"The use of advanced materials in the construction of high-speed craft is becoming more commonplace. However, there are certain requirements set in the High Speed Craft Code (published by IMO) that restrict the use of materials based on results from full scale room fire testing (ISO 9705). An obvious benefit would be gained by simulating the results of these full-scale tests using bench scale data from the Cone Calorimeter and LIFT apparatus. A flame-spread algorithm developed by Henri Mitler at the National Institute of Standards and Technology was selected for implementation into the zone fire model CFAST. This algorithm was modified from its original form, so that it could simulate flame spread on wall/ceiling lining materials for both sidewall and corner scenarios, including ISO 9705 as prescribed in the High Speed Craft Code. Changes to the algorithm included geometry of flame spread across the ceiling, flame height, radiation exchange, ignition burner heat flux maps, and multiple pyrolysis zones. The new flame spread algorithm was evaluated against room corner test data from four different marine composite materials tested per ISO 9705."

Hoje no mercado brasileiro de eletricidade, o preço da energia convencional é composto pela soma do valor do Preço de Liquidação das Diferenças (PLD) divulgado pela Câmara de Comercialização de Energia Elétrica (CCEE) semanalmente com o valor do Spread negociado bilateralmente no mercado à vista (mercado de curto prazo), resultante do equilíbrio entre oferta e demanda. Em alguns momentos, o valor do Spread chega a representar mais de 100% do custo total da energia. Este trabalho faz uma análise do mercado brasileiro, bem como, de alguns mercados no exterior de energia elétrica e destaca os pontos que tem influência direta, na formação do Spread da energia convencional e como isso afeta a decisão de contratação dos agentes. Além disso, o trabalho busca encontrar correlações entre dados divulgados, como carga e oferta de energia, com o ágio negociado no mercado de curto prazo, buscando entender o real impacto de cada um desses fatores e explicar as grandes variações já observadas. Sugere-se também um modelo de regressão linear múltipla para a projeção de valores do ágio. Para tanto, foram utilizadas informações proveniente de um banco de dados de cotações de negócios efetivamente realizados no curto prazo desde janeiro de 2011 até julho de 2014, bem como informações retiradas da CCEE e Operador Nacional do Sistema (ONS). / The Brazilian wholesales energy market price is formed by de sum of the PLD (Market Clearing Price which is released weekly by the Commercial Chamber) and a Spread value, resulting from the negotiation between the market agents. In some cases, the Spread represent more than 100% of the energy total cost. This paper presents an overview about some energy markets, focusing the Brazilian Energy Market, so as to highlight points that affect the Spread value at the spot market and, as consequence, the strategy of the market agents. Additionally, this paper shows the correlation between energy demand and energy offer and energy spread negotiated at the short term market, trying to understand the real impact of each variable trying to get the right explanation regarding the big variations observed. It has been suggested a mathematical model of multiple linear regression to forecast the spread value. In order to accomplish this purpose it was used (i) a historical data of effectively trading situations at the short term market, comprising the period between January 2011 to July 2014, as well as (ii) informations released by the Commercial Chamber (CCEE) and the System Operator (ONS).

