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New quantitative methods are developed for analyser-based phase contrast imaging (ABI) with hard X-rays. In the first instance we show that quantitative ABI may be implemented using an extended incoherent source. Next, we outline how complex Green’s functions may be reconstructed from phase contrast images and we apply this method to reconstruct the thick perfect crystal Green’s function associated with an ABI imaging system. The use of quantitative ABI with incoherent X-ray sources is not widespread and the first set of results pertains to the feasibility of quantitative ABI imaging and phase retrieval using a rotating anode X-ray source. The necessary conditions for observation of ABI phase contrast are deduced from elementary coherence considerations and numerical simulations. We then focus on the problem of extracting quantitative information from ABI images recorded using an extended incoherent X-ray source. The results of an experiment performed at Friedrich-Schiller University, Germany using a rotating anode X-ray source demonstrate the validity of our approach. It is shown that quantitative information may be extracted from such images under quite general and practicable conditions. We then develop a new use for phase contrast imaging systems that allows the Green’s function associated with a linear shift-invariant imaging system to be deduced from two phase contrast images of a known weak object. This new approach is applied to X-ray crystallography where the development of efficient methods of inferring the phase of rocking curves is an important open problem. We show how the complex Green’s function describing Bragg reflection of a coherent scalar X-ray wavefield from a crystal may be recovered from a single image over a wide range of reciprocal space simultaneously. The solution we derive is fast, non-iterative and deterministic. When applied to crystalline structures for which the kinematic scattering approximation is valid, such as thin crystalline films, our technique is shown to solve the famous one-dimensional phase retrieval problem which allows us to directly invert the Green’s function to retrieve the depth-dependent interplanar spacing. Finally we implement our Green’s function retrieval method on experimental data collected at the SPring-8 synchrotron in Hyogo, Japan. In the experiment we recorded analyser-based phase contrast images of a known weak object using a thick perfect silicon analyser crystal. It is then demonstrated that these measurements can be inverted to recover the complex Green’s function associated with the analyser crystal Bragg peak. The reconstructed Green’s function is found to be in good agreement with the prediction of dynamical diffraction theory.

Um novo critério, proposto por Jorge Navaza a partir de considerações teóricas para resolver o problema das fases, é avaliado numericamente. Este critério se baseia na propriedade de atomicidade da função densidade eletrônica, generalizando resultados obtidos por Goedkoop. O problema das fases é resolvido teoricamente pela minimização de uma função, R, que é formada pela soma dos menores autovalores de uma matriz, Q, construída a partir de todos os fatores de estrutura observados. O conjunto de fases procurado é aquele que minimiza R. Como a matriz Q depende em forma relativamente complexa do grupo de simetria espacial do cristal, teoria dos grupos é utilizada para reduzir a ordem desta matriz. O algoritmo e a implantação computacional do cálculo da função R, juntamente com testes numéricos que demonstram a utilidade do critério de Navaza, são descritos em detalhe. Como corolário, que pode talvez resultar de grande importância prática, é mostrado que a função R pode ser utilizada como uma nova figura de mérito nos métodos diretos por multissolução clássicos. Finalmente, é desenvolvida a álgebra correspondente ao cálculo do gradiente da função R, indicando a direção de trabalhos futuros / A new criterion, proposed by Jorge Navaza from theoretical considerations to solve the Phase Problem, is numerically tested. The criterion is based on the atomicity property of the electron density function, generalizing previous results by Goedkoop. The Phase Problem is theoretically solved by the minimization of a function, R, which is formed from the sum of the smallest eigenvalues of a matrix Q, constructed from the set of all observed structure factors. The sought set of phases is that which minimizes R. Because the matrix Q depends in a relatively complex fashion on the space group of the crystal, group theory is employed to reduce the order of Q. The algorithm and computational implementation for the calculation of R, together with numerical tests which demonstrate the usefulness of Navaza´s criterion, are described in detail. As a corollary, that might turn out to be of a practical importance, it is shown that the minimum value of the function R can be used as a novel Figure of Merit in the classical Multisolution Direct Methods. Finally, the rather complex algebra necessary for the calculation of the gradient of the function R is developed, indicating also the possible trends for future work

