Accurate predictions of binding free energies from computer simulations are an invaluable resource for understanding biochemical processes and drug action. The primary aim of the work described in the thesis was to predict and understand ligand binding to several proteins of major pharmaceutical importance using computational methods. We report a computational strategy to quantitatively predict the effects of alanine scanning and ligand modifications based on molecular dynamics free energy simulations. A smooth stepwise scheme for free energy perturbation calculations is derived and applied to a series of thirteen alanine mutations of the human neuropeptide Y1 G-protein coupled receptor and a series of eight analogous antagonists. The robustness and accuracy of the method enables univocal interpretation of existing mutagenesis and binding data. We show how these calculations can be used to validate structural models and demonstrate their ability to discriminate against suboptimal ones. Site-directed mutagenesis, homology modelling and docking were further used to characterize agonist binding to the human neuropeptide Y2 receptor, which is important in feeding behavior and an obesity drug target.  In a separate project, homology modelling was also used for rationalization of mutagenesis data for an integron integrase involved in antibiotic resistance. Blockade of the hERG potassium channel by various drug-like compounds, potentially causing serious cardiac side effects, is a major problem in drug development. We have used a homology model of hERG to conduct molecular docking experiments with a series of channel blockers, followed by molecular dynamics simulations of the complexes and evaluation of binding free energies with the linear interaction energy method. The calculations are in good agreement with experimental binding affinities and allow for a rationalization of three-dimensional structure-activity relationships with implications for design of new compounds. Docking, scoring, molecular dynamics, and the linear interaction energy method were also used to predict binding modes and affinities for a large set of inhibitors to HIV-1 reverse transcriptase. Good agreement with experiment was found and the work provides a validation of the methodology as a powerful tool in structure-based drug design. It is also easily scalable for higher throughput of compounds.

In order to understand the behaviour and function of proteins, their three dimensional structure needs to be known. Determination of macro-molecules’ structures is done using X-ray diffraction or electron microscopy, where the resulting diffraction pattern is used for molecular reconstruction. These methods are however limited by radiation damage.The aim of this work is to study radiation damage of peptides in proteins using computer simulations. Increased understanding of the atomic and molecular dynamics can contribute to an improvement of the method ofimaging biological molecules. To be able to describe the processes that take place as accurately as possible, the problem must treated quantum mechanically.Thus, the simulations are performed with molecular dynamics based on first principles. In order to capture the dynamics of the excited states of the molecule when exposed to X-rays, time-dependent density functional theory with delta self-consistent field is used. These simulations are compared to ground state simulations. The results of the thesis conclude that the excited and ground state simulations result in differences in the dynamics, which are most pronounced for lager molecules.

Cette thèse contient deux parties distinctes, reliées par le thème de l’étude géométrique du problème à trois corps. La première partie présente un point de vue sur les enjeux et les perspectives liés à la diffusion des mathématiques, et illustre ce point de vue à l’aide de deux projets de diffusion « grand public » : une exposition virtuelle autour de la mécanique céleste et du problème à trois corps, et un duo de contes mathématiques pour enfants, l’un sur la forme de la lune, et l’autre sur l’enlacement de courbes fermées. La présentation de ces projets est suivie d’une analyse a priori et d’une étude des observations recueillies lors de différentes expérimentations auprès de publics variés. La deuxième partie est consacrée à l’étude – théorique et numérique – de l’enlacement des trajectoires de quelques systèmes dynamiques sur la 3-sphère, et en particulier de certaines instances du problème à trois corps. On y présente d’abord le problème à trois corps restreint, plan, circulaire, en s’intéressant tout particulièrement au cas où une des deux primaires disparait. On se ramène ainsi à un flot sur la 3-shpère dont on connaît explicitement des sections de Birkhoff en disque ou en anneau, et on met en lumière des éléments qui tendent à montrer le caractère lévogyre de ce flot. On explore ensuite, à l’aide de simulations numériques, la possibilité que le système reste lévogyre sur un domaine assez éloigné de ce cas dégénéré. Enfin, on s’intéresse aux flots sur la 3-sphère qui admettent une section de Birkhoff en disque et on traduit la notion d’enlacement de mesures invariantes pour le flot en termes d’enroulement de mesures invariantes pour le difféomorphisme de premier retour. / This thesis contains two distinct parts, connected by the subject of the geometric study of the three body problem.The first part presents a point of view about the stakes and prospects of the popularization of mathematics, and it illustrates this point of view with two projects of popularization for a general public : a virtual exhibition about celestial mechanics and the three body problem, and a pair of mathematical tales for children, one about the shape of the moon, and the other about the linking number of two closed curves. The presentation of these projects is followed by an initial analysis and by a study of the observations collected during different experimentations towards various publics. The second part is devoted to the theoretical and computational study of the linking number of trajectories from a few dynamical systems on the 3-sphere, and in particular from some cases of the restricted three body problem. We first present the planar, circular, restricted three body problem, with a particular attention to the case where one of the two heavy bodies vanishes. We thus restrict ourselves to a flow on the 3-shpere for which disk-like or annular-like Birkhoff sections are explicitely known, and we bring to light evidences of the right-handedness of this flow. Then we investigate, with the help of computer simulations, the possibility for the system to stay right-handed over a domain rather distant from this degenerate case. Finally, we consider the flows on the 3-sphere which admit a disk-like Birkhoff section, and we translate the notion of linking for measures that are invariant by a flow into the notion of winding for measures that are invariant by the first return map on the disk.

