivement, en fonction des objectifs de l’entreprise et à travers des modules de raisonnements choisis, plusieurs réponses aux questions qui se posent à lui, au titre de la définition du corpus, de la description, de la structuration, de l’interprétation et de la validation des résultats, jusqu’à ce que cette dernière lui paraisse satisfaire aux objectifs de départ. Le modèle établi est validé à travers l’étude de cas du VIIème pylône du temple de Karnak en Égypte. Les résultats obtenus montrent que les modules de raisonnements représentent une solution intéressante pour assister les archéologues dans les projets de reconstitution archéologiques. Ces modules offrent une multiplicité de combinaisons des actions et avantagent ainsi une diversité d’approches et de raisonnements pouvant être mis à contribution pour ces projets tout en maintenant la nature évolutive du système global. / The goal of our research is to explore and study the use of computerized tools in archaeological reconstruction projects of monumental architecture in order to propose new ways in which such technology can be used. The first question we ask is: "How and with which computerized tools can architectural reconstruction projects be conducted in archaeology? In our quest to answer this question, we begin with a study of the different restitution approaches used in various phases of archaeological reconstruction projects. This involves understanding how the different methods of approach have evolved (epistemologically), how those involved in such projects have put information and communication technologies to use in the field of built heritage. This study has identified two main avenues: one whose sole aim is the "representation" of project results and another whose aim is to model this process in order to assist the archaeologist through various phases of a project. We have demonstrated that it is the second approach which combines and offers archaeologists a better utilization of the possibilities offered by computer assisted tools. This allowed us to demonstrate the complex and systemic nature of ICT’s in the field of archaeological reconstruction. The multiple actors, conditions, means and goals considered in archaeological reconstruction projects have led us to explore a new approach that reflects this complexity. In order to achieve the goal of our research, it was necessary to further study the nature of the archaeological process. This involved understanding the links and interrelations between the various components that define the archaeological approach and the various thought processes involved in heritage building archaeological reconstruction projects. This study showed a direct relationship between the subjective nature of the process and the diversity of approaches and thought processes which can be implemented. This exploratory and propositional research reinforces the systemic and complex nature of our approach and prompts us to explore, in practice and through published literature, the elements of known reality. The study of archaeological reasoning through academic publications has allowed us to propose an initial typology of arguments studied. Each of these typologies reflects a methodological approach based on organized actions that can be recorded in a set of reasoning modules. This research has allowed us to highlight phenomena and observed processes, leading to a model representing interrelationships and interactions as well as the specific results of these complex interconnections. This pattern reflects a cyclical process of trial and error, in which the actors consecutively 'experience' (according to the project’s goals and through reasoning modules), several answers to the questions exposed to him under the corpus definition, description, structure, interpretation and validation of the results until the latter would appear to meet the original targets. The model developed was validated through a case study of the seventh pylon of the Karnak temple in Egypt. The results show that the reasoning modules offer an interesting solution assisting archaeologists in archaeological reconstruction projects. The multiple action combinations offered by these modules are an advantage to many approaches and thought processes which could be useful to such projects while maintaining the progressive nature of the overall system.

As a consequence of global environmental change, sustainable management and governance of natural resources face critical challenges, such as dealing with non-linear dynamics, increased resource variability, and uncertainty. This thesis seeks to address some of these challenges by using simulation models. The first line of research focuses on the use of learning-by-doing (LBD) for managing a renewable resource, exemplified by a fish stock, and explores LBD in a theoretical model using artificial intelligence (Paper I and II). The second line of research focuses on the emergence of different forms of self-governance and their interrelation with the dynamics of trust among fishers when harvesting a shared resource, using an agent-based model. This model is informed by qualitative data based on small-scale fisheries in Mexico (Paper III and IV). Paper I and II find that the most sustainable harvesting strategy requires that the actor values current and future yields equally, cautiously experiments around what is perceived as the best harvest action, and rapidly updates its ‘mental model’ to any perceived change in catch. More specifically, Paper II reveals that understanding these aspects in relation to the type of change can yield not only increased performance, but also, and more importantly, increased robustness to both fast and slow changes in resource dynamics. However, when resource dynamics include the possibility of a more fundamental shift in system characteristics (a regime shift), LBD is problematic due to the potential for crossing a threshold, resulting in possible persistent reductions in harvests (Paper I). In Paper III, results indicate that cooperative forms of self-governance are more likely to establish and persist in communities where fishers’ have prior cooperative experience, fishers’ trustworthiness is more or less equal, and that this likelihood increases when resource availability fluctuates seasonally. Finally, to achieve a transformation toward more