A formação espontânea de padrões espaço-temporais auto-organizados longe do equilíbrio termodinâmico é um comportamento característico de sistemas de reação-transporte. De fato, essa estruturação espacial pode ser entendida como um comportamento coletivo de um grande número de elementos individuais no sistema. Consequentemente o padrão emerge como o resultado da interação entre a dinâmica local dessas subunidades e o mecanismo de acoplamento espacial. Dinâmica não-linear do tipo multi-estável, excitável e oscilatória são exemplos típicos de padrões temporais complexos geralmente associados à estruturação espacial. Nesta tese de doutorado são apresentadas duas frentes de trabalho utilizando-se da dinâmica química não-linear na elucidação de mecanismos reacionais longe do equilíbrio termodinâmico: (a) a investigação da natureza química e efeito do drift nas séries temporais transientes em osciladores eletroquímicos. A análise da evolução temporal do parâmetro de bifurcação foi baseada em um método empírico de estabilização, sendo o acúmulo superficial de espécies oxigenadas o principal responsável pelo drift; (b) o desacoplamento das rotas eletroquímicas paralelas na formação de CO2 pela combinação de experimentos, modelagem e simulações numéricas durante a eletro-oxidação oscilatória de metanol em platina policristalina. O efeito dos ânions perclorato e sulfato nas reações paralelas foi investigado por meio da produção global de CO2 e HCOOCH3. Notavelmente, ânions sulfato inibiram mais fortemente a atividade catalítica proveniente da via direta em contraste com a pequena alteração na via indireta. Em paralelo às duas frentes de trabalho, foi construído um setup experimental com a finalidade de acompanhar a evolução espaço-temporal de uma reação eletroquímica com um sistema de aquisição de dados multicanal. A descrição do processo de confecção da célula e eletrodo de trabalho multicanal, o tratamento de dados e alguns resultados experimentais preliminares são inseridos como um capítulo adicional. A ideia central dessa tese converge na obtenção de informações da cinética química envolvida que não é observada em condições próximas ao equilíbrio termodinâmico. Essa interpretação pode ser utilizada como uma metodologia alternativa no estudo da eletrocatálise em reações químicas complexas. / The spontaneous formation of self-organized spatiotemporal patterns under far from thermodynamic equilibrium conditions is a characteristic behavior in reaction-transport systems. Indeed, this spatial structuration can be understood as a collective behavior of a large number of individual elements in the system. Consequently the pattern emerges as a result of the interaction between the local dynamic of these subunits and the spatial coupling. Multistable, excitable and oscillatory nonlinear dynamics are typical examples of complex temporal patterns usually associated to the spatial structuration. In this doctoral thesis, two work fronts are presented using the nonlinear chemical dynamics in the elucidation of reaction mechanisms under far from thermodynamic equilibrium regime: (a) the investigation of the chemical nature and effect of the drift in the transient time-series in electrochemical oscillators. The analysis of the temporal evolution of the bifurcation parameter was based on an empiric method of stabilization, being the slow accumulation of oxygenated species the main responsible for the drift; (b) the decoupling of the parallel electrochemical routes for CO2 production by a combination of experiments, modeling and numerical simulations during the oscillatory electro-oxidation of methanol on polycrystalline platinum. The effect of perchlorate and sulfate anions in the parallel reactions was investigated by the global production of CO2 and HCOOCH3. Remarkably, sulfate anions inhibited more strongly the catalytic activity from direct pathway in contrast to the small alteration in the indirect pathway. In parallel to the two work fronts, an experimental setup was built in order to obtain a spatiotemporal evolution of a electrochemical reaction with a multichannel data acquisition system. A description of the confection process of the cell and the multichannel working electrode, data treatment and some preliminary experimental results are included as an additional chapter. The main idea of this thesis converges in the obtainment of chemical kinetic information which is not observed in conditions close to the thermodynamic equilibrium. This interpretation might be used as an alternative methodology in the study of electrocatalysis in complex chemical reactions.