Dans cette thèse nous avons étudié des indicateurs visant à caractériser les propriétés métalliques ou isolantes de systèmes de basse dimensionnalité à partir de calculs théoriques basés sur la fonction d'onde. Ces systèmes sont intéressants car ils permettent une compréhension en profondeur des phénomènes physiques qui peuvent ensuite être extrapolés à des systèmes plus étendus. Afin de réaliser cette étude nous avons utilisé un nouvel outil basé sur la théorie de la conductivité de Kohn : le tenseur de délocalisation total ou total position spread-tensor (TPS). Ce tenseur est défini comme le second cumulant de l'opérateur position : ? = <?|X2|?> - <?|X|?>2. Divisé par le numéro des électrons, il diverge quand la fonction d'onde est fortement délocalisée (forte fluctuation de la position des électrons) et converge vers une valeur finie dans le cas contraire. Ainsi, la conductivité est relié à la délocalisation de la fonction d'onde. Dans ce travail, deux définitions du TPS ont été abordées : une quantité sommée sur le spin (spin-summed TPS, SS-TPS) d'une part, et une décomposition selon le spin (spin-partitioned TPS, SSP-TSP) d'autre part. Cette dernière s'est avérée être un outil très efficace pour l'étude de systèmes fortement corrélés. Au cours de la thèse, nous avons commencé par étudier plusieurs systèmes diatomiques présentant des liaisons de natures différentes à l'aide de calculs d'interaction de configurations totale (FCI). Le TPS présente alors un maximum dans une zone précédant la rupture de liaison avant de converger asymptotiquement vers les valeurs atomiques, comme la consistance de taille du tenseur le laissait présager. Dans le cas de systèmes pour lesquels l'état électronique présente un croisement évité, le TPS diverge, mettant ainsi en évidence la forte délocalisation de la fonction d'onde. Le SS-TPS est donc un indicateur de choix pour suivre la nature de la liaison chimique. Nous avons ensuite considéré des systèmes à valence mixte de type II pour lesquels l'état fondamental présente un double-puits de potentiel avec un croisement évité avec le premier état excité. Il est donc nécessaire ici d'utiliser un traitement multi-configurationnel. Deux systèmes modèles ont ainsi été étudiés : i) deux di- mères H2 en interaction faible au niveau FCI et ii) un composé du type spiro au niveau CAS-SCF (à l'aide d'un code que nous avons implémenté dans Molpro). Dans les deux cas, le TPS présentait un maximum très marqué dans la région du croisement évité, signature d'une forte mobilité électronique. Nous nous sommes également intéressés à trois types de chaines d'atomes d'hydrogène : i atomes équidistants ii) chaines dimérisées à longueur de liaison H2 fixée et iii) chaines dimérisées. Tant le SS-TPS que le SP-TPS montrent des comportements différents selon le type de chaine considérée. Les premières ont un caractère métallique et une délocalisation de spin prononcée dans le régime fortement corrélé. Les secondes sont de nature isolante avec une délocalisation limitée. Les chaines dimérisées, quant à elle, dissocient très rapidement vers un état isolant mais avec une forte délocalisation de spin. Ces chaines demi-remplies ont aussi été traitées à l'aide d'hamiltonien de Hubbard et de Heisenberg. Nous avons ainsi pu rationaliser le comportement des SS-TPS et SP-TPS en variant le rapport de l'intégrale de saut et de la répulsion électron- électron (-t/U) entre sites adjacents. Le caractère ferromagnétique/anti-ferromagnétique a également pu être suivi en modifiant la valeur de la constante de couplage J dans le cas fortement corrélé. Finalement, ces indicateurs ont été mis en oeuvre pour des polyacenes cycliques. Dans ce cas, le TPS a permis de comprendre la nature des fonctions d'onde de l'état fondamental obtenues au niveau CAS-SCF et NEVPT2. / I carried out a theoretical study to characterize metallic and insulating properties of low-dimensional systems using wave function methods. Low-dimensional systems are particularly important because they allow an understanding that can be extrapolated to higher dimensional systems. We have employed a new tool based on the theory of conductivity of Kohn that we have named: total position-spread tensor (TPS). The TPS is defined as the second moment cumulant of the total position operator: ? = <?|X2|?> - <?|X|?