cooperative forms of self-governance, interventions are required that can strengthen both financial capital and trust among the members of the cooperatives (Paper IV). The unique contribution of this thesis lies in the method for ‘quantitatively’ studying LBD, the stylized model of a small-scale fishery, and the analysis of the two models to advance our understanding of processes of learning and self-governance in uncertain and variable social-ecological environments. Together, the results shed light on how social and ecological factors and processes co-evolve to shape social-ecological outcomes, as well as contributing to the development of novel methods within the emerging field of sustainability science. / I vårt antropocena tidevarv är ett långsiktigt förvaltarskap av naturresurser inom social-ekologiska system av yttersta vikt. Detta kräver en djup förståelse av människan, ekologin, interaktionerna sinsemellan och deras utveckling över tid. Syftet med denna avhandling är att nå en djupare och mer nyanserad förståelse kring två av grundpelarna inom forskningen av hållbar förvaltning av naturresurser–kontinuerligt lärande genom learning-by-doing (LBD) för att förstå naturresursens dynamik, samt vad som kan kallas socialt kapital, i detta sammanhang i betydelsen tillit mellan individer, som naturligtvis ligger till grund för framgångsrik gemensam förvaltning. Denna föresats operationaliseras genom att använda två olika simuleringsmodeller. Den ena modellen undersöker hur en hållbar förvaltning av en förnyelsebar resurs, i denna avhandling exemplifierad av en fiskepopulation, kan uppnås genom LBD. Den andra modellen söker blottlägga det komplexa sociala samspel som krävs för att praktisera gemensam förvaltning genom att använda ett fiskesamhälle som fallstudie. Tidigare forskning på båda dessa två områden är relativt omfattade. Emellertid har den forskning som specialiserat sig på LBD i huvudsak inskränkt sig till empiriska fallstudier. Vad som bryter ny mark i denna avhandling är att vi konstruerar en simuleringsmodell av LBD där vi kan studera lärandeprocessen i detalj för att uppnå en mer hållbar förvaltning över tid. Beträffande modellen som behandlar socialt kapital så har tidigare forskning fokuserat på hur en organisation, eller grupp, kan uppnå hållbar förvaltning. Dock saknas ett helhetsgrepp där som tar hänsyn till alla nivåer; från individnivå (mikro), via gruppnivå (meso), till samhällsnivå (makro). Detta är något som denna avhandling försöker avhjälpa genom att undersöka betydelsen av individers egenskaper, uppbyggnaden av socialt kapital, samt hur detta påverkar emergens av ett samhälle dominerat av mer kooperativa förvaltningsformer respektive mer hierarkiska diton. I papper I and II studeras kärnan av LBD som återkoppling mellan en aktör och en resurs, där aktören lär sig genom upprepade interaktioner med en resurs.  Resultaten visar att LBD är av avgörande betydelse för en hållbar förvaltning, speciellt då naturresursens dynamik är stadd i förändring. I den mest hållbara strategin bör aktören värdera nuvarande och framtida fångster lika högt, försiktigt experimentera kring vad aktören upplever som bästa strategi, för att sedan anpassa sin mentala modell till upplevda förändringar i fångst relativt dess insats någorlunda kraftigt. I papper III och IV behandlas uppbyggnaden av förtroende mellan individer och grupp, samt själv-organiserat styre. Genom att använda småskaligt fiske i Mexiko som en illustrativ fallstudie, utvecklades en agent-baserad modell av ett arketypiskt småskaligt fiskesamhälle. Resultaten indikerar att kooperativa förvaltningsformer är mer dominanta i samhällen där de som utför fisket har liknande pålitlighet, starkt gemensamt socialt kapital vid kooperativets start, och då resursen fluktuerar säsongsmässigt (papper III). Papper IV visar att för att uppnå en transformation från hierarkiska förvaltningsformer till kooperativa diton krävs interventioner som inriktar sig på både socialt och finansiellt kapital. Denna avhandling bidrar således till en djupare förståelse kring hur socialt kapital växer fram, samt hur mer strategiska LBD processer bör utformas när abrupta och osäkra förändringar i ekosystemen blir allt vanligare på grund av människans ökade tryck på planeten. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Submitted. Paper 3: Submitted. Paper 4: Manuscript.</p>

Le modèle Aevol est un modèle d'évolution expérimentale in silico développé par Carole Knibbe et Guillaume Beslon pour étudier l'évolution de la structure des génomes. Aevol a permis d'identifier une très forte pression de sélection indirecte vers un certain niveau de variabilité mutationnelle du phénotype : la survie à long terme d'une lignée étant conditionnée à sa capacité à produire des mutations avantageuses sans pour autant produire trop de mutations délétères, un certain compromis entre robustesse et évolvabilité est indirectement sélectionné. Une conséquence de cette pression de sélection indirecte est le rôle central joué par le taux spontané de réarrangements chromosomiques dans la détermination de la structure du génome. Dans ce travail, nous avons modifié le modèle Aevol pour introduire d'une part un processus explicite de régulation de l'expression des gènes et d'autre part, une sensibilité aux similarités entre séquences dans les événements de recombinaison de l'ADN. Nous avons ainsi pu étudier l'effet de ces variations sur la sélection de second-ordre. Nous avons en particulier observé que celle-ci est extrêmement robuste aux choix de modélisation : les effets liés aux réarrangements sont en effet observés de la même façon lorsque les organismes possèdent un réseau de régulation (qui plus est, ces effets sont visibles sur le réseau lui-même), lorsque les réarrangements se produisent préférentiellement entre séquences similaires et lorsque les transferts horizontaux sont possibles. De plus, les effets de cette pression de sélection de second-ordre ne sont pas limités au niveau génomique : de forts taux de réarrangements tendent à donner lieu à des génomes présentant beaucoup d'opérons, très peu d'ARNs non-codants et des réseaux de régulation très simples. Au contraire, chez les organismes ayant évolué avec de faibles taux de réarrangement, la plupart des gènes sont transcrits sur des ARNs monocistroniques. Ces organismes possèdent un grand nombre d'ARNs