Development of procedures for the simulation of atmospheric flows over complex terrain, using OpenFOAM

The main purpose of this work was the development of procedures for the simulation of atmospheric ows over complex terrain, using OpenFOAM. For this aim, tools and procedures were developed apart from this code for the preprocessing and data extraction, which were thereafter applied in the simulation of a real case. For the generation of the computational domain, a systematic method able to translate the terrain elevation model to a native OpenFOAM format (blockMeshDict) was developed. The outcome was a structured mesh, in which the user has the ability to de ne the number of control volumes and its dimensions. With this procedure, the di culties of case set up and the high computation computational e ort reported in literature associated to the use of snappyHexMesh, the OpenFOAM resource explored until then for the accomplishment of this task, were considered to be overwhelmed. Developed procedures for the generation of boundary conditions allowed for the automatic creation of idealized inlet vertical pro les, de nition of wall functions boundary conditions and the calculation of internal eld rst guesses for the iterative solution process, having as input experimental data supplied by the user. The applicability of the generated boundary conditions was limited to the simulation of turbulent, steady-state, incompressible and neutrally strati ed atmospheric ows, always recurring to RaNS (Reynolds-averaged Navier-Stokes) models. For the modelling of terrain roughness, the developed procedure allowed to the user the de nition of idealized conditions, like an uniform aerodynamic roughness length or making its value variable as a function of topography characteristic values, or the using of real site data, and it was complemented by the development of techniques for the visual inspection of generated roughness maps. The absence and the non inclusion of a forest canopy model limited the applicability of this procedure to low aerodynamic roughness lengths. The developed tools and procedures were then applied in the simulation of a neutrally strati ed atmospheric ow over the Askervein hill. In the performed simulations was evaluated the solution sensibility to di erent convection schemes, mesh dimensions, ground roughness and formulations of the k - ε and k - ω models. When compared to experimental data, calculated values showed a good agreement of speed-up in hill top and lee side, with a relative error of less than 10% at a height of 10 m above ground level. Turbulent kinetic energy was considered to be well simulated in the hill windward and hill top, and grossly predicted in the lee side, where a zone of ow separation was also identi ed. Despite the need of more work to evaluate the importance of the downstream recirculation zone in the quality of gathered results, the agreement between the calculated and experimental values and the OpenFOAM sensibility to the tested parameters were considered to be generally in line with the simulations presented in the reviewed bibliographic sources.

Experimental and numerical study on the evaluation of ventilation efficiency

Buildings account for 40% of total energy consumption in the European Union. The reduction of energy consumption in the buildings sector constitute an important measure needed to reduce the Union's energy dependency and greenhouse gas emissions. The Portuguese legislation incorporate this principles in order to regulate the energy performance of buildings. This energy performance should be accompanied by good conditions for the occupants of the buildings. According to EN 15251 (2007) the four factors that affect the occupant comfort in the buildings are: Indoor Air Quality (IAQ), thermal comfort, acoustics and lighting. Ventilation directly affects all except the lighting, so it is crucial to understand the performance of it. The ventilation efficiency concept therefore earn significance, because it is an attempt to quantify a parameter that can easily distinguish the different options for air diffusion in the spaces. The two indicators most internationally accepted are the Air Change Efficiency (ACE) and the Contaminant Removal Effectiveness (CRE). Nowadays with the developed of the Computational Fluid Dynamics (CFD) the behaviour of ventilation can be more easily predicted. Thirteen strategies of air diffusion were measured in a test chamber through the application of the tracer gas method, with the objective to validate the calculation by the MicroFlo module of the IES-VE software for this two indicators. The main conclusions from this work were: that the values of the numerical simulations are in agreement with experimental measurements; the value of the CRE is more dependent of the position of the contamination source, that the strategy used for the air diffusion; the ACE indicator is more appropriate for quantifying the quality of the air diffusion; the solutions to be adopted, to maximize the ventilation efficiency should be, the schemes that operate with low speeds of supply air and small differences between supply air temperature and the room temperature.

Simulação de sistema de desenfumagem de parques de estacionamento recorrendo ao programa OpenFOAM

