In this thesis I investigate the role of spatial structure, cell-cell interactions and horizontal gene transfer on the genetic composition of growing microbial colonies. In the first part I study how the roughness of the growing layer of the colony depends on the shape of colony-forming cells. To study its impact I develop an off-lattice Eden-like model in which cells are represented as spherocylinders with a variable aspect ratio. I show that the roughness of the expansion front is not significantly affected by the shape of cells and that the dynamic scaling of growing front belongs to the KPZ universality class. Roughness is an important and easy to measure feature which affects the probability of fixation of genetic lineages in the colony. Another feature contributing to the genetic composition of a microbial community is horizontal gene transfer, which is investigated in the second part of this thesis. I develop an agent-based computational model of bacterial cells which grow, divide, and interact mechanically. I focus on plasmid conjugation, in which donors transfer a plasmid (a small, circular DNA molecule) to plasmid-free recipients. I show that bacteria in the expanding colony segregate into sectors of donors and acceptors. Donor sectors grow at the expense of acceptor sectors and that effect can be effectively described by coalescing random walkers that perform biased random walk on the colony expansion front. I use numerical and analytical methods to show that the plasmid eventually spreads to the whole colony given enough time, and I also show that this time is unrealistically long for experimentally determined conjugation rates and therefore real colonies are expected to have both acceptor and donor sectors. Furthermore, my simulations show that segregative plasmid loss at the moment of cell division can counteract the effect of conjugation and can lead to fixation of plasmid free cells. I also show that changes in nutrient concentration and the resultant change in roughness of the expansion front affect the rate of plasmid spread into population. Quantitative and qualitative results obtained in this section may serve as a tool to extract plasmid invasion rates from experimental data. In the last part of this thesis I investigate how the physical factors, such as finite strength of conjugative junctions, affect the conjugation process. I develop a computational model of plasmid transfer in which conjugative junctions are explicitly modelled as short, spring-like tubes that connect conjugating cells. My results show that factors such as junction creation rate and its strength can significantly affect the conjugation performance. I study different situations corresponding to different experimental scenarios (well-mixed colony on a filter paper, colliding colonies) and show that shear forces acting between cells can significantly lower the rate of plasmid transfer. My results can explain why conjugation occurs very rarely in some of these scenarios investigates in laboratory assays.

Automated theorem proving is a method to establish or disprove logical theorems. While these can be theorems in the classical mathematical sense, we are more concerned with logical encodings of properties of algorithms, hardware and software. Especially in the area of hardware verification, propositional logic is used widely in industry. Satisfiability Module Theories (SMT) is a set of logics which extend propositional logic with theories relevant for specific application domains. In particular, software verification has received much attention, and efficient algorithms have been devised for reasoning over arithmetic and data types. Built-in support for theories by decision procedures is often significantly more efficient than reductions to propositional logic (SAT). Most efficient SAT solvers are based on the DPLL architecture, which is also the basis for most efficient SMT solvers. The main shortcoming of both kinds of logics is the weak support for non-ground reasoning, which noticeably limits the applicability to real world systems. The Model Evolution Calculus (ME) was devised as a lifting of the DPLL architecture from the propositional setting to full first-order logic. In previous work, we created the solver Darwin as an implementation of ME, and showed how to adapt improvements from the DPLL setting. The first half of this thesis is concerned with ME and Darwin. First, we lift a further crucial ingredient of SAT and SMT solvers, lemma-learning, to Darwin and evaluate its benefits. Then, we show how to use Darwin for finite model finding, and how this application benefits from lemma-learning. In the second half of the thesis we present Model Evolution with Linear Integer Arithmetic (MELIA), a calculus combining function-free first-order logic with linear integer arithmetic (LIA). MELIA is based on ME and supports similar inference rules and redundancy criteria. We prove the correctness of the calculus, and show how to obtain complete proof procedures and decision procedures for some interesting classes of MELIA's logic. Finally, we explain in detail how MELIA can be implemented efficiently based on the techniques employed in SMT solvers and Darwin.