non-codants et présentent des réseaux de régulation très complexes. Ces effets observés dans le modèle à différents niveaux d'organisation peuvent s'apparenter à de nombreuses caractéristiques observées chez les organismes réels. Ainsi les pressions sélectives indirectes observées grâce au model Aevol permettent de reproduire un large spectre de propriétés biologiques connues en ne modifiant que le seul taux de réarrangements dans le modèle. Ces mécanismes de sélection indirecte apparaissent donc comme de bons candidats pour expliquer ces mêmes observations sur les organismes réels. / The Aevol model is an in silico experimental evolution model that was specifically developped by Carole Knibbe to study the evolution of the structure of the genome. Using Aevol, a very strong second-order selective pressure towards a specific level of mutational variability of the phenotype was revealed: it was shown that since the survival of a lineage on the long term is conditionned to its ability to produce beneficial mutations while not loosing those previously found, a specific trade-off between robustness and evolvability is indirectly selected. A consequence of this indirect selective pressure is the central role played by the spontaneous rate of chromosomal rearrangements in determining the structure of the genome. More specifically, it was shown that because some rearrangements (large duplications and large deletions) have an impact not only arround their breakpoints but on the whole sequence between them, non-coding sequences are actually mutagenic for the coding sequences they surround. The consequence is a clear trend for organisms having evolved under high rearrangement rates to have very short genomes with hardly any non-coding sequences while organisms evolving in the context of low rearrangement rates have huge, mostly non-coding genomes. Here, we modified the Aevol model to introduce an explicit regulation of gene expression as well as a sensitivity to sequence similarity in DNA recombination events. We observed that the effects of the second-order pressure mentioned above are very robust to modelling choices: they are similarly observed when gene regulation is made available, when rearrangements occur preferentially between similar sequences and even when a biologically plausible process of horizontal transfer is allowed. Moreover, the effects of this second-order selective pressure are not limited to the genomic level: high rearrangement rates usually lead to genomes that have many polycistronic RNAs, almost no non-coding RNAs and very simple regulation networks. On the contrary, at low rearrangement rates organisms have most of their genes transcribed on monocistronic RNAs, they own a huge number of coding RNAs and present very complex and intricate regulation networks. These astounding effects at different levels of organization can account for many features found on real organisms. Thus, the indirect selective pressure that was identified thanks to the Aevol model allows to reproduce a large panel of known biological properties by changing the sole spontaneous rearrangement rate, making this pressure a good candidate for explaining these observations on real organisms.

Le déplacement animal joue un rôle déterminant dans la structuration spatiale et la dynamique des populations biologiques, en particulier des espèces fortement mobiles. L’espace et l’environnement font ainsi partie intégrante du cycle de vie des tortues marines. Ce travail de thèse propose de caractériser l’écologie spatiale des tortues marines, du stade juvénile au stade adulte, dans le Sud-ouest de l’océan Indien, principalement par l’usage de deux méthodes : la télémétrie satellitaire et la modélisation individu-centrée. Il montre en premier lieu que la phénologie de la reproduction de la tortue verte à travers la région est principalement liée à la température de surface de la mer au voisinage des sites de reproduction. Sont ensuite étudiés les patrons de dérive des nouveau-nés générés par les courants océaniques qui impacteraient inégalement leurs traits d’histoire de vie selon l’emplacement du site de naissance. Concernant le stade immature, les résultats suggèrent un cycle de développement trans-équatorial pour la tortue caouanne dans l’océan Indien. Pour le stade adulte, cette étude caractérise les couloirs et la connectivité migratoires de la tortue verte dans la région. Enfin, l’intégration de ces résultats permet de comprendre la structuration des patrons migratoires régionaux et leur influence sur la dynamique des populations. L’ensemble des connaissances acquises fournit un support concret d’aide à la décision pour la mise en place de plans de gestion et de conservation des tortues marines dans le Sud-ouest de l’océan Indien. Cela souligne l’importance d’une approche à grande échelle pour la protection d’un patrimoine biologique partagé par plusieurs nations. / Animal movement is crucial to the ecology of spatially structured population, particularly for highly mobile species. Marine turtles’ life cycle is indeed closely related to spatial and environmental factors. This work analyses the spatial ecology of marine turtles, from early juvenile to adult stages, in the Southwest Indian Ocean, primarily through the use of two methods: satellite tracking and individual-based modeling. Firstly, this analysis argues that green turtle’s reproductive phenology across the region is mainly related to the sea surface temperature in the vicinity of the nesting site. Then, it shows how drifting trajectories of hatchlings in oceanic currents unevenly influence their life history traits depending on the position of the natal site. By tracking late juvenile stage, this work also suggests a trans-equatorial developmental cycle for loggerhead turtle in the Indian Ocean. At adult stage, it describes migratory corridors and connectivity for green turtle across the region. Finally, an integrative approach considering all these results allows for an understanding of the regional migratory patterns and their influence on population dynamics. The results of this work provide a practical policy decision tool for management and conservation of marine turtles in the Southwest Indian Ocean and highlight the need for a large-scale approach in the protection of biological resources and heritage shared by multiple nations.

