Simulation of stromatolite growth using diffusion-limited aggregation and a discrete model of biogeochemical exchanges in microbial mat

Resume : Mieux comprendre les stromatolithes et les tapis microbiens est un sujet important en biogéosciences puisque cela aide à l'étude des premières formes de vie sur Terre, a mieux cerner l'écologie des communautés microbiennes et la contribution des microorganismes a la biominéralisation, et même à poser certains fondements dans les recherches en exobiologie. D'autre part, la modélisation est un outil puissant utilisé dans les sciences naturelles pour appréhender différents phénomènes de façon théorique. Les modèles sont généralement construits sur un système d'équations différentielles et les résultats sont obtenus en résolvant ce système. Les logiciels disponibles pour implémenter les modèles incluent les logiciels mathématiques et les logiciels généraux de simulation. L'objectif principal de cette thèse est de développer des modèles et des logiciels pour aider a comprendre, via la simulation, le fonctionnement des stromatolithes et des tapis microbiens. Ces logiciels ont été développés en C++ en ne partant d'aucun pré-requis de façon a privilégier performance et flexibilité maximales. Cette démarche permet de construire des modèles bien plus spécifiques et plus appropriés aux phénomènes a modéliser. Premièrement, nous avons étudié la croissance et la morphologie des stromatolithes. Nous avons construit un modèle tridimensionnel fondé sur l'agrégation par diffusion limitée. Le modèle a été implémenté en deux applications C++: un moteur de simulation capable d'exécuter un batch de simulations et de produire des fichiers de résultats, et un outil de visualisation qui permet d'analyser les résultats en trois dimensions. Après avoir vérifié que ce modèle peut en effet reproduire la croissance et la morphologie de plusieurs types de stromatolithes, nous avons introduit un processus de sédimentation comme facteur externe. Ceci nous a mené a des résultats intéressants, et permis de soutenir l'hypothèse que la morphologie des stromatolithes pourrait être le résultat de facteurs externes autant que de facteurs internes. Ceci est important car la classification des stromatolithes est généralement fondée sur leur morphologie, imposant que la forme d'un stromatolithe est dépendante de facteurs internes uniquement (c'est-à-dire les tapis microbiens). Les résultats avancés dans ce mémoire contredisent donc ces assertions communément admises. Ensuite, nous avons décidé de mener des recherches plus en profondeur sur les aspects fonctionnels des tapis microbiens. Nous avons construit un modèle bidimensionnel de réaction-diffusion fondé sur la simulation discrète. Ce modèle a été implémenté dans une application C++ qui permet de paramétrer et exécuter des simulations. Nous avons ensuite pu comparer les résultats de simulation avec des données du monde réel et vérifier que le modèle peut en effet imiter le comportement de certains tapis microbiens. Ainsi, nous avons pu émettre et vérifier des hypothèses sur le fonctionnement de certains tapis microbiens pour nous aider à mieux en comprendre certains aspects, comme la dynamique des éléments, en particulier le soufre et l'oxygène. En conclusion, ce travail a abouti à l'écriture de logiciels dédiés à la simulation de tapis microbiens d'un point de vue tant morphologique que fonctionnel, suivant deux approches différentes, l'une holistique, l'autre plus analytique. Ces logiciels sont gratuits et diffusés sous licence GPL (General Public License). Abstract : Better understanding of stromatolites and microbial mats is an important topic in biogeosciences as it helps studying the early forms of life on Earth, provides clues re- garding the ecology of microbial ecosystems and their contribution to biomineralization, and gives basis to a new science, exobiology. On the other hand, modelling is a powerful tool used in natural sciences for the theoretical approach of various phenomena. Models are usually built on a system of differential equations and results are obtained by solving that system. Available software to implement models includes mathematical solvers and general simulation software. The main objective of this thesis is to develop models and software able to help to understand the functioning of stromatolites and microbial mats. Software was developed in C++ from scratch for maximum performance and flexibility. This allows to build models much more specific to a phenomenon rather than general software. First, we studied stromatolite growth and morphology. We built a three-dimensional model based on diffusion-limited aggregation. The model was implemented in two C++ applications: a simulator engine, which can run a batch of simulations and produce result files, and a Visualization tool, which allows results to be analysed in three dimensions. After verifying that our model can indeed reproduce the growth and morphology of several types of stromatolites, we introduced a sedimentation process as an external factor. This lead to interesting results, and allowed to emit the hypothesis that stromatolite morphology may be the result of external factors as much as internal factors. This is important as stromatolite classification is usually based on their morphology, imposing that a stromatolite shape is dependant on internal factors only (i.e. the microbial mat). This statement is contradicted by our findings, Second, we decided to investigate deeper the functioning of microbial mats, We built a two-dimensional reaction-diffusion model based on discrete simulation, The model was implemented in a C++ application that allows setting and running simulations. We could then compare simulation results with real world data and verify that our model can indeed mimic the behaviour of some microbial mats. Thus, we have proposed and verified hypotheses regarding microbial mats functioning in order to help to better understand them, e.g. the cycle of some elements such as oxygen or sulfur. ln conclusion, this PhD provides a simulation software, dealing with two different approaches. This software is free and available under a GPL licence.

