Made available in DSpace on 2014-12-17T14:10:23Z (GMT). No. of bitstreams: 1 BrunoGS_DISSERT_partes autorizadas.pdf: 2090858 bytes, checksum: 96c920960475d5970880d27da7b95ada (MD5) Previous issue date: 2011-05-23 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico / Knowledge of the native prokaryotes in hazardous locations favors the application of biotechnology for bioremediation. Independent strategies for cultivation and metagenomics contribute to further microbiological knowledge, enabling studies with non-cultivable about the "native microbiological status and its potential role in bioremediation, for example, of polycyclic aromatic hydrocarbons (HPA's). Considering the biome mangrove interface fragile and critical bordering the ocean, this study characterizes the native microbiota mangrove potential biodegradability of HPA's using a biomarker for molecular detection and assessment of bacterial diversity by PCR in areas under the influence of oil companies in the Basin Petroleum Geology Potiguar (BPP). We chose PcaF, a metabolic enzyme, to be the molecular biomarker in a PCR-DGGE detection of prokaryotes that degrade HPA s. The PCR-DGGE fingerprints obtained from Paracuru-CE, Fortim-CE and Areia Branca-RN samples revealed the occurrence of fluctuations of microbial communities according to the sampling periods and in response to the impact of oil. In the analysis of microbial communities interference of the oil industry, in Areia Branca-RN and Paracuru-CE was observed that oil is a determinant of microbial diversity. Fortim-CE probably has no direct influence with the oil activity. In order to obtain data for better understanding the transport and biodegradation of HPA's, there were conducted in silico studies with modeling and simulation from obtaining 3-D models of proteins involved in the degradation of phenanthrene in the transport of HPA's and also getting the 3-D model of the enzyme PcaF used as molecular marker in this study. Were realized docking studies with substrates and products to a better understanding about the transport mechanism and catalysis of HPA s / O conhecimento sobre os procariotos nativos em locais de risco favorece a aplica??o de biotecnologias para biorremedia??o. Estrat?gias independentes de cultivo, como metagen?mica, contribuem para aprofundar o conhecimento microbiol?gico, possibilitando estudos com organismos n?o cultiv?veis acerca do status microbiol?gico nativo e seu potencial papel na biodegrada??o de, por exemplo, Hidrocarbonetos Arom?ticos Polic?clicos (HAP s). Considerando o bioma de mangue uma interface fr?gil e cr?tica de fronteira com o oceano, este trabalho caracteriza a microbiota nativa de mangue com potencial biodegradador de HAP s utilizando um biomarcador molecular para detec??o e avalia??o da diversidade bacteriana em ?reas sob influ?ncia de ind?strias petrol?feras atrav?s da PCR-DGGE na Bacia Petrol?fera Potiguar (BPP). Foi escolhido um biomarcador molecular metab?lico, enzima PcaF, para detec??o de procariotos degradadores de HAP s. Com o biomarcador, fingerprints foram obtidos de amostras de Paracuru-CE, Fortim-CE e Areia Branca-RN, revelando a ocorr?ncia de flutua??es das comunidades microbianas de acordo com os per?odos de amostragem e em resposta ao impacto por petr?leo. Atrav?s da an?lise das comunidades microbianas frente ? interfer?ncia da ind?stria do petr?leo, em Areia Branca-RN e Paracuru-CE foi observado que o petr?leo ? determinante para a diversidade microbiana. Fortim-CE provavelmente n?o tem influ?ncia direta da atividade petrol?fera. No intuito de obter dados para o melhor entendimento do transporte e biodegrada??o de HAP s, foram desenvolvidos estudos in silico de modelagem e simula??o computacional a partir da obten??o de modelos 3-D de prote?nas envolvidas na degrada??o do fenantreno, no transporte de HAP s e tamb?m a obten??o do modelo 3-D da enzima PcaF. Estudos de dockings com substratos e produtos forneceram dados para o melhor entendimento sobre o mecanismo de transporte e cat?lise de HAP s

