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Molecular dynamics simulation was used to study ion permeation through different membrane proteins embedded in a lipid bilayer (DMPC) with different saline solutions. The potential of mean force (PMF) for ion transport was obtained by umbrella sampling simulations. A revised MacKerell force field for tryptophan residues was studied using gramicidin A (gA) channel as a test model. The revised force field contribution to the Na+ PMF was consonant with the prediction from the experimental results, but in stark contrast to the prediction of the CHARMM force field, version 22, for the tryptophan side-chain. A new grid-based correction map algorithm by MacKerell group, called CMAP, was introduced into the CHARMM force field, version 31. The CMAP algorithm focused on optimizing phi, psi dihedral parameters for the peptide backbone. The CMAP corrections reduced the excessive translocation barrier. Decomposition demonstrated the reduction in the translocation barrier was due to effects on the K+ PMFH2O rather than on K+ PMFgA. The presence of negatively charged sulfonate group at the entrance and exit of the gA channel affected the depth and the location of the highly occupied sites. The negatively charged sulfonate group produced a strong attraction for the cations in the bulk towards the channel mouth. In the M2 transmembrane domain channel (M2-TMD), three M2-TMD structures were studied, differing only in whether the selectivity-filter (four His37 side-chains) was uncharged, +2 charged, or +3 charged. M2-TMD structural properties were compared with the structural properties of other models extracted from NMR and X-ray studies. The spontaneous cation and anion entry into the charged selectivity-filter was different from that into a neutral selectivity-filter. Cl- ions had a lower free-energy barrier in the selectivity-filter than either Na+ or NH4+ ions through the M2-TMD channel. NH4+ ions had a lower free-energy barrier in the selectivity-filter than Na+ ions. Based on accessible rotamer conformations, a revised conductance mechanism was proposed. In this conductance mechanism, the His37 side-chain functioned as an acceptor and donor group, whereas the Trp41 side-chain functioned as a carrying group.

MScEng / Thesis (MScEng (Mechanical and Mechatronic Engineering))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: Accurate dimensional measurement devices are critical for international industrial competitiveness for South Africa. An overview of all the necessary components of a laser tracking system using a multilateration technique for very accurate dimensional metrology is presented. A prototype laser tracker station was built to further investigate this type of system. The prototype successfully tracks a target within a volume of at least 200 200 200 mm3, approximately 300 mm away from the tracker. This system includes the mechanical design of a prototype tracker station, electronic implementation of ampli cation and motor control circuits, a tracking control algorithm, microcontroller programming and interfacing, as well as a user interface. Kinematic modelling along with Monte Carlo analyses nd the main error source of such a tracker as the beam steering mechanism gimbal axes misalignment. Multilateration is also motivated by the results found by the analysis. Furthermore, an initial sequential multilateration algorithm is developed and tested. The results of these tests are promising and motivate the use of multilateration over a single beam laser tracking system. / AFRIKAANSE OPSOMMING: Dit is van kritieke belang dat Suid-Afrika akkurate dimensionele metingstoestelle ontwikkel vir internasionale industriële medinging. 'n Oorsig van al die nodige komponente vir 'n Laser-Volgsisteem, wat slegs van multilaterasie gebruik maak om baie akkurate drie dimensionele metings te kan neem, word in hierdie projek voorgestel. 