Quantum chemistry is plagued by the presence of high-rank quantities, stemming from the N-body nature of the electronic Schrödinger equation. These high-rank quantities present a significant mathematical and computational barrier to the computation of chemical observables, and also drastically complicate the pedagogical understanding of important interactions between particles in a molecular system. The application of physically-motivated rank reduction approaches can help address these to problems. This thesis details recent efforts to apply rank reduction techniques in both of these arenas. With regards to computational tractability, the representation of the 1/r Coulomb repulsion between electrons is a critical stage in the solution of the electronic Schrödinger equation. Typically, this interaction is encapsulated via the order-4 electron repulsion integral (ERI) tensor, which is a major bottleneck in terms of generation, manipulation, and storage. Many rank reduction techniques for the ERI tensor have been proposed to ameliorate this bottleneck, most notably including the order-3 density fitting (DF) and pseudospectral (PS) representations. Here we detail a new and uniquely powerful factorization - tensor hypercontraction (THC). THC decomposes the ERI tensor as a product of five order-2 matrices (the first wholly order-2 compression proposed for the ERI) and offers great flexibility for low-scaling algorithms for the manipulations of the ERI tensor underlying electronic structure theory. THC is shown to be physically-motivated, markedly accurate, and uniquely efficient for some of the most difficult operations encountered in modern quantum chemistry. On the front of chemical understanding of electronic structure theory, we present our recent work in developing robust two-body partitions for ab initio computations of intermolecular interactions. Noncovalent interactions are the critical and delicate forces which govern such important processes as drug-protein docking, enzyme function, crystal packing, and zeolite adsorption. These forces arise as weak residual interactions leftover after the binding of electrons and nuclei into molecule, and, as such, are extremely difficult to accurately quantify or systematically understand. Symmetry-adapted perturbation theory (SAPT) provides an excellent approach to rigorously compute the interaction energy in terms of the physically-motivated components of electrostatics, exchange, induction, and dispersion. For small intermolecular dimers, this breakdown provides great insight into the nature of noncovalent interactions. However, SAPT abstracts away considerable details about the N-body interactions between particles on the two monomers which give rise to the interaction energy components. In the work presented herein, we step back slightly and extract an effective 2-body interaction for each of the N-body SAPT terms, rather than immediately tracing all the way down to the order-0 interaction energy. This effective order-2 representation of the order-N SAPT interaction allows for the robust assignment of interaction energy contributions to pairs of atoms or functional groups (the A-SAPT or F-SAPT partitions), allowing one to discuss the interaction in terms of atom- or functional-group-pairwise interactions. These A-SAPT and F-SAPT partitions can provide deep insight into the origins of complicated noncovalent interactions, e.g., by clearly shedding light on the long-contested question of the nature of the substituent effect in substituted sandwich benzene dimers.

Made available in DSpace on 2014-06-11T19:28:34Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-10-08Bitstream added on 2014-06-13T19:16:36Z : No. of bitstreams: 1 vaz_jcc_me_guara.pdf: 5428958 bytes, checksum: e1d1921d87641ec3a3cb1d276db73cbd (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O objetivo deste trabalho é desenvolver uma ferramenta computacional para a automatização de cálculo para o projeto estrutural de pórticos rolantes. Através de memorial de cálculo analítico, e de um modelo de pórtico rolante, pode ser rapidamente verificado quando ao limite do escoamento do material, suas propriedades geométricas e suas resistências mecânicas, orientando o usuário para a escolha do dimensional da estrutura. Optou-se pelo programa comercial Microsoft Excel, utilizando suas ferramentas e formulações internas, devido a sua facilidade de utilização, permitindo que várias alternativas sejam analisadas para escolha da que melhor atenda aos requisitos de projeto. Para facilitar o uso, as planilhas do Excel forma agrupadas em módulos, visando com isso desenvolver as atividades de informações de dados de forma simples, objetiva e integradas, a fim de se obter uma interface amigável e uma análise estrutural confiável. Para a validação desta ferramenta proposta de cálculo analítico foi utilizado o programa comercial de elementos finitos ANSYS, através da análise de alguns exemplos de pórticos rolantes / The objective of this work is to develop a computational tool to automate the calculation of the structural design of gantry cranes. Through Memorial analytical calculation, and a model gantry crane, can be fast verification against yield of material, its geometric properties and mechanical strength, guiding the user to choose the dimensional. We choose the commercial program Microsoft Excel using its tools and internal formulations due to its ease of use, allowing multiple alternatives are analyzed to choose the one that best meets the design requirements. For ease of use, so Excel spreadsheets grouped into modules, thus aiming to develop the activities of data information in a simple, objective and integrated in order to achieve a friendly interface and reliable structural analysis. For the validation of this proposed tool for analytical calculation we used the commercial finite element program ANSYS, by analyzing some examples of gantry cranes

