Magnetic nerve stimulation is a non-invasive method of exciting a neural tissue which can be achieved by exposing the body to a transient magnetic field. This field is generated by passing a high current through a coil over a short period of time. By positioning this coil in a specific orientation over the targeted nerve, the time variation of the magnetic field will create an electric field in the conductive milieu of the body. Induced currents will result from that electric field. If those currents reach a certain amplitude within a specific time period this will cause a neural depolarization. This depolarization will enable us to test and examine the excited nerve which will provide us with the necessary data for an effective treatment. In my thesis I will analyse the benefits of magnetic nerve stimulation with the objective of designing a coil that provides a focussed magnetic field. This field will excite the targeted nerve with minimal or to no excitation to the surrounding nerves. This means that we can effectively apply or measure the excitation of the targeted nerve without involving the surrounding nerves. It is my intention to bring this application to a practical platform where a simple circuit with lower power requirements can be used. This will enable some patients requiring physiotherapy to safely administer magnetic nerve stimulation to themselves without the help of a therapist. / Thesis / Master of Engineering (ME)

The aim of this thesis is to develop a computer program to design and simulate air conditioning-comfort application of a selected building, for a year period, on an hourly basis. In order to carry out this study, a computer program named AHUSIM.m, is prepared with Matlab computing language. The design and simulation procedure starts with preparing the inputs like indoor, outdoor design states, zone cooling and heating loads, along with the general data for conditioning-comfort equipment. The program, in light of these input data, performs the plotting of the psychrometric processes -including the design and off design processes- on psychrometric charts, air conditioning-comfort system selection and calculating the response of this selected system at varying load conditions for a year. The program also calculates the energy requirements of parts of the selected system throughout the year. Furthermore, it lists dimensions of the parts of the air conditioning-comfort unit, the outdoor supply air and total air flow rates, air and water inlet and exit states. Using numerical tools for heating, ventilating and air conditioning (HVAC) process design and simulation, can improve energy economy and comfort which are the main criteria of HVAC engineering. In such an attempt, major concern is the interaction between the comfort and energy consumption. The program, by designing the system and deciding its behavior throughout a year / provides a means of automatic control considering comfort and energy economy. This program also provides a tool for comparison of different techniques for putting limits to the relation between comfort and energy consumption.

Coiled coils are a well-known protein structure prevalent in eukaryotic function, synthetic applications, and de novo protein design. Coiled-coil folding is often described using heptad repeat positions labeled abcdefg where a and d positions occupy the interface between the coils, e and g positions flank the interface, and the b, c, and f positions face the solvent-exposed surface. The a, d, e, and g positions have been extensively studied in the coiled-coil literature. There is a lack of investigation on the impact of the b, c, and f positions on coiled-coil folding. Chapter 1 is an introduction to the heptad repeat of coiled coils and the impact on folding of each heptad repeat position. In Chapter 2 we introduce a non-covalent interaction among the b, c, and f positions of a coiled-coil trimer that significantly enhances thermodynamic stability. We identify characteristics of the f-position residue (hydrogen bond donating ability and hydrophobicity) that lead to the greatest amount of stability. Chapter 3 introduces crystal structures and molecular dynamic simulations of the interaction to identify the mechanism of stabilization. Further thermodynamic studies find a key salt-bridge interaction between the b and c positions that are influenced by the f-position residue. Chapter 4 explores the impact of salt on the non-covalent interaction and determines that the interaction is sensitive to salt screening and is ionic in nature. It also explores more characteristics of the f-position amino acid, in particular the hydrogen bond donating component. In Chapter 5 we insert the solvent-exposed interaction into helix bundles of differing length and oligomeric state. We find that stability is not only dependent upon amino acid identity but also the length and stoichiometry of a coiled coil.