Enabling Java Connected Device Configuration in Symbian OS

Diplomityön tavoitteena on kehittää Java CDC ajoympäristo Symbian OS käyttöjärjestelmällä varustettuun mobiililaitteeseen. Ajoympäristön tarkoituksena on mahdollistaa kehittyneiden ajoympäristöjen ja sovellusten kehittäminen mobiililaitteiden Java ohjelmistoalustoihin. Diplomityö tarkastelee kahta mobiiliympäristöa, jotka ovat käytössä erittäin laajasti matkapuhelimissa ja kämmenmikroissa: Symbian OS ja Java. Symbian OS on mobiililaitteille tarkoitettu käyttöjärjestelmä, joka on tässä työssä alustana Java ajoympäristölle. Käytännön osuus kuvailee, kuinka CDC ajoympäristö voidaan toteuttaa mobiilissa Symbian OS ympäristössä. Työssä esitellään myös teknologioita, joita CDC ajoympäristön luomalle perustalle voidaan toteuttaa. Mobiililaitteiden ominaisuudet ovat kehittyneet huomattavasti sen jälkeen kun ensimmäiset CLDC ja MIDP Javaa tukevat laitteet tulivat markkinoille. Nykyisin matkapuhelimet ja kämmenmikrot alkavat muistuttaa ominaisuuksiltaan entistä enemmän tavallisia tietokoneita. Myös mobiililaitteiden Java ohjelmistoalustat tarvitsevat uusia teknologioita kasvaneiden vaatimusten tyydyttämiseksi.

Statistical modelling of CSP solving algorithms performance

The goal of this work is to try to create a statistical model, based only on easily computable parameters from the CSP problem to predict runtime behaviour of the solving algorithms, and let us choose the best algorithm to solve the problem. Although it seems that the obvious choice should be MAC, experimental results obtained so far show, that with big numbers of variables, other algorithms perfom much better, specially for hard problems in the transition phase.

Optimizing Mobile Java Location-Based Services in Symbian OS

This thesis evaluates methods for obtaining high performance in applications running on the mobile Java platform. Based on the evaluated methods, an optimization was done to a Java extension API running on top the Symbian operating system. The API provides location-based services for mobile Java applications. As a part of this thesis, the JNI implementation in Symbian OS was also benchmarked. A benchmarking tool was implemented in the analysis phase in order to implement extensive performance test set. Based on the benchmark results, it was noted that the landmarks implementation of the API was performing very slowly with large amounts of data. The existing implementation proved to be very inconvenient for optimization because the early implementers did not take performance and design issues into consideration. A completely new architecture was implemented for the API in order to provide scalable landmark initialization and data extraction by using lazy initialization methods. Additionally, runtime memory consumption was also an important part of the optimization. The improvement proved to be very efficient based on the measurements after the optimization. Most of the common API use cases performed extremely well compared to the old implementation. Performance optimization is an important quality attribute of any piece of software especially in embedded mobile devices. Typically, projects get into trouble with performance because there are no clear performance targets and knowledge how to achieve them. Well-known guidelines and performance models help to achieve good overall performance in Java applications and programming interfaces.