'n Prototipe Laser-Volgsisteem-stasie word gebou om so 'n sisteem verder te ondersoek. Die prototipe slaag wel daarin om 'n teiken, binne 'n volume van 200 200 200 mm3 op 'n afstand van omtrent 300 mm te volg. Die sisteem sluit die meganiese ontwerp van die sodanige stasie, elektroniese seinversterking, motorbeheer, 'n volgingsbeheer algoritme, mikroverwerker programeering en intergrasie, asook 'n gebruikerskoppelvlak program in. Kinematiese modelering, tesame met Monte Carlo simulasies, toon aan dat die hoof oorsaak van metingsfoute by so 'n stasie by die rotasie-asse van die laserstraal-stuurmeganisme, wat nie haaks is nie, lê. Die multilaterasie metode word ook verder ondersteun deur dié modelering. 'n Algoritme wat sekwensiële multilateratsie toepas word boonop ontwikkel en getoets. Die resultate van die toetse dui daarop dat die algoritme funksioneer en dat daar voordele daarin kan wees om so 'n metode in plaas van 'n Enkelstraal-Volgsisteem te gebruik.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: The research presented in this dissertation establishes a micro-CMM parallel manipulator as a viable positioning device for three degree of freedom micro measurement applications. The machine offers the advantages associated with parallel kinematic manipulators, such as light carrying weight, high stiffness and no accumulation of errors, while avoiding some of the traditional disadvantages of parallel manipulators such as the associated effects of angular errors (Abbé error), singularity problems, work space limitation and the extensive use of spherical joints. In this dissertation, the direct position kinematic solution is developed analytically and the solution of the inverse position kinematic is solved numerically. A workspace analysis has been performed. A fully functional prototype demonstrator is fabricated to demonstrate this machine. While the demonstrator was not intended to achieve submicron accuracy, it was intended to validate the error models. Computer controlled measurement is developed and used to position the probe and to record measurements. A reliable kinematic error model based on the theory of error propagation is derived analytically. A numerical method is used to verify the analytical results. Comparison shows that the results of the error model, both analytical and numerical, represent a very good match and follow the same trend. The kinematic position model is validated using a conventional CMM. Results show that an average difference of less than 0.5 mm over a set of 30 points is achieved. This result of the micro-CMM demonstrator measurements falls within the error budget of approximately 0.75 mm estimated by the proposed analytical error model. / AFRIKAANSE OPSOMMING: Die navorsing in hierdie tesis vestig ‘n mikro-CMM parallelle manipuleerder as ‘n lewensvatbare posisioneringstoestel vir drie vryheidsgraad-mikrometing toepassings. Die masjien bied voordele geassosieer met parallelle kinematiese manipuleerders, bv. ligte dra-gewig, hoë styfheid en geen ophoping van foute nie. Die tradisionele nadele van parallelle manipuleerders soos die geassosieerde gevolge van hoekfoute (Abbé fout), enkelvoudigheidsprobleme, werkspasiebeperking en die uitgebreide gebruik van sferiese koppelings word vermy. In hierdie tesis word die direkte posisie kinematiese oplossing analities ontwikkel en die oplossing van die omgekeerde posisie kinematies word numeries opgelos. ‘n Werkspasie analise is uitgevoer. ‘n Ten volle funksionele prototipe demonstrasie-model is vervaardig om hierdie masjien te demonstreer. Die model is nie vervaardig om submikron akkuraatheid te bereik nie, maar eerder om foutmodelle geldig te verklaar. Rekenaar-beheerde metings is ontwerp en gebruik om die toetspen te posisioneer en om metings te neem. ‘n Betroubare kinematiese foutmodel gebaseer op die teorie van foutvoortplanting is analities afgelei. ‘n Numeriese metode word gebruik om die analitiese resultate te bevestig. Vergelyking toon aan dat die resultate van die foutmodel, beide analities en numeries, goeie pasmaats is en dieselfde tendens volg. Die kinematiese posisie model word geldig verklaar deur gebruik te maak van ‘n konvensionele CMM. Resultate wys dat daar ‘n gemiddelde verskil van minder as 0.5 mm oor ‘n stel van 30 punte behaal word. Die resultate van die mikro-CMM model se metings val binne die foutbegroting van ongeveer 0.75 mm geskat by die voorgestelde analitiese foutmodel.