A desigualdade material hereditária teria surgido no registro arqueológico pela primeira vez por volta de 6.500 A.C. na região da Mesopotâmia, tendo posteriormente emergido de maneira independente em diferentes localidades e contextos, dentro de um intervalo de tempo relativamente curto. Muitas teorias foram propostas para explicar os fenômenos, porém sua compreensão permanece em aberto. Buscou-se, aqui, abordar a questão sob a perspectiva dos Sistemas Adaptativos Complexos, construindo um Modelo Baseado em Agentes que teve como base teórica a literatura que trata da questão, focada nos últimos vinte anos do debate, aprofundada em dois estudos de caso: a Mesopotâmia e a Costa Noroeste da América do Norte. Dos nove parâmetros testados oito apresentaram relação direta com a assimetria material dos indivíduos podendo colaborar com a emergência da desigualdade material hereditária, de forma que fomos levados a considerar a igualdade material e a cooperação presente entre os caçadores e coletores como propriedades decorrentes de uma estrutura social de criticalidade auto-organizada / The hereditary material inequality would have emerged for the first time in the archaeological record around 6.500 BC in Mesopotamia, emerging after it repeatedly and independently in different localities and contexts, in a small time period. Many theories have been proposed but the complete understanding of the issue remains open to debate. Thus, we have proposed here an approach of the phenomenon under the Complex Adaptive Systems perspective, through which an agent-based model have been built. Constitutes the background of the model the working papers and text books written in the last two decades, which were later checked agains two case studies: Mesopotamia and Northwest Coast, in North America. Among the nine parameters tested in the model eight presented direct relation to the material asymmetry of individuals, potentially participating of the precesses involved in the emergence of material inequality. This results leads us to consider the possibility of the egalitarian and cooperative social structures of huntergatherers to be one of self-organized criticality

Made available in DSpace on 2016-04-29T14:23:34Z (GMT). No. of bitstreams: 1 Jose Carlos Junqueira.pdf: 2902739 bytes, checksum: 4ec1e0e7a07c0af257870a0ee896add3 (MD5) Previous issue date: 2015-03-11 / This study investigates the impact of processes of co-creation in organizations in general. Based on a multidisciplinary approach, case studies were carried out in four companies in order to investigate different levels of awareness and maturity concerning organizational processes. The focus was on two of the basic concepts that involve co-creation, i.e., self-organization and collective intelligence. A general survey presents the theoretical framework of the state of the art in research in self-organization and collective intelligence. It identifies the intersections and common characteristics between these concepts with reference to authors such as Humberto Maturana, Edgar Morin, Pierre Lévy, Manuel Castells, Lucia Santaella, Edward Hutchins, and Venkat Ramaswamy. The aim of the case studies was to find evidence for the awareness of processes of self-organization and the impact of collective intelligence in organizations. The result of this study shows that the importance of co-creation is only beginning to be acknowledged in organizations. It was found that there is still a lack of methodology and metrics. In particular, maturity curves are not yet being used, as they should. More specific studies to develop a methodology and tools for the interpretation of adherence in collaborative processes are needed / O objeto de estudo desta pesquisa é o impacto dos novos processos de cocriação nas organizações em geral. Baseado numa abordagem transdisciplinar, o trabalho apresenta estudos de caso em quatro organizações específicas que possuem processos em níveis diferenciados de conscientização e maturidade no entendimento de dois dos conceitos básicos que envolvem a cocriação, os quais são a auto-organização e a inteligência coletiva. A demonstração da evidência destes conceitos com os estudos de caso é realizada através do levantamento do referencial teórico em estado da arte dos conceitos e da identificação de intersecções de características comuns entre estes conceitos e sua evidenciação nos processos das organizações analisadas. Os trabalhos que dão sustentação a este estudo são de autores de referência como Humberto Maturana, Edgar Morin, Pierre Lévy, Manuel Castells, Lucia Santaella, Edward Hutchins e Venkat Ramaswamy. O resultado deste trabalho foi a constatação que a utilização de processos de cocriação nas organizações ainda é incipiente e carente de metodologias e métricas, sendo necessários estudos mais específicos para a elaboração de uma metodologia com ferramentas para a interpretação de aderência em processos colaborativos baseada em curvas de maturidade