La Incidencia de las nuevas tecnologías en los hábitos formativos de los estudiantes de magisterio = The Impact of new technologies in the learning habits of teacher students

Este trabajo persigue dos objetivos: el primero es analizar el uso de las TIC en un grupo de estudiantes de segundo curso de Magisterio de la Universidad de Girona; el segundo es analizar los documentos normativos legales que establecen el currículum de educación primaria en Cataluña para observar qué tipo de papel juegan las TIC en las nuevas programaciones educativas. La primera parte se ha llevado a cabo mediante una encuesta, cuyos resultados permiten observar tres aspectos distintos: el primero, que una parte considerable del grupo considera las TIC más como un complemento para el aprendizaje que como una forma de aprendizaje; el segundo, que a pesar de hacer un uso considerable de las TIC, el conocimiento que tienen de ellas es muy básico y utilizan aplicaciones muy genéricas; y el tercero es que una parte de sus propuestas didácticas para el uso de las TIC son propuestas tradicionales simplemente adaptadas a un nuevo instrumento, sin buscar realmente la innovación que puede suponer la incorporación de las TIC. En la segunda parte del artículo, a partir del análisis e interpretación de los documentos legales que establecen el currículum de Educación Primaria, se observa que en un mismo documento conviven aserciones sobre las TIC como complemento al aprendizaje de contenidos con otras formulaciones que consideran las TIC como constructoras de conocimiento. A partir del perfil de los estudiantes y del estado de los documentos legales, al final del artículo se hacen propuestas para formar al futuro maestro teniendo en cuenta las TIC como herramientas básicas de conocimiento

Adaptive optimization schemes for mobile VoIP applications Battery life and call quality aspects

In this thesis programmatic, application-layer means for better energy-efficiency in the VoIP application domain are studied. The work presented concentrates on optimizations which are suitable for VoIP-implementations utilizing SIP and IEEE 802.11 technologies. Energy-saving optimizations can have an impact on perceived call quality, and thus energy-saving means are studied together with those factors affecting perceived call quality. In this thesis a general view on a topic is given. Based on theory, adaptive optimization schemes for dynamic controlling of application's operation are proposed. A runtime quality model, capable of being integrated into optimization schemes, is developed for VoIP call quality estimation. Based on proposed optimization schemes, some power consumption measurements are done to find out achievable advantages. Measurement results show that a reduction in power consumption is possible to achieve with the help of adaptive optimization schemes.

Escrita científica de alunos de graduação em química: análise de relatórios de laboratório

The purpose of this study was to analyze written arguments found within laboratory reports by undergraduate students in a practical inorganic chemistry course. The quality of students' argumentation was analyzed based on the argumentation model developed by Kelly and Takao. Students presented scientific arguments grounded in data and building toward theoretical assertions. This indicates that students have some understanding of the rhetorical power of data in their explanations. The findings of this study also support the idea that Kelly and Takao's model is effective in other disciplines and in other rhetorical tasks distinct from those originally analyzed by them in their domain of oceanography.

QSAR modeling: um novo pacote computacional open source para gerar e validar modelos QSAR

QSAR modeling is a novel computer program developed to generate and validate QSAR or QSPR (quantitative structure- activity or property relationships) models. With QSAR modeling, users can build partial least squares (PLS) regression models, perform variable selection with the ordered predictors selection (OPS) algorithm, and validate models by using y-randomization and leave-N-out cross validation. An additional new feature is outlier detection carried out by simultaneous comparison of sample leverage with the respective Studentized residuals. The program was developed using Java version 6, and runs on any operating system that supports Java Runtime Environment version 6. The use of the program is illustrated. This program is available for download at lqta.iqm.unicamp.br.

Hume, liberty and the object of moral evaluation

Hume's project concerning the conflict between liberty and necessity is ";reconciliatory";. But what is the nature of Hume's project? Does he solve a problem in metaphysics only? And when Hume says that the dispute between the doctrines of liberty and necessity is merely verbal, does he mean that there is no genuine metaphysical dispute between the doctrines? In the present essay I argue for: (1) there is room for liberty in Hume's philosophy, and not only because the position is pro forma compatibilist, even though this has importance for the recognition that Hume's main concern when discussing the matter is with practice; (2) the position does not involve a ";subjectivization"; of every form of necessity: it is not compatibilist because it creates a space for the claim that the operations of the will are non-problematically necessary through a weakning of the notion of necessity as it applies to external objects; (3) Hume holds that the ordinary phenomena of mental causation do not preempt the atribuition of moral responsibility, which combines perfectly with his identification of the object of moral evaluation: the whole of the character of a person, in relation to which there is, nonetheless, liberty. I intend to support my assertions by a close reading of what Hume states in section 8 of the first Enquiry.

