Implementação de um sistema para simulação por Monte Carlo de fotões através do olho humano

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do Grau de Mestre em Engenharia Biomédica

Commissioning de um sistema de planimetria computorizado de Monte Carlo comercial para radioterapia

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Biomédica

Medição e cálculo, utilizando simulações Monte Carlo, das doses em exames de tomografia computorizada

Tese Mestrado Integrado em Engenharia Biomédica

Implementação de um sistema para simulação por Monte Carlo da passagem de fotões através do olho humano mediante a utilização da plataforma GEANT4 - I

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Implementação de um sistema para simulação por Monte Carlo da passagem de fotões através do olho humano mediante a utilização da plataforma GEANT4 – II

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Monte Carlo simulations for dosimetric verification in photon and electron beam radiotherapy

Dissertação para obtenção do Grau de Doutor em Engenharia Biomédica

Simulações Monte Carlo da redução da dose no cristalino e na tiroide em exames de tomografia computorizada utilizando proteções de bismuto

A presente dissertação foi desenvolvida com colaboração do Campus Tecnológico e Nuclear e do Hospital de São José

The Nagasaki-Macao Trade between 1612 and 1618: Carlo Spinola S.J. Procurator of Japan

A nossa dissertação tem como objetivo analisar os compromissos e as obrigações do procurador da Companhia de Jesus no Japão durante os anos em que Carlo Spinola foi escolhido para ocupar tal posição, a segunda em ordem de importância, conforme o jesuíta italiano Francesco Pasio. O ofício de procurador era uma das posições que levavam os missionários da Companhia a lidar diretamente com as autoridades japonesas em Nagasáqui, uma vez que cabia ao procurador receber, verificar e distribuir os bens pertencentes à missão e que eram carregados no navio português de Macau. Além disso, o procurador, juntamente com outros padres superiores, tinha também incumbidas tarefas políticas relativas ao capitão-mor e aos Portugueses no Japão. Spinola assumiu o cargo quando o bakufu começou a mudar a sua atitude em relação à Igreja de Roma, devido a várias causas que, em parte, envolviam também a Companhia de Jesus, com conseqüências negativas para a missão. Para fornecer uma compreensão profunda deste cargo, propomos uma comparação entre o procuradorado de Spinola e outros procuradores no Japão, tendo escolhido em particular o caso do Português João Rodrigues Tçuzu. Além disso, uma vez que o Japão era um caso particular dentro do Padroado Português, parece-nos pertinente efectuar outra comparação e apresentar também o caso - embora mais conciso - do procurador da província brasileira da Companhia de Jesus. Através deste estudo de casos, tentaremos definir o procurador, tanto do ponto de vista prático - ou seja, os seus deveres, os seus compromissos e os seus recursos – como de uma perspectiva moral e filosófica – olhando para a literatura canônica produzida desde os primeiros tempos da Igreja Cristã. Até agora, a históriografia sobre e de autoria jesuítica apenas aborda o cargo de procurador de forma marginal. O nosso trabalho vai preencher essa lacuna. Além disso, o estudo do papel do procurador permite-nos, inevitavelmente, uma melhor compreensão dos mecanismos de participação da Companhia de Jesus no comércio entre Macau e Nagasáqui, desde o seu início – selado por Alessandro Valignano – até ao seu fim – contemporâneo do término do procuradorado de Spínola.

Probabilistic constraint reasoning with Monte Carlo integration to robot localization

This work studies the combination of safe and probabilistic reasoning through the hybridization of Monte Carlo integration techniques with continuous constraint programming. In continuous constraint programming there are variables ranging over continuous domains (represented as intervals) together with constraints over them (relations between variables) and the goal is to find values for those variables that satisfy all the constraints (consistent scenarios). Constraint programming “branch-and-prune” algorithms produce safe enclosures of all consistent scenarios. Special proposed algorithms for probabilistic constraint reasoning compute the probability of sets of consistent scenarios which imply the calculation of an integral over these sets (quadrature). In this work we propose to extend the “branch-and-prune” algorithms with Monte Carlo integration techniques to compute such probabilities. This approach can be useful in robotics for localization problems. Traditional approaches are based on probabilistic techniques that search the most likely scenario, which may not satisfy the model constraints. We show how to apply our approach in order to cope with this problem and provide functionality in real time.

Monte Carlo valuation of worst-of auto-callable equity swaps

This thesis proposes a Monte Carlo valuation method for Worst-of Auto-callable equity swaps. The valuation of this type of swap usually requires complex numerical methods which are implemented in “black-box” valuation systems. The method proposed is an alternative benchmark tool that is relatively simple to implement and customize. The performance of the method was evaluated according to the variance and bias of the output and to the accuracy when compared to a leading valuation system in the market.

Técnicas de codificação/recepção para sistemas de comunicação com espalhamento espectral

Com o advento dos sistemas de comunicação baseados em técnicas de espalhamento espectral, entre os quais se destacam o UMTS e redes sem fios baseadas nas normas 802.11b/g ou 802.16, os requisitos de qualidade vieram incrementados, com consequentes implicações nas técnicas de codificação/desmapeamento adoptadas (turbo códigos no UMTS e 802.16). No contexto dos sistemas baseados em técnicas de espalhamento espectral, são analisados os efeitos da utilização de sequências de espalhamento PN, dando ênfase a aspectos como: Adequação do comprimento face a um cenário multi-percurso e comparação com as técnicas de entrelaçamento usuais; Análise e identificação das sequências mais apropriadas na presença de múltiplos utilizadores; Impacto no desenho de estruturas de recepção apropriadas (nomeadamente estruturas baseadas no receptor RAKE); Associação de técnicas de modulação e codificação adequadas a este tipo de sistemas. Pretendeu-se avaliar o impacto de diferentes técnicas de combinação ao nível do receptor, na presença de um canal dispersivo na frequência. Neste contexto, foram utilizadas técnicas de codificação abrangendo concatenações paralelas, baseadas em códigos constituintes simples, e por sua vez associadas a sequências de espalhamento reais e complexas. No âmbito das técnicas de codificação, são analisados códigos resultantes de concatenações em paralelo, nomeadamente turbo códigos, bem como outros tipos de concatenações derivadas destas com elevada eficiência espectral, como modelações MQAM. Incluem-se resultados numéricos, obtidos por simulação, via método de Monte-Carlo

Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations.

Análise de robustez de estruturas de madeira tradicionais

Dissertação para obtenção do Grau de Mestre em Engenharia Civil – Estruturas e Geotecnia pela Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa

Estudo comparativo de três câmaras de ionização para medição directa do equivalente de dose individual, a 10 mm de profundidade, Hp(10)

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Biomédica