976 resultados para Computational modeling
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This paper focuses on the flexural behavior of RC beams externally strengthened with Carbon Fiber Reinforced Polymers (CFRP) fabric. A non-linear finite element (FE) analysis strategy is proposed to support the beam flexural behavior experimental analysis. A development system (QUEBRA2D/FEMOOP programs) has been used to accomplish the numerical simulation. Appropriate constitutive models for concrete, rebars, CFRP and bond-slip interfaces have been implemented and adjusted to represent the composite system behavior. Interface and truss finite elements have been implemented (discrete and embedded approaches) for the numerical representation of rebars, interfaces and composites.
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Dissertation presented to obtain the Ph.D degree in Biology
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Computational modeling has become a widely used tool for unraveling the mechanisms of higher level cooperative cell behavior during vascular morphogenesis. However, experimenting with published simulation models or adding new assumptions to those models can be daunting for novice and even for experienced computational scientists. Here, we present a step-by-step, practical tutorial for building cell-based simulations of vascular morphogenesis using the Tissue Simulation Toolkit (TST). The TST is a freely available, open-source C++ library for developing simulations with the two-dimensional cellular Potts model, a stochastic, agent-based framework to simulate collective cell behavior. We will show the basic use of the TST to simulate and experiment with published simulations of vascular network formation. Then, we will present step-by-step instructions and explanations for building a recent simulation model of tumor angiogenesis. Demonstrated mechanisms include cell-cell adhesion, chemotaxis, cell elongation, haptotaxis, and haptokinesis.
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We study the properties of the well known Replicator Dynamics when applied to a finitely repeated version of the Prisoners' Dilemma game. We characterize the behavior of such dynamics under strongly simplifying assumptions (i.e. only 3 strategies are available) and show that the basin of attraction of defection shrinks as the number of repetitions increases. After discussing the difficulties involved in trying to relax the 'strongly simplifying assumptions' above, we approach the same model by means of simulations based on genetic algorithms. The resulting simulations describe a behavior of the system very close to the one predicted by the replicator dynamics without imposing any of the assumptions of the mathematical model. Our main conclusion is that mathematical and computational models are good complements for research in social sciences. Indeed, while computational models are extremely useful to extend the scope of the analysis to complex scenarios hard to analyze mathematically, formal models can be useful to verify and to explain the outcomes of computational models.
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Children who sustain a prenatal or perinatal brain injury in the form of a stroke develop remarkably normal cognitive functions in certain areas, with a particular strength in language skills. A dominant explanation for this is that brain regions from the contralesional hemisphere "take over" their functions, whereas the damaged areas and other ipsilesional regions play much less of a role. However, it is difficult to tease apart whether changes in neural activity after early brain injury are due to damage caused by the lesion or by processes related to postinjury reorganization. We sought to differentiate between these two causes by investigating the functional connectivity (FC) of brain areas during the resting state in human children with early brain injury using a computational model. We simulated a large-scale network consisting of realistic models of local brain areas coupled through anatomical connectivity information of healthy and injured participants. We then compared the resulting simulated FC values of healthy and injured participants with the empirical ones. We found that the empirical connectivity values, especially of the damaged areas, correlated better with simulated values of a healthy brain than those of an injured brain. This result indicates that the structural damage caused by an early brain injury is unlikely to have an adverse and sustained impact on the functional connections, albeit during the resting state, of damaged areas. Therefore, these areas could continue to play a role in the development of near-normal function in certain domains such as language in these children.
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Linear programming models are effective tools to support initial or periodic planning of agricultural enterprises, requiring, however, technical coefficients that can be determined using computer simulation models. This paper, presented in two parts, deals with the development, application and tests of a methodology and of a computational modeling tool to support planning of irrigated agriculture activities. Part I aimed at the development and application, including sensitivity analysis, of a multiyear linear programming model to optimize the financial return and water use, at farm level for Jaíba irrigation scheme, Minas Gerais State, Brazil, using data on crop irrigation requirement and yield, obtained from previous simulation with MCID model. The linear programming model outputted a crop pattern to which a maximum total net present value of R$ 372,723.00 for the four years period, was obtained. Constraints on monthly water availability, labor, land and production were critical in the optimal solution. In relation to the water use optimization, it was verified that an expressive reductions on the irrigation requirements may be achieved by small reductions on the maximum total net present value.