The relativity of evaluative sentences: disagreeing over disagreement

Evaluative sentences (moral judgments, expressions of taste, epistemic modals) are relative to the speaker's standards. Lately, a phenomenon has challenged the traditional explanation of this relativity: whenever two speakers disagree over them they contradict each other without being at fault. Hence, it is thought that the correction of the assertions involved must be relative to an unprivileged standard not necessarily the speaker's. I will claim instead that so far, neither this nor any other proposal has provided an explanation of the phenomenon. I will point out several problems presented by them and I will hint to how this phenomenon could be explained by making minor adjustments to our semantic theory.

Evaluation of an indicator for water yield in a watershed of Alto Rio Grande Region, State of Minas Gerais , Brazil

The Brazilian Law stipulates that water is a limited natural resource doted of economic value, thus it is necessary to develop mechanisms for its adequate management. Actions that encourage the farmers to apply soil conservation practices with the purpose of increase water yield from springs and to promote improvement of its quality, reducing production of sediment transportation, is being encouraged by governments, even with financial compensation for owners. From these assertions, this study aims to quantify the benefits of the conservation actions of the management units and to characterize a Water Yield Indicator (WYI) to support sustainable actions in the watershed of Alto Rio Grande region, in the state of Minas Gerais (MG). To assess the impact of actions it were identified four scenarios of land use and occupation of the watershed from Marcela stream which is located in Alto Rio Grande Region. After analyzing the results, it can be stated that the scenarios simulation has demonstrated important changes in water yield and that the definition of the Water Yield Index from the junction of the erosion potential with the water storage potential, has proved effective, as it integrate quantity and quality of water.

Trustworthy context dependency in ubiquitous systems

The modern society is getting increasingly dependent on software applications. These run on processors, use memory and account for controlling functionalities that are often taken for granted. Typically, applications adjust the functionality in response to a certain context that is provided or derived from the informal environment with various qualities. To rigorously model the dependence of an application on a context, the details of the context are abstracted and the environment is assumed stable and fixed. However, in a context-aware ubiquitous computing environment populated by autonomous agents, a context and its quality parameters may change at any time. This raises the need to derive the current context and its qualities at runtime. It also implies that a context is never certain and may be subjective, issues captured by the context’s quality parameter of experience-based trustworthiness. Given this, the research question of this thesis is: In what logical topology and by what means may context provided by autonomous agents be derived and formally modelled to serve the context-awareness requirements of an application? This research question also stipulates that the context derivation needs to incorporate the quality of the context. In this thesis, we focus on the quality of context parameter of trustworthiness based on experiences having a level of certainty and referral experiences, thus making trustworthiness reputation based. Hence, in this thesis we seek a basis on which to reason and analyse the inherently inaccurate context derived by autonomous agents populating a ubiquitous computing environment in order to formally model context-awareness. More specifically, the contribution of this thesis is threefold: (i) we propose a logical topology of context derivation and a method of calculating its trustworthiness, (ii) we provide a general model for storing experiences and (iii) we formalise the dependence between the logical topology of context derivation and its experience-based trustworthiness. These contributions enable abstraction of a context and its quality parameters to a Boolean decision at runtime that may be formally reasoned with. We employ the Action Systems framework for modelling this. The thesis is a compendium of the author’s scientific papers, which are republished in Part II. Part I introduces the field of research by providing the mending elements for the thesis to be a coherent introduction for addressing the research question. In Part I we also review a significant body of related literature in order to better illustrate our contributions to the research field.

Reusable formal architectures for networked systems

Today's networked systems are becoming increasingly complex and diverse. The current simulation and runtime verification techniques do not provide support for developing such systems efficiently; moreover, the reliability of the simulated/verified systems is not thoroughly ensured. To address these challenges, the use of formal techniques to reason about network system development is growing, while at the same time, the mathematical background necessary for using formal techniques is a barrier for network designers to efficiently employ them. Thus, these techniques are not vastly used for developing networked systems. The objective of this thesis is to propose formal approaches for the development of reliable networked systems, by taking efficiency into account. With respect to reliability, we propose the architectural development of correct-by-construction networked system models. With respect to efficiency, we propose reusable network architectures as well as network development. At the core of our development methodology, we employ the abstraction and refinement techniques for the development and analysis of networked systems. We evaluate our proposal by employing the proposed architectures to a pervasive class of dynamic networks, i.e., wireless sensor network architectures as well as to a pervasive class of static networks, i.e., network-on-chip architectures. The ultimate goal of our research is to put forward the idea of building libraries of pre-proved rules for the efficient modelling, development, and analysis of networked systems. We take into account both qualitative and quantitative analysis of networks via varied formal tool support, using a theorem prover the Rodin platform and a statistical model checker the SMC-Uppaal.