Cette thèse a pour sujet la biologie cellulaire, et plus particulièrement l'organisation interne des cellules eucaryotes. Bien que les différents acteurs régissant cette organisation aient été en grande partie identifiées, on ignore encore comment une architecture si complexe et dynamique peut émerger de simples interactions entres molécules. Un des objectifs des différentes études présentées dans cette thèse est de construire un cadre théorique permettant d'appréhender cette auto-organisation. Pour cela, nous étudions des problèmes spécifiques à différentes échelles allant du nanomètre (dynamique des hétérogénéités dans les membranes biologiques) au micromètre (organisation des organelles cellulaires), en utilisant des simulations numériques stochastiques et des méthodes analytiques. Le texte est organisé pour présenter les résultats des plus petites au plus grandes échelles. Dans le premier chapitre, nous étudions l'organisation de la membrane d'un seul compartiment en modélisant la dynamique d'hétérogénéités membranaires. Dans le second chapitre, nous étudions la dynamique d'un compartiment unique échangeant des vésicules avec le milieu extérieur. Nous étudions également comment deux compartiments différents peuvent être générés par les mêmes mécanismes d'échanges de vésicules. Enfin, dans le troisième chapitre, nous développons un modèle global de la dynamique des organelles cellulaires, dans le contexte particulier de la biogenèse de l'appareil de Golgi. / This thesis deals with cell biology, and particularly with the internal organization of eukaryotic cells. Although many of the molecular players contributing to the intra-cellular organization have been identified, we are still far from understanding how the complex and dynamical intra-cellular architecture emerges from the self-organization of individual molecules. One of the goals of the different studies presented in this thesis is to provide a theoretical framework to understand such self-organization. We cover specific problems at different scales, ranging from membrane organization at the nanometer scale to whole organelle structure at the micron scale, using analytical work and stochastic simulation algorithms. The text is organized to present the results from the smallest to the largest scales. In the first chapter, we study the membrane organization of a single compartment by modeling the dynamics of membrane heterogeneities. In the second chapter we study the dynamics of one membrane-bound compartment exchanging vesicles with the external medium. Still in the same chapter, we investigate the mechanisms by which two different compartments can be generated by vesicular sorting. Finally in the third chapter, we develop a global model of organelle biogenesis and dynamics in the specific context of the Golgi apparatus

This paper demonstrates that it is possible to generate a reasonably accurate coordinate system on randomly distributed processors, using only local information and local communication. By coordinate systems we imply that each element assigns itself a logical coordinate that maps to its global physical location, starting with no apriori knowledge of position or orientation. The algorithm presented is inspired by biological systems that use chemical gradients to determine the position of cells. Extensive analysis and simulation results are presented. Two key results are: there is a critical minimum average neighborhood size of 15 for good accuracy and there is a fundamental limit on the resolution of any coordinate system determined strictly from local communication. We also demonstrate that using this algorithm, random distributions of processors produce significantly better accuracy than regular processor grids - such as those used by cellular automata. This has implications for discrete models of biology as well as for building smart sensor arrays.

Cell-cell and cell-environment interactions are controlled by a set of local rules that dictate cell behavior. With such local rules, emergence of computationally meaningful building blocks and hierarchies can be observed. For example, at the cellular level organization in the visual system, receptive field of a retinal ganglion cell displays an activation inhibition behavior that can be modeled as Mexican Hat wavelet or Difference of Gaussians. This precise organization is the product of a harmonious collaboration of different cell types located at the lower levels in a hierarchical structure for each ganglion cell. Moreover, a similar hierarchical organization is observed at higher levels in the visual system. This thesis investigates the visual system from several perspectives in an effort to explore the biological/computational principles underlying these local rules. The investigation results in a hybrid computer model that can combine the advantages of evolutionary and developmental principles to explore the effects of local rules on cellular differentiation, retinal mosaics, layered structures and network topology.

