The sequence-dependent curvature and flexibility of DNA is critical for many biochemically important processes. However, few experimental methods are available for directly probing these properties at the base-pair level. One promising way to predict these properties as a function of sequence is to model DNA with a set of base-pair parameters that describe the local stacking of the different possible base-pair step combinations. In this dissertation research, we develop and study a computational model for predicting the diffusion coefficients of short, relatively rigid DNA fragments from the sequence and the base-pair parameters. We focus on diffusion coefficients because various experimental methods have been developed to measure them. Moreover, these coefficients can also be computed numerically from the Stokes equations based on the three-dimensional shape of the macromolecule. By comparing the predicted diffusion coefficients with experimental measurements, we can potentially obtain refined estimates of various base-pair parameters for DNA. Our proposed model consists of three sub-models. First, we consider the geometric model of DNA, which is sequence-dependent and controlled by a set of base-pair parameters. We introduce a set of new base-pair parameters, which are convenient for computation and lead to a precise geometric interpretation. Initial estimates for these parameters are adapted from crystallographic data. With these parameters, we can translate a DNA sequence into a curved tube of uniform radius with hemispherical end caps, which approximates the effective hydrated surface of the molecule. Second, we consider the solvent model, which captures the hydrodynamic properties of DNA based on its geometric shape. We show that the Stokes equations are the leading-order, time-averaged equations in the particle body frame assuming that the Reynolds number is small. We propose an efficient boundary element method with a priori error estimates for the solution of the exterior Stokes equations. Lastly, we consider the diffusion model, which relates our computed results from the solvent model to relevant measurements from various experimental methods. We study the diffusive dynamics of rigid particles of arbitrary shape which often involves arbitrary cross- and self-coupling between translational and rotational degrees of freedom. We use scaling and perturbation analysis to characterize the dynamics at time scales relevant to different classic experimental methods and identify the corresponding diffusion coefficients. In the end, we give rigorous proofs for the convergence of our numerical scheme and show numerical evidence to support the validity of our proposed models by making comparisons with experimental data. / text

Les questions de sûreté et d'incertitudes sont au centre des études de faisabilité pour un site de stockage souterrain de déchets nucléaires, en particulier l'évaluation des incertitudes sur les indicateurs de sûreté qui sont dues aux incertitudes sur les propriétés du sous-sol et des contaminants. L'approche globale par les méthodes probabilistes de type Monte Carlo fournit de bons résultats, mais elle demande un grand nombre de simulations. La méthode déterministe étudiée ici est complémentaire. Reposant sur la décomposition en valeurs singulières de la dérivée du modèle, elle ne donne qu'une information locale, mais elle est beaucoup moins coûteuse en temps de calcul. Le modèle d'écoulement suit la loi de Darcy et le transport des radionucléides autour du site de stockage est modélisé par une équation de diffusion-convection linéaire. Différentiation à la main et différentiation automatique sont comparées sur ces modèles en mode direct et en mode adjoint. Une étude comparée des deux approches probabiliste et déterministe pour l'analyse de la sensibilité des flux de contaminants aux exutoires par rapport aux variations des paramètres d'entrée est menée sur des données réalistes fournies par l'ANDRA. Des outils génériques d'analyse de sensibilité et de couplage de code sont développés en langage Caml. Ils permettent à l'utilisateur de ces plates-formes génériques de ne fournir que la partie spécifique de l'application dans le langage de son choix. Une étude sur les écoulements diphasiques eau/air partiellement saturés en hydrogéologie porte sur les limitations des approximations de Richards et de la formulation en pression globale issue du domaine pétrolier.