Migrating legacy applications to cloud: case TOAS

Cloud computing, despite its success and promises, presents issues for businesses mi­grating their legacy applications to cloud. In this research legacy-to-cloud migration issues are reviewed based on literature findings and an experience report. Solutions are applied to Tieto Open Application Suite (TOAS) software development platform running on cloud infrastructure. It is observed that the migration strategy heavily affects the migration approach. For TOAS a strategy of redesigning the applications for cloud is suggested. Common migration-driven application level modifications in­clude adaptation to service-oriented architecture, load balancing, and runtime and technology changes. A cloud platform such as TOAS might introduce additional needs. Decision making on migration strategy is found to be an issue to be solved case by case. Use of assistive decision making tools is suggested.

Design and validation of stateful composite RESTful web services

A web service is a software system that provides a machine-processable interface to the other machines over the network using different Internet protocols. They are being increasingly used in the industry in order to automate different tasks and offer services to a wider audience. The REST architectural style aims at producing scalable and extensible web services using technologies that play well with the existing tools and infrastructure of the web. It provides a uniform set of operation that can be used to invoke a CRUD interface (create, retrieve, update and delete) of a web service. The stateless behavior of the service interface requires that every request to a resource is independent of the previous ones facilitating scalability. Automated systems, e.g., hotel reservation systems, provide advanced scenarios for stateful services that require a certain sequence of requests that must be followed in order to fulfill the service goals. Designing and developing such services for advanced scenarios with REST constraints require rigorous approaches that are capable of creating web services that can be trusted for their behavior. Systems that can be trusted for their behavior can be termed as dependable systems. This thesis presents an integrated design, analysis and validation approach that facilitates the service developer to create dependable and stateful REST web services. The main contribution of this thesis is that we provide a novel model-driven methodology to design behavioral REST web service interfaces and their compositions. The behavioral interfaces provide information on what methods can be invoked on a service and the pre- and post-conditions of these methods. The methodology uses Unified Modeling Language (UML), as the modeling language, which has a wide user base and has mature tools that are continuously evolving. We have used UML class diagram and UML state machine diagram with additional design constraints to provide resource and behavioral models, respectively, for designing REST web service interfaces. These service design models serve as a specification document and the information presented in them have manifold applications. The service design models also contain information about the time and domain requirements of the service that can help in requirement traceability which is an important part of our approach. Requirement traceability helps in capturing faults in the design models and other elements of software development environment by tracing back and forth the unfulfilled requirements of the service. The information about service actors is also included in the design models which is required for authenticating the service requests by authorized actors since not all types of users have access to all the resources. In addition, following our design approach, the service developer can ensure that the designed web service interfaces will be REST compliant. The second contribution of this thesis is consistency analysis of the behavioral REST interfaces. To overcome the inconsistency problem and design errors in our service models, we have used semantic technologies. The REST interfaces are represented in web ontology language, OWL2, that can be part of the semantic web. These interfaces are used with OWL 2 reasoners to check unsatisfiable concepts which result in implementations that fail. This work is fully automated thanks to the implemented translation tool and the existing OWL 2 reasoners. The third contribution of this thesis is the verification and validation of REST web services. We have used model checking techniques with UPPAAL model checker for this purpose. The timed automata of UML based service design models are generated with our transformation tool that are verified for their basic characteristics like deadlock freedom, liveness, reachability and safety. The implementation of a web service is tested using a black-box testing approach. Test cases are generated from the UPPAAL timed automata and using the online testing tool, UPPAAL TRON, the service implementation is validated at runtime against its specifications. Requirement traceability is also addressed in our validation approach with which we can see what service goals are met and trace back the unfulfilled service goals to detect the faults in the design models. A final contribution of the thesis is an implementation of behavioral REST interfaces and service monitors from the service design models. The partial code generation tool creates code skeletons of REST web services with method pre and post-conditions. The preconditions of methods constrain the user to invoke the stateful REST service under the right conditions and the post condition constraint the service developer to implement the right functionality. The details of the methods can be manually inserted by the developer as required. We do not target complete automation because we focus only on the interface aspects of the web service. The applicability of the approach is demonstrated with a pedagogical example of a hotel room booking service and a relatively complex worked example of holiday booking service taken from the industrial context. The former example presents a simple explanation of the approach and the later worked example shows how stateful and timed web services offering complex scenarios and involving other web services can be constructed using our approach.