We have investigated the noncovalent interactions in carbohydrate-aromatic interactions which are pivotal to the recognition of carbohydrates in proteins. We have employed quantum mechanical methods to study carbohydrate-aromatic complexes. Due to the importance of dispersion contribution to the interaction energy, we mainly use density functional theory augmented with an empirical correction for the dispersion interactions (DFT-D). We have validated this method with a limited number of high level ab initio calculations. We have also analysed the vibrational and NMR chemical shift characteristics using the DFT-D method. We have mainly studied the complexes involving β-glucose with 3-methylindole and p-hydroxytoluene, which are analogues of tryptophan and tyrosine, respectively. We find that the contribution for interaction energy mainly comes from CH/π and OH/π interactions. We find that the interaction energy of complexes involving CH/π and OH/π interactions is reflected in the associated blue and red shifts of vibrational spectrum. We also find that the interactions involving 3-methylindole are somewhat greater than those for p-hydroxytoluene. The C-H blueshifts are also in parallel with the predicted NMR proton shift. We have also tested different density functionals including both standard density functionals and newly developed M0x functionals and MP2 method for studying carbohydrate-aromatic complexes. The DFT-D method and M06 functionals of the M0x family are found to perform better, while B3LYP and BLYP functionals perform poorly. We find that the inclusion of a dispersion term to BLYP is found to perform better. The dispersion energy dominates over the interaction energy of carbohydrate-aromatic complexes. From the DFT-D calculations, we found that the complexes would be unstable without the contribution from dispersive energy. We have also studied the importance of noncovalent interactions in functionalization of nanotubes by nucleic acid bases and aromatic amino acids by using semi-empirical methods with dispersion term such asPM3-D and PM3-D*. We find that the both semi-empirical schemes give reasonable interaction energies with respect to DFT-D interaction energies. We have also used PM3-D method to study the adsorption of organic pollutants on graphene sheet and on nanotubes. We found that the semi-empirical schemes, which are faster and cheaper, are suitable to study these larger molecules involving noncovalent interactions and can be used as an alternative to DFT-D method. We have also studied the importance of dispersion interaction and the effect of steric hindrance in aggregation of functionalized anthracenes and pentacenes. We have also employed molecular dynamics simulation methods to study the aggregation of anthracene molecules in toluene solution.

Like other animals, humans explore to learn about the world, and exploit what we have learned in order to maximize reward. The trade-off between exploration and exploitation is a widely-studied topic that cuts across multiple domains, including animal ecology, economics, and computer science. This work approaches the explore-exploit dilemma from the perspective of cognitive neuroscience. In particular, how are our decisions to explore or exploit represented computationally? And how is that representation implemented in the brain? Experiment 1 examined neural signals following outcomes in a risk-taking task. Explorations – defined as slower responses – were preceded by an enhancement of the P300, a component of the human event-related brain potential thought to reflect a phasic release of norepinephrine from locus coeruleus. Experiment 2 revealed that the same neural signal precedes feedback in a learning task called a two-armed bandit. There, a reinforcement learning model was used to classify responses as either exploitations or explorations; exploitations were driven by previous rewards, and explorations were not. Experiments 3 and 4 extended these results in three important ways. First, evidence is presented that the neural signal observed in Experiments 1 and 2 was driven not only by the upcoming decision, but also by the preceding decision (perhaps even more so). Second, Experiments 3 and 4 involved increasingly larger action spaces. Experiment 3 involved choosing from among either 4, 9, or 16 options. Experiment 4 involved searching for rewards in continuous two-dimensional map. In both experiments, the feedback-locked P300 was enhanced following exploration. Third, exploitation was the more common strategy in Experiments 1 and 2. Thus, it was unclear whether the exploration-related P300 enhancement observed there was due to exploration per se, to exploration rate, or to the fact that exploration was rare compared to exploitation. Experiment 3 partially address this by eliciting different rates of exploration; the exploration-related P300 effect correlated with rate of exploration. In Experiment 4, exploration was more common than exploitation (in contrast to Experiments 1–3); even so, exploration was followed by a P300 enhancement. Together, Experiments 1–4 suggest the presence of a general neural system related to exploration that operates across multiple task types (discrete to continuous), regardless of whether exploration or exploitation is the more common task strategy. The proposed purpose of this neural signal is to interrupt one mode of decision-making (exploration) in favour of another (exploitation). / Graduate

