Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-04-26T13:52:48Z No. of bitstreams: 1 danielaluciaferreira.pdf: 2001864 bytes, checksum: baa9c94a0457494a3f6bf721819ac7fe (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-04-26T13:53:59Z (GMT) No. of bitstreams: 1 danielaluciaferreira.pdf: 2001864 bytes, checksum: baa9c94a0457494a3f6bf721819ac7fe (MD5) / Made available in DSpace on 2017-04-26T13:53:59Z (GMT). No. of bitstreams: 1 danielaluciaferreira.pdf: 2001864 bytes, checksum: baa9c94a0457494a3f6bf721819ac7fe (MD5) Previous issue date: 2016-09-19 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O uso de álcoois como combustíveis tem sido considerado uma promissora fonte de energia renovável. Considerável atenção tem sido dada às reações de metanol, uma vez que é um combustível alternativo importante. Nessa dissertação foi feito primeiramente um estudo dos sistemas moleculares que envolvem a reação entre o metanol e o radical hidroxila, otimizando-se as geometrias envolvidas em diferentes níveis teóricos como o Density Functional Theory (DFT), Hartree Fock (HF) e Coupled Cluster (CCSD(T)) calculados pelo MOLPRO [1]. A partir destes resultados foram construídos gráficos energéticos, que caracterizam a superfície de energia potencial de forma não-analítica. Utilizou-se métodos clássicos no estudo da dinâmica de reações químicas, gerando condições iniciais pelo método Quasiclassical Trajetory (QCT), em seguida, passamos ao estudo de trajetórias on-the-fly, que possui um custo computacional muito elevado inviabilizando um estudo estatístico das velocidades de reação. A partir daí, os procedimentos para calcular as constantes de velocidade em função das propriedades moleculares teóricas passou a ser investigado usando o pressuposto fundamental de que o perfil da reação pode ser descrito a um nível teórico pela Teoria do Estado de Transição (TST) usando-se para isto o programa kcvt [28]. Obtivemos as geometrias otimizadas, os gráficos energéticos de todos os pontos das reações OH+CH3OH→H2O+CH2OH e OH+CH3OH→H2O+CH3O nos níveis DFT - funcional BHLYP, HF e CCSD(T), assim como as constantes de velocidade canônica para uma faixa de temperatura de 120K a 3000k. / The use of alcohol as fuel has been considered a promising source of renewable energy. Considerable attention has been given to the reactions of methanol, since it is an important alternative fuel. In this dissertation, firstly it was studied molecular systems involving the reaction between methanol and the hydroxyl radical, optimizing the geometries involved in different theoretical levels like Density Functional Theory (DFT), Hartree Fock (HF) end Coupled Cluster (CCSD(T)) calculated by MOLPRO [1] . From these results it were built energy graphics that characterize the potential energy surface which is not analytical. We used standard methods to study the dynamics of chemical reactions, generating initial conditions by Quasiclassical Trajetory (QCT) method, passing to the study of trajectories on-the-fly, which has a very high computational cost invalidating a statistical study of reaction rates . Thereafter, the procedures to calculate the rate constants on the basis of theoretical molecular properties has been investigated using the fundamental assumption that the profile of the reaction can be described in a theoretical level by The Theory of State Transition (TST) using- to this the kcvt program [28]. We obtained the optimized geometries, the energy graphs of all the points of the reactions OH+CH3OH→H2O+CH2OH and OH+CH3OH→+H2OCH3O in the DFT-BHLYP, HFandCCSD(T)levels, as well as the canonical rates constants for a temperature range from 120K to 3000K.

While the spin trapping properties of thiols have been investigated through EPR analysis and kinetics studies, few groups have studied these properties using strictly computational methods. In particular, α-lipoic acid (ALA) and its reduced form, dihydrolipoic acid (DHLA), one of the strongest endogenously produced antioxidants, show potential for being effective, naturally occurring spin traps for the trapping of reactive oxygen species. This research covers electronic structure calculations of ALA, DHLA, and their corresponding hydroxyl radical spin adducts, performed at the cc-pVDZ/B3LYP/DFT level of theory. The effects on DHLA introduced by other radicals such as ·OOH, ·OCH3, and ·OOCH3 are reported. Explicit solvation was carried out using open-source molecular packing software and was studied using MOPAC PM6 semi-empirical geometry optimizations. Complete Basis Set (CBS) limit extrapolations were performed using cc-pVXZ (X = D, T, Q) Dunning basis sets under the DFT/B3LYP level of theory, and results are compared to the literature.