Much research effort has been devoted to producing algorithms that contribute directly or indirectly to the extraction of 3D information from a wide variety of types of scenes and conditions of image capture. The research work presented in this thesis is aimed at three distinct applications in this area: interactively extracting 3D points from a pair of uncalibrated images in a flexible way; finding corresponding points automatically in high resolution images, particularly those of archaeological scenes captured from a freely moving light aircraft; and improving a correlation approach to dense disparity mapping leading to 3D surface reconstructions. The fundamental concepts required to describe the principles of stereo vision, the camera models, and the epipolar geometry described by the fundamental matrix are introduced, followed by a detailed literature review of existing methods. An interactive system for viewing a scene via a monochrome or colour anaglyph is presented which allows the user to choose the level of compromise between amount of colour and ghosting perceived by controlling colour saturation, and to choose the depth plane of interest. An improved method of extracting 3D coordinates from disparity values when there is significant error is presented. Interactive methods, while very flexible, require significant effort from the user finding and fusing corresponding points and the thesis continues by presenting several variants of existing scale invariant feature transform methods to automatically find correspondences in uncalibrated high resolution aerial images with improved speed and memory requirements. In addition, a contribution to estimating lens distortion correction by a Levenberg Marquard based method is presented; generating data strings for straight lines which are essential input for estimating lens distortion correction. The remainder of the thesis presents correlation based methods for generating dense disparity maps based on single and multiple image rectifications using sets of automatically found correspondences and demonstrates improvements obtained using the latter method. Some example views of point clouds for 3D surfaces produced from pairs of uncalibrated images using the methods presented in the thesis are included.

This thesis investigates the mechanisms behind the control of a typical two line kite, where the lines are attached to the kite side by side. This arrangement gives the kite flyer the ability to apply a roll angle to the kite, which then results in a yawing motion. The reason for this yaw rotation has not been adequately described previously. The definitions of roll and yaw for a kite have been re-defined to match the real world behaviour of the kite-bridle-line system. Specifically, these are defined as rotations relative to the lines rather than the kite itself. This detail has been neglected in previous research, and has a significant effect on the turning behaviour of a kite. A static model of a kite represented by flat disks was created. This model allows the out of balance forces and moments to be found for a kite when it is held at any position. When the kite is held with a roll angle applied, the disk angles of attack become unequal. This causes a change in the magnitude, direction, and point of action of the aerodynamic forces on each disk, which can lead to a yaw moment. While this does not give a complete picture of how a kite turns, it does explain one of the two mechanisms that cause a kite to begin to yaw when a roll angle is applied. The other mechanism is due to the velocity of the roll rotation, and is out of the scope of this thesis since a dynamic analysis would be required. The static model showed that any variation to kite geometry or any parameter that affects the equilibrium position of the kite will affect turning response. The most important of these parameters for a simple kite represented by two disks is the dihedral angle. A minimum negative dihedral angle (or anhedral) is required for a kite to turn in the expected direction when a roll angle is applied. The value of the minimum anhedral angle required for this behaviour varies with other parameters, but is generally between 8° and 20°. Other parameters such as bridle geometry also affect the turning response of a kite, primarily because they alter the equilibrium positions of the kite and line. Altering these equilibrium positions has a strong effect on turning response, since it changes the initial disk angles of attack. Additionally, if the kite and line are not aligned perpendicular to each other (which is a rare condition for a kite) a roll angle further changes the disk angles of attack, since the roll angle is applied about an axis relative to the line rather than the kite. An investigation into the effect of varying wind velocity on turning response showed that it has an important effect. Some kites will reverse their response to a given roll angle at some wind velocities, which could make the kite very difficult to control. Additionally, some kites can alter their equilibrium positions sharply with wind velocity, again causing varying turning behaviour as the wind conditions change. Future work should examine the dynamic turning response of kites. A dynamic simulation could be used to examine how the turning response of a kite is influenced by the rate at which a control input is applied. Additionally, the behaviour of the kite once the initial turning movement has begun could be assessed.