Title: Adaptive choice of parameters in stabilization methods for convection- diffusion equations Author: Bc. Petr Lukáš (e-mail: luk.p@post.cz) Department: Department of Numerical Mathematics Supervisor: Doc. Mgr. Petr Knobloch, Dr. (e-mail: knobloch@karlin.mff.cuni.cz) Abstract: The aim of the work is to propose suitable approaches for adap- tive choice of parameters in stabilization methods for convection-difusion equations discretized by the finite element method. We introduce the L-SR1 method, compare it with other nonlinear methods of minimizing functions with large number of variables, and introduce and compare the adaptive methods based on minimizing of the error indicator. Keywords: Adaptive choice of parameters, finite element method, stabiliza- tion methods, convection-diffusion equation, L-SR1 method, error indicator

Title: Numerical analysis of approximation of nonpolygonal domains for discon- tinuous Galerkin method Author: Filip Klouda Department: Department of Numerical Mathematics Supervisor: prof. RNDr. Vít Dolejší, Ph.D., DSc., KNM MFF UK Abstract: In this work we use the discontinuous Galerkin finite element method for the semidiscretization of a nonlinear nonstationary convection-diffusion pro- blem defined on a nonpolygonal two-dimensional domain. Using so called appro- ximating curved elements we define a piecewise polynomial approximation of the boundary of the domain and a space on which we search for a solution. We study the convergence of the method considering a symmetric as well as nonsymmetric discretization of diffusion terms and with the interior and boundary penalty. The obtained results allow us to derive an error estimate for the Discontinuous Galer- kin method employing the approximating curved elements. This estimate depends on the order of the approximation of the solution and also on the order of the approximation of the boundary. We describe one possibility of the construction of the approximating curved elements with the aid of a polynomial mapping given by an interpolation of points on the boundary. We present numerical experiments. Keywords: nonlinear convection-diffusion equation, discontinuous...

Ce mémoire est un exposé synthétique d'une partie des travaux que j'ai accomplis après la fin de ma thèse. Au cours des dernières années, j'ai été amené à m'intéresser à la discrétisation de problèmes provenant de différentes applications en mécanique des fluides. L'élément commun à tous ces problèmes est la présence de termes diffusifs du second ordre. Pour des raisons différentes, j'ai considéré des discrétisations non conformes, c'est-à-dire, basées sur des espaces discrets non contenus dans l'espace continu naturellement associé à la formulation faible du problème. Plus précisément, dans les travaux présentés dans ce mémoire on retrouve essentiellement deux grandes familles de méthodes : les méthodes dites de Galerkine discontinues et les méthodes volumes finis. Ce document s'organise comme suit. Les Chapitres 1–3 fournissent les renseignements administratifs relatifs au dossier de demande d'habilitation, dont un <EM>curriculum vitæ</EM>, une description succincte de l'ensemble de mes travaux et la liste complète des publications. Les Chapitres 4–5 relatent les efforts entrepris au sujet de la discrétisation de problèmes avec diffusion par des méthodes non conformes. Plus précisément, le Chapitre 4 est consacré aux méthodes de Galerkine discontinues, tandis que le Chapitre 5 traite des méthodes volumes finis. Même si l'accent est généralement mis sur les motivations des travaux et sur le développement de la ligne de pensée, des détails sont fournis quand cela s'avère nécessaire pour apporter un complément d'information par rapport aux publications, ou bien pour indiquer des pistes de recherche futures. Le rapport contient aussi une annexe contenant les résumés des thèses actuellement en cours. Dans la dernière partie de ce mémoire on peut trouver le texte intégral des publications. Pour faciliter la lecture, mes publications sont citées dans le texte avec un numéro progressif, tandis que les articles de la bibliographie générale sont cités avec les initiales des auteurs.

While moment matching can effectively reduce the dimension of a linear, time-invariant system, it can simultaneously fail to improve the stable time-step for the forward Euler scheme. In the context of a semi-discrete heat equation with spatially smooth forcing, the high frequency modes are virtually insignificant. Eliminating such modes dramatically improves the stable time-step without sacrificing output accuracy. This is accomplished by modal filtration, whose computational cost is relatively palatable when applied following an initial reduction stage by moment matching. A bound on the norm of the difference between the transfer functions of the moment-matched system and its modally-filtered counterpart yields an intelligent choice for the mode of truncation. The dual-stage algorithm disappoints in the context of highly nonnormal semi-discrete convection-diffusion equations. There, moment matching can be ineffective in dimension reduction, precluding a cost-effective modal filtering step.