>2 . The tensor divided by the number of electrons diverges when the wave function is delocalized (high fluctuation of electrons' positions), and it takes finite values for localized ones. In this way, the electrical conductivity is related to the proper delocalization of the wave function. In addition, the tensor can be divided in spin-summed (SS-TPS) and spin-partitioned tensors (SP-TPS). The latter one becomes a powerful tool to the study of strongly correlated systems. In this dissertation, we started to investigate at full configuration interaction (FCI) level diatomic molecules showing different types of bond. The TPS presented a marked maximum before the bond was broken and in the asymptotic limit one recovers the TPS values of isolated atoms (size consistency). For the case of diatomic systems showing avoided-crossing electronic states, the TPS diverges evidencing the high delocalization of the wave function. Therefore, the SS-TPS is capable of monitoring and characterizing molecular wave functions. We considered mixed-valence systems that are often distinguished by a double-well potential energy surface presenting an avoided-crossing. Thus, such a configuration possesses a strongly multireference nature involving at least two states of the same symmetry. Two different systems were investigated: i) two weakly interacting hydrogen dimers that were investigated at Full CI level, and ii) a spiro like molecule where the TPS tensor was evaluated in a CAS-SCF state-averaged wave function using our implementation of the SS- TPS formalism in MOLPRO. We found that the tensor's component in the direction of the electron transfer (ET) shows a marked maximum in the avoided-crossing region, evidencing the presence of a high electron mobility. The formalisms of the SS- and SP-TPS was applied to one dimensional systems composed by three types of half-filled hydrogen chains: i) equally-spaced chains, ii) fixed-bond dimerized chains, and iii) homothetic dimerized chains. Both the SS- and SP-TPS showed different signatures associated to the three types of systems. Equally-spaced chains have metallic wave functions and a high spin delocalization in the strongly correlated regime. In contrast, fixed-bond dimerized chains have an insulating character and a restricted spin delocalization. Finally, homothetic dimerized chains dissociate very quickly which renders them in the insulating state but with a high spin delocalization. We also studied half-filled chains by using the Hubbard and the Heisenberg Hamiltonians. On the one hand, we were able to depict the response of the SS- and SP-TPS by varying the ratio between the hopping and electron-electron repulsion (-t/U parameter) of topological connected sites. On the other hand, the ferromagnetic and anti-ferromagnetic character of the wave functions were evaluated by varying the coupling constant (J) in the strongly correlated systems. A theoretical study of closed polyacenes (PAH) structures was performed at CAS-SCF and NEVPT2 level. Our methodology for choosing the active space using the Hückel Hamiltonian was able to characterize the ground state of the systems that indeed fulfilled the Ovchinnikov rule. Finally, we applied the SS-TPS to understand the nature of the wave functions of these PAHs.

The aim of our work was to provide a robust method for evaluating imaging performance of positron emission tomography (PET) systems and particularly to estimate the modulation transfer function (MTF) using the line spread function (LSF) method. A novel plane source was prepared using thin layer chromatography (TLC) of a fluorine-18-fluorodeoxyglucose (18F-FDG) solution. The source was placed within a phantom, and imaged using the whole body (WB) two dimensional (2D) and three dimensional (3D) standard imaging protocols in a hybrid PET/CT scanner. Modulation transfer function was evaluated by determining the LSF, for various reconstruction methods and filters. The proposed MTF measurement method was validated against the conventional method, based on point spread function (PSF). Higher MTF values were obtained with 3D scanning protocol and 3D iterative reconstruction algorithm. All MTF obtained using 3D reconstruction algorithms showed better preservation of higher frequencies than the 2D algorithms. They also exhibited better contrast and resolution. MTF derived from LSF were more precise compared with those obtained from PSF since their reproducibility was better in all cases, providing a mean standard deviation of 0.0043, in contrary to the