La simulation d'écoulements dans des cavités cylindriques en rotation présente une difficulté particulière en raison de l'apparition de singularités sur l'axe. Le présent travail propose une méthode collocative pseudospectrale suffisamment efficace et précise pour surmonter cette difficulté et résoudre les équations 3D de Navier-Stokes écrites en coordonnées cylindriques. Cette méthode a été développée dans le cadre des différentes études menées au laboratoire M2P2, utilisant une méthode collocative de type Chebychev dans les directions radiale et axiale et Fourier-Galerkin dans la direction azimutale [thêta]. Pour éviter de prescrire des conditions sur l'axe, une nouvelle approche a été développée. Le domaine de calcul est défini par (r,[thêta],z)∈[-1,1]×[0,2π]×[-1,1] avec un nombre N pair de points de collocation dans la direction radiale. Ainsi, r=0 n'est pas un point de collocation. La distribution de points de type Gauss-Lobatto selon r et z densifie le maillage seulement près des parois ce qui rend l'algorithme bien adapté pour simuler les écoulements dans des cavités cylindriques en rotation. Dans la direction azimutale, le chevauchement des points dû à la discrétisation est évitée par l'introduction d'un décalage égal à π/2K à [thêta]>π dans la transformée de Fourier. La méthode conserve la convergence spectrale. Des comparaisons avec des résultats expérimentaux et numériques de la littérature montrent un très bon accord pour des écoulements induits par la rotation d'un disque dans des cavités cylindriques fermées. / When simulating flows in cylindrical rotating cavities, a difficulty arises from the singularities appearing on the axis. In the same time, the flow field itself does not have any singularity on the axis and this singularity is only apparent. The present work proposes an efficient and accurate collocation pseudospectral method for solving the 3D Navier-Stokes equations using cylindrical coordinates. This method has been developed in the framework of different studies of rotor-stator flows, using Chebyshev collocation in the radial and axial directions and Fourier-Galerkin approximation in the azimuthal periodic direction [thêta]. To avoid the difficulty on the axis without prescribing any pole and parity conditions usually required, a new approach has been developed. The calculation domain is defined as (r,[thêta];,z)∈[-1,1]×[0,2π]×[-1,1] using an even number N of collocation points in the radial direction. Thus, r=0 is not a collocation point. The method keeps the spectral convergence. The grid-point distribution densifies the mesh only near the boundaries that makes the algorithm well-suited to simulate rotating cavity flows where thin layers develop along the walls. In the azimuthal direction, the overlap in the discretization is avoided by introducing a shift equal to π/2K for [thêta]>π in the Fourier transform. Comparisons with reliable experimental and numerical results of the literature show good quantitative agreements for flows driven by rotating discs in cylindrical cavities. Associated to a Spectral Vanishing Viscosity, the method provides very promising LES results of turbulent cavity flows with or without heat transfer.

Muitos grupos de pesquisa já trabalharam com o desenvolvimento de conjuntos de bases, no intuito de obter melhores resultados em tempo e custo de cálculo computacional reduzidos. Para tal finalidade, o tamanho e a precisão são fatores a ser considerados, para que o número de funções do conjunto gerado proporcione uma boa descrição do sistema em estudo, num tempo de convergência reduzido. Esta dissertação tem como objetivo apresentar os conjuntos de bases obtidos pelo Método da Coordenada Geradora, para os átomos Na, Mg, Al, Si, P, S e Cl, e avaliar a qualidade de tais conjuntos pela comparação da energia eletrônica total, em nível atômico e molecular. Foi realizada uma busca para a obtenção do melhor conjunto contraído e do melhor conjunto de funções de polarização. A qualidade do conjunto gerado foi avaliada pelo cálculo DFT-B3LYP, cujos resultados foram comparados aos valores obtidos por cálculos que utilizam funções de bases conhecidas na literatura, tais como: cc-pVXZ do Dunning e pc-n do Jensen. Pelos resultados obtidos, pode-se notar que os conjuntos de bases gerados neste trabalho, denominados MCG-3d2f, podem representar sistemas atômicos ou moleculares. Tanto os valores de energia quanto os de tempo computacional são equivalentes e, em alguns casos, melhores que os obtidos aqui com os conjuntos de bases escolhidos como referência (conjuntos de Dunning e Jensen). / Many research groups have been working with the development of basis sets in order to get the best results in reduced time and cost of computational calculation. It is known that for such purpose, size and accuracy are the primary factors to be considered, so that the number of the generated set of functions allows a good description of the system being studied in a small convergence time. This essay aims to present the basis sets obtained by the Generator Coordinate Method for the atoms Na, Mg, Al, Si, P, S and Cl, as well as evaluating the quality of such clusters by comparing the electron energy at atomic and molecular levels. A research was also performed to obtain the best set contracted as well as the best set of polarization functions. The quality of the generated set was evaluated by calculating DFT-B3LYP results, which were compared to values obtained through calculation using basis functions such as cc-pVXZ of Dunning and pcn of Jensen. It can be noted, from the results obtained, that the basis sets generated in this study, named MCG-3d2f, may well represent atomic or molecular systems. Energy values and the computational time are equivalent and in some cases, even better than those obtained with the sets of bases chosen here as reference sets (Dunning and Jensen).

