The work described in this dissertation was motivated by a desire to better understand the cellular pathology of ischemic stroke. Two of the three bodies of research presented herein address and issue directly related to the investigation of ischemic stroke through the use of diffusion weighted magnetic resonance imaging (DWMRI) methods. The first topic concerns the development of a computationally efficient finite difference method, designed to evaluate the impact of microscopic tissue properties on the formation of DWMRI signal. For the second body of work, the effect of changing the intrinsic diffusion coefficient of a restricted sample on clinical DWMRI experiments is explored. The final body of work, while motivated by the desire to understand stroke, addresses the issue of acquiring large amounts of MRI data well suited for quantitative analysis in reduced scan time. In theory, the method could be used to generate quantitative parametric maps, including those depicting information gleaned through the use of DWMRI methods. Chapter 1 provides an introduction to several topics. A description of the use of DWMRI methods in the study of ischemic stroke is covered. An introduction to the fundamental physical principles at work in MRI is also provided. In this section the means by which magnetization is created in MRI experiments, how MRI signal is induced, as well as the influence of spin-spin and spin-lattice relaxation are discussed. Attention is also given to describing how MRI measurements can be sensitized to diffusion through the use of qualitative and quantitative descriptions of the process. Finally, the reader is given a brief introduction to the use of numerical methods for solving partial differential equations. In Chapters 2, 3 and 4, three related bodies of research are presented in terms of research papers. In Chapter 2, a novel computational method is described. The method reduces the computation resources required to simulate DWMRI experiments. In Chapter 3, a detailed study on how changes in the intrinsic intracellular diffusion coefficient may influence clinical DWMRI experiments is described. In Chapter 4, a novel, non-steady state quantitative MRI method is described.

Optical precursor is the sharp optical pulse front that does not show delay in absorptive media. In this thesis, optical precursor behavior in rubidium (Rb) vapor was investigated in the picoseconds regime. An amplified femtosecond laser was shaped to a 7-ps square pulse with sharp rising and trailing edges. This pulse was then sent into a hot rubidium vapor, and the center frequency of the laser pulse was absorbed. The output pulses were measured by a fast streak camera with 2-picosecond resolution. By varying the temperature of the Rb vapor, the measured pulse shapes showed the progression of formation of optical precursors. The measured pulses shapes showed good agreement with theory. On the other hand, a connection between optical precursors and femtosecond laser pumped 3-photon superradiance was investigated in this thesis. Maxwell-Bloch equations were numerically solved in two steps with commercial software Mathematica 8. A good agreement was found between simulation and experiment. It was confirmed that, at low excitation regime, superradiance generated from hot rubidium vapor, which were pumped by a femtosecond laser, can be understood as the formation of optical precursors.

The semiconductor Bloch equations (SBEs) are an insightful and well-established formalism for studying light-matter interactions in solids. When Coulomb interactions between electrons are omitted, the SBEs are simplified to a single particle model. The SBEs in this single electron approximation have been used extensively to model strong-field interactions in condensed matter. The SBEs in the length gauge provide an intuitive and numerically efficient model of high harmonic generation (HHG) in solids. In this approach, the SBEs involve Berry connections and transition dipole moments, which are gauge dependent structural quantities. This thesis studies the role of gauge symmetry in the SBEs, and how it can be exploited to facilitate efficient numerical analysis of HHG in solids. In the length gauge, the macroscopic current describing HHG can be decomposed into physically intuitive contributions. In particular, this leads to a contribution known as the "mixture" current, which has been overlooked by the HHG community until recently. We study the influence of this contribution using the analytic tight-binding model for gapped graphene. We derive an analytic gauge transformation that removes singular behaviour from the gapped graphene model, thus enabling efficient numerical integration of the SBEs. We also present an alternative approach for simulating dynamics in tight-binding models. Instead of simulating the SBEs in the usual basis of Bloch functions, we transform to the basis in which the tight-binding Hamiltonian is represented. The dipole matrix elements necessarily vanish in this basis, and the SBEs can be integrated using only the Hamiltonian matrix elements. We first generalize the SBEs to accomodate a non-diagonal Hamiltonian matrix, and we demonstrate this formalism numerically using two different tight-binding models. Finally, we derive a novel formulation of the SBEs which involve only gauge invariant matrix elements. Specifically, the Berry connections and transition dipole phases are replaced by a gauge invariant quantity known as the shift vector. This yields a fully gauge invariant description of HHG in solids, and the shift vector provides intuitive insight for HHG in systems with broken inversion symmetry. Further, the ability to describe HHG solely in terms of gauge invariant quantities raises new possibilities for tomographic reconstruction of crystal band structure, and this idea is discussed as a possible direction of future work.