This dissertation presents a unique approach to human behavior analysis based on expert guidance and intervention through interactive construction and modification of behavior models. Our focus is to introduce the research area of behavior analysis, the challenges faced by this field, current approaches available, and present a new analysis approach: Interactive Relevance Search and Modeling (IRSM). More intelligent ways of conducting data analysis have been explored in recent years. Ma- chine learning and data mining systems that utilize pattern classification and discovery in non-textual data promise to bring new generations of powerful "crawlers" for knowledge discovery, e.g., face detection and crowd surveillance. Many aspects of data can be captured by such systems, e.g., temporal information, extractable visual information - color, contrast, shape, etc. However, these captured aspects may not uncover all salient information in the data or provide adequate models/patterns of phenomena of interest. This is a challenging problem for social scientists who are trying to identify high-level, conceptual patterns of human behavior from observational data (e.g., media streams). The presented research addresses how social scientists may derive patterns of human behavior captured in media streams. Currently, media streams are being segmented into sequences of events describing the actions captured in the streams, such as the interactions among humans. This segmentation creates a challenging data space to search characterized by non- numerical, temporal, descriptive data, e.g., Person A walks up to Person B at time T. This dissertation will present an approach that allows one to interactively search, identify, and discover temporal behavior patterns within such a data space. Therefore, this research addresses supporting exploration and discovery in behavior analysis through a formalized method of assisted exploration. The model evolution presented sup- ports the refining of the observer\'s behavior models into representations of their understanding. The benefit of the new approach is shown through experimentation on its identification accuracy and working with fellow researchers to verify the approach\'s legitimacy in analysis of their data. / Ph. D.

Konzeptuelle Modelle sind zur Gestaltung und Steuerung von Informationssystemen ein akzeptiertes und weit verbreitetes Instrument. Sie werden sowohl zur Gestaltung der Organisationsstruktur als auch zur Entwicklung der unterstützenden IT-Systeme verwendet. Für diesen Aufgabenbereich existiert eine hohe Nachfrage nach externer Unterstützung, da spezifische Fachkenntnisse und Erfahrungen notwendig sind. In diesem Zusammenhang werden seit Jahrzehnten Ansätze zur Wiederverwendung in Wissenschaft und Praxis diskutiert. Die Akzeptanz und Verbreitung von explizit zur Wiederverwendung konstruierten Modellen (Referenzmodelle) bleiben jedoch deutlich hinter den Erwartungen zurück. Die vorliegende Arbeit trägt zur Untersuchung möglicher Ursachen für den ausbleibenden Erfolg von Referenzmodellen bei. Der Forschung liegt die Vermutung zugrunde, dass die Potentiale von Referenzmodellen nicht zufriedenstellend ausgeschöpft werden können, weil die existierenden bzw. verwendeten Modellierungsmethoden die theoretischen Anforderungen an die Wiederverwendung von modellhaft dargestellten Lösungen zur Unternehmensgestaltung nicht erfüllen. Die vorliegende Arbeit fasst neun Einzelpublikationen zum Themenbereich Evolutionäre Referenzmodelle zu einer kumulativen Dissertation zusammen. Es werden in einem argumentativdeduktiven Verfahren konstruktivistische Theorien zur systematischen Weiterentwicklung und Wiederverwendung konzeptueller Unternehmensmodelle untersucht. Die auf dieseWeise resultierende Erweiterung der allgemeinen Modelltheorie wurde ihrerseits argumentativ-konzeptionell mit Hilfe von semiformalen Argumentationsmodellen aufbereitet. Im Ergebnis werden ein theoretisches Rahmenwerk zur evolutionären Referenzmodellierung präsentiert und 23 konzeptionelle Anforderungen definiert, die eine gezielte Methodenentwicklung für die evolutionäre Referenzmodellierung steuern sollen.

