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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
1

Conception d'outils bioinformatiques pour la modélisation de voies métaboliques et de leur régulation / Designing bioinformatic tools to model metabolic pathways and their regulation

Dupont, Pierre-Yves 15 December 2011 (has links)
La biologie des systèmes actuelle s’appuie sur des techniques d’analyse biologique à haut débit comme la transcriptomique ou la métabolomique. Cependant, ces techniques haut débit ont leurs limites et peuvent générer des erreurs. En croisant les résultats de différentes techniques d’analyse biologique, nous espérons pallier une partie de leurs limites. À cet effet, nous avons commencé à développer une plateforme de modélisation, MPSA (Metabolic Pathways Software Analyzer), permettant d’intégrer les données générées à des réseaux métaboliques. MPSA permet de représenter les graphes de voies métaboliques, d’effectuer des simulations basées sur la résolution de systèmes d’équations différentielles et d’étudier la structure des réseaux métaboliques par le calcul et la représentation des modes élémentaires. Nous avons développé différentes applications web permettant, d’une part, l’interprétation des résultats biologiques en utilisant des bases de données et, d’autre part, leur export vers MPSA. La base de données centrale de ce développement est myKegg, incluant l’ensemble des voies métaboliques humaines de la base de données publique KEGG ainsi qu’une base de synonymes construite elle aussi à partir de KEGG. Cette base permet d’identifier des voies métaboliques et de les importer dans MPSA. Une base de données de métabolomique, BioNMR, a aussi été construite spécifiquement pour organiser les résultats générés à partir de spectres de RMN. Une autre application web, GeneProm, a été développée pour l’analyse de promoteurs de gènes ou promotologie. Un protocole d’étude a été mis au point et testé sur un groupe de 4 gènes codant pour les isoformes 1 à 4 de la protéine ANT, transporteur mitochondrial d’ATP, chacune ayant un rôle et un profil d’expression spécifique dans la bioénergétique cellulaire. L’étude par promotologie de ces 4 gènes a permis d’identifier des éléments de régulation spécifiques dans leurs séquences promotrices et d’identifier des gènes potentiellement co-régulés. Ces gènes peuvent ensuite être exportés vers notre plateforme MPSA. L’ensemble de ce développement sera inclus au projet de plateforme intégrative de l’Unité de Nutrition Humaine de l’INRA. / Current systems biology relies on high-throughput biological analysis techniques such as transcriptomics or metabolomics. However, these techniques may generate errors. By crossing results from different analysis techniques, we hope to avoid at least part of these limits. For that purpose, we started to develop a modeling platform, MPSA (Metabolic Pathways Software Analyzer). MPSA allows integrating biological data on metabolic pathways. MPSA also ensures the display of metabolic pathways graphs, the simulation of models based on ordinary differential equations systems solving and the study of network structures using elementary flux modes. We have developed several web applications allowing on the one hand to interpret biological results by using databases, and on the other hand to export these data to MPSA. The main database of this work is myKegg. It includes all human KEGG metabolic pathways and a list of synonyms for human KEGG entries. This base allows to identify metabolic pathways from a list of biological compounds and to import them in MPSA. Another database, BioNMR, has been developed to organize the data extracted from NMR spectra. Another web application named GeneProm has been developed to analyze gene promoters. A promotology protocol was developed and tested on a set of four genes coding for the four ANT (adenine nucleotide translocator) protein isoforms. Each ANT isoform has a specific expression profile and role in cell bioenergetics. The promotology study of these four genes led us to construct specific regulatory models from identified regulatory elements in their promoter sequence. Potentially co-regulated genes were deduced from these models. Then they can be exported to our MPSA platform. This whole development will be included in the project of Integrative Biology platform in the INRA Human Nutrition Unit.
2

MPSA Effects on Copper Electrodeposition: Understanding Molecular Behavior at the Electrochemical Interface

Guymon, Clint Gordon 21 November 2005 (has links) (PDF)
In this work the structure of the electrochemical metal-liquid interface is determined through use of quantum mechanics, molecular simulation, and experiment. Herein are profiled the molecular dynamics details and results of solid-liquid interfaces at flat non-specific solid surfaces and copper metal electrodes. Ab initio quantum-mechanical calculations are reported and define the interatomic potentials in the simulations. Some of the quantum-mechanical calculations involve small copper clusters interacting with 3-mercaptopropanesulfonic acid (MPSA), sodium, chloride, bisulfate and cuprous ions. In connection with these I develop the electrode charge dynamics (ECD) routine to treat the charge mobility in a metal. ECD bridges the gap between small-scale metal-cluster ab initio calculations and large-scale simulations of metal surfaces of arbitrary geometry. As water is the most abundant surface species in aqueous systems, water determines much of the interfacial dynamics. In contrast to prior simulation work, simulations in this work show the presence of a dense 2D ice-like rhombus structure of water on the surface that is relatively impervious to perturbation by typical electrode charges. I also find that chloride ions are adsorbed at both positive and negative electrode potentials, in agreement with experimental findings. Including internal modes of vibration in the water model enhances the ion contact adsorption at the solid surface. In superconformal filling of copper chip interconnects, organic additives are used to bottom-up fill high-aspect ratio trenches or vias. I use molecular dynamics and rotating-disk-electrode experiments to provide insight into the function of MPSA, one such additive. It is concluded that the thiol head group of MPSA inhibits copper deposition by preferentially occupying the active surface sites. The sulfonate head group participates in binding the copper ions and facilitating their transfer to the surface. Chloride ions reduce the work function of the copper electrode, reduce the binding energy of MPSA to the copper surface, and attenuate the binding of copper ions to the sulfonate head group of MPSA.

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