Understanding the electronic structure and dynamics of cyclic organic molecules is becoming increasingly the subject of investigations from different perspectives due to their unique chemical and physical properties. Since they are largely involved in the biochemistry of living organisms, studies on this class of compounds are also valuable to understand biologically relevant complex systems. Compared to other techniques, high-order harmonic generation (HHG) has been increasingly considered as a powerful spectroscopic tool with Angstrom spatial and attosecond temporal resolutions. This thesis demonstrates that high-order harmonic spectroscopy is capable of providing structural and dynamical information on the electronic systems of representative cyclic organic molecules comprising randomly oriented five-membered or six-membered rings. The first part of this thesis shows that the HHG from these molecules is sensitive to their aromatic character, which results from the de-localized pi electrons, and can potentially be a useful qualitative measure of aromaticity. We show that the advantage of utilizing HHG in this direction stems from the result that only pi molecular orbitals, associated with aromatcity, are responsible for the HHG emission in aromatic systems. The capability of HHG to distinguish cyclic isomers is demonstrated in the case of xylene molecules. Supported by numerical calculations, differences in the isomers are attributed to both tunnel ionization and photorecombination, the first and last steps of HHG. These results enable further HHG-based time-resolved studies of the dynamics associated with isomeric effects that these molecules exhibit. The present work also challenges the well-established prediction that strong field ionization from a molecular orbital is suppressed along nodal planes, where the electron density is zero. In fact, our study shows that considerable tunnel ionization in some cyclic molecules can occur near or along nodal planes. This unusual ionization is reported to have its signature on the quantitative and qualitative dependence of harmonic yield on laser ellipticity. The high symmetry displayed by the cyclic molecule, 1,4 cyclohexadiene, is shown to leave its imprints on the HHG in the form of structural interferences even if the target is randomly oriented. Two-color HHG from this molecule also indicates that hole dynamics could be involved in the generation process. A general study on high harmonic spectroscopy of the Cooper minimum in molecules is also reported. The presence of this minimum could affect the interpretation of harmonics spectra in any molecule containing S or Cl atoms. The molecular environment is shown to influence the position of this spectral modulation.

