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

La profilométrie optique est une technique de métrologie de surface rapide et non destructive. Dans ce mémoire, nous avons abordé cette problématique par des méthodes inverses de diffraction électromagnétique et dans une configuration de type Microscopie Tomographique Optique par Diffraction (ODTM). La surface est sondée par un éclairement sous plusieurs angles d'incidences ; la mesure en amplitude et en phase du champ lointain diffracté constitue les données du problème. Des profils de surfaces ont été reconstruits en considérant différents modèles de diffraction, parmi lesquelles une méthode approchée fondée sur les approximations de diffusion simple et de paraxialité. La résolution latérale de cette méthode et des techniques classiques de profilométrie est limitée par le critère d'Abbe-Rayleigh, défini sur la base de l'ouverture numérique pour l'éclairement et la détection du champ. Afin de dépasser cette limite de résolution, nous avons développé une méthode itérative de Newton-Kantorovitch régularisée. L'opérateur de diffraction y est rigoureusement modélisé par une méthode des moments, résolution numérique des équations du formalisme intégral de frontière, et l'expression de la dérivée de Fréchet de cet opérateur est obtenue par la méthode des états adjoints, à partir du théorème de réciprocité. Pour les surfaces unidimensionnelles métalliques, notre technique permet d'inverser à partir de données synthétiques des surfaces très rugueuses avec une résolution au delà du critère d'Abbe-Rayleigh. / Optical profilometry is a nondestructive and fast noncontact surface metrology technique. In this thesis, we have tackled this issue with inverse scattering electromagnetic methods and in an Optical Digital Tomographic Microscopy (ODTM) configuration. The surface is probed with illuminations under several incidence angles; the measure of far scattered field amplitude and phase constitutes the problem data. Surface profiles have been reconstructed using different scattering models among which an approximate theory based on single scattering and paraxiality. The lateral resolution of this technique and classical profilometric approaches is limited by the so-called Abbe-Rayleigh's criterion defined out of the numerical aperture for illumination and field detection. In order to overpass this resolution limit, we have developed a regularized iterative Newton-Kantorovitch's method. The scattering operator is rigorously modelized with the method of moments, that is a numerical solution of boundary integral equations, and its Fréchet derivative adjoint states expression is deduced from the reciprocity theorem. For one-dimensional metallic surfaces, our method succeeds in inverting from synthetic data very rough surfaces with the resolutions beyond the Abbe-Rayleigh's criterion. The performance of this technique and inversion conditions clearly differ from one polarization to the other : in the TM case, interactions at longer distance than in the TE case improve yet the resolution. This work includes also an experimental validation of our inverse model on grooves in indium phosphure substrate at 633 nm.