Made available in DSpace on 2016-10-13T14:10:04Z (GMT). No. of bitstreams: 1 Leonardo Yuji Tamura.pdf: 2018327 bytes, checksum: dca70d285f6272ea72951fe189bab096 (MD5) Previous issue date: 2016-03-22 / The aim of this work is to deepen the understanding of the process of adaptation of firms in the international environment. For such it relied on studies that faced the firm as a complex adaptive system and utilized the Stuart Kauffman s NK model. The NK model was originally conceived to study biological phenomena but has been applied by scholars in strategy and organizational studies since 1997. To enable the use of the NK model for the study of multinational firms, the model was extended to embrace specific international business concepts such as the gaining of competitive advantage in different countries from the adaptation of the firm s internal characteristics to the local environment. The chosen methodology is based on the paradigm of agent-based modeling and simulation. Accordingly, the firms were modeled as autonomous agents that search for the optimization of their competitive advantage by the means of the adaptation process. This approach allowed the study the emergent properties of the system from the agents interaction and behavior. The results of the simulation showed that gaining competitive advantage from the firm s attributes in different countries enabled the emergence of new viable organizational forms. It was also noted that one organizational form that does not provides optimal competitive advantage in a particular country may still be viable in a global context. Another result was the emergence of the complexity catastrophe, which is the degradation of the competitive advantage resulted from the addition of conflicting constraints. Such conflicting constraints are a result of the simultaneous optimization of the competitive advantage in many countries in many different ways due to the possibility of local adaptation. / O objetivo deste trabalho é aprofundar o entendimento sobre o processo de adaptação de empresas no ambiente internacional. Para isto foram utilizados estudos que encararam a empresa como um sistema adaptativo complexo e utilizaram o modelo NK de Stuart Kauffman. O modelo NK foi originalmente concebido para o estudo de fenômenos biológicos, mas vem sendo aplicado por acadêmicos em trabalhos de estratégia e organizações desde 1997. Para que fosse possível utilizar o modelo NK para o estudo de empresas multinacionais, o modelo foi estendido para abarcar conceitos específicos de negócios internacionais como, por exemplo, a obtenção de vantagem competitiva em diferentes países a partir da adaptação de caraterísticas internas da empresa ao ambiente local. A metodologia utilizada foi baseada no paradigma da modelagem e simulação baseado em agentes. Com base neste paradigma as empresas foram modeladas como agentes autônomos que, por meio de um processo de adaptação buscam otimizar sua vantagem competitiva. Esta abordagem permite estudar propriedades emergentes do sistema a partir da interação e do comportamento dos agentes. Os resultados das simulações mostraram que a obtenção de vantagem competitiva a partir dos atributos organizacionais da empresa em diversos países possibilita o surgimento de novas formas organizacionais viáveis. Também se observou que uma forma organizacional que não propicia vantagem competitiva ótima em um país específico, ainda pode ser viável num contexto global. Outro resultado obtido foi a emergência da catástrofe da complexidade, que é a degradação da vantagem competitiva em decorrência da adição de restrições conflitantes. Tais restrições conflitantes são resultado da necessidade de otimizar simultaneamente a vantagem competitiva em diversos países de diversas formas diferentes devido à possibilidade de adaptação local.