A representação de malhas por meio de estrutura de dados e operadores topológicos e um dos focos principais da modelagem geométrica, onde permite uma implementação robusta e eficiente de mecanismos de refinamento adaptativo, alinhamento de células e acesso as relações de incidência e adjacência entre os elementos da malha, o que é de grande importância na maioria das aplicações em mecânica dos fluidos. No caso de malhas não estruturadas, a não uniformidade da decomposição celular e melhor representada por uma estrategia mais sofisticada, que são as estruturas de dados topológicas. As estruturas de dados topológicas indexam elementos de uma malha representando relações de incidência e adjacência entre elementos, garantindo acesso rápido às informações. Um dos aspectos mais comuns aos problemas tratados pela mecânica dos fluidos computacional é a complexidade da geometria do domínio onde ocorre o escoamento. O uso de estruturas de dados para manipular malhas computacionais e de grande importância pois realiza de modo eficiente as consultas às informações da malha e centraliza todas as operações sobre a malha em um único módulo, possibilitando sua extensão e adaptação em diversas situações. Este trabalho visou explorar o acoplamento de uma estrutura de dados topológica, a Mate Face, em um módulo simulador existente, de modo a gerenciar todos os acessos à malha e dispor operações e iteradores para pesquisas complexas nas vizinhanças de cada elemento na malha. O módulo simulador resolve as equações governantes da mecânica dos fluidos através da técnica de volumes finitos. Foi utilizada uma formulação que atribui os valores das propriedades aos centroides dos volumes de controle, utiliza métodos de alta ordem, os esquemas ENO e WENO, que tem a finalidade de capturar com eficiência descontinuidades presentes em problemas governados por equações diferenciais parciais hiperbólicas. As equações de Euler em duas dimensões representam os escoamentos de interesse no presente trabalho. O acoplamento da estrutura de dados Mate Face ao simulador foi realizada através da criação de uma biblioteca desenvolvida que atua como uma interface de comunicação entre os dois módulos, a estrutura de dados e o simulador, que foram implementados em diferentes linguagens de programação. Deste modo, todas as funcionalidades existentes na Mate Face tornaram-se acessíveis ao simulador na forma de procedimentos. Um estudo sobre malhas dinâmicas foi realizado envolvendo o método das molas para movimentação de malhas simulando-se operações de arfagem. A idéia foi verificar a aplicabilidade deste método para auxiliar simulações de escoamentos não estacionarios. Uma outra vertente do trabalho foi estender a estrutura Mate Face de forma a representar elementos não suportados a priori, de modo a flexibilizar o seu uso em simulações de escoamentos baseados no método de volumes finitos espectrais. O método dos volumes espectrais e utilizado para se obter alta resolução espacial do domínio computacional, que também atribui valores das propriedades aos centroides dos volumes de controle, porém, os volumes de controle são particionados em volumes menores de variadas topologias. Assim, uma extensão da Mate Face foi desenvolvida para representar a nova malha para a aplicação do método, representando-se cada particionamento localmente em cada volume espectral. Para todas as etapas deste trabalho, realizaram-se experimentos que validaram a utilizaação da estrutura de dados Mate Face junto a métodos numéricos. Desta forma, a estrutura pode auxiliar as ferramentas de simulações de escoamentos de fluidos no gerenciamento e acesso à malha computacional / The storage and access of grid files by data structures and topologic operators is one of the most important goals of geometric modeling research field, which allows an efficient and stable implementation of adaptive refinement mechanisms, cells alignment and access to incidence and adjacency properties from grid elements, representing great concernment in the majority of applications from fluid mechanics. In the case of non-structured grids, the cellular decomposition if non-uniform and is better suited by a more sophisticated strategy - the topologic data structs. The topologic data structs index grid elements representing incidence and adjacency properties from grid elements, ensuring quick access to information. One of most common aspects from problems solved by computational fluid mechanic is the complexity of the domain geometry where the fluid ows. The usage of data structures to manipulate computational grids is of great importance because it performs efficiently queries on grid information and centers all operations to the grid on a unique module, allowing its extension and flexible usage on many problems. This work aims at exploring the coupling of a topologic data structure, the Mate Face, on a solver module, by controlling all grid access providing operators and iterators that perform complex neighbor queries at each grid element. The solver module solves the governing equations from fluid mechanics though the finite volume technique with a formulation that sets the property values to the control volume centroids, using high order methods - the ENO and WENO schemes, which have the purpose of efficiently capture the discontinuities appearing in problems governed by hyperbolic conservation laws. The two dimensional Euler equations are considered to represent the flows of interest. The coupling of the Mate Face data structure to the solver module was achieved by a creation of a library that acts as an interface layer between both modules, the Mate Face and the solver, which had been implemented using different programming languages. Therefore, all Mate Face class methods are available to the solver module though the interface library in the form of procedures. A study of dynamic grids was made by using spring methods for the moving grid under pitch movement case. The goal was to analyze the applicability of such method to aid non stationary simulations. Another contribution of this work was to show how the Mate Face can be extended in order to deal with non-supported types of elements, allowing it to aid numeric simulations using the spectral finite volume method. The spectral nite volume method is used to obtain high spatial resolution, also by setting the property values to the control volume centroids, but here the control volumes are partitioned into smaller volumes of different types, from triangles to hexagons. Then, an extension of the Mate Face was developed in order to hold the new generated grid by the partitioning specfied by the spectral finite volume method. The extension of Mate Face represents all partitioned elements locally for each original control volume. For all implementations and proposals from this work, experiments were performed to validate the usage of the Mate Face along with numeric methods. Finally, the data structure can aid the fluid flow simulation tools by managing the grid file and providing efficient query operators

The object of this work is to meet readers with the basic principle and solution of high order digital modulator with integrated circuit AD9957 produced by the company Analog Devices. Block diagram and final scheme of the modulator and device construction is presented. Standard USB interface for communication, control and data transmission between modulator and host represented by personal computer is applied. The project describes following parts of the designed system: PCB layout, control firmware of MCU and application program running under PC. In the conclusion, chosen results of measurement are described and evaluated.

