Open channel confluences are common geographical structures in surface runoff. Most natural rivers originate from mountains and hills, flow into a main stream at confluences and finally head into the sea. Confluences are major sites for a main stream to obtain sediment and water from a tributary. Complex turbulence structures such as vortices, flow stagnation, secondary flow, flow re-circulation and water exchange both in vertical and lateral directions result in complicated sedimentation, erosion, mixing and contaminant transport at open channel confluences. The detailed study of flow dynamics and morphodynamics in confluences is of great significance to the urban flood control, scour of the river bed, design and maintenance of the channel and sediment and pollutants transport. This thesis describes a novel flume experiment on the sediment transport patterns in channel confluences as a function of different flow and geometry conditions. The initial equilibrium bed geometry was developed in a mobile bed confluence flume under four cases including two junction angles and two discharge ratios. The equilibrium bed was fixed for each case allowing for detailed flow velocimetry. The observed spatial patterns of turbulence statistics are evaluated with respect to the equilibrium bathymetry. Sediment were then fed instantaneously to the tributary channel at three different feeding sites in order to study the sediment deposition patterns. It was observed that although the sediment initiated at different feeding sites move along different paths through the confluence, all sediment tend to deposit at the face of the dune in the flow separation zone. This thesis also investigated how the deposition pattern would change versus time when feeding at the same site from the tributary channel. The time history of deposition pattern was also investigated for one of the cases. The sediment that initially deposit at the face of the dune eventually moved to the back of the dune and deposit around the post-confluence scour hole, demonstrating that over time the deposition pattern evolves to a state which is similar with the original bed morphology.

Cette thèse étudie la confluence des systèmes de récriture en l'absence de propriété de terminaison, pour des applications aux langages fonctionnels de premier ordre comme MAUDE, ou aux langages d'ordre supérieur comportant des types dépendants, comme Dedukti. Dans le premier cas, les calculs opérant sur des structures de données infinies ne terminent pas. Dans le second, les calculs non typés ne terminent pas à cause de la beta-réduction. Dans le cas où les calculs terminent, la confluence se réduit à celle des pics critiques, divergences minimales du calcul, obtenues à partir d'un terme médian appellé superposition qui se récrit de deux manière différentes en une paire de termes appellée critique. Dans le cas où les calculs ne terminent pas, le résultat majeur est que les calculs définis par des règles linéaires à gauche et sans paires critiques confluent. Il s'agit donc d'étendre ce résultat aux systèmes dont les règles peuvent être non-linéaires à gauche et avoir des paires critiques.L'étude la confluence est faite à partir de la méthode des diagrammes décroissants, qui généralise les techniques utilisées antérieurement aussi bien pour des calculs qui terminent que pour des calculs qui ne terminent pas. Cette technique est abstraite, en ce sens qu'elle s'applique à des relations arbitraires opérant sur un ensemble abstrait. Elle consiste à équipper chaque étape de calcul d'un label pris dans un ensemble bien fondé. Un pic de calcul, composé d'un terme se récrivant de deux manières différentes, possède un diagramme décroissant lorsque ses extémités peuvent se récrire en un terme commun avec des étapes de calcul satisfaisant des conditions de comparaison avec les labels du pic. La force de cette technique est sa complétude, c-a-d que toute relation confluente peut-être équippée d'un système de labels (par des entiers) pour lequel tous ses pics possèdent des diagrammes décroissants. Ce résultat est basé sur un théorème assez ancien de Klop, qui définit pour les systèmes non-terminant, uneespèce de forme normale sous la forme d'une suite infinie de récritures élémentaires, appellée "dérivation cofinale".Dans une première partie, nous révisitons les résultats de van Oostrom, et en proposons une preuve différente dans le but de les généraliser au cas des calculs dits "modulo", c-a-d dans des quotients, qui mèlent des règles et deséquations. Cette généralisation inclue la complétude, en faisant intervenir une généralisation de lanotion de dérivation cofinale dans le cas des calculs cohérents au sens de Jouannaud et Kirchner.La second partie de la thèse applique le théorème de van Oostrom et sa généralisation à des système (concrets) de récriture de termes, ainsi qu'à plusieurs priblèmes ouverts du domaine. L'application récente à des problèmes d'ordre supérieur tirés de la théorie des types dépendants ne fait pas partie de la thèse. / This thesis is devoted to the confluence of rewrite systems in the absence of termination, for applications in first-order functional languages like MAUDE or higher-order languages with dependent types, as Dedukti. In the first case, the computations on infinite data structures do not terminate, while in the second case, untyped computations do not terminate because of beta-reduction. In the case where the computations terminate, confluence is reduced to that of critical peaks, the "minimal diverging computations", made of a minimal middle term called "overlap" which computes in two different ways, resulting in a so-called "critical pair". In the case of non-terminating computations, a main result is that left-linear rewrite rules that have no critical pairs are always confluent. This suggests that the notion of critical pairs plays a key role there too, but a general understanding of the confluence of non-terminating computations in terms of critical pairs is still missing.Our investigation of confluence is based on the decreasing diagrams method due to van Oostrom, which generalizes the techniques used previously for both terminating and non-terminating computations. The method is abstract in the sense that it applies to arbitrary relations on an abstract set. It equips each step of computations with a label taken from a well-founded set. A diverging computation, called peak, has a decreasing diagram if its extremities can be joined by steps whose direction and labels satisfy some constraints with respect to the peak's rewrites and labels. The strength of this technique is its completeness, that is, any confluent relation can be equipped with a well-founded set of labels such that all peaks have decreasing diagrams. The proof of completeness is based on Klop's notion of cofinal derivations, which is an infinite derivation playing the role of a normal form when computations do not terminate.In the first part, we revise the results of van Oostrom, and propose an alternative proof that extends the method to the "modulo" case, in which computations mix rewrite steps and equational steps. The completeness result is extended as well, via a generalization of cofinal derivations and the notion of strong coherence due to Jouannaud and Kirchner.The second part of the thesis applies the decreasing diagrams method and its generalization to concrete systems rewriting terms, as well as to several open problems. The recent application to the problems of higher-order computations in dependent type theory is not part of the thesis.