On the first part, we consider nonlinear operators I depending on a family of nonlocal linear operators [mathematical equations]. We study the solutions of the Dirichlet initial and boundary value problems [mathematical equations]. We do not assume even symmetry for the kernels. The odd part bring some sort of nonlocal drift term, which in principle competes against the regularization of the solution. Existence and uniqueness is established for viscosity solutions. Several Hölder estimates are established for u and its derivatives under special assumptions. Moreover, the estimates remain uniform as the order of the equation approaches the second order case. This allows to consider our results as an extension of the classical theory of second order fully nonlinear equations. On the second part, we study two phase problems posed over a two dimensional cone generated by a smooth curve [mathematical symbol] on the unit sphere. We show that when [mathematical equation] the free boundary avoids the vertex of the cone. When [mathematical equation]we provide examples of minimizers such that the vertex belongs to the free boundary. / text

abstract: Phase problem has been long-standing in x-ray diffractive imaging. It is originated from the fact that only the amplitude of the scattered wave can be recorded by the detector, losing the phase information. The measurement of amplitude alone is insufficient to solve the structure. Therefore, phase retrieval is essential to structure determination with X-ray diffractive imaging. So far, many experimental as well as algorithmic approaches have been developed to address the phase problem. The experimental phasing methods, such as MAD, SAD etc, exploit the phase relation in vector space. They usually demand a lot of efforts to prepare the samples and require much more data. On the other hand, iterative phasing algorithms make use of the prior knowledge and various constraints in real and reciprocal space. In this thesis, new approaches to the problem of direct digital phasing of X-ray diffraction patterns from two-dimensional organic crystals were presented. The phase problem for Bragg diffraction from two-dimensional (2D) crystalline monolayer in transmission may be solved by imposing a compact support that sets the density to zero outside the monolayer. By iterating between the measured stucture factor magnitudes along reciprocal space rods (starting with random phases) and a density of the correct sign, the complex scattered amplitudes may be found (J. Struct Biol 144, 209 (2003)). However this one-dimensional support function fails to link the rod phases correctly unless a low-resolution real-space map is also available. Minimum prior information required for successful three-dimensional (3D) structure retrieval from a 2D crystal XFEL diffraction dataset were investigated, when using the HIO algorithm. This method provides an alternative way to phase 2D crystal dataset, with less dependence on the high quality model used in the molecular replacement method. / Dissertation/Thesis / Doctoral Dissertation Physics 2016

Um novo critério, proposto por Jorge Navaza a partir de considerações teóricas para resolver o problema das fases, é avaliado numericamente. Este critério se baseia na propriedade de atomicidade da função densidade eletrônica, generalizando resultados obtidos por Goedkoop. O problema das fases é resolvido teoricamente pela minimização de uma função, R, que é formada pela soma dos menores autovalores de uma matriz, Q, construída a partir de todos os fatores de estrutura observados. O conjunto de fases procurado é aquele que minimiza R. Como a matriz Q depende em forma relativamente complexa do grupo de simetria espacial do cristal, teoria dos grupos é utilizada para reduzir a ordem desta matriz. O algoritmo e a implantação computacional do cálculo da função R, juntamente com testes numéricos que demonstram a utilidade do critério de Navaza, são descritos em detalhe. Como corolário, que pode talvez resultar de grande importância prática, é mostrado que a função R pode ser utilizada como uma nova figura de mérito nos métodos diretos por multissolução clássicos. Finalmente, é desenvolvida a álgebra correspondente ao cálculo do gradiente da função R, indicando a direção de trabalhos futuros / A new criterion, proposed by Jorge Navaza from theoretical considerations to solve the Phase Problem, is numerically tested. The criterion is based on the atomicity property of the electron density function, generalizing previous results by Goedkoop. The Phase Problem is theoretically solved by the minimization of a function, R, which is formed from the sum of the smallest eigenvalues of a matrix Q, constructed from the set of all observed structure factors. The sought set of phases is that which minimizes R. Because the matrix Q depends in a relatively complex fashion on the space group of the crystal, group theory is employed to reduce the order of Q. The algorithm and computational implementation for the calculation of R, together with numerical tests which demonstrate the usefulness of Navaza´s criterion, are described in detail. As a corollary, that might turn out to be of a practical importance, it is shown that the minimum value of the function R can be used as a novel Figure of Merit in the classical Multisolution Direct Methods. Finally, the rather complex algebra necessary for the calculation of the gradient of the function R is developed, indicating also the possible trends for future work

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