The main focus of the thesis are approaches to technical analysis, trading systems and it summarizes interesting findings, according to which a FOREX automated trading system was designed and implemented. Optimization and testing were a prerequisite for a real-world deployment, so the automated trading system was tested on historical data and some of its input parameters were optimized for maximum stability and profit.

Durch neue, hochflexible Fertigungsverfahren wie das Freiformfräsen eröffnet sich für Kegelradverzahnungen ein großes geometrisches Optimierungspotenzial. Diese Arbeit widmet sich daher der Ermittlung einer optimalen Makro-, Mikro- und Zahnfußgeometrie für bogenverzahnte Kegelräder. Neben dem Zahnprofil und der Zahnfußkurve wird besonderes Augenmerk auf die Ermittlung topologischer Flankenmodifikationen zur Maximierung der Tragfähigkeit gelegt. Gleichzeitig bietet der gezeigte Optimierungsalgorithmus die Möglichkeit zur Minimierung der Geräuschanregung, wodurch der bisher existierende Zielkonflikt zwischen diesen beiden Aspekten aufgehoben werden kann.

This thesis presents numerical optimization of geometries of axially symmetric ion trap mass analyzers. The motivation for this thesis is two fold. First is to demonstrate how the automated scheme can be applied to achieve geometry parameters of axially symmetric ion traps for a desired field configuration. Second is, through the Geometries investigated in this thesis, to present practically achievable geometries for mass spectroscopists to use. Here the underlying thought has been to keep the design simple for ease of fabrication (with the possibility of miniaturization) and still ensure that the performance of these analyzers is similar to the stretched geometry Paul traps. Five geometries have been taken up for investigation: one is the well known Cylindrical ion trap (CIT), three are new geometries and the last is the Paul trap under development in our laboratory. Two of these newer geometries have a step in the region of the midline of the cylindrical ring electrode (SRIT) and the third geometry has a step in its endcap electrodes (SEIT). The optimization has been carried out around deferent objective functions composed of the desired weights of higher order multiples. The Nelder-Mead simplex method has been used to optimize trap geometries. The multipoles included in the computations are quadrupole, octopole, dodecapole, hexadecapole,ikosipole and tetraikosipole having weights A2, A4, A6, A8, A10 and A12, respectively.Poincare sections have been used to understand dynamics of ions in the traps investigated. For the CIT, it has been shown that by changing the aspect ratio of the trap the harmful ejects of negative dodecapole superposition can be eliminated, although this results in a large positive A4=A2 ratio. Improved performance of the optimized CIT is suggested by the ion dynamics as seen in Poincare sections close to the stability boundary. With respect to the SRIT, two variants have been investigated. In the first geometry, A4=A2 and A6=A2 have been optimized and in the second A4=A2, A6=A2 and A8=A2 have been optimized; in both cases, these ratios have been kept close to their values reported for stretched hyperboloid geometry Paul traps. In doing this, however, it was seen that the weights of still higher order multipole not included in the objective function, A10=A2 and A12=A2, are high; additionally, A10=A2 has a negative sign. In spite of this, for both these configurations, the Poincare sections predict good performance. In the case of the SEIT, a geometry was obtained for which A4=A2 and A6=A2 are close to their values in the stretched geometry Paul trap and the higher even multipole (A8=A2, A10=A2 and A12=A2) are all positive and small in magnitude. The Poincare sections predict good performance for this con¯guration too. Direct numerical simulations of coupled nonlinear axial/radial dynamics also predict good performance for the SEIT, which seems to be the most promising among the geometries proposed here. Finally, for the Paul trap under development in our laboratory, Poincare sections and numerical simulations of coupled ion dynamics suggest a stretch of 79:7% is the best choice.