Wir untersuchen ein Defektkorrekturverfahren, das ein einfaches Upwind-Differenzenverfahren erster Ordnung mit einem zentralen Differenzenverfahren kombiniert, für ein- und zweidimensionale singulär gestörte Konvektions-Diffusions-Probleme auf einer Klasse von Shishkin-Typ-Gittern. Im eindimensionalen Fall wird nachgewiesen, dass das Verfahren von (fast) zweiter Ordnung, gleichmäßig bezüglich des Diffusionsparameters $\epsilon$ konvergiert. Zur Konvergenzanalyse für das zweidimensionale Modellproblem werden verschiedene Techniken diskutiert. In einem Spezialfall kann auf einem stückweise uniformen Shishkin-Gitter die $\epsilon$-gleichmäßige Konvergenz des Verfahrens von fast zweiter Ordnung gezeigt werden. Ferner sind die bisher bekannten Stabilitätsaussagen und ihre Verwendung zur Konvergenzanalysis der betrachteten Differenzenverfahren sowie Methoden zur Analyse von Defektkorrekturverfahren zusammengestellt. Einige Bemerkungen zu Defektkorrekturverfahren und Finite-Elemente-Methoden schließen die Arbeit ab. Numerische Experimente untermauern die theoretischen Resultate. / We consider a defect correction method that combines a first-order upwinded difference scheme with a second-order central difference scheme for model singularly perturbed convection-diffusion problems in one and two dimensions on a class of Shishkin-Type meshes. In one dimension, the method is shown to be convergent uniformly in the diffusion parameter $\epsilon$ of second order in the discrete maximum norm. To analyze the two-dimensional case, we discuss several proof techniques for defect correction methods. For a special problem with constant coefficients on a piecewise uniform Shishkin-mesh we can show the second order convergence of the considered scheme, uniformly with respect to the diffusion parameter. Moreover the known stability properties and their impact on the convergence analysis of the considered differnce schemes are compiled. Some remarks on defect correction and finite elements conclude the theses. Numerical experiments support our theoretical results.

Cette thèse porte sur la modélisation, pour le contrôle, des profils de compositions dans les colonnes de distillation cryogénique. Nous obtenons un modèle non-linéaire de convection-diffusion par réduction d'un modèle d'équations-bilans singulièrement perturbé. Du point de vue de l'automatique, nous nous intéressons à la stabilité des profils de compositions résultants, ainsi qu'à leur observabilité. Du point de vue du procédé, la nouvauté de notre modèle réside dans la prise en compte d'une efficacité de garnissage dépendant des conditions d'opération de la colonne. Le modèle est validé par des comparaisons avec des données de fonctionnement dynamique issues d'une unité de séparation réelle, pour la séparation d'un mélange binaire. Sur le cas plus complexe d'une cascade de colonnes séparant un mélange ternaire, le modèle montre une grande sensibilité aux erreurs d'estimation des taux de reflux. Des résultats adaptés du champ de la chromatographie nous permettent de relier cette sensibilité à des erreurs d'estimation des vitesses d'ondes de compositions cohérentes. En parallèle, nous proposons et testons également un modèle de fonctions de transfert simple (fondé sur des gains statiques et des retards purs uniquement) pour les petites dynamiques de compositions, qui dépend explicitement de valeurs mesurables ou observables sur le procédé