PSF method which gave 0.0405. By using our novel plane source we developed a method for measuring the image registration shift between the CT and the PET images in fusion. The method gave results that are comparable to the manufacturers’ method for image registration and has the advance that is applicable to all scanner models. Through the MTF it is also feasible to compare commercially available scanners in terms of image quality. In conclusion, the proposed method is novel and easy to implement for characterization of the signal transfer properties and image quality of PET/CT systems. It provides an easy way to evaluate the frequency response of each kernel available. The proposed method requires cheap and easily accessible materials, available to the medical physicist in the nuclear medicine department. Furthermore, it is robust to aliasing and since this method is based on the LSF, is more resilient to noise due to greater data averaging than conventional PSF-integration techniques. In this study was used to assess the image quality. But it can also be used as a method of quality control and stability of system performance over time. / Σκοπός της παρούσας μελέτης ήταν να εισαγάγει μια νέα μέθοδο για την αξιολόγηση των χαρακτηριστικών της ποιότητας εικόνας στην τομογραφία εκπομπής ποζιτρονίων (PET). Ειδικότερα, έγινε εκτίμηση της συνάρτησης διαμόρφωσης μεταφοράς (MTF) σε PET εικόνες με χρήση της συνάρτησης διασποράς γραμμής (LSF). Κατασκευάστηκε μία πρότυπη επίπεδη πηγή, Λεπτού Χρωματογραφικού Χάρτη (TLC), υψηλής ομοιογένειας. Οι καμπύλες της MTF υπολογίστηκαν από την ανακατασκευή των εγκάρσιων τομών της επίπεδης πηγής. Η ανακατασκευή έγινε για όλους τους διαθέσιμους αλγόριθμους ανακατασκευής και φίλτρα καθώς και για τους δύο τρόπους σάρωσης (2D και 3D). Τα αποτελέσματα συγκρίθηκαν με την MTF που προκύπτει μέσω της συνάρτησης διασποράς σημείου (PSF). Με την χρήση της επίπεδης πηγής αναπτύχθηκε μέθοδος με την οποία μπορεί να ελεγχθεί η σύμπτωση της εικόνας του CT και της εικόνας του PET κατά την σύντηξη. Η μέθοδος συγκρίθηκε με τον τρόπο ελέγχου που καθορίζει ο κατασκευαστής του συστήματος. Επιπλέον, πραγματοποιήθηκε σύγκριση μεταξύ δύο εμπορικών συστημάτων από διαφορετικούς κατασκευαστές. Η σύγκριση πραγματοποιήθηκε για τα διαθέσιμα πρωτόκολλα σάρωσης και τους προτεινόμενους αλγόριθμους ανακατασκευής κάθε συστήματος. Η σάρωση του αντικειμένου σε 3D και η χρήση τρισδιάστατων αλγορίθμων ανασύστασης είχε ως αποτέλεσμα την δημιουργία εικόνων με υψηλότερες τιμές MTF. Όλες οι καμπύλες MTF που προέκυψαν από τρισδιάστατους αλγόριθμούς ανασύστασης έδειξαν καλύτερη απόκριση στις υψηλότερες συχνότητες από τους δισδιάστατους αλγόριθμους. Οι εικόνες που προέρχονται από τρισδιάστατους αλγόριθμους έχουν καλύτερη αντίθεση (contrast) και διακριτική ικανότητα (resolution). Οι καμπύλες MTF που προέρχονται από την LSF έχουν καλύτερη ακρίβεια σε σχέση με τις καμπύλες MTF που προέρχονται από την PSF και η επαναληψιμότητα τους ήταν καλύτερη σε όλες τις περιπτώσεις. Η μέση τιμή της τυπικής απόκλισης των καμπυλών MTF που προέρχονται από την LSF βρέθηκε ίση με 0,0043, ενώ η μέση τιμή της τυπικής απόκλισης των καμπυλών MTF που προέρχονται από την χρήση της PSF ήταν 0,0405. Με την προτεινόμενη μέθοδο αξιολόγησης είναι δυνατόν να συγκριθούν δύο ή περισσότερα εμπορικά διαθέσιμα συστήματα ως προς τα ποιοτικά χαρακτηριστικά της εικόνας τους. Τέλος, η μέτρηση της απόκλιση της εικόνας του CT και του PET στην εικόνα σύντηξης με την μέθοδο που αναπτύχθηκε ήταν συγκρίσιμη με την τιμή που μετρήθηκε εφαρμόζοντας την μέθοδο του κατασκευαστή. Συμπερασματικά, η παρούσα εργασία έδειξε ότι η χρήση της MTF, που προέρχεται από την LSF, μπορεί να χαρακτηρίσει πλήρως την ποιότητα εικόνας PET. Με τη προτεινόμενη μέθοδο αξιολόγησης της ποιότητας εικόνας, η διερεύνηση των διαφόρων στοιχείων της αλυσίδας απεικόνισης μπορεί να γίνει πιο απλή και να βελτιωθεί περαιτέρω και η συνολική απόδοση συστημάτων PET. Η προτεινόμενη μέθοδος αξιολόγησης απαιτεί υλικά που είναι συνηθισμένα στο κλινικό περιβάλλον, μπορεί να εφαρμοστεί πειραματικά και να χρησιμοποιηθεί στην κλινική πράξη. Επιπλέον, επειδή η μέθοδος βασίζεται στην LSF, είναι πιο ανθεκτική στο θόρυβο από τις συμβατικές τεχνικές που κάνουν χρήση της συνάρτησης διασποράς σημείου. Σε αυτή τη μελέτη χρησιμοποιήθηκε για την εκτίμηση της ποιότητας εικόνας. Μπορεί όμως να χρησιμοποιηθεί και ως μέθοδος ελέγχου ποιότητας και σταθερότητας της απόδοσης του συστήματος στον χρόνο.