Les troubles du spectre de l’autisme (TSA) sont caractérisés par des difficultés persistantes dans les domaines de la communication et des interactions sociales. Les individus atteints de TSA ont notamment des difficultés à décoder les émotions d’autrui et il est souvent suggéré qu’un déficit général du traitement des visages émotionnels est à l’origine de ces difficultés. Cependant, les résultats de la littérature sont incohérents et soulignent l'importance de facteurs méthodologiques qui pourraient influencer la performance des personnes TSA. Deux théories actuelles sont pertinentes au regard de ces difficultés rencontrées dans les interactions sociales : 1) la théorie de la régulation comportementale propose que ces difficultés résultent de dysfonctionnements du traitement des émotions et/ou des mécanismes permettant de répondre de façon appropriée à ces émotions; et 2) la théorie de la motivation sociale propose au contraire que ces mécanismes sont intacts et que les difficultés rencontrées sont le résultat d’un déficit de motivation sociale. Cette thèse avait pour but de départager ces deux théories, tout en contrôlant de nombreux facteurs méthodologiques qui pourraient influencer la performance des personnes TSA. L’expérience 1 visait à étudier l’impact de la direction du regard sur le traitement de la peur et de la colère. L’expérience 2 étudiait les choix d’actions spontanées en présence de visages de peur ou de colère et la catégorisation de ces émotions présentées en vision périphérique. Ces deux études révèlent des résultats similaires chez des adolescents neuro-typiques et TSA. Ces deux groupes sont capables de décoder des expressions de peur et de colère, présentées au centre de l’écran ou en périphérie, ils sont aussi sensibles aux variations d’intensité de ces émotions et aux variations de contexte (ici étudié sous la forme de la direction du regard). D’autre part, les deux groupes répondent de façon similaire à ces émotions, notamment en choisissant des actions qui leur permettent d’éviter des individus menaçants. Pris dans leur ensemble, ces résultats indiquent que les mécanismes impliqués dans le traitement des émotions, l’intégration des facteurs contextuels, et dans l’adaptation de son comportement en réponses à ces signaux sociaux sont intacts chez des adolescents atteints de TSA. Ces résultats sont discutés au regard des théories de la motivation sociale et de la régulation comportementale. / Autism spectrum disorders (ASD) are neurodevelopmental conditions characterised by persistent deficits in social reciprocity. Deficits in emotion perception are common in ASD and suggested to stem from a generalised deficit in the processing of facial affect. The literature however is inconsistent, stressing the importance of methodological factors that might bring individuals with ASD to a disadvantage. Two relevant theoretical frameworks are considered: 1) the behavioural self-regulation account proposes that affective atypicalities stem from deficits in the processing of the emotional signals and/or the regulation of appropriate responses to these signals; and 2) the social motivation account proposes that the mechanisms behind either of these two stages of emotion understanding are intact and that behavioural deficits stem from reduced weighting of social information. This Ph.D. aimed to disentangle between the two theories in the context of social threats by taking into account the necessary methodological factors. Experiment 1 investigated the contextual impact of gaze direction on the categorisation of facial expressions of anger and fear. Experiment 2 investigated both free action choice in response to implicit social threats –facial expressions of anger and fear- and their emotion categorisation accuracy in visual periphery. Across both studies ASD and typically developing (TD) adolescents demonstrated intact processing of both anger and fear in direct view and in visual periphery and were sensitive to the changes in emotional intensity of the stimuli. In Experiment 1, although the control group was overall more accurate than the ASD group in emotion decoding, gaze direction impacted the processing of threat similarly in both groups. Specifically, gaze direction raised the saliency of the threat for the observer and enhanced their sensitivity to the most salient ones. In Experiment 2, both groups demonstrated an overall tendency to avoid emotional agents, which was particularly evident in the case of anger. Taken together, the mechanisms behind the processing of facial social threats appear relatively spared in ASD adolescents and the impact of contextual factors are similar ASD and typical development. Adolescents with ASD are able to use social threats to adapt their behaviour by avoiding the emotional agent, which is not surprising during a developmental period characterised by enhanced reactivity to threat. These findings are discussed in terms of the social motivation and behavioural self-regulation frameworks and future directions are proposed.