Master of Science / Department of Biology / Martha E. Mather / Determining patterns and drivers of organismal distribution and abundance are fundamental and enduring challenges in ecology, especially for mobile organisms at a ‘scape scale. To address the problem presented by individuals whose distributions are dynamic across large geographic areas, here I tracked 59 acoustically-tagged migratory striped bass (Morone saxatilis) with an array of 26 stationary receivers in Plum Island Estuary (PIE), MA. Specifically, I asked (1) how these predators were distributed across the estuarine seascape, (2) if these fish used three types of geomorphic sites (exits, confluences, and non-confluences) differently, (3) if distinct types of individual distributional “types” existed, and (4) if fish within distinct distributional groups used geomorphic site types and regions differently. Based on three components of predator trajectories (site specific numbers of individuals, residence time, and number of movements), striped bass were not distributed evenly throughout PIE. Confluences attracted tagged striped bass although not all confluences or all parts of confluences were used equally. Use of non-confluences sites was more variable than exits or confluences. Thus, geomorphic drivers and regions link mobile organisms to physical conditions across the seascape. Based on spatial and spatial-temporal cluster analyses, these striped bass predators clustered into four seasonally-resident distributional types. These included the (1) Rowley River group (fish that primarily resided in the Rowley River), (2) Plum Island Sound group (fish that primarily resided in the Middle Sound region), (3) Extreme Fidelity group (fish that spent most of their time in PIE at a single receiver location), and (4) the Exploratory group (fish that showed no affiliation with any particular location). These distributional groups used geomorphic site types and regions differently. Thus, my data show a rare link between behavioral (i.e., individual animal personalities) and field ecology (seascape geomorphology) that can advance the understanding of field-based patterns and drivers of organismal distribution.

La biologie des systèmes cherche à comprendre et analyser des systèmes biologiques à l'aide de modèles mathématiques et informatiques. L'explosion des données expérimentales entraîne des modèles de plus en plus grands. Afin de pouvoir les analyser facilement ou les simuler rapidement, il est alors nécessaire de pouvoir les simplifier. Dans cette thèse, nous proposons des méthodes de simplifications de réseaux de réactions biochimiques. Ces méthodes sont suffisamment riches pour pouvoir simplifier un grand nombre de réseaux provenant d'applications biologiques. Elles sont contextuelles, permettant de considérer un réseau comme un sous-module d'un modèle plus grand, et de le simplifier sans modifier le comportement du modèle global. Enfin, nos simplifications sont correctes, c'est-à-dire qu'elles préservent la sémantique des réseaux. Dans un premier temps, nous nous intéressons à une sémantique non déterministe, basée sur la possibilité de converger vers les attracteurs du réseau. Nous étudions ensuite des simplifications pour la sémantique déterministe, permettant par exemple de supprimer des espèces intermédiaires à l'équilibre. Enfin, nous nous intéressons à la confluence d'une telle simplification, ainsi qu'au lien entre l'élimination des espèces intermédiaires et le calcul des modes élémentaires d'un réseau. / System biology aims at understanding and analyzing biological systems using mathematical and computational models. The explosion of the number of experimental data leads to larger and larger models. In order to be able to easily analyze them and quickly simulate them, it is necessary to be able to simplify them. In this thesis, we propose simplification methods for biochemical reaction networks. These methods are sufficiently rich to be able to simplify an important number of networks from biological applications. They are contextual, allowing to consider a network as a sub-module of a larger model, and to simplify it without modifying the behavior of the global model. Finally, our simplifications are sound, meaning that they preserve the semantics of the networks. Firstly, we are interested in a non deterministic semantics, based on the capability to converge to some attractors of the network. Then we study some simplifications for the deterministic semantics, allowing for instance to remove intermediate species at steady-state. Finally, we are interested by the confluence of this simplification, as well as the relation between the elimination of intermediate species and the computation of the elementary modes of a network.