Os parques de estacionamento cobertos estão obrigados por legislação a terem sistemas de desenfumagem. Assim, nesta dissertação desenvolve-se um procedimento computacional para a analise e verificação de funcionamento de sistemas de desenfumagem com ventiladores de impulso para parques de estacionamento, recorrendo ao software de mecânica dos fluidos computacional OpenFOAM. Actualmente nos sistemas de desenfumagem de parques de estacionamento estão a ser aplicados ventiladores de impulso. Este tipo de ventiladores não estão contemplados pela legislação em vigor. Assim, para serem utilizados é necessário verificar se estes podem substituir as redes de condutas. A verificação do funcionamento de sistemas de desenfumagem com ventiladores de impulso e efectuada com recurso a programas de simulação de mecânica dos fluidos computacional. O software OpenFOAM não tem tutoriais para ventiladores de impulso. Assim, foi executado um procedimento para validação dos ventiladores de impulso. A validação consistiu em reproduzir-se uma experiência executada por Giesen et al. (2011). Executaram-se várias simulações com diferentes modelos de turbulência, verificando-se que o programa buoyantpimplefoam do software OpenFOAM ao utilizar o modelo de turbulência k -ɛ simulou quase na perfeição os ventiladores de impulso. O desenvolvimento do procedimento computacional foi executado para um parque de estacionamento com uma geometria bastante complexa. O parque de estacionamento foi criado com um software em 3D e posteriormente inserido numa malha j a criada com as dimensões exteriores do parque. Foram estipuladas as condições de fronteira e executou-se uma simulação de seiscentos segundos com parâmetros determinados previamente. O processamento da simulação teve a duração de aproximadamente oito dias. Dos resultados obtidos concluiu-se que o procedimento computacional apresentado simula adequadamente sistemas de desenfumagem em parques de estacionamento.

Desenvolvimento de um procedimento de Numerical Site Calibration para um Parque Eólico usando Dinâmica de Fluidos Computacional

Esta dissertação descreve o desenvolvimento e avaliação de um procedimento de \Numerical Site Calibration" (NSC) para um Parque Eólico, situado a sul de Portugal, usando Dinâmica de Fluídos Computacional (CFD). O NSC encontra-se baseado no \Site Calibration" (SC), sendo este um método de medição padronizado pela Comissão Electrónica Internacional através da norma IEC 61400. Este método tem a finalidade de quantificar e reduzir os efeitos provocados pelo terreno e por possíveis obstáculos, na medição do desempenho energético das turbinas eólicas. Assim, no SC são realizadas medições em dois pontos, no mastro referência e no local da turbina (mastro temporário). No entanto, em Parques Eólicos já construídos, este método não é aplicável visto ser necessária a instalação de um mastro de medição no local da turbina e, por conseguinte, o procedimento adequado para estas circunstâncias é o NSC. O desenvolvimento deste método é feito por um código CFD, desenvolvido por uma equipa de investigação do Instituto Superior de Engenharia do Porto, designado de WINDIETM, usado extensivamente pela empresa Megajoule Inovação, Lda em aplicações de energia eólica em todo mundo. Este código é uma ferramenta para simulação de escoamentos tridimensionais em terrenos complexos. As simulações do escoamento são realizadas no regime transiente utilizando as equações de Navier-Stokes médias de Reynolds com aproximação de Bussinesq e o modelo de turbulência TKE 1.5. As condições fronteira são provenientes dos resultados de uma simulação realizada com Weather Research and Forecasting, WRF. Estas simulações dividem-se em dois grupos, um dos conjuntos de simulações utiliza o esquema convectivo Upwind e o outro utiliza o esquema convectivo de 4aordem. A análise deste método é realizada a partir da comparação dos dados obtidos nas simulações realizadas no código WINDIETM e a coleta de dados medidos durante o processo SC. Em suma, conclui-se que o WINDIETM e as suas configurações reproduzem bons resultados de calibração, ja que produzem erros globais na ordem de dois pontos percentuais em relação ao SC realizado para o mesmo local em estudo.

Using cilia mutants to study left-right asymmetry in zebrafish

A thesis submitted in fulfillment of the requirements for the degree of the Masters in Molecular Genetics and Biomedicine

Fiber functionalization for biomedical applications

Deep-eutectic solvents (DES) are considered novel renewable and biodegradable solvents, with a cheap and easy synthesis, without waste production. Later it was discovered a new subclass of DES that even can be biocompatible, since their synthesis uses primary metabolites such as amino acids, organic acids and sugars, from organisms. This subclass was named natural deep-eutectic solvents (NADES). Due to their properties it was tried to study the interaction between these solvents and biopolymers, in order to produce functionalized fibers for biomedical applications. In this way, fibers were produced by using the electrospinning technique. However, it was first necessary to study some physical properties of NADES, as well as the influence of water in their properties. It has been concluded that the water has a high influence on NADES properties, which can be seen on the results obtained from the rheology and viscosity studies. The fluid dynamics had changed, as well as the viscosity. Afterwards, it was tested the viability of using a starch blend. First it was tested the dissolution of these biopolymers into NADES, in order to study the viability of their application in electrospinning. However the results obtained were not satisfactory, since the starch polymers studied did not presented any dissolution in any NADES, or even in organic solvents. In this way it was changed the approach, and it was used other biocompatible polymers. Poly(ethylene oxide), poly(vinyl alcohol) and gelatin were the others biopolymers tested for the electrospinning, with NADES. All polymers show good results, since it was possible to obtain fibers. However for gelatin it was used only eutectic mixtures, containing active pharmaceutical ingredients (API’s), instead of NADES. For this case it was used mandelic acid (antimicrobial properties), choline chloride, ibuprofen (anti-inflammatory properties) and menthol (analgesic properties). The polymers and the produced fibers were characterized by scanning electron microscope (SEM), Transmission electron microscopy (TEM) and Fourier transform infrared spectroscopy (FTIR). With the help of these techniques it was possible to conclude that it was possible to encapsulate NADES within the fibers. Rheology it was also study for poly(ethylene oxide) and poly(vinyl alcohol), in a way to understand the influence of polymer concentration, on the electrospinning technique. For the gelatin, among the characterization techniques, it was also performed cytotoxicity and drug release studies. The gelatin membranes did not show any toxicity for the cells, since their viability was maintained. Regarding the controlled release profile experiment no conclusion could be drawn from the experiments, due to the rapid and complete dissolution of the gelatin in the buffer solution. However it was possible to quantify the mixture of choline chloride with mandelic acid, allowing thus to complete, and confirm, the information already obtained for the others characterization technique.