Vertical external-cavity surface-emitting lasers are ideal testbeds for studying the influence of the non-equilibrium many-body dynamics on mode locking. As we will show in this thesis, ultra short pulse generation involves a marked departure from Fermi carrier distributions assumed in prior theoretical studies. A quantitative model of the mode locking dynamics is presented, where the semiconductor Bloch equations with Maxwell’s equation are coupled, in order to study the influences of quantum well carrier scattering on mode locking dynamics. This is the first work where the full model is solved without adiabatically eliminating the microscopic polarizations. In many instances we find that higher order correlation contributions (e.g. polarization dephasing, carrier scattering, and screening) can be represented by rate models, with the effective rates extracted at the level of second Born-Markov approximations. In other circumstances, such as continuous wave multi-wavelength lasing, we are forced to fully include these higher correlation terms. In this thesis we identify the key contributors that control mode locking dynamics, the stability of single pulse mode-locking, and the influence of higher order correlation in sustaining multi-wavelength continuous wave operation.

A systematic study of microscopic many-body dynamics is used to analyze a strategy for how to generate ultrashort mode locked pulses in the vertical external-cavity surface-emitting lasers with a saturable absorber mirror. The field propagation is simulated using Maxwell's equations and is coupled to the polarization from the quantum wells using the semiconductor Bloch equations. Simulations on the level of second Born-Markov are used to fit coefficients for microscopic higher order correlation effects such as dephasing of the polarization, carrier-carrier scattering and carrier relaxation. We numerically examine recent published experimental results on mode locked pulses, as well as the self phase modulation in the gain chip and SESAM.

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Este trabalho aborda o problema da inversão do vetor momento magnético, com ampla aplicação na Ressonância Nuclear Magnética (RNM). Em vez de uma sequência de impulsos e de abordarmos somente o problema de conduzir o vetor de -e3 para +e3, escolhemos uma lei de controle limitada e analisamos o processo de várias iterações (voltas completas). Através do método da medianização, obtemos uma solução explícita aproximada para o sistema e, através dela e de alguns teoremas auxiliares sobre rotações, discutimos a propagação do erro em módulo e fase cometido após a realização dessas iterações. / This dissertation considers the problem of inversion of the magnetic moment vector, with wide application in Nuclear Magnetic Resonance (NMR). Instead of a pulse sequence and only approach the problem of driving the vector from -e3 to +e3, we choose limited controls and we analyze several iterations of the process (laps). By the averaging method, we obtain an approximate explicit solution for the system and through this method, together with some auxiliary theorems on rotations, we discuss the propagation of error in magnitude and phase committed after performing these iterations.

A metodologia GMAX, (Gradient-Modulated Adiabatic Excitation), caracteriza-se pelo uso de pulsos adiabáticos para localização de volumes em espectroscopia e seleção de fatias em MRI. A sua utilidade surge do interessante perfil de inversão da magnetização transversal induzido ao longo da amostra. Entretanto, a interpretação desse comportamento tem sido dada apenas de forma qualitativa, através da utilização da condição de adiabaticidade como ponto de partida. Neste trabalho é apresentada uma descrição analítica partindo da solução em termos da função hipergeométrica para os pulsos sech e tanh. A partir desse procedimento encontramos um conjunto de resultados com os quais é possível inferir analiticamente o comportamento característico da magnetização, tendo como objetivo obter um maior controle da magnetização a partir dos parâmetros da metodologia que proporcionam interpretação física. / The Gradient-Modulated Adiabatic Excitation (GMAX) methodology is characterized by the use of adiabatic pulses for volume localization in spectroscopy and slice selection in MRI. Its use derives from the interesting nodal point transverse magnetization profile induced throughout the sample. Nevertheless, the interpretation of such behavior for the magnetization has been of qualitative purpose only, using the adiabatic condition as a starting point. Here, we present an analytical description, starting from the solution in terms of the hypergeometric functions for sech and tanh pulses. From this procedure we found a set of results with which is possible to infer analytically the characteristic behavior of the magnetization. This is on the purpose of obtaining greater control of the magnetization from parameters of the methodology that carry physical interpretation.

Au cours des dernières décennies, l'angiographie par résonance magnétique a été utilisée comme routine clinique pour l'exploration précise et non invasive des vaisseaux sanguins, ainsi que pour le diagnostic des affections neurovasculaires les plus courantes. Plusieurs méthodes spécifiques ont été développées pour simuler numériquement le procédé de formation des angiographies. Cependant, à ce jour, la plupart des logiciels de simulation IRM avancés sont exclusivement spécialisés dans l'imagerie des tissus statiques. Le présent travail a donc été réalisé pour étendre les possibilités d'un logiciel existant afin de proposer un outil complet pour la simulation IRM des écoulements fluides. L'efficacité de cette approche est démontrée en reproduisant les principales séquences angiographiques et les artéfacts de flux les plus courants. Pour finir, des applications sur des simulations de flux sanguins dans des géométries de vaisseaux réalistes sont présentées. / During the last decades, magnetic resonance angiography has been used as a clinical routine for precise and non-invasive exploration of vessels, as well as for diagnosis of the most common neurovascular diseases. Several dedicated methods were developed to simulate specifically the process of angiographic acquisitions. Though, currently, most of advanced MRI simulators are exclusively specialized in static tissues imaging. This work was carried out to expand the possibilities of one of those simulators in order to propose a complete tool for MRI simulation of flow motion.The efficiency of this approach is proven by replicating the main angiographic pulse sequences and the most common flow artifacts. Finally, applications are provided on simulations of blood flow in realistic vessels geometries.