Le présent mémoire porte sur la conception et le développement de deux antennes RF utilisées en imagerie par résonance magnétique. Ces antennes ont pour but de guider le futur développement d’une plateforme d’imagerie multi-animal qui servira les chercheurs du nouveau CRCHUM. Plus spécifiquement, ces antennes ont été conçues pour l’imagerie du proton à 1.5T. La première utilise une birdcage de type lowpass pour la partie émettrice et utilise 8 éléments de surface pour la partie réceptrice. La seconde antenne est une birdcage de type lowpass polarisée circulairement qui est utilisée à la fois pour l’émission et pour la réception. Cette dernière a présenté de bonnes performances, générant des images avec un SNR élevé et avec une bonne homogénéité, la rendant une bonne candidate pour la future plateforme. La première a présenté quelques problèmes au niveau de la désyntonisation de la birdcage et du couplage entre les éléments. Dans le cas où ces problèmes venaient à être surmontés, cette antenne aurait l’avantage de pouvoir utiliser des techniques d’imagerie parallèle et possiblement d’avoir un SNR plus élevé. / This master thesis focuses on the design and development of two RF coils used in magnetic resonance imaging. These coils are designed to guide the future development of a multi-animal imaging platform that will serve researchers of the new CRCHUM. More specifically, these coils were designed for proton imaging at 1.5T. The first uses a lowpass birdcage as transmitter and uses 8 surface elements for the receiving part. The second coil is a circularly polarized lowpass birdcage which is used both for transmission and for reception. The latter presented good performances, generating images with high SNR and good homogeneity, making it a good candidate for the future platform. The first one presented a few problems at the detuning of the birdcage and the coupling between the elements. In the case where these problems would be overcome, this coil would have the advantage of being able to use parallel imaging techniques and possibly to have a higher SNR.

Esta dissertação apresenta modelagem matemática e um método de solução numérica para problemas de conformação eletromagnética de chapas metálicas finas circulares utilizando uma bobina em espiral plana. O método foca especificamente o cálculo do campo eletromagnético gerado pela bobina e análise do circuito que modela o sistema de estampagem eletromagnética. A bobina plana é aproximada por círculos concêntricos carregando a corrente de descarga dos capacitores. Os cálculos das correntes induzidas e perfil da força eletromagnética na chapa e acoplamentos magnéticos entre a bobina e chapa metálica são realizados para o instante inicial, antes da deformação plástica da chapa. O método utiliza a lei de Biot-Savart, sendo que a solução das integrais obtidas para indução magnética é realizada através de métodos numéricos, considerando as simetrias do problema. Para verificação da modelagem matemática, da solução numérica e comprovação da viabilidade técnica deste processo, um dispositivo de estampagem eletromagnética foi desenvolvido e diversos experimentos foram realizados com chapas de alumínio. Os parâmetros investigados foram a espessura da chapa a ser deformada e a influência da presença de vácuo na cavidade da ferramenta. Os resultados experimentais demonstram concordância com os resultados da modelagem proposta. A presença de vácuo também demonstrou um incremento na deformação da chapa. A rotina desenvolvida no software Matlab fornece informações importantes para o processo e permite que se faça ajustes no dispositivo. / This dissertation presents a mathematical model and numerical method to solve the problems of electromagnetic forming of thin circular metal sheets by using a flat spiral coil. The method focuses specifically on the calculation of the electromagnetic field generated by the coil flat and circuit analysis modeling system electromagnetic forming. The flat coil is approximated by concentric circles carrying a discharge current of capacitors. The calculations of induced currents and profile of the electromagnetic force on the plate and magnetic coupling between the coil and sheet metal are made to the initial time, before the plastic deformation of the plate. The method uses the law of Biot-Savart, and the solution of the integral obtained for magnetic induction is performed by numerical methods, considering the symmetries of the problem. To verify the mathematical model, the numerical solution and proving the technical feasibility of this process, a electromagnetic forming device was developed and several experiments were made with aluminum plates. The parameters investigated were the thickness of the plate to be deformed and the influence of the vacuum in the cavity of the tool. The experimental results show agreement with the results of the proposed model. The presence of vacuum also showed an increase in the deformation of the plate. A routine developed in software Matlab provide important information for the process and allow to make adjustments on the device.

Le présent mémoire porte sur la conception et le développement de deux antennes RF utilisées en imagerie par résonance magnétique. Ces antennes ont pour but de guider le futur développement d’une plateforme d’imagerie multi-animal qui servira les chercheurs du nouveau CRCHUM. Plus spécifiquement, ces antennes ont été conçues pour l’imagerie du proton à 1.5T. La première utilise une birdcage de type lowpass pour la partie émettrice et utilise 8 éléments de surface pour la partie réceptrice. La seconde antenne est une birdcage de type lowpass polarisée circulairement qui est utilisée à la fois pour l’émission et pour la réception. Cette dernière a présenté de bonnes performances, générant des images avec un SNR élevé et avec une bonne homogénéité, la rendant une bonne candidate pour la future plateforme. La première a présenté quelques problèmes au niveau de la désyntonisation de la birdcage et du couplage entre les éléments. Dans le cas où ces problèmes venaient à être surmontés, cette antenne aurait l’avantage de pouvoir utiliser des techniques d’imagerie parallèle et possiblement d’avoir un SNR plus élevé. / This master thesis focuses on the design and development of two RF coils used in magnetic resonance imaging. These coils are designed to guide the future development of a multi-animal imaging platform that will serve researchers of the new CRCHUM. More specifically, these coils were designed for proton imaging at 1.5T. The first uses a lowpass birdcage as transmitter and uses 8 surface elements for the receiving part. The second coil is a circularly polarized lowpass birdcage which is used both for transmission and for reception. The latter presented good performances, generating images with high SNR and good homogeneity, making it a good candidate for the future platform. The first one presented a few problems at the detuning of the birdcage and the coupling between the elements. In the case where these problems would be overcome, this coil would have the advantage of being able to use parallel imaging techniques and possibly to have a higher SNR.