The whole in a complex system is the sum of its parts, plus the interactions between the parts. Understanding social, biological, and economic systems therefore often depends on understanding their patterns of interactions---their networks. In this thesis, the approach is to understand complex systems by making simple network models with nodes and links. It is first of all an attempt to investigate how the communication over the network affects the network structure and, vice versa, how the network structure affects the conditions for communication. To explore the local mechanism behind network organization, we used simplified social systems and modeled the response to communication. Low communication levels resulted in random networks, whereas higher communication levels led to structured networks with most nodes having very few links and a few nodes having very many links. We also explored various models where nodes merge into bigger units, to reduce communication costs, and showed that these merging models give rise to the same kind of structured networks. In addition to this modeling of communication networks, we developed new ways to measure and characterize real-world networks. For example, we found that they in general favor communication on short distance, two-three steps away in the network, within what we call the information horizon. / Helheten i ett komplext system är mer än summan av dess delar, då den även inbegriper interaktionerna mellan dem. Att studera sociala, biologiska och ekonomiska system blir därför ofta en fråga om att förstå deras interaktionsmönster, d.v.s. deras nätverk av noder och länkar. Med utgångspunkt i enkla nätverksmodeller undersöker avhandlingen i huvudsak hur kommunikation i nätverk påverkar nätverksstrukturen och, vice versa, hur nätverksstrukturen påverkar villkoren för kommunikation. Vi utforskade mekanismerna bakom hur nätverk är organiserade genom att modellera effekten av kommunikation i förenklade sociala system. En låg kommunikationsnivå visade sig ge upphov till kaotiska nätverk där ingen nod i princip hade fler länkar än någon annan. En hög kommunikationsnivå resulterade däremot i strukturerade nätverk, med några få centrala noder med många länkar, medan flertalet noder var perifera med enbart några få länkar. Det visade sig också att alla aktörer i nätverket gynnades av kommunikation, även när den var ojämnt fördelad. Kvaliteten på kommunikationen, d.v.s. informationens giltighet, var också avgörande för vilka positioner som gynnades i ett nätverk, vilket vi visade genom att studera aktörer som spred falsk information. Eftersom effektiv kommunikation är en viktig del i många nätverk betraktar vi utvecklingen av dem som en optimeringsprocess. Varje kommunikationshandling mellan noderna tar tid och genom att slå sig samman till större enheter begränsas dessa kostnader och gör nätverket effektivare. Dessa s.k. sammanslagningsmodeller gav upphov till samma typ av strukturerade nätverk som ovan. Genom att utveckla olika sätt att mäta nätverksstrukturer visade vi bland annat att många verkliga system främjar kommunikation över korta avstånd, två-tre steg bort i nätverket, innanför det vi kallar informationshorisonten. Vi uppskattade också den mängd information som krävs för att orientera sig i städer, och fann att det är lättare att hitta i moderna, planerade städer än i äldre städer som utvecklats under lång tid.

This thesis investigates designs that enable individual components of a distributed system to work together and coordinate their actions towards a common goal. While the basic motivation for our research is to develop engineering principles for large-scale autonomous systems, we address the problem in the context of resource management in server clusters that provide web services. To this end, we have developed, implemented and evaluated a decentralized design for resource management that follows four principles. First, in order to facilitate scalability, each node has only partial knowledge of the system. Second, each node can adapt and change its role at runtime. Third, each node runs a number of local control mechanisms independently and asynchronously from its peers. Fourth, each node dynamically adapts its local configuration in order to optimize a global utility function. The design includes three fundamental building blocks: overlay construction, request routing and application placement. Overlay construction organizes the cluster nodes into a single dynamic overlay. Request routing directs service requests towards nodes with available resources. Application placement partitions the cluster resources between applications, and dynamically adjusts the allocation in response to changes in external load, node failures, etc. We have evaluated the design using complexity analysis, simulation and prototype implementation. Using complexity analysis and simulation, we have shown that the system is scalable, operates efficiently in steady state, quickly adapts to external events and allows for effective service differentiation by a system administrator. A prototype has been built using accepted technologies (Java, Tomcat) and evaluated using standard benchmarks (TPC-W and RUBiS). The evaluation results show that the behavior of the prototype matches closely that of the simulated design for key metrics related to adaptability and robustness, therefore validating our design and proving its feasibility. / QC 20100629

Self-organizing overlay networks have emerged as a powerful paradigm for providing network services. While most approaches assume that overlay networks are built over a single substrate network, generally, the Internet, this thesis addresses the construction of overlay networks over multiple substrate networks. We present the design, implementation and evaluation of Cross-Substrate Advertisement (CSA) mechanisms for overlay networks over multiple heterogeneous substrate networks. A key difficulty arises from the more complex address bindings, since a single logical identifier is bound to multiple substrate addresses. We present mechanisms for exchanging information on address bindings and evaluate their effectiveness. The CSA mechanisms have been implemented in the HyperCast overlay protocol architecture, and have been evaluated in measurement experiments on an Emulab testbed. The experiments show that our CSA methods are effective in disseminating address information in large networks and are robust in the presence of network disruptions.

Self-organizing overlay networks have emerged as a powerful paradigm for providing network services. While most approaches assume that overlay networks are built over a single substrate network, generally, the Internet, this thesis addresses the construction of overlay networks over multiple substrate networks. We present the design, implementation and evaluation of Cross-Substrate Advertisement (CSA) mechanisms for overlay networks over multiple heterogeneous substrate networks. A key difficulty arises from the more complex address bindings, since a single logical identifier is bound to multiple substrate addresses. We present mechanisms for exchanging information on address bindings and evaluate their effectiveness. The CSA mechanisms have been implemented in the HyperCast overlay protocol architecture, and have been evaluated in measurement experiments on an Emulab testbed. The experiments show that our CSA methods are effective in disseminating address information in large networks and are robust in the presence of network disruptions.