Made available in DSpace on 2016-06-02T19:02:39Z (GMT). No. of bitstreams: 1 2372.pdf: 3456814 bytes, checksum: 7894f1e8062bb948621e2d222d01e3b0 (MD5) Previous issue date: 2008-11-06 / Financiadora de Estudos e Projetos / The Molecular Evolution of the living organisms is a slow process that occurs over the years producing mutations and recombinations at the genetic material, i.e. at the DNA. The mutations can occur as nucleotide remotion, insertion and/or substitution at the DNA chain. The Directed Molecular Evolution is an in vitro process that tries to improve biological functions of specific molecules producing mutations at the molecule s genetic material, mimicking the natural process of evolution. Many technics that simulate in vitro molecular evolution, among them the DNA shuffling, have been used aiming to improve specific properties of a variety of commercially important products as pharmaceutical proteins, vaccines and enzymes used in industries. The original DNA shuffling methodology can be sumarized by the following steps: 1) selection of the parental sequences; 2) random fragmentation of the parental sequences by an enzyme; 3) repeated cycles of PCR (Polymerase Chain Reaction), in order to reassemble the DNA fragments produced in the previous step; 4) PCR amplification of the reassembled sequences obtained in step 3). The DNA shuffling technic success can be measured by the number of recombinat molecules found at the DNA shuffling library obtained, since these recombinant molecules potentially have improved functionalities in relation to their parent since their sequence may accumulate beneficial mutations originated from distinct parent sequences. Nowadays some few models can be found in the literature whose purpose is to suggest optimization to this process aiming the increase of the genetic diversity of the DNA shuffling library obtained. This research work presents a comparative study of four models used to predict/estimate the DNA shuffling results. In addition a computational tool for simulating the DNA shuffling proccess is proposed and implemented in an environment where other functionalities related to the analyses of the parental sequences and the resulting sequences from the DNA shuffling library is also implemented. / A Evolução Molecular dos organismos vivos é um processo lento que ocorre ao longo dos anos e diz respeito às mutações e recombinações sofridas por um determinado organismo em seu material genético, ou seja, em seu DNA. As mutações ocorrem na forma de remoções, inserções e/ou substituições de nucleotídeos ao logo da cadeia de DNA. A Evolução Molecular Direta é um processo laboratorial, ou seja, in vitro, que visa melhorar funções biológicas específicas de moléculas por meio de mutações/recombinações em seu material genético, imitando o processo natural de evolução. Diversas técnicas que simulam a evolução molecular em laboratório, entre elas a técnica de DNA shuffling, têm sido amplamente utilizadas na tentativa de melhorar determinadas propriedades de uma variedade de produtos comercialmente importantes como vacinas, enzimas industriais e substâncias de interesse famacológico. A metodologia original de DNA shuffling pode ser sumarizada pelas seguintes etapas: 1) seleção dos genes de interesse, dito parentais; 2) fragmentação enzimática dos genes; 3) ciclos de PCR (Polymerase Chain Reaction), para que ocorra a remontagem dos fragmentos; 4) amplificação das seqüências remontadas cujo tamanho é igual a dos parentais. O sucesso ou não da técnica de DNA shuffling pode ser medido pelo número de moléculas recombinantes encontradas na biblioteca de DNA shuffling obtida, uma vez que estas podem apresentar melhorias funcionais em relação aos parentais pelo fato de, possivelmente, acumularem em sua seqüência mutações benéficas presentes em parentais distintos. Atualmente podem ser encontradas na literatura algumas poucas modelagens computacionais capazes de sugerir otimizações para o processo, com vistas em aumentar a diversidade genética da biblioteca resultante. O presente trabalho apresenta um estudo comparativo de quatros modelos para predição/estimativa de resultados de experimentos de DNA shuffling encontrados na literatura bem como a proposta e implementação de uma ferramenta computacional de simulação para o processo de DNA shuffling. A ferramenta de simulação foi implementada em um ambiente que disponibiliza outras funcionalidades referentes à análise das seqüências a serem submetidas ao shuffling bem como ferramentas para análise das seqüências resultantes do processo.