Esta dissertação apresenta modelagem matemática e um método de solução numérica para problemas de conformação eletromagnética de chapas metálicas finas circulares utilizando uma bobina em espiral plana. O método foca especificamente o cálculo do campo eletromagnético gerado pela bobina e análise do circuito que modela o sistema de estampagem eletromagnética. A bobina plana é aproximada por círculos concêntricos carregando a corrente de descarga dos capacitores. Os cálculos das correntes induzidas e perfil da força eletromagnética na chapa e acoplamentos magnéticos entre a bobina e chapa metálica são realizados para o instante inicial, antes da deformação plástica da chapa. O método utiliza a lei de Biot-Savart, sendo que a solução das integrais obtidas para indução magnética é realizada através de métodos numéricos, considerando as simetrias do problema. Para verificação da modelagem matemática, da solução numérica e comprovação da viabilidade técnica deste processo, um dispositivo de estampagem eletromagnética foi desenvolvido e diversos experimentos foram realizados com chapas de alumínio. Os parâmetros investigados foram a espessura da chapa a ser deformada e a influência da presença de vácuo na cavidade da ferramenta. Os resultados experimentais demonstram concordância com os resultados da modelagem proposta. A presença de vácuo também demonstrou um incremento na deformação da chapa. A rotina desenvolvida no software Matlab fornece informações importantes para o processo e permite que se faça ajustes no dispositivo. / This dissertation presents a mathematical model and numerical method to solve the problems of electromagnetic forming of thin circular metal sheets by using a flat spiral coil. The method focuses specifically on the calculation of the electromagnetic field generated by the coil flat and circuit analysis modeling system electromagnetic forming. The flat coil is approximated by concentric circles carrying a discharge current of capacitors. The calculations of induced currents and profile of the electromagnetic force on the plate and magnetic coupling between the coil and sheet metal are made to the initial time, before the plastic deformation of the plate. The method uses the law of Biot-Savart, and the solution of the integral obtained for magnetic induction is performed by numerical methods, considering the symmetries of the problem. To verify the mathematical model, the numerical solution and proving the technical feasibility of this process, a electromagnetic forming device was developed and several experiments were made with aluminum plates. The parameters investigated were the thickness of the plate to be deformed and the influence of the vacuum in the cavity of the tool. The experimental results show agreement with the results of the proposed model. The presence of vacuum also showed an increase in the deformation of the plate. A routine developed in software Matlab provide important information for the process and allow to make adjustments on the device.

Esta dissertação apresenta modelagem matemática e um método de solução numérica para problemas de conformação eletromagnética de chapas metálicas finas circulares utilizando uma bobina em espiral plana. O método foca especificamente o cálculo do campo eletromagnético gerado pela bobina e análise do circuito que modela o sistema de estampagem eletromagnética. A bobina plana é aproximada por círculos concêntricos carregando a corrente de descarga dos capacitores. Os cálculos das correntes induzidas e perfil da força eletromagnética na chapa e acoplamentos magnéticos entre a bobina e chapa metálica são realizados para o instante inicial, antes da deformação plástica da chapa. O método utiliza a lei de Biot-Savart, sendo que a solução das integrais obtidas para indução magnética é realizada através de métodos numéricos, considerando as simetrias do problema. Para verificação da modelagem matemática, da solução numérica e comprovação da viabilidade técnica deste processo, um dispositivo de estampagem eletromagnética foi desenvolvido e diversos experimentos foram realizados com chapas de alumínio. Os parâmetros investigados foram a espessura da chapa a ser deformada e a influência da presença de vácuo na cavidade da ferramenta. Os resultados experimentais demonstram concordância com os resultados da modelagem proposta. A presença de vácuo também demonstrou um incremento na deformação da chapa. A rotina desenvolvida no software Matlab fornece informações importantes para o processo e permite que se faça ajustes no dispositivo. / This dissertation presents a mathematical model and numerical method to solve the problems of electromagnetic forming of thin circular metal sheets by using a flat spiral coil. The method focuses specifically on the calculation of the electromagnetic field generated by the coil flat and circuit analysis modeling system electromagnetic forming. The flat coil is approximated by concentric circles carrying a discharge current of capacitors. The calculations of induced currents and profile of the electromagnetic force on the plate and magnetic coupling between the coil and sheet metal are made to the initial time, before the plastic deformation of the plate. The method uses the law of Biot-Savart, and the solution of the integral obtained for magnetic induction is performed by numerical methods, considering the symmetries of the problem. To verify the mathematical model, the numerical solution and proving the technical feasibility of this process, a electromagnetic forming device was developed and several experiments were made with aluminum plates. The parameters investigated were the thickness of the plate to be deformed and the influence of the vacuum in the cavity of the tool. The experimental results show agreement with the results of the proposed model. The presence of vacuum also showed an increase in the deformation of the plate. A routine developed in software Matlab provide important information for the process and allow to make adjustments on the device.