V této práci je prezentována studie fragmentačního procesu zvolené molekuly a jeho vztah ke složení fragmentačních produktů. Práce je zaměřená na výpočet fragmentační energie molekuly pomocí ab initio kvantově chemických metod, metodou „density functional theory (DFT)“ a také srovnáním s experimentem. Je prezentován vliv výpočetní metody, bázového setu, a geometrie molekuly na simulaci. Byla porovnána fragmentace methylfenylsilanu (MPS), dimethylfenylsilanu (DMPS), a trimetylfenylsilanu (TMPS). Fragmentace byla iniciována monochromatickým elektronovým svazkem (EII). Hmotnostní spektrometrie byla využita ke studiu složení fragmentačních produktů MPS a TMPS. Fragmentační produkty MPS a TMPS měřené v rámci této práce byly doplněny o experimentální studii DMPS, která byla prezentována v literatuře. Takto byla získána řada molekul, které jsou strukturně podobné, ale mají výrazně rozdílné chování během fragmentace. Pomocí měření účinného průřezu byly měřeny disociační energie vazeb a tyto disociační energie byly vypočteny pomocí metody DFT. Kombinací teoretického výpočtu metodou DFT a experimentálního měření jsme poukázali na společné rysy a na rozdíly ve fragmentačním schématu všech tří molekul. Navrhli jsme odštěpení dvou vodíkových atomů během plazmově indukovaného fragmentačního procesu. Vodíky mohou být odštěpeny pomocí dvou mechanismů: i. odštěpení dvou vodíků jeden po druhém a ii. odštěpení molekuly H2 v jednom kroku. Z profilů energie dokážeme určit, který mechanismus bude v tom konkrétním případě pravděpodobnější. Předpokládaný mechanismus je v korelaci s experimentálními výsledky fragmentace zjištěnými z hmotnostních spekter.

Designing structures for lightness is an intelligent and responsible way for engineers and architects to conceive structural systems. Lightweight structures are able to bridge wide spans with a least amount of material. However, the quest for lightness remains an utopia without the driving constraints that give sense to contemporary structural design.<p><p>Previously proposed computational methods for designing lightweight structures focused either on finding an equilibrium shape, or are restricted to fairly small design applications. In this work, we aim to develop a general, robust, and easy-to-use method that can handle many design parameters efficiently. These considerations have led to truss layout optimization, whose goal is to find the best material distribution within a given design domain discretized by a grid of nodal points and connected by tentative bars. <p><p>This general approach is well established for topology optimization where structural component sizes and system connectivity are simultaneously optimized. The range of applications covers limit analysis and identification of failure mechanisms in soils and masonries. However, to fully realize the potential of truss layout optimization for the design of lightweight structures, the consideration of geometrical variables is necessary. <p><p>The resulting truss geometry and topology optimization problem raises several fundamental and computational challenges. Our strategy to address the problem combines mathematical programming and structural mechanics: the structural properties of the optimal solution are used for devising the novel formulation. To avoid singularities arising in optimal configurations, the present approach disaggregates the equilibrium equations and fully integrates their basic elements within the optimization formulation. The resulting tool incorporates elastic and plastic design, stress and displacements constraints, as well as self-weight and multiple loading.<p><p>Besides, the inherent slenderness of lightweight structures requires the study of stability issues. As a remedy, we develop a conceptually simple but efficient method to include local and nodal stability constraints in the formulation. Several numerical examples illustrate the impact of stability considerations on the optimal design.<p><p>Finally, the investigation on realistic design problems confirms the practical applicability of the proposed method. It is shown how we can generate a range of optimal designs by varying design settings. In that regard, the computational design method mostly requires the designer a good knowledge of structural design to provide the initial guess. / Doctorat en Sciences de l'ingénieur / info:eu-repo/semantics/nonPublished

Wave energy conversion technology has gained popularity due to its potential to be-come one of the most preferred energy sources. Its high energy density and low car-bon footprint have inspired the development of many wave energy converter (WEC) technologies, few of which have made their way to commercialisation, and many are progressing. The Floating Power Plant (FPP) device is a combined floating wind and wave converter. The company, Floating Power Plant, was established in 2004 and has developed and patented a floating device that consists of a semi-submersible that serves as a foundation for a single wind turbine and hosts four wave energy converters (WECs). Each WEC consists of a partially submerged wave absorber whose pitching motion generates energy from incoming waves. The wave absorbers are connected to an oil hydraulic power take-off system located in a dry “engine room” above the free water surface, where the mechanical energy in the absorber is converted to electricity. When undergoing pitching movements, there are interactions between individual wave absorbers and the surrounding platform. This thesis focuses on developing methods to improve the FPP WEC’s hydrodynamic interactions. The first part of this thesis optimises the wave absorber (WA) ballast. An ana-lytical model is developed to enable systematic selection of WA ballast combination with significantly less computational effort when compared with the more conven-tional means, such as using CAD software. The study suggests an algorithm with which the absorbed power and resonance frequency can be improved and adjusted by manipulating the ballasts’ mass, the position of its centre of gravity, placement and inclination of the WA. The proposed method is generic and can be applied to other WEC concepts or submerged bodies in general. The results show the feasibility of designing the absorber ballast to offer passive control for increased wave absorption. It demonstrates the effect of ballast on the WA inclination, resonance frequency and response amplitude operator (RAO). The second part focuses on the optimisation of the FPP platform geometry. The genetic algorithm optimisation technique is implemented to maximise the annual en-ergy produced by the relative pitch motion of the WA to the floating platform. The optimised variables are characteristic lengths of the floating platform, most of which are part of the immediate surrounding walls of the absorber. The objective function is a function of the WA’s annual energy production (AEP) and RAO. Results show the feasibility of improving the hydrodynamic interaction between the floating platform and its integrated wave absorbers for a given wave climate by using a heuristic search technique. The number of iterations to convergence tends towards increased values when considering more optimised variables. It is also observed that the computational time appears to be independent of the number of variables but is significantly impacted by the computational power of the machine used.