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Techniques of evaluation of risks coming from inherent uncertainties to the agricultural activity should accompany planning studies. The risk analysis should be carried out by risk simulation using techniques as the Monte Carlo method. This study was carried out to develop a computer program so-called P-RISCO for the application of risky simulations on linear programming models, to apply to a case study, as well to test the results comparatively to the @RISK program. In the risk analysis it was observed that the average of the output variable total net present value, U, was considerably lower than the maximum U value obtained from the linear programming model. It was also verified that the enterprise will be front to expressive risk of shortage of water in the month of April, what doesn't happen for the cropping pattern obtained by the minimization of the irrigation requirement in the months of April in the four years. The scenario analysis indicated that the sale price of the passion fruit crop exercises expressive influence on the financial performance of the enterprise. In the comparative analysis it was verified the equivalence of P-RISCO and @RISK programs in the execution of the risk simulation for the considered scenario.
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In this study we discuss the electronic, structural, and optical properties of titanium dioxide nanoparticles, and also the properties of Ni(II) diimine dithiolato complexes as dyes in dye-sensitized TiO2 based solar cells. The abovementioned properties have been modeled by using computational codes based on the density functional theory. The results achieved show slight evidence on the structure-dependent band gap broadening, and clear blue-shifts in absorption spectra and refractive index functions of ultra-small TiO2 particles. It is also shown that these properties are strongly dependent on the shape of the nanoparticles. Regarding the Ni(II) diimine dithiolato complexes as dyes in dye-sensitized TiO2 based solar cells, it is shown that based on the experimental electrochemical investigation and DFT studies all studied diimine derivatives could serve as potential candidates for the light harvesting, but the e ciencies of the dyes studied are not very promising.
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The application of computational fluid dynamics (CFD) and finite element analysis (FEA) has been growing rapidly in the various fields of science and technology. One of the areas of interest is in biomedical engineering. The altered hemodynamics inside the blood vessels plays a key role in the development of the arterial disease called atherosclerosis, which is the major cause of human death worldwide. Atherosclerosis is often treated with the stenting procedure to restore the normal blood flow. A stent is a tubular, flexible structure, usually made of metals, which is driven and expanded in the blocked arteries. Despite the success rate of the stenting procedure, it is often associated with the restenosis (re-narrowing of the artery) process. The presence of non-biological device in the artery causes inflammation or re-growth of atherosclerotic lesions in the treated vessels. Several factors including the design of stents, type of stent expansion, expansion pressure, morphology and composition of vessel wall influence the restenosis process. Therefore, the role of computational studies is crucial in the investigation and optimisation of the factors that influence post-stenting complications. This thesis focuses on the stent-vessel wall interactions followed by the blood flow in the post-stenting stage of stenosed human coronary artery. Hemodynamic and mechanical stresses were analysed in three separate stent-plaque-artery models. Plaque was modeled as a multi-layer (fibrous cap (FC), necrotic core (NC), and fibrosis (F)) and the arterial wall as a single layer domain. CFD/FEA simulations were performed using commercial software packages in several models mimicking the various stages and morphologies of atherosclerosis. The tissue prolapse (TP) of stented vessel wall, the distribution of von Mises stress (VMS) inside various layers of vessel wall, and the wall shear stress (WSS) along the luminal surface of the deformed vessel wall were measured and evaluated. The results revealed the role of the stenosis size, thickness of each layer of atherosclerotic wall, thickness of stent strut, pressure applied for stenosis expansion, and the flow condition in the distribution of stresses. The thicknesses of FC, and NC and the total thickness of plaque are critical in controlling the stresses inside the tissue. A small change in morphology of artery wall can significantly affect the distribution of stresses. In particular, FC is the most sensitive layer to TP and stresses, which could determine plaque’s vulnerability to rupture. The WSS is highly influenced by the deflection of artery, which in turn is dependent on the structural composition of arterial wall layers. Together with the stenosis size, their roles could play a decisive role in controlling the low values of WSS (<0.5 Pa) prone to restenosis. Moreover, the time dependent flow altered the percentage of luminal area with WSS values less than 0.5 Pa at different time instants. The non- Newtonian viscosity model of the blood properties significantly affects the prediction of WSS magnitude. The outcomes of this investigation will help to better understand the roles of the individual layers of atherosclerotic vessels and their risk to provoke restenosis at the post-stenting stage. As a consequence, the implementation of such an approach to assess the post-stented stresses will assist the engineers and clinicians in optimizing the stenting techniques to minimize the occurrence of restenosis.