Higher Education Institutions are spaces for planning strategies deployment and sustainable best practices implementation in teaching, research, outreach, management and operations, behaving as a role model to society. The innovation of this work relies on deploying tools to aid waste management decision-making, considering that higher education institutions community are potential sustainability agent promoters, and that strategies to integrate HEIs educational dimension with engagement, operational, and policy & management dimensions, is this works innovation from other frameworks already deployed. It is important to understand that HEIs, different than other institutions, have the obligation to build knowledge and to train its community to serve society. HEIs responsibility to prepare new leaders, given the opportunity for raising awareness and sustainable culture by engaging its community in daily activities, by preparing them to see daily challenges and solve it through more sustainable approaches. This works tools were deployed using social sciences, engineering, and computational modeling interfaces. This thesis products are a literature review regard solid waste management at Higher Education Institutions; The description of the solid waste management at University of São Paulo &#8211; São Carlos Campus, a study describing strengthening and weakening factors for the University of São Paulo Recicla recycle program; A framework for solid waste management at Higher Education Institutions; The use of survey as a tool to assess culture of sustainability at the University of São Paulo &#8211; São Carlos Campus; The Waste Management Index for Brazilian Higher Education Institutions; and the use of Agent-Based Modeling methodology as a decision-making tool for recycling initiatives. The main conclusions are that there is a gap on tools to help decision-making regard solid waste management and that consider higher education institutions specificities, this lead to creation of tools to address these necessities. By working to deploy tools with social sciences and engineering interfaces, researchers can find an innovative, rich, and barely exploited field. / Instituições de ensino superior são espaços para implantação de estratégias de planejamento e melhores práticas sustentáveis no ensino, pesquisa, extensão, gerenciamento e operações, comportando-se como modelo para a sociedade. A inovação deste trabalho baseia-se na elaboração e implantação de ferramentas para auxiliar na tomada de decisão referente a gerenciamento de resíduos, considerando que a comunidade de instituições de ensino superior são potenciais agentes promotores de sustentabilidade. Além disso, estratégias para integrar a dimensão educacional das IES com o engajamento, as dimensões operacional e de políticas e gestão é o que diferencia o modelo aqui proposto de outros modelos existentes. É importante entender que as IES, diferentes das outras instituições, têm a obrigação de construir conhecimento e treinar sua comunidade para servir a sociedade. A responsabilidade da IES em preparar novos líderes, tem a oportunidade de aumentar a conscientização e a cultura sustentável, envolvendo sua comunidade nas atividades diárias, preparando-as para ver desafios diários e resolvê-lo através de abordagens mais sustentáveis. As ferramentas foram elaboradas usando interfaces de ciências sociais, engenharia e modelagem computacional. Os produtos desta tese são: A revisão da literatura sobre o gerenciamento de resíduos sólidos nas Instituições de Ensino Superior; A descrição da gestão de resíduos sólidos no campus da Universidade de São Paulo - São Carlos, um estudo que descreve os fatores de fortalecimento e fragilização do programa de reciclagem de Recicla da Universidade de São Paulo; Um modelo para a gestão de resíduos sólidos nas Instituições de Ensino Superior; O uso da questionários como ferramenta para avaliar a cultura de sustentabilidade na Universidade de São Paulo - Campus de São Carlos; O Índice de Gestão de Resíduos Sólidos para Instituições de Ensino Superior Brasileiras; e O uso da metodologia de modelagem baseada em agentes como uma ferramenta de tomada de decisão para iniciativas de reciclagem. As principais conclusões são que há uma lacuna em ferramentas para ajudar a tomada de decisão em relação ao gerenciamento de resíduos sólidos e que consideram as especificidades das instituições de ensino superior, o que leva à criação de ferramentas para atender a essas necessidades. Trabalhando para implantar ferramentas com interface entre as ciências sociais, engenharia, e modelagem computacional os pesquisadores puderam trabalhar em um campo inovador, rico e pouco explorado.

Inventée en 1983, comme procédé de prototypage rapide, la fabrication additive (FA) est aujourd’hui considérée comme un procédé de fabrication quasiment au même titre que les procédés conventionnels. On trouve par exemple des pièces obtenues par FA dans des structures d’aéronef. Cette évolution de la FA est due principalement à la liberté de forme permise par le procédé. Le développement de diverses techniques sur le principe de fabrication couche par couche et l’amélioration en quantité et en qualité de la palette de matériaux pouvant ainsi être mis en forme, ont été les moteurs de cette évolution. De nombreuses autres techniques et matériaux de FA continuent de voir le jour. Dans le sillage de la FA (communément appelée impression 3D) a émergé un autre mode de fabrication : l’impression 4D (I4D). L’I4D consiste à explorer l’interaction matériaux intelligents (MIs) – FA. Les MIs sont des matériaux dont l’état change en fonction d’un stimulus ; c’est le cas par exemple des matériaux thermochromiques dont la couleur change en réponse à la chaleur ou des hydrogels qui peuvent se contracter en fonction du pH d’un milieu aqueux ou de la lumière. Les objets ainsi obtenus ont – en plus d’une forme initiale (3D) – la capacité de changer d’état (en fonction des stimuli auxquels