本文利用向量自我迴歸模型所得出來的殘差值來模擬未預期到的總體經濟訊息，以期限利差和一個月定存利率來捕捉殖利率曲線，以違約利差和股利收益率來描繪資產報酬的條件機率分布，本文實證未預期到的期限利差和未預期到的違約風險與淨值市價比因子和市值規模因子包含相同的訊息，因此後續檢驗這些能夠捕捉未來投資機會的總體經濟訊息比起Fama-French三因子模型是否對台灣股票橫斷面的平均報酬更具有解釋能力。 實證方法採用Fama-MacBeth(1973)兩階段迴歸方法，Fama-French三因子模型實證結果顯示台灣股票市場存在著負向的淨值市價比效果，但卻不存在著規模效果，這與國外一些學者研究1980年代之後規模效果逐漸消失的結論相同。在實證未預期到的總體經濟訊息模型時，由於被解釋變數為股票超額報酬率，因此常數項應該為不顯著的關係，但此假設強烈的被未預期到的總體經濟訊息模型拒絕，代表此模型可能遺漏了重要的解釋變數。因此，Fama-French 三因子模型對台灣股票橫斷面平均報酬率的解釋能力比未預期到的總體經濟訊息模型更佳。 / The Fama and French factors HML and SMB are correlated with innovations in variables that describe investment opportunities. I find that shocks to term spread and shocks to default spread have the same information with the Fama and French factors HML and SMB. This paper investigates whether a model that includes shocks to the aggregate dividend yield and term spread, default spread, and one-month deposit interest rate can explain the cross section of average return on Taiwan stock market as well as the Fama and French can. Using the Fama-MacBeth (1973) two steps cross-sectional regressions, I find there exists the negative book-to-market effect on Taiwan stock market, but the size effect disappears. Since the dependent variables in the regression is excess returns, the intercept of the cross-sectional regression should be zero. This hypothesis is strongly rejected in the case of the model includes shocks to the Macroeconomics variables and the market portfolio. It means this model omits some important variables, so the Fama and French three-factor model can explain the cross section of average returns better.

Eventi come l’ultima crisi finanziaria sono una delle principali cause di perdite inattese negli investimenti finanziari. Infatti, durante una crisi finanziaria, la volatilità dei rendimenti azionari aumenta a causa degli shock dei mercati, incrementando la probabilità di perdita. Per fronteggiare gli effetti della crisi gli investitori , sfruttando possibili informazioni provenienti dai mercati, dovrebbero impostare con anticipo le proprie strategie di investimento e gestirli in modo appropriato per limitare gli effetti degli shock. In base a tali considerazioni si è analizzato, con tale studio, la capacità di predizione da parte di alcune variabili finanziarie/economiche ( BSEYD e Term Yield Spread) dell’andamento dei principali mercati europei ( Germania, Francia e Spagna) e si è definita un appropriata strategia di investimento per i periodi di crisi, costruendo un modello di portafoglio neutrale agli shock. I periodi analizzati sono stati rispettivamente : 1994-2013 e 2003-2014. I risultati hanno dimostrato che le variabili analizzate presentano diverso potere di predizione dei mercati considerati e che la perfomance del portafoglio neutrale agli shock di mercato è migliore di quella del portafoglio market neutral nei periodi di crisi. / Events like the last financial crisis are one of the principal causes of unexpected loss in investments. During a financial crisis period the stock return volatility increases for effect of internal and external shocks and the probability of reaching the expected return become lower , increasing the probability of loss. To face crisis effects, international investors should consider possible signals and information present in the market about possible crashes or declining period to set in advance their investment strategies and to manage them properly to limit the shock effects. On the basis of these considerations, with this study, we analyzed the predictive power of 2 economic/ financial variables( BSEYD and Term spread yield) on principal European stock markets (France, Germany and Spain) and defined a proper investment strategy for financial crisis period, building a portfolio model that is neutral to the international market shocks. The study has been conducted in two periods: 1994-2013 ( prediction analysis) and 2003-2014 (shock neutral portfolio mode). Results show different predictive power on the of the variables on the different markets analyzed and a better performance of the shock neutral portfolio than the market neutral portfolio strategy in declining period of the market.