Desde sua criação por Ferranti, cerca de 50 anos atrás, as tecnologias de projeto e de fabricação das Máquinas de Medir a Três Coordenadas evoluíram muito. Entretanto, ainda é possível fabricar equipamentos livres de erros. Para garantir a acuracidade das medições realizadas é necessário que se conheça tais erros e que rotinas de compensação sejam implementadas. O levantamento dos erros de qualquer equipamento é feito através de procedimentos de calibração. Entretanto, devido à complexidade das MM3Cs, ainda não existem procedimentos internacionalmente aceitos, por usuários e fabricantes, para avaliar o desempenho metrológico desses equipamentos. Técnicas normalizadas existentes, a exemplo, JIS B 7440 de 1987, B89.4.1 de 1997, VDI/VDE 2617 de 1986 entre outras, propõem testes de desempenho que na maioria das vezes superestimam os erros da MM3C. Além disso, dificultam a rastreabilidade para quaisquer condições de medição diferente daquelas em que foi realizado o teste. Assim, diante do exposto, este trabalho tem por objetivo principal apresentar um novo modelo de sintetização de erros para MM3Cs, o Modelo Reduzido de Sintetização de erros. Este modelo possui equações de sintetização, para Ex, Ey e Ez, reduzidas, em comparação à outros modelos conhecidos, necessita de pequeno tempo na calibração o que reduz o custo desta atividade, possibilita o diagnóstico das fontes de erros e garante a rastreabilidade dos erros calculados. / Since the introduction of coordinate measuring machines by Ferranti in late fifties, the CMM design and manufacturing technology have enormously developed. Nevertheless, it is stile impossible to produce mechanical devices that are exempted from errors. In order to ensure measurements accuracy, it becomes necessary to understand such errors and establish compensation routines. The errors survey of any piece of equipment is performed by means of calibration procedures. However, due to the complexity of CMMs, there are not, until the present time, procedures that are internationally accepted by uses and manufactures to evaluate the metrological performance of this sort of equipment. Current standardized techniques, for instance, JIS B 7440 from 1987, B89.4.1. from 1997, VDI/VDE 2617 from 1986, among others, propose performance tests that usually overestimate CMM errors. Furthermore, they obstruct traceability to whatever measurement condition that is different from the ones used to perform the test. This being the case, the aim of this work comprises the presentation of the new error sinthetization model. This model deals with sinthetization equations for Ex, Ey and Ez that are reduced if compared to other known models, requires short calibration periods, reducing its expenses, allow the determination of the sources of errors and ensures traceability of calculated errors.

Nesta dissertação, definimos a geometria hiperbólica usando o disco de Poincaré (D2) e o semiplano superior (H2) com as respectivas propriedades. Além disso, apresentamos algumas funções e relações importantes da geometria hiperbólica; conceituamos as superfícies de Riemann, analisando suas propriedades e representações; estudamos o espaço de Teichmüller com a devida decomposição em calças. Esses temas são ferramentas necessárias para atingir o objetivo da dissertação: definir as coordenadas de Fenchel Nielsen como um sistema de coordenadas locais do espaço de Teichmüller Tg. / In this dissertation, we defined the hyperbolic geometry using the Poincares disk (D2) and upper half-plane (H2) with its properties. Besides, we presented some functions and important relations of the hyperbolic geometry; we conceptualize the Riemann surfaces, analyzing its properties and representations; we studied the Teichmüller Space with proper decomposition pants. These themes are essential tools to reach the goal of the work: The definition of the Fenchel Nielsen coordenates as local coordinate system of the Teichmüller space Tg.