sont sensibles les MIs dont ils sont faits) d’où la 4e dimension (temps). L’I4D fait – à juste titre – l’objet d’intenses recherches concernant l’aspect fabrication (exploration de nouveaux procédés et matériaux, caractérisation, etc.). Cependant très peu de travaux sont entrepris pour accompagner les concepteurs (qui, a priori, ne sont ni experts FA ni des experts de MIs) à l’utiliser dans leurs concepts. Cette nouvelle interaction procédé-matériau requiert en effet des modèles, des méthodologies et outils de conception adaptés. Cette thèse sur la conception pour l’impression 4D a pour but de combler ce vide méthodologique. Une méthodologie de conception pour la FA a été proposée. Cette méthodologie intègre les libertés (forme, matériaux, etc.) et les contraintes (support, résolution, etc.) spécifiques à la FA et permet aussi bien la conception de pièces que celle d’assemblages. En particulier, la liberté de forme a été prise en compte en permettant la génération d’une géométrie minimaliste basée sur les flux fonctionnels (matière, énergie, signal) de la pièce. Par ailleurs, les contributions de cette thèse ont porté sur la conception avec les matériaux intelligents. Parce que les MIs jouent plus un rôle fonctionnel que structurel, les préoccupations portant sur ces matériaux doivent être menées en amont du processus de conception. En outre, contrairement aux matériaux conventionnels (pour lesquels quelques valeurs de paramètres peuvent suffire comme information au concepteur), les MIs requièrent d’être décrits plus en détails (stimulus, réponse, fonctions, etc.). Pour ces raisons un système d’informations orientées conception sur les MIs a été mis au point. Ce système permet, entre autre, d’informer les concepteurs sur les capacités des MIs et aussi de déterminer des MIs candidats pour un concept. Le système a été matérialisé par une application web. Enfin un cadre de modélisation permettant de modéliser et de simuler rapidement un objet fait de MIs a été proposé. Ce cadre est basé sur la modélisation par voxel (pixel volumique). En plus de la simulation des MIs, le cadre théorique proposé permet également le calcul d’une distribution fonctionnelle de MIs et matériau conventionnel ; distribution qui, compte tenu d’un stimulus, permet de déformer une forme initiale vers une forme finale désirée. Un outil – basé sur Grasshopper, un plug-in du logiciel de CAO Rhinoceros® – matérialisant ce cadre méthodologique a également été développé. / Invented in 1983, as a rapid prototyping process, additive manufacturing (AM) is nowadays considered as a manufacturing process almost in the same way as conventional processes. For example, parts obtained by AM are found in aircraft structures. This AM evolution is mainly due to the shape complexity allowed by the process. The driving forces behind this evolution include: the development of various techniques on the layer-wise manufacturing principle and the improvement both in quantity and quality of the range of materials that can be processed. Many other AM techniques and materials continue to emerge. In the wake of the AM (usually referred to as 3D printing) another mode of manufacturing did emerge: 4D printing (4DP). 4DP consists of exploring the smart materials (SM) – AM interaction. SMs are materials whose state changes according to a stimulus; this is the case, for example, with thermochromic materials whose color changes in response to heat or hydrogels which can shrink as a function of an aqueous medium’s pH or of light. The objects thus obtained have – in addition to an initial form (3D) – the capacity to shift state (according to the stimuli to which the SMs of which they are made are sensitive) hence the 4th dimension (time). 4DP is – rightly – the subject of intense research concerning the manufacturing aspect (exploration of new processes and materials, characterization, etc.). However, very little work is done to support the designers (who, in principle, are neither AM experts nor experts of SMs) to use it in their concepts. This new process-material interaction requires adapted models, methodologies and design tools. This PhD on design for 4D printing aims at filling this methodological gap. A design methodology for AM (DFAM) has been proposed. This methodology integrates the freedoms (shape, materials, etc.) and the constraints (support, resolution, etc.) peculiar to the AM and allows both the design of parts and assemblies. Particularly, freedom of form has been taken into account by allowing the generation of a minimalist geometry based on the functional flows (material, energy, and signal) of the part. In addition, the contributions of this PhD focused on designing with smart materials (DwSM). Because SMs play a functional rather than a structural role, concerns about these materials need to be addressed in advance of the design process (typically in conceptual design phase). In addition, unlike conventional materials (for which a few parameter values may suffice as information to the designer), SMs need to be described in more detail (stimulus, response, functions, etc.). For these reasons a design-oriented information system on SMs has been developed. This system makes it possible, among other things, to inform designers about the capabilities of SMs and also to determine SMs candidates for a concept. The system has been materialized by a web application. Finally, a modeling framework allowing quickly modeling and simulating an object made of SMs has been proposed. This framework is based on voxel modeling (volumetric pixel). In addition to the simulation of SMs behaviors, the proposed theoretical framework also allows the computation of a functional distribution of SMs and conventional material; distribution which, given a stimulus, makes it possible to deform an initial form towards a desired final form. A tool – based on Grasshopper, a plug-in of the CAD software Rhinoceros® – materializing this methodological framework has also been developed.