PKO: alternative method for isolating mycobacteria from sputum

We elaborated an alternative culture method, which we denominated PKO (initials in tribute of respect to Petroff, Kudoh and Ogawa), for isolating Mycobacterium tuberculosis from sputum for diagnosis of pulmonary tuberculosis (TB), and to compare its performance with the Swab and Petroff methods. For the technique validation, sputum samples from patients suspected of pulmonary TB cases were examined by acid-fast microscopy (direct and concentrated smear), PKO, Swab and Petroff methods. We found that Petroff and PKO methods have parity in the effectiveness of M. tuberculosis isolation. However, by the PKO method, 65% of isolated strains were detected in a period of £15 days, while by the Petroff method the best detection was in an interval of 16-29 days (71%). In positive smear samples, the average time of PKO isolation is only superior to the one related for Bactec 460TB. In conclusion, the exclusion of the neutralization stage of pH in the PKO reduces the manipulation of the samples, diminishes the execution time of the culture according to the Petroff method and facilitates the qualification of professionals involved in the laboratorial diagnosis of Tuberculosis.

Development of a thermoelectric generator for the exhaust of a vehicle

Dissertação de mestrado integrado em Engenharia Mecânica

Developing discontinuous Galerkin methods for the resolution of the incompressible Navier-Stokes equations

Informe de investigación elaborado a partir de una estancia en el Laboratorio de Diseño Computacional en Aeroespacial en el Massachusetts Institute of Technology (MIT), Estados Unidos, entre noviembre de 2006 y agosto de 2007. La aerodinámica es una rama de la dinámica de fluidos referida al estudio de los movimientos de los líquidos o gases, cuya meta principal es predecir las fuerzas aerodinámicas en un avión o cualquier tipo de vehículo, incluyendo los automóviles. Las ecuaciones de Navier-Stokes representan un estado dinámico del equilibrio de las fuerzas que actúan en cualquier región dada del fluido. Son uno de los sistemas de ecuaciones más útiles porque describen la física de una gran cantidad de fenómenos como corrientes del océano, flujos alrededor de una superficie de sustentación, etc. En el contexto de una tesis doctoral, se está estudiando un flujo viscoso e incompresible, solucionando las ecuaciones de Navier- Stokes incompresibles de una manera eficiente. Durante la estancia en el MIT, se ha utilizado un método de Galerkin discontinuo para solucionar las ecuaciones de Navier-Stokes incompresibles usando, o bien un parámetro de penalti para asegurar la continuidad de los flujos entre elementos, o bien un método de Galerkin discontinuo compacto. Ambos métodos han dado buenos resultados y varios ejemplos numéricos se han simulado para validar el buen comportamiento de los métodos desarrollados. También se han estudiado elementos particulares, los elementos de Raviart y Thomas, que se podrían utilizar en una formulación mixta para obtener un algoritmo eficiente para solucionar problemas numéricos complejos.

Efficacy of an enzyme-linked immunosorbent assay as a diagnostic tool for schistosomiasis mansoni in individuals with low worm burden

IgM-ELISA is an immunoenzymatic method useful for detection of IgM antibodies against a fraction of Schistosoma mansoni adult worm antigen (AWA) that is soluble in trichloroacetic acid (AWA-TCA). This method was applied to three groups of individuals with different clinical and epidemiological characteristics, and the results compared with those obtained by other diagnostic methods: immunofluorescence test for detection of IgM antibodies (IgM-IFT) or IgG antibodies (IgG-IFT), ELISA for detection of IgG antibodies (IgG-ELISA), and two parasitological methods, Kato-Katz and miracidium hatching. The IgM-ELISA presented a sensitivity of 98%, when the parasitologic fecal examination was defined as reference diagnostic method, and a specificity of 98 and 97.3%, respectively for the group of clinically healthy individuals and other helminth carriers. A comparative analysis between the results of IgM-ELISA and those obtained by other serologic tests showed a good degree of agreement, with Kappa indices ranging from 0.95 to 0.98. The diagnostic efficacy of 97.8%, as determined with schistosomiasis patients with low parasitic burden, suggests the excellent performance of the IgM-ELISA and its usefulness for the diagnosis of schistosomiasis when applied in low endemic areas.