L’objectif de la thèse est de développer un dispositif de micro positionnement intégrant à la fois les actionneurs et les capteurs. Un dispositif a été conçu afin de réaliser des déplacements dans les plans sur une course millimétrique. Le dispositif compact ne nécessite pas de système de guidage additionnel et selon le mode d’utilisation de ces moteurs, il est capable de réaliser des translations dans le plan ou des rotations autour d’un axe perpendiculaire au plan. Le dispositif comprend quatre moteurs électromagnétiques linéaires fixés orthogonalement sur une structure en forme de croix. Chaque moteur consiste en une paire de bobines planes entrelacées fixe et une barre ’aimants mobile. Un capteur de déplacement intégré dans la structure en croix permettant de mesurer le déplacement de celle-ci a été conçu et fabriqué. Ce capteur est constitué d’une tête de mesure à fibres optiques placé face à un réseau en silicium réalisé par des techniques de microfabrication. Afin de minimiser les erreurs d’assemblage, la structure en croix a également été micro fabriquée. Le dispositif est capable de réaliser un déplacement de 10 mm et une rotation de ±11° autour de l’axe perpendiculaire au plan du dispositif. La résolution de déplacement du dispositif est de 1,4 µm avec une précision de 31 nm en boucle fermée. Le dispositif peut également atteindre une vitesse de déplacement de 12 mm/s. / The objective of thesis is to develop an integrated micro positioning system for micro applications. A unique micro positioning system design capable to deliver millimeter level strokes with pre-embedded auto guidance feature in micro application has been realized. The design integrates, a stack of orthogonally arranged four electromagnetic linear motors. Each linear motor consists of a fixed planar electric drive coil and mobile permanent magnet array. The optimal design of the system delivers a small footprint size. In addition, to measure and control the displacement, a high resolution compact optical displacement measurement sensor has been designed and fabricated in silicon material using microfabrication technology. Furthermore, a light weight silicon cross structure was fabricated using dry etching technology to reduce components assembly errors. The device is capable to deliver 10 mm displacement stroke with a rotation of ±11° about an axis perpendicular to the plane of the device. The displacement resolution of the device is 1.4 µm with a precision of 31 nm in closed loop control. The device can realize displacement with a speed of 12 mm/s.

In this study, RF coil geometries are designed for MRI applications using inhomogeneous main magnetic fields. The current density distributions that can produce the desired RF magnetic field characteristics are obtained on predefined cubic, cylindrical and planar surfaces and Tikhonov, CGLS, TSVD and Rutisbauer regularization methods are applied to match the desired and generated magnetic fields. The conductor paths, which can produce the current density distribution calculated for each surface selection and regularization technique, are determined using stream functions. The magnetic fields generated by the current distributions are calculated and the error percentages between the desired and generated magnetic fields are found. Optimum conductor paths that are going to be produced on cubic, cylindrical and planar surfaces and the required regularization method are determined on the basis of error percentages and realizability of the conductor paths. The optimum conductor path calculated for the planar coil is realized and in the measurement done by LakeShore 3-Channel Gaussmeter, an average error percentage of 11 is obtained between the theoretical and measured magnetic field. The inductance values of the realized RF coil are measured / the tuning and matching capacitance values are calculated and the frequency characteristics of the system is tested using Electronic Workbench 5.1. The quality factor value of the tested system is found to be 162.5, which corresponds to a bandwidth of 39,2 KHz at 6,387 MHz (operating frequency of METU MRI system). The techniques suggested in this study can be used in order to design and realize RF coils on prede&macr / ned arbitrary surfaces for inhomogeneous main magnetic fields. In addition, a hand held MRI device can be manufactured which uses a low cost permanent magnet to provide a magnetic field and generates the required RF field with the designed RF coil using the techniques suggested in this study.