Le diagnostic et la prise en charge des infections ostéo-articulaires (IOA) sont souvent complexes occasionnant une perte osseuse irréversible. La variabilité intra et inter-patient en terme de présentation clinique rend impossible le recours à une description systématique ou à une analyse statistique pour le diagnostic et l'étude de cette pathologie. Le développement d'IOA résulte d'interactions complexes entre les mécanismes cellulaires et moléculaires du tissu osseux et les bactéries. L'objectif de cette thèse est de modéliser l'IOA afin de simuler le comportement du système suite à des interactions au niveau cellulaire et moléculaire en utilisant l'approche de modélisation à base d'agents. Nous avons utilisé une méthode basée sur l'analyse bibliographique pour extraire les caractéristiques du modèle et les utiliser pour deux aspects. Le premier consiste en l'élaboration de la structure du modèle en identifiant les agents et les interactions, et le deuxième concerne l'estimation quantitative des différents paramètres du modèle. La réponse du système BJI aux différentes tailles d’inoculum bactérien a été simulée par la variation de différents paramètres. L'évolution des agents simulés a ensuite été analysée en utilisant une modélisant par des systèmes dynamiques non linéaires et une méthodologie "Datadriven", grâce auxquelles nous avons décrit le système d'IOA et identifié des relations plausibles entre les agents. Le modèle a réussi à présenter la dynamique des bactéries, des cellules immunitaires innées et des cellules osseuses au cours de la première étape de l'IOA et pour différentes tailles d'inoculum bactérien. La simulation a mis en évidence les conséquences sur le tissu osseux résultant du processus de remodelage osseux au cours de l'IOA. Ces résultats peuvent être considérés comme une base pour une analyse plus approfondie et pour la proposition de différentes hypothèses et scénarios de simulation qui pourraient être étudiés dans ce laboratoire virtuel. / Bone and joint infections are one of the most challenging bone pathologies that associated with irreversible bone loss and long costly treatment. The high intra and inter patient's variability in terms of clinical presentation makes it impossible to rely on the systematic description or classical statistical analysis for its diagnosis or studying. The development of BJI encompasses a complex interplay between the cellular and molecular mechanisms of the host bone tissue and the infecting bacteria. The objective of this thesis is to provide a novel computational modeling framework that simulates the behavior resulting from the interactions on the cellular and molecular levels to explore the BJI dynamics qualitatively and comprehensively, using an agent-based modeling approach. We relied on a meta-analysis-like method to extract the quantitative and qualitative data from the literature and used it for two aspects. First, elaborating the structure of the model by identifying the agents and the interactions, and second estimating quantitatively the different parameters of the model. The BJI system’s response to different microbial inoculum sizes was simulated with respect to the variation of several critical parameters. The simulation output data was then analyzed using a data-driven methodology and system dynamics approach, through which we summarized the BJI complex system and identified plausible relationships between the agents using differential equations. The BJI model succeeded in imitating the dynamics of bacteria, the innate immune cells, and the bone cells during the first stage of BJI and for different inoculum size in a compatible way. The simulation displayed the damage in bone tissue as a result of the variation in bone remodeling process during BJI. These findings can be considered as a foundation for further analysis and for the proposition of different hypotheses and simulation scenarios that could be investigated through this BJI model as a virtual lab.

The continuous progression of urbanization has resulted in an increasing number of people living in cities or towns. In parallel, advancements in technologies, such as the Internet, telecommunications, and transportation, have allowed for better connectivity among people. This has engendered drastic changes in urban systems during the recent decades. From a social geographic perspective, the changes in urban systems are primarily characterized by intensive contacts among people and their interactions with the surrounding urban environment, which further leads to subsequent challenging problems such as traffic jams, environmental pollution, urban sprawl, etc. These problems have been reported to be heterogeneous and non-deterministic. Hence, to cope with them, massive amounts of geographic data are required to create new knowledge on urban systems. Due to the thriving of Volunteer Geographic Information (VGI) in recent years, this thesis presents knowledge on urban systems based on extensive VGI datasets from three sources: highway dataset from the OpenStreetMap (OSM) project, photo location dataset from the Flickr website, and GPS tracking datasets from volunteers, taxicabs, and air flights. The knowledge primarily relates to two issues of urban systems: the urban space and the corresponding human dynamics. In accordance, on one hand, urban space acts as a carrier for associated geographic activities and knowledge of it benefits our understanding of current social and economic problems in urban systems. On the other hand, human dynamics reflect human behavior in urban space, which leads to complex mobility or activity patterns. Its investigation allows a derivation of the underlying driving force that is very instructive to urban planning, traffic management, and infectious disease control. Therefore, to fully understand the two issues, this thesis conducts a thorough investigation from multiple aspects. The first issue is investigated from four aspects. First, at the city level, the controversial topic of city size regularity is investigated in terms of natural cities, and the conclusion is that Zipf’s law holds stably for all US cities. Second, at the sub-city level, the size distribution of spatial units within different cities in terms of the clusters formed by street nodes, photo locations, and taxi static points are explored, and the result shows a remarkable scaling property of these spatial units. Third, enlightened by the scaling property of the urban space at the city or sub-city level, this thesis devises a novel tool that can demarcate the cities into three categories: compact cities, normal cities, and