Submitted by Viviani Bacchmi (vbacchmi@uol.com.br) on 2018-05-04T23:43:50Z No. of bitstreams: 1 Dissertação versão final pdf_maio2018.pdf: 2165181 bytes, checksum: 07d81c83d220ec75dc2dd926c48b8896 (MD5) / Approved for entry into archive by Thais Oliveira (thais.oliveira@fgv.br) on 2018-05-10T17:24:21Z (GMT) No. of bitstreams: 1 Dissertação versão final pdf_maio2018.pdf: 2165181 bytes, checksum: 07d81c83d220ec75dc2dd926c48b8896 (MD5) / Approved for entry into archive by Suzane Guimarães (suzane.guimaraes@fgv.br) on 2018-05-10T17:35:37Z (GMT) No. of bitstreams: 1 Dissertação versão final pdf_maio2018.pdf: 2165181 bytes, checksum: 07d81c83d220ec75dc2dd926c48b8896 (MD5) / Made available in DSpace on 2018-05-10T17:35:37Z (GMT). No. of bitstreams: 1 Dissertação versão final pdf_maio2018.pdf: 2165181 bytes, checksum: 07d81c83d220ec75dc2dd926c48b8896 (MD5) Previous issue date: 2018-04-18 / Este estudo tem por objetivo analisar em que medida os tributos incidentes sobre as operações de crédito e sobre a atividade bancária interferem no spread bancário, considerando que tais tributos devem observar determinados limites e princípios constitucionais e legais para sua criação e majoração. Tendo em vista que na atividade de concessão de crédito, uma das principais realizadas pelos bancos, estes captam recursos no mercado e os repassam aos tomadores de crédito, o que lhes gera um 'ganho', que é conhecido como spread bancário: o presente trabalho prestou-se a analisar como esse ganho é calculado. Essa diferença entre custo e margem dos bancos, o spread, é calculado a partir de determinados componentes que afetam o seu percentual e, portanto, o custo do crédito. Entre os principais componentes do spread destacam-se os tributos incidentes sobre o crédito e sobre a atividades dos bancos. Para determinar se os tributos afetam ou não o valor do spread, optou-se por analisar, primeiramente, o papel do Estado como agente regulador da economia o papel dos Bancos como agente de fomento do mercado financeiro, para então comentar sobre o mercado de crédito e o spread bancário, que interfere no custo desse crédito. Passando por considerações sobre o crédito brasileiro e a interferência dos tributos na apuração do spread, o trabalho parte para a avaliação da observância dos princípios constitucionais que regem a criação e a majoração dos tributos bancários frente à necessidade de reduzir o spread para cumprimento da finalidade de desenvolver a atividade econômica de pessoas e de empresas. / The aim of this study is to analyse how much credit operation and bank activities incident taxes interfere on bank spread, considering these taxes must observe some constitutional and legal limitation to its creation and increase. In view of credit grant activity, one of the most important realized by banks, they raise funds in the Market and pass along them to credit borrowers, what generates a 'gain', called bank spread: the present study analysed how this gain in calculated. This difference between bank’s cost and margin, the spread, is calculated from certain components that affect its rates, and so the cost of credit. One of the main component of the spread is tax incident on credit and on bank activities. In order to determine if tax affects spread value, it was analysed, first of all, the Estate as an economy regulator agente and the banks as agents of economy development, and so make comments about credit market and spread that interferes in the credit cost. After making considerations on brazilian credit and the interference of taxes on spread apuration, this study analyses if the constitutional principles that rule the creation and increase of bank taxes are observed, considering the necessity to reduce spread to accomplish the objective of developing economic activities of people and companies.