Programmers don't just have to write programs, they are have to reason about them. Programming languages aren't just tools for instructing computers what to do, they are tools for reasoning. And, it isn't just programmers who reason about programs: compilers and other tools reason similarly as they transform from one language into another one, or as they optimize an inefficient program into a better one. Languages, both surface languages and intermediate ones, need therefore to be both efficiently implementable and to support effective logical reasoning. However, these goals often seem to be in conflict. This dissertation studies programming language calculi inspired by the Curry-Howard correspondence, relating programming languages to proof systems. Our focus is on calculi corresponding logically to classical sequent calculus and connected computationally to abstract machines. We prove that these calculi have desirable properties to help bridge the gap between reasoning and implementation. Firstly, we explore a persistent conflict between extensionality and effects for lazy functional programs that manifests in a loss of confluence. Building on prior work, we develop a new rewriting theory for lazy functions and control which we first prove corresponds to the desired equational theory and then prove, by way of reductions into a smaller system, to be confluent. Next, we turn to the inconsistency between weak-head normalization and extensionality. Using ideas from our study of confluence, we develop a new operational semantics and series of abstract machines for head reduction which show us how to retain weak-head reduction's ease of implementation. After demonstrating the limitations of the above approach for call-by-value or types other than functions, we turn to typed calculi, showing how a type system can be used not only for mixing different kinds of data, but also different evaluation strategies in a single program. Building on variations of the reducibility candidates method such as biorthogonality and symmetric candidates, we present a uniform proof of strong normalization for our mixed-strategy system which works so long as all the strategies used satisfy criteria we isolate. This dissertation includes previously published co-authored material.

Cette thèse porte sur l’étude des paléoenvironnements et des dynamiques morphologiques holocènes dans le bassin versant du Massengh et de ses confluences avec les oueds Sbiba et el Hathob (Tunisie du centre-ouest). Après l’étude du cadre physique de l’évolution des environnements holocènes et actuels, la thèse se concentre dans un premier temps, sur la chronostratigraphie des héritages et des archives sédimentaires. La reconstitution des paléoenvironnements et de la morphogenèse Holocène est tentée, dans un deuxième temps. En dernier lieu, la thèse fait porter l’analyse sur l’évolution morphodynamique actuelle du milieu fluvial à l’échelle de l’espace de confluences. / This thesis focuses on the study of paleoenvironmental and Holocene morphological dynamics in the watershed Massengh and its confluence with the wadis and Sbiba el Hathob (Tunisia's center-west). After studying the physical part of the evolution of Holocene and current environments, the thesis focusesinitiallyon chronostratigraphy inheritances and sedimentary archives. The reconstruction of paleoenvironmentaland morphogenesis Holocene is attempted, in a second step. To summarize, the thesis studies in depth the currentmorphodynamic evolution of the fluvial environment across the space of confluences.

Software tools such as Build systems and project management tools are sometimes notwell designed when it comes to usability. This paper investigates the possibility of creatingcustom solutions for the three Atlassian products Jira, Confluence, and BitBucket, in orderto increase the efficiency when performing common tasks at the Atlassian administration atSaab AB. It was discovered that the main issue was performing reoccurring project-accesspermission audits, which was a very repetitive task with many manual steps involved.The solution to the issue was a Python script that, through the use of the Atlassian RESTAPI, could collect all the necessary information automatically and present it in a readablesummarized view. The amount of manual steps was significantly decreased to just a fewsteps which made a huge difference for the Atlassian administrators at Saab AB.

This master’s thesis deals with an analysis of information system of the company DATA-Software, spol s.r.o. After evaluating the strengths and weaknesses of the system, changes will be proposed in order to increase the added value the information system generates for the company or to lower its costs while retaining the same functionality.

Potential sites lies not only in its location but also the dominant position it holds to their surroundings. Undeveloped plot represents a "node" or "island" ... loosening strictly linear character Bakery. It is a place which brings together three disparate streams - Classical serious at the running part of Mendel Square, dramatically quarreling upper section flowing into the area from Hus class and insignificant Anenská that, if there "just got lost." All "three" street, however, are closely connected with the plot and the transformation of space clearly indicates their transformation. A distinctive feature of the property is its visual exposure of looking from Mendel Square, the plot creates a "picture" to which the pawn closer. This image should be interesting, changing to attract one's attention for more than just one or two seconds. The image should not least communicate - what is happening on the ground, what links are individual objects ... a landmark and should, for use by infantrymen use. It should also not be attractive from a distance - when one zooms in close proximity, should be surprised by the discovery of something new, something that was not noticeable from a distance, it should be attention to detail, or idea that can be seen only at close contact.

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