<div>The Boltzmann equation, an integro-differential equation for the molecular distribution function in the physical and velocity phase space, governs the fluid flow behavior at a wide range of physical conditions, including compressible, turbulent, as well as flows involving further physics such as non-equilibrium internal energy exchange and chemical reactions. Despite its wide applicability, deterministic solutions of the Boltzmann equation present a huge computational challenge, and often the collision operator is simplified for practical reasons, hereby, referred to as linear kinetic models. These models utilize the moment of the underlying probability distribution to mimic some properties of the original collision operator. But, just because we know the moments of a distribution, doesn't mean we know the actual distribution. The approximation of reality can never supersede the reality itself. Because, all the facts (moments) about the world (distribution) cannot explain the world. The premise lies not in the fact that a certain flow behavior can be correctly predicted; but rather that the Boltzmann equation can reveal and explain previously unsuspected aspects of reality.</div><div><br></div><div>Therefore, in this work, we introduce accurate, efficient, and robust numerical schemes for solving the multi-species Boltzmann equation which can model general repulsive interactions. These schemes are high order spatially and temporally accurate, spectrally accurate in molecular velocity space, exhibit nearly linear parallel efficiency on the current generation of processors; and can model a wide-range of rarefied flows including flows involving momentum, heat, and diffusive transport. The single-species variant formed the basis of author's Masters' thesis.</div><div><br></div><div>While the first part of the dissertation is targeted towards multi-species flows that exhibit rich non-equilibrium phenomenon; the second part focuses on single-species flows that do not depart significantly from equilibrium. This is the case, for example, in micro-nozzles, where a portion of flow can be highly rarefied, whereas others can be in near-continuum regime. However, when the flow is in near-continuum regime, the traditional deterministic numerical schemes for kinetic equations encounter two difficulties: a) since the near-continuum is essentially an effect of large number of particles in an infinitesimal volume, the average time between successive collisions decrease, and therefore the discrete simulation timestep has to be made smaller; b) since the number of molecular collisions increase, the flow acquires steady state slowly, and therefore one needs to carry out time integration for large number of time steps. Numerically, the underlying issue stems from stiffness of the discretized ordinary differential equation system. This situation is analogous to low Reynolds number scenario in traditional compressible Navier-Stokes simulations. To circumvent these issues, we introduce a class of high order spatially and temporally accurate implicit-explicit schemes for single-species Boltzmann equation and related kinetic models with the following properties: a) since the Navier-Stokes can be derived from the asymptotics of the Boltzmann equation (using Chapman-Enskog expansion~\cite{cercignani2000rarefied}) in the limit of vanishing rarefaction, these schemes preserve the transition from Boltzmann to Navier-Stokes; b) the timestep is independent of the rarefaction and therefore the scheme can handle both rarefied and near-continuum flows or combinations thereof; c) these schemes do not require iterations and therefore are easy to scale to large problem sizes beyond thousands of processors (because parallel efficiency of Krylov space iterative solvers deteriorate rapidly with increase in processor count); d) with use of high order multi-stage time-splitting, the time integration over sufficiently long number of timesteps can be carried out more accurately. The extension of the present methodology to the multi-species case can be considered in the future. </div><div><br></div><div>A series of numerical tests are performed to illustrate the efficiency and accuracy of the proposed methods. Various benchmarks highlighting different scattering models, different mass ratios, momentum transport, heat transfer, and diffusive transport have been studied. The results are directly compared with the direct simulation Monte Carlo (DSMC) method. As an engineering use-case, the developed methodology is applied for the study of thermal processes in micro-systems, such as heat transfer in electronic-chips; and primarily, the ingeniously Purdue-developed, Microscale In-Plane Knudsen Radiometric Actuator (MIKRA) sensor, which can be used for flow actuation and measurement.</div>

Development of a novel high-order flux correction method on strand grids is presented. The method uses a combination of flux correction in the unstructured plane and summation-by-parts operators in the strand direction to achieve high-fidelity solutions. Low-order truncation errors are cancelled with accurate flux and solution gradients in the flux correction method, thereby achieving a formal order of accuracy of 3, although higher orders are often obtained, especially for highly viscous flows. In this work, the scheme is extended to high-Reynolds number computations in both two and three dimensions. Turbulence closure is achieved with a robust version of the Spalart-Allmaras turbulence model that accommodates negative values of the turbulence working variable, and the Menter SST turbulence model, which blends the k-ε and k-ω turbulence models for better accuracy. A major advantage of this high-order formulation is the ability to implement traditional finite volume-like limiters to cleanly capture shocked and discontinuous flow. In this work, this approach is explored via a symmetric limited positive (SLIP) limiter. Extensive verification and validation is conducted in two and three dimensions to determine the accuracy and fidelity of the scheme for a number of different cases. Verification studies show that the scheme achieves better than third order accuracy for low and high-Reynolds number flow. Cost studies show that in three-dimensions, the third-order flux correction scheme requires only 30% more walltime than a traditional second-order scheme on strand grids to achieve the same level of convergence. In order to overcome meshing issues at sharp corners and other small-scale features, a unique approach to traditional geometry, coined "asymptotic geometry," is explored. Asymptotic geometry is achieved by filtering out small-scale features in a level set domain through min/max flow. This approach is combined with a curvature based strand shortening strategy in order to qualitatively improve strand grid mesh quality.