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第14639号 / 工博第3107号 / 新制||工||1462(附属図書館) / 26991 / UT51-2009-D351 / 京都大学大学院工学研究科分子工学専攻 / (主査)教授 榊 茂好, 教授 田中 庸裕, 教授 村上 正浩 / 学位規則第4条第1項該当

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第15396号 / 工博第3275号 / 新制||工||1493(附属図書館) / 27874 / 京都大学大学院工学研究科分子工学専攻 / (主査)教授 榊 茂好, 教授 白川 昌宏, 教授 北川 進 / 学位規則第4条第1項該当

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第17162号 / 工博第3652号 / 新制||工||1555(附属図書館) / 29901 / 京都大学大学院工学研究科分子工学専攻 / (主査）教授 佐藤 啓文, 教授 横尾 俊信, 教授 梶 弘典 / 学位規則第4条第1項該当

Optical and spectroscopic molecular properties are key to characterizing the behavior of molecules interacting with an applied electromagnetic field of light. Response theory has been used for a long time to calculate such properties in the frequency domain. Real-time (RT) methods solve for the frequency-dependent properties in the time domain by explicitly propagating the time-dependent wave function. Various quantum chemical methods can be incorporated with the RT formalism, including Hartree-Fock, density functional theory, configurational interaction, coupled cluster, etc. Among these, coupled cluster (CC) methods provide high accuracy for systems with strong electron correlation, making RT-CC implementations intriguing. All applications of CC methods face a substantial challenge due to their high-order polynomial scaling. For RT-CC methods, two aspects may be explored to improve the efficiency, the numerical techniques regarding the RT propagation and the reduced-scaling methods regarding CC itself. In this work, we start with the exploration of the hardware used for the calculations and the numerical integration methods for propagating the wave function parameters. Firstly, a GPU-enabled Python implementation has been developed by conducting the tensor contractions on GPUs utilizing PyTorch, a machine learning package, that has similar syntax as NumPy for tensor operations. A speedup of a factor of 14 is obtained for the RT-CCSD/cc-pVDZ absorption spectrum calculation of the water tetramer. Furthermore, to optimize the performance on GPUs, single-precision arithmetic is added to the implementation to achieve an additional speedup of a factor of two. Lastly, a group of integrators for solving differential equations are introduced to the RT framework, including regular explicit integrators, adaptive integrators, and a mixed-step-size approach customized for strong-field simulations. The optimal choice of the integrator depends on the requiring accuracy, stability and efficiency. In addition to being highly accurate, CC methods are also systematically improvable and provide a hierarchy of accuracy. Based upon the RT-CCSD implementation, the coupled cluster singles, doubles and approximate triples (CC3) method, favorable for calculating frequency-dependent properties, is tailored to the RT framework for high excitation and approximate orbital relaxation. The calculation is tested on both CPUs and GPUs, with a significant speedup gained from GPUs for the water cluster test cases. To further expand the range of applications of our RT-CC implementation, dynamic polarizabilities, first hyperpolarizabilities, and the G' tensor are calculated from induced electric and magnetic dipole moments using finite-difference methods. A discussion has also been conducted to compare RT-CC3 with RT-CCSD, and time-dependent nonorthogonal orbital-optimized coupled cluster doubles (TDNOCCD) method. Additionally, electron dynamics, including the Rabi oscillation and exited state to excited state transitions, have also been explored utilizing the well-developed RT-CC framework. / Doctor of Philosophy / Theoretical studies aim to match experiments, but more importantly, provide insights to interpret and predict experimental data. Calculating optical properties related to light-matter interactions is one of the most crucial tasks for characterizing molecular properties. In experiments, electromagnetic radiation in the form of light is applied to the system. The absorption or emission of light can be measured to identify, for example, the electronic structure of the molecule. In theoretical simulations, this applied radiation is represented by a perturbation operator that is added to the Hamiltonian in the Schrödinger equation. Quantum chemists are dedicated to developing methods that provide a better description of the spectroscopy. In the current work, the frequency, shape and the intensity of the radiation can all be finely-tuned, similar to experimental setups. The framework for extracting optical properties from time-dependent trajectories of induced dipole moments is established for accurate and efficient simulations. To improve efficiency and make the method feasible for real-world applications, a strong understanding of light-matter interactions on a quantum level and proper utilization of computational resources are both necessary. Improvements achieved and presented in this dissertation demonstrate a powerful tool for a better understanding of the nature of the interaction between the system and the electromagnetic radiation.