Made available in DSpace on 2016-12-23T14:37:34Z (GMT). No. of bitstreams: 1 ANGELO ANTONIO CAMPOS.pdf: 660395 bytes, checksum: 449c13f957ade5ea58be1aee63b345e2 (MD5) Previous issue date: 2007-03-30 / The interest in studying problems of underground drainage and solutos transport not in soils saturated it has been increasing significantly in the last years, mainly because of the growing concern with the quality of the soil and of the environment in general. Applied fertilizers in agricultural lands move below the zone radicular of the plants and they can contaminate underground water tables and aqüíferos. One of the most significant challenges of the current agriculture is the increase of the competitiveness associated to the preservation of the environment, allowing maintainable benefits in the agricultural explorations. The impact of pollutants in the quality of the underground water has been research object and of public health, especially in areas where she is to main source of drinking water. The mathematical models appear as useful tool in the prediction of as and when she should proceed the irrigation and the behavior of the solutos in solo.Devido to the complexity involved in these physical phenomena, it is used now beside the experimental work, the numeric simulation as forecast tool. The numeric simulation of the problem of infiltration of water and solutos in soil not saturated it is of great importance, because the growth of the agricultural production demands transformations with technological innovations that allow the improvement of the productivity of the cultures. To simulate the transport transiente of fertilizers, defensive, herbicidas and pollutant in an agricultural soil not saturated it is necessary the solution of two equations you not differentiate lineal. One of them is the equation of Richards, that governs the movement of water in the soil and, after your solution for a certain time, the results obtained for humidity, they are used for the solution of the other equation that treats of the transport of a certain soluto in matter. This work had for objective, to solve the proposed model of infiltration of water and soluto in the soil for the method of finite volumes, being used programming FORTRAN 90, to treat the case of the non linearidade of the movement of the water and a certain soluto not in soils saturated. Among the analyzed solutos, we used samples of abrasive mud coming of the sawmills and politrizes of the companies of marbles and granites of the municipal district of Cachoeiro of Itapemirim, where several rehearsals and analyses were accomplished, to feed the program and to evaluate the material in subject it is a pollutant in potential of the soil. The proposed method was shown appropriate to solve problems of infiltration of water and solutos transport not in soils saturated. / O interesse em estudar problemas de escoamento subterrâneo e transporte de solutos em solos não saturados tem aumentado significativamente nos últimos anos, principalmente por causa da preocupação crescente com a qualidade do solo e do meio ambiente em geral. Fertilizantes aplicados em terras agrícolas movem-se abaixo da zona radicular das plantas e podem contaminar lençóis de água subterrâneos e aqüíferos. Um dos desafios mais significativos da agricultura atual é o aumento da competitividade associada à preservação do meio ambiente, permitindo benefícios sustentáveis nas explorações agrícolas. O impacto de contaminantes na qualidade da água subterrânea tem sido objeto de pesquisa e de saúde pública, especialmente em regiões onde ela é a principal fonte de água potável. Os modelos matemáticos surgem como ferramenta útil na predição de quanto e quando se deve proceder a irrigação e o comportamento dos solutos no solo.Devido à complexidade envolvida nestes fenômenos físicos, utiliza-se atualmente ao lado do trabalho experimental, a simulação numérica como ferramenta de previsão. A simulação numérica do problema de infiltração de água e solutos em solo não saturado é de grande importância, pois o crescimento da produção agrícola exige transformações com inovações tecnológicas que permitam a melhoria da produtividade das culturas. Para simular o transporte transiente de fertilizantes, defensivos, herbicidas e poluentes num solo agrícola não saturado é necessária a solução de duas equações diferenciais não lineares. Uma delas é a equação de Richards, que governa o movimento de água no solo e, após a sua solução para um determinado tempo, os resultados obtidos para umidade, são empregados para a solução da outra equação que trata do transporte de um determinado soluto em particular. Este trabalho teve por objetivo, resolver o modelo proposto de infiltração de água e soluto no solo pelo método de volumes finitos, utilizando-se programação FORTRAN 90, para tratar o caso da não inearidade da movimentação da água e um determinado soluto em solos não saturados. Dentre os solutos analisados, utilizamos amostras de lama abrasiva provenientes das serrarias e politrizes das empresas de mármores e granitos do município de Cachoeiro de Itapemirim, onde foram realizados vários ensaios e análises, para alimentar o x programa e avaliar se o material em questão é um contaminante em potencial do solo. O método proposto mostrou-se adequado para resolver problemas de infiltração de água e transporte de solutos em solos não saturados.

We present the analysis for the higher order continuous Galerkin−Petrov (cGP) time discretization schemes in combination with the one-level local projection stabilization in space applied to time-dependent convection-diffusion-reaction problems. Optimal a priori error estimates will be proved. Numerical studies support the theoretical results. Furthermore, a numerical comparison between continuous Galerkin−Petrov and discontinuous Galerkin time discretization schemes will be given.