Submitted by Renato Lago Pereira Chaves (renatochaves.jazz@gmail.com) on 2016-12-07T12:00:08Z No. of bitstreams: 1 Dissertação versão final - completa.pdf: 944839 bytes, checksum: 8b600dfc73c30bb2aa4684d3725ced47 (MD5) / Approved for entry into archive by Janete de Oliveira Feitosa (janete.feitosa@fgv.br) on 2016-12-07T19:18:46Z (GMT) No. of bitstreams: 1 Dissertação versão final - completa.pdf: 944839 bytes, checksum: 8b600dfc73c30bb2aa4684d3725ced47 (MD5) / Made available in DSpace on 2016-12-20T16:02:44Z (GMT). No. of bitstreams: 1 Dissertação versão final - completa.pdf: 944839 bytes, checksum: 8b600dfc73c30bb2aa4684d3725ced47 (MD5) Previous issue date: 2016-10-31 / The impacts of the so-called craft beer revolution reached Brazilian beer industry in the first years of this century. As a result, a group of new entrepreneurs emerged in the country, who argue that they are restoring beer to its rightful status, not only as a local business but also as a product that may bring a specific regional personality. The recent evolution of the craft beer segment is paving the way to the development of different forms of organizing, such as contract brewing, designed for companies which do not own physical brewing facilities. Although most companies still understand contract brewing as a transitional business model, it did change into a permanent form of organizing. Limited to contract breweries from the Rio de Janeiro metropolitan area, this research attempts to assess how contract breweries changed from a temporary, transitional business model into a permanent form of organizing. Furthermore, in view of some distinctive features observed in the models adopted by contract breweries, which may differ from each other considerably with regard to their temporariness and the ability to survive in the long term, I propose a typology of contract breweries. / Os impactos da chamada revolução da cerveja artesanal chegaram à indústria de cerveja brasileira nos primeiros anos deste século. Por conseguinte, um grupo de novos empreendedores surgiu no país, segundo os quais eles estariam retornando a cerveja a seu devido lugar, não apenas como um negócio local, mas também como um produto que pode conferir uma personalidade regional específica. A recente evolução do segmento de cerveja artesanal está abrindo caminho para o desenvolvimento de diferentes formas de se organizar, tais como produção por contrato, modelo desenhado para empresas que não dispõem de instalações fabris próprias. Embora a maior parte das empresas ainda perceba produção por contrato como um modelo de negócio de transição, este modelo evoluiu até tornar-se uma forma permanente de organização. Limitada a cervejarias por contrato da região metropolitana do Rio de Janeiro, esta pesquisa busca analisar como as cervejarias por contrato evoluíram de um modelo de negócio temporário e de transição para uma forma permanente de organização. Ademais, haja vista algumas características específicas observadas nos modelos de negócio adotados pelas cervejarias por contrato, que podem diferir consideravelmente uma das outras no que concerne a sua temporariedade e capacidade de sobreviver a longo prazo, uma tipologia de cervejarias por contrato é proposta.

Le système PLM est l’un des outils stratégiques de l’entreprise. Ces systèmes sont sujets à des changements récurrents dans l’entreprise. Les évolutions organisationnelles, le changement de l’offre produit ou encore le remplacement de logiciels PLM peuvent déclencher l’évolution du système d’information PLM. Une des structures les plus importantes dans les systèmes PLM est le modèle du produit, autour duquel s’articule les informations et processus. C’est autour du modèle produit que se concentrent nos recherches. Les causes d’évolution des modèles produits sont des éléments signifiants qui différencient les étapes de la démarche à suivre. Les méthodes d’IDM sont utilisées afin de formaliser la transformation des modèles. En plus, cette démarche bénéfice d’un cadre de similarité spécialement développé pour la configuration de produit. Un exemple industriel est illustré et résolu en appliquant cette démarche. Il s’agit de l’évolution d’un système gérant les modèles spécifiques de produit vers un système qui est capable de construire et d’utiliser les modèles génériques de produit. Un outil informatique support à nos travaux est développé dans le cadre d'Eclipse. / PLM systems are among the strategic components of enterprise’s information system architecture. These systems undergo frequent evolutions of enterprise. Organizational evolution or product offer variation as well as PLM application replacement may launch PLM systems’ evolution.One of the important structures in PLM systems is the product configuration, which organize and structure all product’s information and processes. Our research activities concern product model evolution. Reasons of product model evolution specify the appropriate methodology and necessary steps in order to handle it. MDE methods are used to formalize the model transformation process.Moreover, our methodology contains a specific similarity framework dedicated to product configuration. An industrial example was illustrated and resolved by this methodology. The problematic of this example is the migration of a system which manage only specific product configuration to a new system that is capable to construct and use generic models of product.