sprawling cities. The tool is then applied to cities in both the US and three European countries. In the last, another representation of urban space is taken into account, namely the transportation network. The findings report that the US airport network displays the properties of scale-free, small-world, and disassortative mixing and that the individual natural airports show heterogeneous patterns that are probably subject to geographic constraints and socioeconomic factors. The second issue is examined from four perspectives. First, at the city level, the movement flow contributed by agents using two types of behavior is investigated through an agent-based simulation, and the result conjectures that the human mobility behavior is mainly shaped by the underlying street network. Second, at the country level, this thesis reports that the human travel length by air can be approximated well by an exponential distribution, and subsequent simulations indicate that human mobility behavior is largely constrained by the underlying airport network. Third, at the regional level, the length that humans travel by car is demonstrated to agree well with a power law with exponential cutoff distribution, and subsequent simulation further reproduces this levy flight characteristic. Based on the simulation, human mobility behavior is again revealed to be primarily shaped by the underlying hierarchical spatial structure. Finally, taxicab static points are adopted to explore human activity patterns, which can be characterized as the regularities in space and time, the heterogeneity and predictability in space. From a complex system perspective, this thesis presents the knowledge discovered in urban systems using massive volumes of geographic data. Together with new knowledge from empirical findings, the development of methods, and the design of theoretic models, this thesis also shares the research community with geographic data generated from extensive VGI datasets and the corresponding source codes. Moreover, this study is aligned with a paradigm shift in that it analyzes large-size datasets using high processing power as opposed to analyzing small-size datasets with low processing power. / <p>QC 20121113</p>

Despite their important ecosystem benefits for terrestrial and marine flora and fauna and the human livelihood mangrove forests suffer a high loss rate mainly due to human activity. Aside from these impacts, natural forest disturbances exist more commonly in mangroves compared to other forests as a direct consequence of their exposed coastal location. Within this thesis I investigate the influence of natural disturbance regimes on the mangrove forest dynamics focusing in particular on the ecological role of disturbances, disturbance patterns, forest structure, succession behavior and long-term vulnerability evaluation. The study areas were set in the Indian River Lagoon in Florida (USA) and in Can Gio an UNESCO Biosphere Reserve (Vietnam). In addition, theoretical simulation studies were carried out to complement the field studies. Thereby, in our study at the Indian River Lagoon site I investigated the ecosystem response to hurricane events of an artificially impounded mangrove forest. In Can Gio, the suitability of lightning strike – caused gaps for setting a homogenous plantation into more natural-like state according to species composition and forest structure was analyzed. Finally, a theoretical simulation study was carried out to compare lightning strike and hurricane events regarding their homogenization and heterogenization effects on the spatio-temporal forest structure. The findings of the field study in the Indian River Lagoon indicate that hurricane events had a severe impact on forest areas in higher successional stages by creating open patches, whereas areas in lower successional stages remained largely undisturbed. Furthermore, the impoundment determines the species selection of the post-hurricane succession by favoring flooding-tolerant species. However, regeneration was found to be impaired by the artificially high inundation regime at some disturbed patches. The lightning-strike disturbances enhance the species composition in the monospecific plantation in Can Gio by providing a sufficient light regime for entering seeds to establish. In addition, lightning-strike gaps increased the plantation structure complexity. Regenerating lightning-strike gaps remained as “green islands” within windthrow sites in the plantation due to their low stature and provided seeds for surrounding disturbed areas thereby accelerating their recolonization. The results of the simulation analysis of a theoretical landscape showed that in the simulated highly complex natural mature forests all disturbance regimes entail homogenization on the spatial structure compared to an undisturbed scenario. The hurricane scenario showed an increased temporal variation of the forest dynamics whereas lightning-strike gaps were not able to contribute to additional heterogeneity in the simulated area, despite of having the same tree mortality probability during disturbances. The interaction of the large-scale impoundment in the Indian River Lagoon and medium-sized hurricane events is characterized by partially impeded post-hurricane regeneration. In contrast, small-scaled lightning strikes influenced the regeneration of medium-sized windthrow sites positively within the homogenous plantation. We therefore suggest management activities aimed at creating small clearances within the plantation in Can Gio to simulate additional small-scale disturbances in order to facilitate heterogenization of the plantation structure. Natural disturbances are found to be able to enhance the species diversity and the interactions of ecological processes. In particular, where sustainable management strategies focused on maintaining ecosystem services especially in restored sites or plantations act as a supportive part. Natural disturbances are an integral component of mangrove forests and fulfill specific ecological functions. However, our findings indicate that these disturbances, on top of altered environmental conditions associated with climate change and direct human impacts, might jeopardize the natural development in unnatural forest structures as on plantations or restored sites. This thesis gives an extensive overview about the effect of various disturbances in different mangrove forest systems, including semi-natural forests and strongly modified plantations, on species composition and forest structure. Field studies and simulation analyses contribute in equal parts to the results of the thesis.