This thesis deals with computational modelling of rubber damper using Finite element method (FEM). This thesis includes experimental measurement of material properties of rubber subjected to static and dynamic loading and their implementation into viscoelastic and hyperelastic material models with respect to given task. Dependance of dynamic stiffness on loading frequency obtained from the simulation is validated with experimental measurement. In the end the difference between results is investigated and possible causes of that are introduced.

The diploma thesis deals with the assessment of the prediction of brain aneurysm rupture based on its geometrical and material properties. In the first part of the thesis there is a~detailed research study of cardiovascular systems with a focus on the cerebral artery and aneurysm occurring on their bifurcates. The second part of the thesis is focused on the creation of two models of arterial cerebral bifurcation with the presence of aneurysm and on obtaining their geometry in unloaded state. Emphasis is placed on the most realistic constitutive model of the artery wall material based on real data from uniaxial tensile tests and on a suitably chosen blood pressure load. This blood pressure may be step-changed, for example, in bungee jumping. In the work, a calculation of the increase in blood pressure during the step-change is performed, which is subsequently used in calculations of tension in the wall of the cerebral aneurysm. In conclusion, the risk of rupture is evaluated in two model idealized brain aneurysms and a discussion of the credibility of the results is given.

The diploma thesis deals with the design of an artificial heart based on the principle of gas accumulators. The introductory part describes the anatomy and physiology of the human cardiovascular system, mechanical heart replacement and the basic properties of pneumatic mechanisms. Furthermore, there is shown the procedure of pneumatic circuit design and its simulation in the program Simulink. The experimental part contains verification of the functionality of the pneumatic circuit, designed the positive displacement pump, and the measured characteristics of both ventricles. The last part of the work deals with the reduction possibilities of dimensions and weight of the whole mechanism. There is also included computational modelling of the pneumatic circuit using helium as a working medium.

This master thesis is aimed at computational modeling of ballistic resistant layered laminate. The introductory sections of the thesis are aimed at understanding the individual topics that are closely related to the interaction of the projectile and target and computational modeling of this process. The main goal of this thesis was to create a computational model that is able to reflect the behavior of aramid fabric during the interaction with the projectile. During the development of the computational model were used more methods of modeling and also more material models were used. For the purposes of the development of the computational model were used the available data of the companies SVS FEM s.r.o. and VVÚ s.p. The outcome of the diploma thesis is a computational model of aramid fabric which is designed for ballistic protection simulations. This model is validated on the basis of available experiments. The validated computational model is then applied to the simulation of ballistic protection.

Work occupies computational modelling mechanical behavior elastomers and composits with rubber matrix and their utilization for compute model of tire creation. MATADOR tire 165/65 R13 Axisymetric 2D model was created in two geometric variants. For the computational modeling is applying the Finite element method (FEM). The model was in different variants distinctive grade of modeling material. At first was done inner pressure analyst impact on deformation of each of model. Then was count influence on tire load with angular velocity meanwhile with inner pressure. The impact thickness of tire protector layer on global deformation tyre casing was verified too.

The master’s thesis deals with the computational modelling of the mechanical testing of isolated smooth muscle cells. The main aims are to create computational model of a cell, to simulate single-axis tensile test and to modify the model so that the model reflects real mechanical response. The model of the cell includes cytoplasm, nucleus, cell membrane and cytoskeleton which is modelled as a tensegrite structure. On this model the tensile test was simulated in case of the cell with cytoskeleton and the cell with distributed the cytoskeleton. Force-elongation curves, which were obtained from this simulation, were compared with experimental data which were taken from literature. Tensile properties were measured on freshly isolated cells from rat thoracic aorta, cultured cells, and cells treated with cytochalasin D to disrupt their actin filaments. It was found that the cytoskeleton influence on the cell load in computational model was smaller than in the real cell. Therefore the model was modified by changing material propreties and geometry so that the model of the cell corresponded with the different types of experimentally measured cells.