Konzeptuelle Modelle sind zur Gestaltung und Steuerung von Informationssystemen ein akzeptiertes und weit verbreitetes Instrument. Sie werden sowohl zur Gestaltung der Organisationsstruktur als auch zur Entwicklung der unterstützenden IT-Systeme verwendet. Für diesen Aufgabenbereich existiert eine hohe Nachfrage nach externer Unterstützung, da spezifische Fachkenntnisse und Erfahrungen notwendig sind. In diesem Zusammenhang werden seit Jahrzehnten Ansätze zur Wiederverwendung in Wissenschaft und Praxis diskutiert. Die Akzeptanz und Verbreitung von explizit zur Wiederverwendung konstruierten Modellen (Referenzmodelle) bleiben jedoch deutlich hinter den Erwartungen zurück. Die vorliegende Arbeit trägt zur Untersuchung möglicher Ursachen für den ausbleibenden Erfolg von Referenzmodellen bei. Der Forschung liegt die Vermutung zugrunde, dass die Potentiale von Referenzmodellen nicht zufriedenstellend ausgeschöpft werden können, weil die existierenden bzw. verwendeten Modellierungsmethoden die theoretischen Anforderungen an die Wiederverwendung von modellhaft dargestellten Lösungen zur Unternehmensgestaltung nicht erfüllen. Die vorliegende Arbeit fasst neun Einzelpublikationen zum Themenbereich Evolutionäre Referenzmodelle zu einer kumulativen Dissertation zusammen. Es werden in einem argumentativdeduktiven Verfahren konstruktivistische Theorien zur systematischen Weiterentwicklung und Wiederverwendung konzeptueller Unternehmensmodelle untersucht. Die auf dieseWeise resultierende Erweiterung der allgemeinen Modelltheorie wurde ihrerseits argumentativ-konzeptionell mit Hilfe von semiformalen Argumentationsmodellen aufbereitet. Im Ergebnis werden ein theoretisches Rahmenwerk zur evolutionären Referenzmodellierung präsentiert und 23 konzeptionelle Anforderungen definiert, die eine gezielte Methodenentwicklung für die evolutionäre Referenzmodellierung steuern sollen.

[EN] Renewing software systems is one of the most cost-effective ways to protect software investment, which saves time, money and ensures uninterrupted access to technical support and product upgrades. There are several motivations to promote investment and scientific effort for specifying systems by means of conceptual models and supporting its evolution. In order to contribute to the requirements engineering field with automated software production methods, we design TraceME to cover the spectrum of activities from requirements to code focusing on organisational evolution. In this sense, the spectrum of activities involves various information system perspectives of analysis that need to be integrated. In this complex setting, traceability and conceptual models are key concepts. Mechanisms to trace software specifications from requirements to code are important to justify evolution processes; versions of information systems should be traced in order to get the connection between old and new specifications. Moreover, it is necessary to find mechanisms to facilitate change specifications, measurement, and interpretation. To design this thesis we follow Design Science by Roel Wieringa. Design Science gives us the hints on how to conduct the research, be rigorous, and put in practice scientific rules. Besides Design Science has been a key factor for structuring our research, we acknowledge the application of this framework since it has helps us to report clearly our findings. We build TraceME by making a method engineering effort, which shapes its fragmented nature in chunks. The architecture of TraceME opens a wide window of opportunities for its application in real world situations. To facilitate industrial adoption, we develop open source tools to support the implementation of the TraceME chunks. For example, one case study and one action-research protocols have been executed in two different organisations in Spain. The validation of TraceME has taken place in laboratory demonstrations, controlled experiments, action research and case study experiences in industry. Thanks to the validations various lessons learnt have been gathered and greatly influenced the maturity of the method. For example: the importance to consider end-users' perceptions for discovering needs to mitigate, and the significance to get knowledge from the application of TraceME in different contexts. The evidences from the validations demonstrate that TraceME is feasible to be applied to support evolution projects. In addition, future research is needed for promoting the implementation of TraceME. We envision short term and future-term work that motivate us to tackle the challenge to support evolution projects. / [ES] La evolución de sistemas software es una de las actividades mas importantes que permiten minimizar el tiempo de puesta en producción de actualizaciones y nuevos desarrollos, reducir los costos que implica desarrollar una aplicación desde cero, y además asegura el acceso ininterrumpido de servicios. Existen variadas motivaciones para promover la investigación y desarrollo de soluciones para especificar y evolucionar sistemas de información mediante modelos conceptuales. Para contribuir al campo de la ingeniería de requisitos con métodos automáticos de producción de software, hemos diseñado el método TraceME para cubrir el espectro de actividades desde requisitos a código con un enfoque de evolución organizacional. De este modo, el espectro