En sjukdom kan många gånger härledas till en kaskadereaktion mellan proteiner, co-faktorer och substrat. Denna kaskadreaktion blir många gånger målet för att behandla sjukdomen med läkemedel. För att designa nya läkemedelsmoleyler används vanligen datorbaserade verktyg. Denna design av läkemedelsmolekyler drar stor nytta av att målproteinet är känt och då framförallt dess tredimensionella (3D) struktur. Är 3D-strukturen känd kan man utföra så kallad struktur- och datorbaserad molekyldesign, 3D-geometrin (f.f.a. för inbindningsplatsen) blir en vägledning för designen av en ny molekyl. Många faktorer avgör interaktionen mellan en molekyl och bindningsplatsen, till exempel fysikalisk-kemiska egenskaper hos molekylen och bindningsplatsen, flexibiliteten i molekylen och målproteinet, och det omgivande lösningsmedlet. För att strukturbaserad molekyldesign ska fungera väl måste två viktiga steg utföras: i) 3D anpassning av molekyler till bindningsplatsen i ett målprotein (s.k. dockning) och ii) prediktion av molekylers affinitet för bindningsplatsen. Huvudsyftena med arbetet i denna avhandling var som följer: i) skapa modeler för att prediktera affiniteten mellan en molekyl och bindningsplatsen i ett målprotein; ii) förfina molekyl-protein-geometrin som skapas vid 3D-anpassning mellan en molekyl och bindningsplatsen i ett målprotein (s.k. dockning); iii) karaktärisera proteiner och framför allt deras sekundärstruktur; iv) bedöma effekten av olika matematiska beskrivningar av lösningsmedlet för förfining av 3D molekyl-protein-geometrin skapad vid dockning och prediktion av molekylers affinitet för proteiners bindningsfickor. Ett övergripande syfte var att använda kemometriska metoder för modellering och dataanalys på de ovan nämnda punkterna. För att sammanfatta så presenterar denna avhandling metoder och resultat som är användbara för strukturbaserad molekyldesign. De rapporterade resultaten visar att det är möjligt att skapa kemometriska modeler för prediktion av molekylers affinitet för bindningsplatsen i ett protein och att dessa presterade lika bra som andra vanliga metoder. Dessutom kunde kemometriska modeller skapas för att beskriva effekten av hur inställningarna för olika parametrar i dockningsprogram påverkade den 3D molekyl-protein-geometrin som dockingsprogram skapade. Vidare kunde kemometriska modeller andvändas för att öka förståelsen för deskriptorer som beskrev sekundärstrukturen i proteiner. Förfining av molekyl-protein-geometrin skapad genom dockning gav liknande och ickesignifikanta resultat oberoende av vilken matematisk modell för lösningsmedlet som användes, förutom för ett fåtal (sex av 30) fall. Däremot visade det sig att användandet av en förfinad geometri var värdefullt för prediktion av molekylers affinitet för bindningsplatsen i ett protein. Förbättringen av prediktion av affintitet var markant då en Poisson-Boltzmann beskrivning av lösningsmedlet användes; jämfört med prediktionerna gjorda med ett dockningsprogram förbättrades korrelationen mellan beräknad affintiet och uppmätt affinitet med 0,7 (R2). / A disease is often associated with a cascade reaction pathway involving proteins, co-factors and substrates. Hence to treat the disease, elements of this pathway are often targeted using a therapeutic agent, a drug. Designing new drug molecules for use as therapeutic agents involves the application of methods collectively known as computer-aided molecular design, CAMD. When the three dimensional (3D) geometry of a macromolecular target (usually a protein) is known, structure-based CAMD is undertaken and structural information of the target guides the design of new molecules and their interactions with the binding sites in targeted proteins. Many factors influence the interactions between the designed molecules and the binding sites of the target proteins, such as the physico-chemical properties of the molecule and the binding site, the flexibility of the protein and the ligand, and the surrounding solvent. In order for structure-based CAMD to be successful, two important aspects must be considered that take the abovementioned factors into account. These are; i) 3D fitting of molecules to the binding site of the target protein (like fitting pieces of a jigsaw puzzle), and ii) predicting the affinity of molecules to the protein binding site. The main objectives of the work underlying this thesis were: to create models for predicting the affinity between a molecule and a protein binding site; to refine the geometry of the molecule-protein complex derived by or in 3D fitting (also known as docking); to characterize the proteins and their secondary structure; and to evaluate the effects of different generalized-Born (GB) and Poisson-Boltzmann (PB) implicit solvent models on the refinement of the molecule-protein complex geometry created in the docking and the prediction of the molecule-to-protein binding site affinity. A further objective was to apply chemometric methodologies for modeling and data analysis to all of the above. To summarize, this thesis presents methodologies and results applicable to structure-based CAMD. Results show that predictive chemometric models for molecule-to-protein binding site affinity could be created that yield comparable results to similar, commonly used methods. In addition, chemometric models could be created to model the effects of software settings on the molecule-protein complex geometry using software for molecule-to-binding site docking. Furthermore, the use of chemometric models provided a more profound understanding of protein secondary structure descriptors. Refining the geometry of molecule-protein complexes created through molecule-to-binding site docking gave similar results for all investigated implicit solvent models, but the geometry was significantly improved in only a few examined cases (six of 30). However, using the geometry-refined molecule-protein complexes was highly valuable for the prediction of molecule-to-binding site affinity. Indeed, using the PB solvent model it yielded improvements of 0.7 in correlation coefficients (R2) for binding affinity parameters of a set of Factor Xa protein drug molecules, relative to those obtained using the fitting software.