Lors de cette thèse, je me suis intéressée aux modèles et aux algorithmes pour étudier l'histoire évolutive commune des hôtes et des symbiotes. Le premier objectif était d'analyser la robustesse des méthodes de réconciliation des arbres phylogénétiques, qui sont très utilisées dans ce type d'étude. Celles-ci associent (ou lient) un arbre, d'habitude celui des symbiotes, à l'autre, en utilisant un modèle dit basé sur des évènements. Les évènements les plus utilisés sont la cospéciation, la duplication, le saut et la perte. Les phylogénies des hôtes et des symbiotes sont généralement considérés comme donnés, et sans aucune erreur. L'objectif était de comprendre les forces et les faiblesses du modèle parcimonieux utilisé et comprendre comment les résultats finaux peuvent être influencés en présence de petites perturbations ou d'erreurs dans les données en entrée. Ici deux cas sont considérés, le premier est le choix erroné d'une association entre les feuilles des hôtes et des symbiotes dans le cas où plusieurs existent, le deuxième est lié au mauvais choix de l'enracinement de l'arbre des symbiotes. Nos résultats montrent que le choix des associations entre feuilles et le choix de l'enracinement peuvent avoir un fort impact sur la variabilité de la réconciliation obtenue. Nous avons également remarqué que l'evènement appelé “saut” joue un rôle important dans l'étude de la robustesse, surtout pour le problème de l'enracinement. Le deuxième objectif de cette thèse était d'introduire certains evènements peu ou pas formellement considérés dans la littérature. L'un d'entre eux est la “propagation”, qui correspond à l'invasion de différents hôtes par un même symbiote. Dans ce cas, lorsque les propagations ne sont pas considérés, les réconciliations optimales sont obtenues en tenant compte seulement des coûts des évènements classiques (cospeciation, duplication, saut, perte). La nécessité de développer des méthodes statistiques pour assigner les coûts les plus appropriés est toujours d'actualité. Deux types de propagations sont introduites : verticaux et horizontaux. Le premier type correspond à ce qu'on pourrait appeler aussi un gel, à savoir que l'évolution du symbiote s'arrête et “gèle” alors que le symbiote continue d'être associé à un hôte et aux nouvelles espèces qui descendent de cet hôte. Le second comprend à la fois une invasion, du symbiote qui reste associé à l'hôte initial, mais qui en même temps s'associe (“envahit”) un autre hôte incomparable avec le premier, et un gel par rapport à l'évolution des deux l'hôtes, celui auquel il était associé au début et celui qu'il a envahi. Nos résultats montrent que l'introduction de ces evènements rend le modèle plus réaliste, mais aussi que désormais il est possible d'utiliser directement des jeux de données avec un symbiote qui est associé plusieurs hôtes au même temps, ce qui n'était pas faisable auparavant / In this Ph.D. work, we proposed models and algorithms to study the common evolutionary history of hosts and symbionts. The first goal was to analyse the robustness of the methods of phylogenetic tree reconciliations, which are a common way of performing such study. This involves mapping one tree, most often the symbiont’s, to the other using a so-called event-based model. The events considered in general are cospeciation, duplication, host switch, and loss. The host and the symbiont phylogenies are usually considered as given and without any errors. The objective here was to understand the strengths and weaknesses of the parsimonious model used in such mappings of one tree to another, and how the final results may be influenced when small errors are present, or are introduced in the input datasets. This may correspond either to a wrong choice of present-day symbiont-host associations in the case where multiple ones exist, or to small errors related to a wrong rooting of the symbiont tree. Our results show that the choice of leaf associations and of root placement may have a strong impact on the variability of the reconciliation output. We also noticed that the host switch event has an important role in particular for the rooting problem. The second goal of this Ph.D. was to introduce some events that are little or not formally considered in the literature. One of them is the spread, which corresponds to the invasion of different hosts by a same symbiont. In this case, as when spreads are not considered, the optimal reconciliations obtained will depend on the choice made for the costs of the events. The need to develop statistical methods to assign