de actividades involucra diferentes perspectivas de análisis de sistemas de información que necesitan ser integradas. En este escenario tan complejo, la trazabilidad y los modelos conceptuales son conceptos clave. Es necesario disponer de mecanismos para trazar especificaciones de software desde requisitos a código con el fin de justificar procesos de evolución. Las versiones de los sistemas de información deben ser trazables con el fin de establecer la conexión entre especificaciones obsoletas y actuales. Adicionalmente, es necesario encontrar mecanismos para facilitar la especificación del cambio, su medición e interpretación. Para diseñar esta tesis hemos seguido el marco de Design Science de Roel Wieringa. Design Science nos ha proporcionado las claves para conducir esta investigación, ser rigurosos y poner en práctica reglas científicas. Además de que Design Science ha sido un factor clave para estructurar nuestra investigación, reconocemos que la aplicación de este marco nos ha ayudado a reportar claramente nuestros hallazgos. Hemos aplicado ingeniería de métodos para diseñar y construir TraceME. Gracias a esto, la naturaleza de TraceME es conformada mediante fragmentos de método. La arquitectura de TraceME abre una amplia ventana de oportunidades para su aplicación en situaciones de la vida real. Para facilitar la adopción industrial de TraceME, hemos desarrollado herramientas de software libre para dar soporte a los fragmentos de TraceME. Por ejemplo, un caso de estudio y una experiencia de action research han sido ejecutadas en dos organizaciones en España. La validación de TraceME ha sido llevada a cabo mediante demostraciones de laboratorio, experimentos controlados, un caso de estudio y una experiencia de action research en industria. Como resultado, TraceME ha sido mejorado considerablemente; además hemos descubierto investigaciones a realizar a corto, mediano y largo plazo con el fin de implementar TraceME en la industria. Las evidencias obtenidas como resultado de las validaciones demuestra la factibilidad de TraceME para ser aplicado en proyectos de evolución organizacional. El trabajo futuro nos motiva a afrontar los retos que conlleva el soporte de proyectos de evolución de sistemas de información. / [CAT] L'evolució dels sistemes programari és una de les activitats més importants que permeten minimitzar el temps de posada en producció d'actualitzacions i nous desenvolupaments, reduir els costos que involucra desenvolupar una aplicació des de cero, a més d' assegurar l'accés ininterromput de serveis. Existixen diverses motivacions per promoure la investigació i desenvolupament de solucions per a especificar i evolucionar sistemes de informació mitjançant models conceptuals. Per tal de contribuir al camp de l'enginyeria de requisits amb mètodes automàtics de producció de programari, hem dissenyat el mètode TraceME per cobrir l'espectre d'activitats des de requisits a codi en un enfocament d'evolució organitzacional. Així, l'espectre d'activitats involucra diferents perspectives d'anàlisi de sistemes d'informació que necessiten ser integrades. En aquest escenari tan complex, la traçabilitat i els models conceptuals són conceptes clau. És necessari disposar de mecanismes per traçar especificacions de programari des de requisits a codi amb la fi de justificar processos d'evolució. Les versions dels sistemes d'informació deuen ser traçables amb la fi d'establir la connexió entre especificacions obsoletes i actuals. Addicionalment, és necessari trobar mecanismes per facilitar l'especificació del canvi, la seua mesura i interpretació. Per tal de dissenyar aquesta tesi, hem seguit el marc de Design Science de Roel Wieringa. Design Science ens ha proporcionat les claus per conduir aquesta investigació, ser rigorosos i posar en pràctica regles científiques. A més a més, Design Science ha sigut un factor clau per estructurar la nostra investigació, reconeixem que l'aplicació de aquest marc ens a ajudat a reportar clarament els nostres resultats. Hem aplicat enginyeria de mètodes per dissenyar i construir TraceME. Gràcies a açò, la natura de TraceME es conforma mitjançant fragments de mètodes. L'arquitectura de TraceME obri una ampla finestra d'oportunitats per a la seua aplicació en situacions de la vida real. Per facilitar l'adopció industrial de TraceME, hem desenvolupat ferramentes de programari lliure per tal de donar suport als fragments de TraceME. Per exemple, un cas d'estudi i una experiència de action research han sigut executades en dos organitzacions a Espanya. La validació de TraceME ha sigut portada a cap mitjançant demostracions de laboratori, experiments controlats , un cas d'estudi i una experiència de action research en l'industria. Com a resultat, TraceME ha sigut millorada considerablement; a més a més, hem descobert investigacions a realitzar a curt, mig i llarg termini amb la fi d'implementar TraceME a l'industria. Les evidències obtingudes com a resultat de les validacions, demostren la factibilitat de TraceME per ser aplicat en projectes d'evolució organitzacional. El treball futur presenta nous reptes que ens motiven a afrontar el suport de projectes d'evolució de sistemes d'informació. / Ruiz Carmona, LM. (2016). TraceME: Traceability-based Method for Conceptual Model Evolution [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/64553 / TESIS