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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
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Die Wechselwirkung zwischen Proteinen und anorganischen Oberflächen fasziniert sowohl aus angewandter als auch theoretischer Sicht. Sie ist ein wichtiger Aspekt in vielen Anwendungen, unter anderem in chirugischen Implantaten oder Biosensoren. Sie ist außerdem ein Beispiel für theoretische Fragestellungen betreffend die Grenzfläche zwischen harter und weicher Materie. Fest steht, dass Kenntnis der beteiligten Mechanismen erforderlich ist um die Wechselwirkung zwischen Proteinen und Oberflächen zu verstehen, vorherzusagen und zu optimieren. Aktuelle Fortschritte im experimentellen Forschungsbereich ermöglichen die Untersuchung der direkten Peptid-Metall-Bindung. Dadurch ist die Erforschung der theoretischen Grundlagen weiter ins Blickfeld aktueller Forschung gerückt. Eine Möglichkeit die Wechselwirkung zwischen Proteinen und anorganischen Oberflächen zu erforschen ist durch Computersimulationen. Obwohl Simulationen von Metalloberflächen oder Proteinen als Einzelsysteme schon länger verbreitet sind, bringt die Simulation einer Kombination beider Systeme neue Schwierigkeiten mit sich. Diese zu überwinden erfordert ein Mehrskalen-Verfahren: Während Proteine als biologische Systeme ausreichend mit klassischer Molekulardynamik beschrieben werden können, bedarf die Beschreibung delokalisierter Elektronen metallischer Systeme eine quantenmechanische Formulierung. Die wichtigste Voraussetzung eines Mehrskalen-Verfahrens ist eine Übereinstimmung der Simulationen auf den verschiedenen Skalen. In dieser Arbeit wird dies durch die Verknüpfung von Simulationen alternierender Skalen erreicht. Diese Arbeit beginnt mit der Untersuchung der Thermodynamik der Benzol-Hydratation mittels klassischer Molekulardynamik. Dann wird die Wechselwirkung zwischen Wasser und den [111]-Metalloberflächen von Gold und Nickel mittels eines Multiskalen-Verfahrens modelliert. In einem weiteren Schritt wird die Adsorbtion des Benzols an Metalloberflächen in wässriger Umgebung studiert. Abschließend wird die Modellierung erweitert und auch die Aminosäuren Alanin und Phenylalanin einbezogen. Dies eröffnet die Möglichkeit realistische Protein- Metall-Systeme in Computersimulationen zu betrachten und auf theoretischer Basis die Wechselwirkung zwischen Peptiden und Oberflächen für jede Art Peptide und Oberfläche vorauszusagen.
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The cardiomyocyte is a complex biological system where many mechanisms interact non-linearly to regulate the coupling between electrical excitation and mechanical contraction. For this reason, the development of mathematical models is fundamental in the field of cardiac electrophysiology, where the use of computational tools has become complementary to the classical experimentation. My doctoral research has been focusing on the development of such models for investigating the regulation of ventricular excitation-contraction coupling at the single cell level. In particular, the following researches are presented in this thesis: 1) Study of the unexpected deleterious effect of a Na channel blocker on a long QT syndrome type 3 patient. Experimental results were used to tune a Na current model that recapitulates the effect of the mutation and the treatment, in order to investigate how these influence the human action potential. Our research suggested that the analysis of the clinical phenotype is not sufficient for recommending drugs to patients carrying mutations with undefined electrophysiological properties. 2) Development of a model of L-type Ca channel inactivation in rabbit myocytes to faithfully reproduce the relative roles of voltage- and Ca-dependent inactivation. The model was applied to the analysis of Ca current inactivation kinetics during normal and abnormal repolarization, and predicts arrhythmogenic activity when inhibiting Ca-dependent inactivation, which is the predominant mechanism in physiological conditions. 3) Analysis of the arrhythmogenic consequences of the crosstalk between β-adrenergic and Ca-calmodulin dependent protein kinase signaling pathways. The descriptions of the two regulatory mechanisms, both enhanced in heart failure, were integrated into a novel murine action potential model to investigate how they concur to the development of cardiac arrhythmias. These studies show how mathematical modeling is suitable to provide new insights into the mechanisms underlying cardiac excitation-contraction coupling and arrhythmogenesis.