This thesis is at the beginning about designing hardware of I/O card with module \-Rabbit3200 equipped by ethernet. Programs were created in programming languages such as assembler, C and C\#. At the end card was tested by generator, multimeter and oscilloscope.

The area is located in the city of Brno - Tuřany. It is defined from the west Černovice river with natural monument Holásky Lake, from east by railway line from the south street U Potoka. The aim is a comprehensive urban design of the development area. The existing area is a typical structure of the former village connected to Brno. Location is convenient for the development of residential functions and optional equipment. The main objective of the solution is to design urban areas, which would carry on the original structure of the village and effective form of use of the available unused area.

This diploma thesis is a part of a project of two students. The aim of the project is to design safer electronics for the unstable balancing vehicle HUMMER and implementation of advanced diagnostics and fault detection. In the first part of the project we analysed the original vehicle using the FMEA analyse and created a new concept of the vehicle. The second part of the project describes a new hardware. I designed and tested the power electronics, control unit and supplies. The outputs of the work are prototypes which allow testing a new concept.

The Diploma thesis is focused on reballing of BGA packages with the device PACE TF 2700. It describes the general types of BGA packages, their defects, importance of thermal management to the solder techniques, where it is also talked about the meaning of solders and fluxes for the joint. The work informs about the most common methods of reballing, the proper handling of components and the current situation with BGA stencils on the market. It briefly describes the device operation of PACE TF 2700, that is working on the convection and IR principle of heating components. It deals with the manufacturing of the template, dummy BGA packages, the test plates, creation of the thermo profile, comparing and examining the defects and their causes, which had the most significant impact on the results. The achievements would serve for comparing them with the results of the future laboratory exercises or as a subject for further works.

This master thesis deals with the design and realization of a drive for a 500 W BLDC motor powered with a battery power supply. It also deals with the possibilities of realization of drives and other possibilities to control these motors. Describes the implementation of the inverter using Atmel's AVR microcontroller. The thesis also deals with the design of an auxiliary switching inverter. Communication with UART and CAN interface is also implemented.

With the development of information technology, power management for telecom and computer applications become a large market for power supply industries. To meet the performance and reliability requirement, distributed power system (DPS) is widely adopted for telecom and computer systems, because of its modularity, maintainability and high reliability. Due to limited space and increasing power consumption, power supplies for telecom and server systems are required to deliver more power with smaller volume. As the key component of DPS system, front-end AC/DC converter is under the pressure of continuously increasing power density. For conventional industry practices, some limitations prevents front-end converter meeting the power density requirement. In this dissertation, different techniques have been investigated to improve power density of front-end AC/DC converters. For PFC stage, at low switching frequency, PFC inductor size is large and limits the power density. Although increasing switching frequency can dramatically reduce PFC inductor size, EMI filter size might be larger at higher switching frequency because of the change of noise spectrum. Since the relationship between EMI filter size and PFC switching frequency is unclear for industry, PFC circuits always operate with switching frequency lower than 150 kHz. Based on the EMI filter design method, together with a simple EMI noise prediction model, relationship between EMI filter corner frequency and PFC switching frequency was revealed. The analysis shows that switching frequency of PFC circuit should be higher than 400 kHz, so that both PFC inductor and EMI filter size can be reduced. Although theoretical analysis and experimental results verify the benefits of high switching frequency PFC, it is essential to find a suitable topology that allows high switching frequency operation while maintains high efficiency. Three PFC topologies, single switch PFC, three-level PFC with range switch and dual Boost PFC, were evaluated with analysis and experiments. By using advanced semiconductor devices, together with proposed control methods, these topologies could achieve high efficiency at high switching frequency. Thus, the benefits of high frequency PFC can be realized. In front-end converter, large holdup time capacitor size is another barrier for power density improvement. To meet the holdup time requirement, bulky holdup time capacitor is normally used to provide energy during holdup time. Holdup time capacitor requirement can be reduced by using wider input voltage range DC/DC converte. Because LLC resonant converter can realized with input voltage range without sacrificing its normal operation efficiency, it becomes an attractive solution for DC/DC stage of front-end converters. Moreover, its small switching loss allows it operating at MHz switching frequency and achieves smaller passive component size. However, lack of design methodology makes the topology difficult to be implemented. An optimal design methodology for LLC resonant converter has been developed based on the analysis on the circuit during normal operation condition and holdup time. The design method is verified by a 1 MHz switching frequency LLC resonant converter with 76W/in3 power density. When front-end converter operates at high switching frequency, negative effects of circuit parasitics become more pronounced. By integrating active devices together with their gate drivers, Active Integrated power electronics module (IPEM) can largely reduce circuit parasitics. Therefore, switching loss and voltage stress on switching devices can be reduced. Moreover, IPEM concept can be extended into passive integration and EMI filter integration By using this power integration technology, power density and circuit performance of front-end converter can be improved, which is verified by theoretical analysis and experimental results. / Ph. D.