The efficient computation of dynamic (time-dependent) molecular properties is a broad field with numerous applications in aiding molecular synthesis and design, with a particular preva- lence in spectroscopic predictions. Typical methods for computing the response of a molecu- lar system to an electromagnetic field (EMF) considers a quantum mechanical description of the molecule and a classical approximation for the EMF. Methods for describing light-matter interactions with high-accuracy electronic structure methods, such as coupled cluster (CC), are discussed, with a focus on improving the efficiency of such methods. The CC method suffers from high-degree polynomial scaling. In addition to the ground-state calculation, computing dynamic properties requires the description of sensitive excited-state effects. The cost of such methods often prohibits the accurate calculation of response prop- erties for systems of significant importance, such as large-molecule drug candidates or chiral species present in biological systems. While the literature is ripe with reduced-scaling meth- ods for CC ground-state calculations, considerably fewer approaches have been applied to excited-state properties, with even fewer still providing adequate results for realistic systems. This work presents three studies on the reduction of the cost of molecular property evalu- ations, in the hopes of closing this gap in the literature and widening the scope of current theoretical methods. There are two main ways of simulating time-dependent light-matter interactions: one may consider these effects in the frequency domain, where the response of the system to an EMF is computed directly; or, the response may be considered explicitly in the time domain, where wave function (or density) parameters can be propagated in time and examined in detail. Each methodology has unique advantages and computational bottlenecks. The first two studies focus on frequency-domain calculations, and employ fragmentation and machine- learning techniques to reduce the cost of single-molecule calculations or sets of calculations across a series of geometric conformations. The third study presents a novel application of the local correlation technique to real-time CC calculations, and highlights deficiencies and possible solutions to the approach. / Doctor of Philosophy / Theoretical chemistry plays a key role in connecting experimental results with physical inter- pretation. Paramount to the success of theoretical methods is the ability to predict molecular properties without the need for costly high-throughput synthesis, aiding in the determina- tion of molecular structure and the design of new materials. Light-matter interactions, which govern spectroscopic techniques, are particularly complicated, and sensitive to the theoreti- cal tools employed in their prediction. Compounding the issue of accuracy is one of efficiency — accurate theoretical methods typically incur steep scaling of computational cost (memory and processor time) with respect to the size of the system. An important aspect in improving the efficiency of these methods is understanding the nature of light-matter interactions at a quantum level. Many unanswered questions still remain, such as, "Can light-matter interactions be thought of as a sum of interactions be- tween smaller fragments of the system?" and "Can conventional methods of accelerating ground-state calculations be expected to perform well for spectroscopic properties?" The present work seeks to answer these questions through three studies, focusing on improving the efficiency of these techniques, while simultaneously addressing their fundamental flaws and providing reasonable alternatives.

The present work describes coherence structure of English and Czech book introductions. The account of coherence is based on Rhetorical Structure Theory (Mann and Thompson, 1988; Mann and Taboada, 2006) which posits that majority of texts have one main effect which can be described by one of their inventory of thirty-two rhetorical relations; other relations are organized in a hierarchical structure and contribute to the main effect. Out of thirty monographs compiled for each language, four book introductions were chosen to represent the English language and four to represent the Czech language. The data were annotated in terms of rhetorical structure. The qualitative analysis showed that the genre of book introduction does not differ across languages as all texts were described by the same top-level relations; the only difference concerns the position of the goal of the monograph. The queantitative analysis showed that the difference on lower levels concerns the presentation of past research: Czech focused more on presenting elements of subject-matter. Key words: coherence, rhetorical relations, Rhetorical Structure Theory, book introductions, English, Czech, monographs, genre