the most appropriate ones therefore remains of actuality. Two types of spread are introduced: vertical and horizontal. The first case corresponds to what could be called also a freeze in the sense that the evolution of the symbiont “freezes” while the symbiont continues to be associated with a host and with the new species that descend from this host. The second includes both an invasion, of the symbiont which remains with the initial host but at the same time gets associated with (“invades”) another one incomparable with the first, and a freeze, actually a double freeze as the evolution of the symbiont “freezes” in relation to the evolution of the host to which it was initially associated and in relation to the evolution of the second one it “invaded”. Our results show that the introduction of these events makes the model more realistic, but also that it is now possible to directly use datasets with a symbiont that is associated with more than one host at the same time, which was not feasible before

Tato diplomová práce se zabývá modelováním bodové rozptylové funkce (point spread function, PSF) u skenovacího transmisního elektronového mikroskopu (STEM). Nejprve je provedena teoretická rešerše, kde jsou popsány všechny důležitě aspekty, potřebné k následnému modelování. Je tedy proveden základní popis konstrukce přístroje a určeny jeho klíčové komponenty, které mají hlavní vliv na tvar výsledné PSF. Následně jsou popsány hlavní zobrazovací vady, které ovlivňují výslednou PSF. Ty jsou popsány z hlediska vlnové optiky. Na základě toho je pak navržen a zrealizován poměrně přesný model PSF u mikroskopu STEM. Poté je vytvořeno GUI, které umožňuje plné využití daného vytvořeného modelu. Na závěr je získaný model otestován na modelových a reálných datech, pomocí metody Lucy-Richardson.

Coherence scanning interferometry (CSI) is a non-contacting optical technique which is widely used for the measurement of surface topography. CSI combines the lateral resolution of a high power microscope with the axial resolution of an interferometer. As with any other metrology instrument, CSI is calibrated to define measurement uncertainty. The traditional calibration procedure, as recommended by instrument manufacturers, consists of calibration of the axial and lateral scales of the instrument. Although calibration in this way provides uncertainties for the measurement of rectilinear artefacts, it does not give information about tilt-related uncertainty. If an object with varying slope is measured, significant errors are observed as the surface gradient increases. In this thesis a novel approach of calibration and adjustment for CSI using a spherical object is introduced. This new technique is based on three dimensional linear filtering theory. According to linear theory, smooth surface measurement in CSI can be represented as a linear filtering operation, where the filter is characterised either by point spread function (PSF) in space domain or by transfer function (TF) in spatial frequency domain. The derivation of these characteristics usually involves making the Born approximation, which is strictly only applicable for weakly scattering objects. However, for the case of surface scattering and making use of the Kirchhoff approximation, the system can be considered linear if multiple scattering is assumed to be negligible. In this case, the object is replaced by an infinitely thin foil-like object, which follows the surface topography and, therefore, is called the foil model of the surface. For an ideal aberration free instrument, the linear characteristics are determined by the numerical aperture of the objective lens and the bandwidth of the source. However, it is found that the PSF and TF of a commercial instrument can depart significantly from theory and result in a significant measurement error. A new method, based on modified inverse filter to compensate the phase and amplitude-related errors in the system PSF/TF, is demonstrated. Finally, a method based on de-warping to compensate distortion is discussed. The application of the linear theory as well as modified inverse filter is dependent on the assumption of the shift invariance. As distortion introduces a field dependent magnification, the presence of distortion for CSI with relatively large field of view, restricts the applicability of the linear theory. Along with this restriction, distortion also introduces erroneous height measurement for objects with gradients. This new approach, based on de-warping, resolves the problems associated with distortion.