La thèse présente le développement de CPS (CMOS Pixel Sensors) intégré avec CAN au niveau du pixel pour les couches externes du détecteur de vertex de l’ILD (International Large Detector). Motivé par la physique dans l’ILC (International Linear Collider), une précision élevée est nécessaire pour les détecteurs. La priorité des capteurs qui montre sur les couches externes est une faible consommation d’énergie en raison du rapport élevé de couverture de la surface sensible (~90%) dans le détecteur de vertex. Le CPS intégré avec CAN est un choix approprié pour cette application. L’architecture de CAN de niveau colonne ne fournit pas une performance optimisée en termes de bruit et la consommation d’énergie. La conception de CAN au niveau du pixel a été proposée. Bénéficiant des sorties de pixels tout-numérique, CAN au niveau des pixels présentent les mérites évidents sur le bruit, la vitesse, la zone sensible et la consommation d’énergie. Un prototype de capteur, appelé MIMADC, a été implémenté par un processus de 0.18 μm CIS (CMOS Image Sensor). L’objectif de ce capteur est de vérifier la faisabilité du CPS intégré avec les CAN au niveau des pixels. Trois matrices sont incluses dans ce prototype, mais avec deux types différents de CAN au niveau de pixel: une avec des CAN à registre à approximations successives (SAR), et les deux autres avec des CAN à une seule pente (Single-Slope, SS) CAN. Toutes les trois possédant les pixels de la même taille de 35×35 μm2 et une résolution de 3-bit. Dans ce texte, des analyses théoriques et le prototype sont présentés, ainsi que la conception détaille des circuits. / This thesis presents the development of CMOS pixel sensors (CPS) integrated with pixel-level ADCs for the outer layers of the ILD (International Large Detector) vertex detector. Driven by physics in the ILC (International Linear Collider), an unprecedented precision is required for the detectors. The priority of the sensors mounted on the outer layers is low power consumption due to the large coverage ratio of the sensitive area (~90%) in the vertex detector. The CPS integrated with ADCs is a promising candidate for this application. The architecture of column-level ADCs, exists but do not provide an optimized performance in terms of noise and power consumption. The concept of pixel-level ADCs has been proposed. Benefiting from the all-digital pixel outputs, pixel-level ADCs exhibit the obvious merits on noise, speed, insensitive area, and power consumption. In this thesis, a prototype sensor, called MIMADC, has been implemented by a 0.18 μm CIS (CMOS Image Sensor) process. The target of this sensor is to verify the feasibility of the CPS integrated with pixel-level ADCs. Three matrices are included in this prototype but with two different types of pixel-level ADCs: one with successive approximation register (SAR) ADCs, and the other two with single-slope (SS) ADCs. All of them feature a same pixel size of 35×35 μm2 and a resolution of 3-bit. In this thesis, the prototype is presented for both theoretical analyses and circuit designs. The test results of the prototype are also presented.

The thesis deals with the development and realization of a multimedia module with a microcontroller for radio controlled models of ships, cars, and fighting techniques. The module uses commands from the RC transmitter to control the model illumination and accompanying sounds. The thesis summarizes principles generally used in RC models. Based on these general principles, a new control element for the RC transmitter is designed. A relevant multimedia module is designed and implemented. The last part of the thesis is devoted to the description of the basic parts of microcontroller firmware.