O presente trabalho tem por objetivo a caracterização dinâmica dos sistemas múltiplos de planetas extrassolares. O critério de classificação escolhido é baseado na proposta publicada inicialmente em Ferraz-Mello et al. (2005) e posteriormente modicada em Michtchenko et al. (2007). Para a obtenção dos parâmetros planetários orbitais foi feita uma pesquisa em diversos catálogos e artigos disponíveis para posterior criação de um catálogo próprio. Este incluiu somente sistemas extrassolares múlltiplos, ou seja, sistemas que contêm dois ou mais planetas orbitando a estrela. Foram feitas simulações numéricas de estabilidade dinâmica dos sistemas do catálogo próprio com tempos de integração de 200 mil até 21 milhões de anos. Ao todo, foram analisados 37 sistemas múltiplos extrassolares, divididos em 50 subsistemas considerando-se a estrela e dois planetas em órbitas consecutivas. Ao todo, foram analisados 37 sistemas múltiplos extrassolares, divididos em 50 subsistemas considerando-se a estrela e dois planetas em órbitas consecutivas. Estes foram submetidos ao total de 68 simulações computacionais. Os sistemas que apresentaram um cenário de estabilidade dinâmica foram posteriormente separados em três classes: ressonantes, seculares ou hierárquicos. Mais ainda, o comportamento secular desses sistemas foi classificado conforme o movimento do ângulo \"Deltavarpi\" : oscilatório em torno de 0º, oscilatório em torno de 180º ou circulatório. Os resultados das simulações são mostrados para todos os sistemas estudados. / The aim of the present work is a dynamic classification of multiple extrasolar systems. The characterization criterion used is based on a criterion proposed initially in Ferraz-Mello et al. (2005) and modified in Michtchenko et al. (2007). To obtain orbital parameters of the extrasolar systems, a search was done into several available catalogues and the scientific literature. A new catalogue was compiled containing only multiple extrasolar systems, that is, systems with two or more planets in orbit of the host star. Numerical simulations of dynamical stability of the cataloged systems were done considering pairs of planets on the consecutive orbits. Totally, 37 multiple extrasolar systems were analyzed, decomposed in 50 sub-systems each one consisting of the host star and two planets. The time evolution of those were simulated over time spans from 200 thousand years to 21 million years in 68 numerical simulations. The systems which have presented a dynamical stability were subsequently classified in resonants, secular or hierarchical and their secular behavior was classified with respect of the angle \"Deltavarpi\" as oscillation around 0º, oscillation around 180º or circulation. The result of all simulations are presented here for the analyzed systems.

<p>The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented.</p><p>For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions.</p><p>A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands.</p><p>A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding.</p><p>The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.</p>

The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented. For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions. A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands. A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding. The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.

Over the last few decades, computer simulation techniques have been established as an essential tool for understanding biochemical processes. This thesis deals mainly with the application of free energy calculations to ribosomal complexes and a cardiac ion channel. The linear interaction energy (LIE) method is used to explore the energetic properties of the essential process of codon–anticodon recognition on the ribosome. The calculations show the structural and energetic consequences and effects of first, second, and third position mismatches in the ribosomal decoding center. Recognition of stop codons by ribosomal termination complexes is fundamentally different from sense codon recognition. Free energy perturbation simulations are used to study the detailed energetics of stop codon recognition by the bacterial ribosomal release factors RF1 and RF2. The calculations explain the vastly different responses to third codon position A to G substitutions by RF1 and RF2. Also, previously unknown highly specific water interactions are identified. The GGQ loop of ribosomal RFs is essential for its hydrolytic activity and contains a universally methylated glutamine residue. The structural effect of this methylation is investigated. The results strongly suggest that the methylation has no effect on the intrinsic conformation of the GGQ loop, and, thus, that its sole purpose is to enhance interactions in the ribosomal termination complex. A first microscopic, atomic level, analysis of blocker binding to the pharmaceutically interesting potassium ion channel Kv1.5 is presented. A previously unknown uniform binding mode is identified, and experimental binding data is accurately reproduced. Furthermore, problems associated with pharmacophore models based on minimized gas phase ligand conformations are highlighted. Generalized Born and Poisson–Boltzmann continuum models are incorporated into the LIE method to enable implicit treatment of solvent, in an effort to improve speed and convergence. The methods are evaluated and validated using a set of plasmepsin II inhibitors.