No description available.

Truncation errors and computational cost are obstacles that still hinder large-scale applications of the Computational Fluid Dynamics method. The discontinuous Galerkin method is one of the high-order schemes utilized extensively in recent years, which is locally conservative, stable, and high-order accurate. Besides that, it can handle complex geometries and irregular meshes with hanging nodes. In this document, the nondimensional compressible Euler equations and Reynolds- Averaged Navier-Stokes equations are discretized by discontinuous Galerkin methods with a two-equations turbulence model on both structured and unstructured meshes. The traditional equation of state for an ideal gas model is substituted by a multispecies thermodynamics model in order to complete the governing equations. An approximate Riemann solver is used for computing the convective flux, and the diffusive flux is approximated with some internal penalty based schemes. The temporal discretization of the partial differential equations is either performed explicitly with the aid of Rung-Kutta methods or with semi-implicit methods. Inspired by the artificial viscosity diffusion based limiter for shock-capturing method, which has been extensively studied, a novel and robust technique based on the introduction of mass diffusion to the species governing equations to guarantee that the species mass fractions remain positive has been thoroughly investigated. This contact-surface-capturing method is conservative and a high order of accuracy can be maintained for the discontinuous Galerkin method. For each time step of the algorithm, any trouble cell is first caught by the contact-surface discontinuity detector. Then some amount of mass diffusions are added to the governing equations to change the gas mixtures and arrive at an equilibrium point satisfying some conditions. The species properties are reasonable without any oscillations. Computations are performed for many steady and unsteady flow problems. For general non-mixing fluid flows, the classical air-helium shock bubble interaction problem is the central test case for the high-order discontinuous Galerkin method with a mass diffusion based limiter chosen. The computed results are compared with experimental, exact, and empirical data to validate the fluid dynamic solver.

This dissertation focuses on the development of adaptive time-stepping and high-order parallel stages exponential Runge–Kutta methods for discretizing stiff partial differential equations (PDEs). The design of exponential Runge–Kutta methods relies heavily on the existing stiff order conditions available in the literature, primarily up to order 5. It is well-known that constructing higher-order efficient methods that strictly satisfy all the stiff order conditions is challenging. Typically, methods up to order 5 have been derived by relaxing one or more order conditions, depending on the desired accuracy level. Our approach will be based on a comprehensive investigation of these conditions. We will derive novel and efficient exponential Runge–Kutta schemes of orders up to 5, which not only fulfill the stiff order conditions in a strict sense but also support the implementation of variable step sizes. Furthermore, we develop the first-ever sixth-order exponential Runge–Kutta schemes by leveraging the exponential B-series theory. Notably, all the newly derived schemes allow the efficient computation of multiple stages, either simultaneously or in parallel. To establish the convergence properties of the proposed methods, we perform an analysis within an abstract Banach space in the context of semigroup theory. Our numerical experiments are given on parabolic PDEs to confirm the accuracy and efficiency of the newly constructed methods.

DNA中の二本鎖切断(DSB)に対するアスコルビン酸(AA)およびDMSOの保護効果を、蛍光顕微鏡による巨大DNA(T4 DNA; 166kbp)の単分子観察によって評価した。凍結／解凍の状態に対して3つの異なる形態の放射源、可視光、γ線、および超音波の環境下にさらした。1‐プロパノールと2‐プロパノールの間で異なる効果が表れた。ゲノムDNA分子の高次構造の変化は、1−プロパノールを用いると、長軸長が濃度60％で最小を示し、次にアルコール含有量の増加と共に増加する傾向があることを見出した。一方、2−プロパノールを用いると、長軸長はアルコール含有量の増加と共にほぼ単調な減少を示した。 / The protective effect of ascorbic acid (AA) and DMSO against double-strand breaks (DSBs) in DNA was evaluated by single-molecule observation of giant DNA (T4 DNA; 166kbp) through fluorescence microscopy. Samples were exposed to three different forms of radiation: visible light, γ-ray, and ultrasound or freeze/thawing. The change of the higher-order structure of genomic DNA molecules in the presence of alcohols by use of single DNA observation with fluorescence microscopy, by focusing our attention to unveil the different effect between 1-propanol and 2-propanol. / 博士(工学) / Doctor of Philosophy in Engineering / 同志社大学 / Doshisha University

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