Dans cette thèse sont montrés des développements de l'approximation de la phase aléatoire (RPA) dans le contexte de théories à séparation de portée. On présente des travaux sur le formalisme de la RPA en général, et en particulier sur le formalisme "matrice diélectrique" qui est exploré de manière systématique. On montre un résumé d'un travail sur les équations RPA dans le contexte d'orbitales localisées, notamment des développements des orbitales virtuelles localisées que sont les "orbitales oscillantes projetées" (POO). Un programme a été écrit pour calculer des fonctions telles que le trou de d'échange, la fonction de réponse, etc... sur des grilles de l'espace réel (grilles parallélépipédiques ou de type "DFT"). On montre certaines de ces visualisations. Dans l'espace réel, on expose une adaptation de l'approximation du dénominateur effectif (EED), développée originellement dans l'espace réciproque en physique du solide. Également, les gradients analytiques des énergies de corrélation RPA dans le contexte de la séparation de portée sont dérivés. Le formalisme développé ici à l'aide d'un lagrangien permet une dérivation tout-en-un des termes courte- et longue-portée qui émergent dans les expressions du gradient, et qui montrent un parallèle intéressant. Des applications sont montrées, telles que des optimisations de géométries aux niveaux RSH-dRPA-I et RSH-SOSEX d'un ensemble de 16 petites molécules, ou encore le calcul et la visualisation des densités corrélées au niveau RSH-dRPA-I / In this thesis are shown developments in the random phase approximation (RPA) in the context of range-separated theories. We present advances in the formalism of the RPA in general, and particularly in the "dielectric matrix" formulation of RPA, which is explored in details. We show a summary of a work on the RPA equations with localized orbitals, especially developments of the virtual localized orbitals that are the "projected oscillatory orbitals" (POO). A program has been written to calculate functions such as the exchange hole, the response function, etc... on real space grid (parallelepipedic or of the "DFT" type) ; some of those visualizations are shown here. In the real space, we offer an adaptation of the effective energy denominator approximation (EED), originally developed in the reciprocal space in solid physics. The analytical gradients of the RPA correlation energies in the context of range separation has been derived. The formalism developed here with a Lagrangian allows an all-in-one derivation of the short- and long-range terms that emerge in the expressions of the gradient. These terms show interesting parallels. Geometry optimizations at the RSH-dRPA-I and RSH-SOSEX levels on a set of 16 molecules are shown, as well as calculations and visualizations of correlated densities at the RSH-dRPA-I level