No description available.

We report a class of the mathematics in which an animation technology (calculating and plotting capabilities) of the software Mathematica is utilized. This class is taught for university students in a computer laboratory during a second semester. It is our purpose to make a student realize the usefulness and the importance of mathematics easily through visualization. In addition, we hope that students will acquire a new power of mathematics needed in the 21st century. For several years, we have continued this kind of class, and have continued to investigate the effectiveness that our teaching method (especially visualization) brings in the understanding of the mathematics. In this paper, we present some of this teaching method, which is performed in our class. From the questionnaire survey, it is found that our teaching method not only convinces students that the mathematics is useful or important but also deepens the mathematic understanding of students more.

Submitted by Daniele Amaral (daniee_ni@hotmail.com) on 2016-10-21T16:40:39Z No. of bitstreams: 1 DissAFR.pdf: 2278033 bytes, checksum: c7c90860ad15e7ba874ca20e2461507d (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-11-08T18:58:03Z (GMT) No. of bitstreams: 1 DissAFR.pdf: 2278033 bytes, checksum: c7c90860ad15e7ba874ca20e2461507d (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-11-08T18:58:30Z (GMT) No. of bitstreams: 1 DissAFR.pdf: 2278033 bytes, checksum: c7c90860ad15e7ba874ca20e2461507d (MD5) / Made available in DSpace on 2016-11-08T19:01:16Z (GMT). No. of bitstreams: 1 DissAFR.pdf: 2278033 bytes, checksum: c7c90860ad15e7ba874ca20e2461507d (MD5) Previous issue date: 2016-08-03 / Não recebi financiamento / The student learning obtained by memorizing the information transmitted by the teacher's narrative, for further reproduction in the assessment, shows that the classic way of teaching, leads to a mechanical and not significant learning. The proposal of this study is to report the development and application of a Potentially Meaningful Teaching Unit (PMTU) proposed by Moreira, based on the Theory of Meaningful Learning of Ausubel. The proposal was drawn up using the PMTU steps in which, at first the survey of students' prior knowledge about the theme vectors was performed through the collective construction of a conceptual map and then the content of vectors was presented more generally through problem- situations. From that on, each vector operation was addressed more specifically, aiming the progressive differentiation and the integrative reconciliation. The students' performance was accomplished through their active participation and motivation in solving the problem-situations, in class debates, in the construction of maps, in simulations and video productions, that is with the use of The Information and Communication New Technologies of (ICNT). The concepts that were discussed and presented in accordance with the steps of PMTU: scalar greatness, vector greatness, trigonometric relationships in the triangle rectangle, vector addition by the polygon, the parallelogram and components methods, scalar product (real number) by one vector, scalar product and vector product of two vectors. The use of this sequence showed the evidence of occurrence of significant learning by the students and, therefore, many of the difficulties of high school students understanding have been overcome, since they are now familiar with the determination of some physical greatness, through operations with vectors presented in analytical geometry. / A aprendizagem do aluno obtida somente através da memorização das informações transmitidas pela narrativa do professor, para posterior reprodução na avaliação, mostra que a maneira clássica de ensinar, leva a uma aprendizagem mecânica e não significativa. A proposta deste trabalho é relatar o desenvolvimento e a aplicação de uma Unidade de Ensino Potencialmente Significativa (UEPS) proposta por Moreira, baseada na Teoria da Aprendizagem Significativa de Ausubel. A mesma foi elaborada seguindo os passos da UEPS onde, num primeiro momento fez-se o levantamento dos conhecimentos prévios dos alunos acerca do tema vetores através da construção de um mapa mental e, em seguida foi apresentado o conteúdo de vetores de forma mais geral, através de situações-problemas. A partir daí, cada operação com vetores foi abordada de maneira mais específica, visando à diferenciação progressiva e à reconciliação integradora. O desempenho dos alunos se deu pela participação ativa e motivação dos mesmos nas resoluções das situações-problemas, nos debates em sala, nas construções de mapas, nas simulações e na produção de vídeo, ou seja, no uso das Novas Tecnologias da Informação e Comunicação (NTIC). Os conceitos que foram abordados e apresentados de acordo com os passos da UEPS: grandeza escalar, grandeza vetorial, relações trigonométricas no triângulo retângulo, adição vetorial pelos métodos do polígono, do paralelogramo e das componentes, produto de escalar (número real) por um vetor, produto escalar e produto vetorial de dois vetores. A utilização dessa sequência apontou evidências da ocorrência de aprendizagem significativa por parte dos alunos e, com isso, muitas das dificuldades de compreensão dos alunos do Ensino Médio foram superadas, uma vez que agora estão familiarizados com a determinação de algumas grandezas físicas, através de operações com vetores, apresentadas na Geometria Analítica.