Proteins orchestrate a number of cellular processes either alone or in concert with other biomolecules like nucleic acids, carbohydrates, and lipids. They exhibit an intrinsic ability to fold de novo to their functional states. The three–dimensional structure of a protein, dependent on its amino acid sequence, is important for its function. Understanding this sequence– structure–function relationship has become one of the primary goals in biophysics. Various experimental techniques like X–ray crystallography, Nuclear Magnetic Resonance (NMR), and site–directed mutagenesis have been used extensively towards this goal. Computational studies include mainly sequence based, and structure based approaches. The sequence based approaches such as sequence alignments, phylogenetic analysis, domain identification, statistical coupling analysis etc., aim at deriving meaningful information from the primary sequence of the protein. The structure based approaches, on the other hand, use structures of folded proteins. Recent advances in structure determination and efforts by various structural consortia have resulted in an enormous amount of structures available for analysis. Innumerable observations such as the allowed and disallowed regions in the conformations of a peptide unit, hydrophobic core in globular proteins, existence of regular secondary structures like helices, sheets, and turns and a limited fold space have been landmarks in understanding the characteristics of protein structures. The uniqueness of protein structure is attained through non–covalent interactions among the constituent amino acids. Analyses of protein structures show that different types of non–covalent interactions like hydrophobic interactions, hydrogen bonding, salt bridges, aromatic stacking, cation–π interactions, and solvent interactions hold protein structures together. Although such structure analyses have provided a wealth of information, they have largely been performed at a pair–wise level and an investigation involving such pair–wise interactions alone is not sufficient to capture all the determinants of protein structures, since they happen at a global level. This consideration has led to the development of graphs/networks for proteins. Graphs or Networks are a collection of nodes connected by edges. Protein Structure Networks (PSNs) can be constructed using various definitions of nodes and edges. Nodes may vary from atoms to secondary structures in Synopsis proteins, and the edges can range from simple atom–atom distances to distance between secondary structures. To study the interplay of amino acids in structure formation, the most commonly used PSNs consider amino acids as nodes. The criterion for edge definition, however, varies. PSNs can be constructed at a course grain level by considering the distances between Cα/Cβ atoms, any side–chain atoms, or the centroids of the amino acids. At a finer level, PSNs can be constructed using atomic details by considering the interaction types or by computing the extent of interaction between amino acids. Representation of proteins as networks and their analyses has given us a unique perspective on various aspects such as protein structure organization, stability, folding, function, oligomerization and so on. A variety of network properties like the degree distribution, clustering coefficient, characteristic path lengths, clusters, and hubs have been investigated. Most of these studies are carried out on protein structures alone. However, the interaction of proteins with other biopolymers like nucleic acids is vital for many crucial biological processes like transcription and translation. In this thesis, we have attempted to address this problem by constructing and analyzing combined graphs of the structures of protein and DNA. Also, in almost all of the PSN studies, the connections have been made solely on the basis of geometric criteria. In the later part of the thesis, we have taken PSN a step further by defining the non–covalent connections based on chemical considerations in the form of the energies of interactions. The thesis contains two sections. The first part mainly involves the construction and application of PSNs to study DNA binding proteins. The DNA binding proteins are involved in several high fidelity processes like DNA recombination, DNA replication, and transcription. Although the protein– DNA interfaces have been extensively analyzed using pair–wise interactions, we gain additional global perspective from network approach. Furthermore, most of the earlier investigations have been carried out from the protein point of view (protein centric) and the present network approach aims to combine both the protein centric and the DNA centric view points by construction and analyses of protein–DNA graphs. These studies are described in Chapters 3 and 4. The second part of the thesis discusses the development, characterization, and application of protein structure networks based on non– covalent interaction energies. The investigations are presented in chapters 5 and 6. Chapter 3 discusses the development of Protein–DNA Graphs (PDGs) where the protein–DNA interfaces are represented as networks. PDG is a bipartite network in which amino