Com uma quantidade quase incontável de informação textual disponível na web, a automatização de diversas tarefas referentes ao processamento automático de textos é uma necessidade inegável. Em abordagens superficiais do PLN (Processamento da Linguagem Natural), importantes propriedades do texto são perdidas, como posição, ordem, adjacência e contexto dos segmentos textuais. Uma análise textual mais profunda, como a realizada no nível do discurso, ocupa-se da busca e identificação da organização retórica do texto, gerando uma estrutura hierárquica em que as intenções do autor são explicitadas e relacionadas entre si. Para a automatização dessa tarefa, tem-se utilizado técnicas de aprendizado automático, predominantemente do paradigma supervisionado. Nesse paradigma, são necessários dados rotulados manualmente para a geração dos modelos de classificação. Como a anotação para essa tarefa é algo custoso, os resultados obtidos no aprendizado são insatisfatórios, pois estão bem aquém do desempenho humano na mesma tarefa. Nesta tese, o uso massivo de dados não rotulados no aprendizado semissupervisionado sem fim foi empregado na tarefa de identificação das relações retóricas. Foi proposto um framework que utiliza textos obtidos continuamente da web. No framework, realiza-se a monitoração da mudança de conceito, que pode ocorrer durante o aprendizado contínuo, e emprega-se uma variação dos algoritmos tradicionais de semissupervisão. Além disso, foram adaptados para o Português técnicas do estado da arte. Sem a necessidade de anotação humana, a medida-F melhorou, por enquanto, em 0,144 (de 0,543 para 0,621). Esse resultado consiste no estado da arte da análise discursiva automática para o Português. / Considering the almost uncountable textual information available on the web, the auto- matization of several tasks related to the automatic text processing is an undeniable need. In superficial approaches of NLP (Natural Language Processing), important properties of the text are lost, as position, order, adjacency and context of textual segments. A de- eper analysis, as carried out in the discursive level, deals with the identification of the rhetoric organization of the text, generating a hierarchical structure. In this structure, the intentions of the author are identified and related among them. To the automati- zation of this task, most of the works have used machine learning techniques, mainly from the supervised paradigm. In this paradigm, manually labeled data is required to obtain classification models, specially to identify the rhetorical relations. As the manual annotation is a costly process, the obtained results in the task are unsatisfactory, because they are below the human perfomance. In this thesis, the massive use of unlabeled data was applied in a semi-supervised never-ending learning to identify the rhetorical relations. In this exploration, a framework was proposed, which uses texts continuously obtained from the web. In the framework, a variation of traditional semi-supervised algorithms was employed, and it uses a concept-drift monitoring strategy. Besides that, state of the art techniques for English were adapted to Portuguese. Without the human intervention, the F-measure increased, for while, 0.144 (from 0.543 to 0.621). This result consists in the state-of-the-art for Discourse Analysis in Portuguese.

Com uma quantidade quase incontável de informação textual disponível na web, a automatização de diversas tarefas referentes ao processamento automático de textos é uma necessidade inegável. Em abordagens superficiais do PLN (Processamento da Linguagem Natural), importantes propriedades do texto são perdidas, como posição, ordem, adjacência e contexto dos segmentos textuais. Uma análise textual mais profunda, como a realizada no nível do discurso, ocupa-se da busca e identificação da organização retórica do texto, gerando uma estrutura hierárquica em que as intenções do autor são explicitadas e relacionadas entre si. Para a automatização dessa tarefa, tem-se utilizado técnicas de aprendizado automático, predominantemente do paradigma supervisionado. Nesse paradigma, são necessários dados rotulados manualmente para a geração dos modelos de classificação. Como a anotação para essa tarefa é algo custoso, os resultados obtidos no aprendizado são insatisfatórios, pois estão bem aquém do desempenho humano na mesma tarefa. Nesta tese, o uso massivo de dados não rotulados no aprendizado semissupervisionado sem fim foi empregado na tarefa de identificação das relações retóricas. Foi proposto um framework que utiliza textos obtidos continuamente da web. No framework, realiza-se a monitoração da mudança de conceito, que pode ocorrer durante o aprendizado contínuo, e emprega-se uma variação dos algoritmos tradicionais de semissupervisão. Além disso, foram adaptados para o Português técnicas do estado da arte. Sem a necessidade de anotação humana, a medida-F melhorou, por enquanto, em 0,144 (de 0,543 para 0,621). Esse resultado consiste no estado da arte da análise discursiva automática para o Português. / Considering the almost uncountable textual information available on the web, the auto- matization of several tasks related to the automatic text processing is an undeniable need. In superficial approaches of NLP (Natural Language Processing), important properties of the text are lost, as position, order, adjacency and context of textual segments. A de- eper analysis, as carried out in the discursive level, deals with the identification of the rhetoric organization of the text, generating a hierarchical structure. In this structure, the intentions of the author are identified and related among them. To the automati- zation of this task, most of the works have used machine learning techniques, mainly from the supervised paradigm. In this paradigm, manually labeled data is required to obtain classification models, specially to identify the rhetorical relations. As the manual annotation is a costly process, the obtained results in the task are unsatisfactory, because they are below the human perfomance. In this thesis, the massive use of unlabeled data was applied in a semi-supervised never-ending learning to identify the rhetorical relations. In this exploration, a framework was proposed, which uses texts continuously obtained from the web. In the framework, a variation of traditional semi-supervised algorithms was employed, and it uses a concept-drift monitoring strategy. Besides that, state of the art techniques for English were adapted to Portuguese. Without the human intervention, the F-measure increased, for while, 0.144 (from 0.543 to 0.621). This result consists in the state-of-the-art for Discourse Analysis in Portuguese.