Measurement of the dynamics in ski jumping using a wearable inertial sensor-based system.

Abstract Dynamics is a central aspect of ski jumping, particularly during take-off and stable flight. Currently, measurement systems able to measure ski jumping dynamics (e.g. 3D cameras, force plates) are complex and only available in few research centres worldwide. This study proposes a method to determine dynamics using a wearable inertial sensor-based system which can be used routinely on any ski jumping hill. The system automatically calculates characteristic dynamic parameters during take-off (position and velocity of the centre of mass perpendicular to the table, force acting on the centre of mass perpendicular to the table and somersault angular velocity) and stable flight (total aerodynamic force). Furthermore, the acceleration of the ski perpendicular to the table was quantified to characterise the skis lift at take-off. The system was tested with two groups of 11 athletes with different jump distances. The force acting on the centre of mass, acceleration of the ski perpendicular to the table, somersault angular velocity and total aerodynamic force were different between groups and correlated with the jump distances. Furthermore, all dynamic parameters were within the range of prior studies based on stationary measurement systems, except for the centre of mass mean force which was slightly lower.

Stoneley wave modeling in heterogeneous porous media with viscous pore fluids

We implemented Biot-type porous wave equations in a pseudo-spectral numerical modeling algorithm for the simulation of Stoneley waves in porous media. Fourier and Chebyshev methods are used to compute the spatial derivatives along the horizontal and vertical directions, respectively. To prevent from overly short time steps due to the small grid spacing at the top and bottom of the model as a consequence of the Chebyshev operator, the mesh is stretched in the vertical direction. As a large benefit, the Chebyshev operator allows for an explicit treatment of interfaces. Boundary conditions can be implemented with a characteristics approach. The characteristic variables are evaluated at zero viscosity. We use this approach to model seismic wave propagation at the interface between a fluid and a porous medium. Each medium is represented by a different mesh and the two meshes are connected through the above described characteristics domain-decomposition method. We show an experiment for sealed pore boundary conditions, where we first compare the numerical solution to an analytical solution. We then show the influence of heterogeneity and viscosity of the pore fluid on the propagation of the Stoneley wave and surface waves in general.

The diagnostic dilemma of hyperintense fetal lung on prenatal MRI : 12.03

Purpose: In the last years, MRI appears as a complementary diagnostic method to US in the diagnosis of congenital lung lesions. Focal homogeneous pulmonary hyperintensity on T2-WI constitutes a frequent pattern observed. Our purpose is to determine if this finding is associated with a characteristic pulmonary lesion. Materials and methods: Between 01.01.00 and 31.12.07, a total of 50 prenatal MRI in fetuses with echographic diagnosis of thoracic pathology were performed in our institution, including 12 cases of suspected congenital pulmonary lesions. Prenatal images were correlated with post-natal diagnosis. Results: In 12 cases, fetal MRI detected congenital pulmonary lesions. In 8 patients, typical signs (cystic lesions, septations, anomalous vasculature) clearly suggested a specific pathology. In 4 cases, MRI showed a focal homogeneous increase of the signal intensity (SI) on T2-WI of the pathologic lung related to the normal one. The final diagnosis of these fetuses included 1 patient with congenital cystic adenomatoid malformation type III, 1 patient with segmental emphysema and 2 cases of bronchial atresia. In all 4 cases, a significant post-natal reduction of the lesion size related to prenatal MRI studies was observed. Conclusion: Our study suggests that a focal increment of the SI of the lung on T2-WI is a non specific sign of congenital lung disease, present in different pathologies. Therefore, a prospective diagnosis is not possible.

Dynamics of turing patterns under spatiotemporal forcing

We study, both theoretically and experimentally, the dynamical response of Turing patterns to a spatiotemporal forcing in the form of a traveling-wave modulation of a control parameter. We show that from strictly spatial resonance, it is possible to induce new, generic dynamical behaviors, including temporally modulated traveling waves and localized traveling solitonlike solutions. The latter make contact with the soliton solutions of Coullet [Phys. Rev. Lett. 56, 724 (1986)] and generalize them. The stability diagram for the different propagating modes in the Lengyel-Epstein model is determined numerically. Direct observations of the predicted solutions in experiments carried out with light modulations in the photosensitive chlorine dioxide-iodine-malonic acid reaction are also reported.