Les systèmes d’assistance à la réverbération sont des dispositifs électroacoustiques installés dans les salles de spectacle pour moduler leur acoustique en fonction du type de représentation qui s’y déroule. Afin de pouvoir dimensionner ces systèmes en amont de leur installation, ce travail s’intéresse au développement, à la mise en œuvre et à la mise à l’épreuve de modèles prévisionnels de l’effet de ses systèmes sur les caractéristiques acoustiques d’une salle, en se concentrant sur les systèmes dits régénératifs diagonaux. Le premier modèle présenté est basé sur une approche systémique exacte et sur l’utilisation de simulations numériques. Il s’agit d’un modèle dont le principe est déjà décrit dans la littérature spécialisée, mais auquel est intégré ici un algorithme de détermination automatique des paramètres de réglage d’un système d’assistance à la réverbération reproduisant la méthode manuelle. Parce que l’utilisation de simulations numériques impose une modélisation détaillée de la salle et un important temps de calcul, ce modèle n’est pas compatible avec la réactivité demandée lors d’une phase d’avant-projet. Dans cette optique, deux autres modèles bases sur les hypothèses de champ diffus et, par là même, plus rapides d’exécution, sont développés. L’un repose aussi sur une approche systémique exacte, mais utilise la théorie stochastique de l’acoustique géométrique des salles plutôt que des simulations numériques. L’autre repose sur une approche énergétique simple. Les confrontations de ces deux modèles avec celui reposant sur des simulations numériques sont exposées pour cinq salles, en considérant la prévision d’évolution de six indices acoustiques courants due à l’introduction d’un système d’assistance à la réverbération. Il en ressort que ces deux modèles aboutissent à des erreurs prévisionnelles comparables et que celles-ci sont équivalentes à celles des formules de Sabine ou d’Eyring ou de la théorie révisée des champs diffus de Barron et Lee appliquées dans une salle sans système. Parallèlement, l’étude et la prévision de l’effet d’un système d’assistance à la réverbération régénératif en augmentation du couplage de deux espaces mal couples au sein d’une même salle sont présentées. Il est montré que ce type d’utilisation permet effectivement une augmentation du couplage et que celle-ci peut être correctement abordée à partir d’un modèle énergétique développé ici. Il est aussi montré à partir de simulations numériques, que cette utilisation permet d’homogénéiser les caractéristiques acoustiques entre les deux espaces couplés. / Reverberation enhancement systems (RES) are electro-acoustic devices installed in auditoria to adapt the listening conditions according to the performances. In order to design these systems before their installation, this work deals with the development, the implementation and the testing of prediction tools of the effect of these systems on the acoustic characteristics of a room, by focusing on diagonal regenerative RES. The first proposed tool is based on a systemic approach and numerical simulations. This tool, whose principle is already described in the literature, is here enhanced by the use of an algorithm that automatically fine-tunes the system parameters. As numerical simulations require detailed 3D models of rooms and high computation times, this tool is not compatible with the responsiveness needed for a preliminary design stage. With this in mind, two other models based on the diffuse field assumptions are also developed to predict the action of a RES. One of them is also based on a systemic approach but it uses the stochastic geometric theory of room acoustics instead of numerical simulations. The other model is based on a simple energetic approach. The confrontation of the results given by these two models with the results given by the model based on numerical simulations has been carried out in five rooms considering the effect of a RES on six common room acoustic criteria. It appeared that these two models lead to prediction errors similar to those obtained with the Sabine or Eyring’s formula, or the Barron and Lee’s revised theory applied in a room without RES. In the same time, the study of the effect of a RES used to enhance the coupling between two poor coupled room is presented. It is shown that this particular use of a RES actually increases the coupling effect, and that this effect can be correctly described and predicted by an energetic model developed here. It is also shown by numerical simulations that this system can balance the listening conditions between two coupled rooms.