A mechanistic model is developed to determine the habitat needs of drift-feeding stream salmonids from the direct cause-and- effect relationships of environmental and physiological variables on net energy intake (NEI). The model determines NEI by subtracting energy costs (basal metabolism , swimming cost, digestion cost) and losses (egestion and excretion) from the gross energy intake obtained as a result of simulated prey capture. The prey capture portion of the model utilizes components o f the predation model of C.S. Holling and the prey capture model of N.F. Hughes and L.M. Dill to determine the rate of prey capture (gross energy intake) as a function of fish size, water velocity, water depth, water temperature, and the amount of drift. Physiological input parameters for the model are estimated from the literature. Two separate validation tests of the model's ability to predict stream habitat use of trout, primarily cutthroat trout (Oncorhynchus clarki), in St. Charles Creek, Idaho, are presented. In both cases, the NEI model closely predicts the stream habitat that different size classes of fish utilize. The validation tests provide strong evidence that drift-feeding fish utilize stream habitats that provide high rates of NEI as determined by the model. Sensitivity and simulation analyses of the model are used to identify the most important input parameters and to illustrate in terms of energetics why drift-feeding fish utilize various habitats. Model simulations explain why fish utilize deeper and faster habitats as they get larger and why they utilize slower habitats in the winter. In addition, it is shown that streams with high drift rates should theoretically provide more usable salmonid habitat than similar streams with lower drift rates.

Les cytokinines sont des hormones régulant de nombreux processus physiologiques. Elles sont en particulier impliquées dans certaines interactions plantes-microorganismes pathogènes. Leur perception est assurée par les récepteurs Histidine Kinases (HK) dont la fonction est prédominante dans la transduction de signaux moléculaires et environnementaux. Ce travail a permis une caractérisation complète des cinq récepteurs aux cytokinines de type CHASE-Histidine Kinase (MdCHK) et d’un osmosenseur (MdHK1) chez le pommier, espèce d’intérêt économique soumise à l’attaque de nombreux pathogènes. La combinaison d’approches moléculaires et bio-informatiques a révélé les particularités fonctionnelles et les rôles spécifiques des MdCHK. Ces connaissances ont permis de sélectionner une souche de levures exprimant le récepteur MdCHK2 en tant que biosenseur de cytokinines. Ce nouvel outil biotechnologique optimisé pour la détection rapide de cytokinines a conduit à la mise en évidence d’une production de ces composés par Erwinia amylovora, bactérie pathogène du pommier. Le criblage de bactéries pathogènes humaines grâce au biosenseur a également révélé leur production par Staphylococcus aureus et Streptococcus agalactiae. Afin d’optimiser ce biosenseur, une approche mécanistique de MdCHK2 a été entreprise et dévoile l’importance de certains domaines dans ses spécificités de perception. / Cytokinins are hormones regulating numerous physiological processes. They are particularly involved in some plant-pathogen interactions. Their perception is ensured by Histidine Kinase (HK) receptors which play a prevailing role in transducing molecular and environmental signals. This work enabled the full characterization of the five cytokinin CHASE-Histidine Kinase receptors (MdCHK) and the osmosensor (MdHK1) in apple tree, a species of economic interest subjected to many pathogen attacks. Combining molecular and bioinformatics approaches led us to reveal the functional features and specific roles of the MdCHK. This knowledge allowed us to select a yeast expressing the MdCHK2 receptor as a cytokinin biosensor. This new biotechnological tool optimized for fast cytokinin detection led us to expose the production of such molecules in Erwinia amylovora, a pathogenic bacterium of apple. Screening human pathogenic bacteria with the biosensor also unveiled their production in Staphylococcus aureus and Streptococcus agalactiae. In order to optimize this biosensor, we initiated a mechanistic approach on MdCHK2 and showed the importance of some domains in its perception specificities.

Fatigue cracking is one of the most common distresses of asphalt pavements, whereas healing is a counter process to cracking which alleviates cracking damage and extends fatigue life of asphalt pavements. Most of existing methods to characterize fatigue cracking and healing are generally empirical or phenomenological in nature, which does not satisfy the need to develop mechanistic-based pavement design methods. The objective of this study is to characterize fatigue cracking and healing of asphalt mixtures using an energy-based mechanistic approach. A controlled-strain repeated direct tension (RDT) test is selected to generate both fatigue cracking and permanent deformation in an asphalt mixture specimen. Fatigue cracking is separated from permanent deformation from a mechanical viewpoint. The development of fatigue cracking is described by the evolution of the damage density and the increase of the average crack size with the increase of loading cycles. A creep and step-loading recovery (CSR) test is designed to measure the internal stress in the recovery phase of an asphalt mixture specimen. The internal stress and the strain measured in the recovery phase are used to conduct the mechanistic analysis of recovery and healing of the asphalt mixture specimen. Then healing is described using the decrease of the damage density and average crack size with time. Different types of asphalt mixtures produce distinctly different fatigue cracking and healing characteristics. The effect of mixture composition, temperature, and aging are evaluated using the approach above. The entire series of tests for fatigue, permanent deformation and healing can be completed in one day, with the healing part requiring only a matter of minutes. The methods proposed in this study characterize fatigue cracking and healing of asphalt mixtures using its essential cause and effect relationship.

Ce travail porte sur l’étude expérimentale et la modélisation de la sédimentation des boues activées. Un pilote expérimental associant une colonne de sédimentation et un transducteur ultrasonore est proposé. Des profils de vitesse de sédimentation et de concentration en particules sont obtenus grâce à ce dispositif, ce qui permet de mieux comprendre les mécanismes de décantation des boues. Ces résultats sont utilisés afin de développer une approche numérique. Un modèle de sédimentation est construit en intégrant des fonctions expérimentales. Une méthodologie mettant en œuvre la différentiation automatique du modèle est ensuite élaborée et appliquée, d'une part, à l'analyse de sensibilité du modèle aux paramètres des fonctions utilisées et, d'autre part, à l'identification des valeurs de ces paramètres à l'aide des résultats expérimentaux. La conjonction des approches expérimentale et numérique proposées constitue un processus efficace pour le développement des modèles de sédimentation. / This work deals with the experimental investigation and modelling of activated sludge settling. An experimental setup combining a settling column and an ultrasonic transducer is proposed. Settling velocity and concentration profiles are obtained using this setup, allowing for a better understanding of the mechanisms of activated sludge settling. These results are applied to the development of a numerical approach. A settling model using experimental functions is built. A methodology based on the automatic differentiation of the model is developed. This methodology is used, on the one hand, to analyse the sensitivity of the results to the model parameters and, on the other hand, to identify the parameter values on the basis of experimental data. The combination of the proposed experimental and numerical methods yields an efficient process for the development of sedimentation models.