acids form a set of nodes and the nucleotides form the other set. The extent of interaction between the two diverse types of biopolymers is normalized to define the strength of interaction. Edges are then constructed based on the interaction strength between amino acids and nucleotides. Such a representation, reported here for the first time, provides a holistic view of the interacting surface. The developed PDGs are further analyzed in terms of clusters of interacting residues and identification of highly connected residues, known as hubs, along the protein–DNA interface and discussed in terms of their interacting motifs. Important clusters have been identified in a set of protein–DNA complexes, where the amino acids interact with different chemical components of DNA such as phosphate, deoxyribose and base with varying degrees of connectivity. An analysis of such fragment based PDGs provided insights into the nature of protein–DNA interaction, which could not have been obtained by conventional pair–wise analysis. The predominance of deoxyribose–amino acid clusters in beta–sheet proteins, distinction of the interface clusters in helix–turn–helix and the zipper type proteins are some of the new findings from the analysis of PDGs. Additionally, a potential classification scheme has been proposed for protein–DNA complexes on the basis of their interface clusters. This classification scheme gives a general idea of how the proteins interact with different components of DNA in various complexes. The present graph–based method has provided a deeper insight into the analysis of the protein–DNA recognition mechanisms from both protein and DNA view points, thus throwing more light on the nature and specificity of these interactions (Sathyapriya, Vijayabaskar et al. 2008). Chapter 4 delineates the application of PSN to an important problem in molecular biology. An analysis of interface clusters from multimeric proteins provides a clue to the important residues contributing to the stability of the oligomers. One such prediction was made on the DNA binding protein under starvation from Mycobacterium smegmatis (Ms–Dps) using PSNs. Two types of trimers, Trimer A (tA) and Trimer B (tB) can be derived from the dodecamer because of the inherent three fold symmetry of the spherical crystal structure. The irreversible dodecamerization of these native Ms--Dps trimers, in vitro, is known to be directly associated with the bimodal function (DNA binding and iron storage) of this protein. Interface clusters which were Synopsis identified from the PSNs of the derived trimers, allowed us to convincingly predict the residues E146 and F47 for mutation studies. The prediction was followed up by our experimental collaborators (Rakhi PC and Dipankar Chatterji), which led to the elucidation of the molecular mechanism behind the in vitro oligomerization of Ms--Dps. The F47E mutant was impaired in dodecamerization, and the double mutant (E146AF47E) was a native monomer in solution. These two observations suggested that the two trimers are important for dodecamerization and that the residues selected are important for the structural stability of the protein in vitro. From the structural and functional characterizations of the mutants, we have proposed an oligomerization pathway of Ms–Dps (Chowdhury, Vijayabaskar et al. 2008). The second part of the thesis involves the development, characterization (Chapter 5) and application (Chapter 6) of Protein Energy Networks (PENs). As mentioned above, the PSNs constructed on the geometric basis efficiently capture the topology and associated properties at the level of atom–atom contact. The chemistry, however, is not completely captured by these network representations, and a wealth of information can be extracted by incorporating the details of chemical interactions. This study is an advancement over the existing PSNs, in terms of edges being defined on the basis of interaction energies among the amino acids. This interaction energy is the resultant of various types of interactions within a protein. Use of such realistic interaction energies in a weighted network captures all the essential features responsible for maintaining the protein structure. The methodology involved in representing proteins as interaction energy weighted networks, with realistic edge weights obtained from standard force fields is described in Chapter 5. The interaction energies were derived from equilibrium ensembles (obtained using molecular dynamics simulations) to account for the structural plasticity, which is essential for function elucidation. The suitability of this method to study single static structures was validated by obtaining interaction energies on minimized crystal structures of proteins. The PENs were then characterized using network parameters like edge weight distributions, clusters, hubs, and shortest paths. The PENs exhibited three distinct behaviors in terms of the size of the largest connected cluster as a function of interaction energy; namely, the pre–transition, transition, and post transition regions, irrespective of the topology of the proteins. The pre– transition region (energies<–20 kJ/mol) comprises smaller clusters with mainly charged and polar residues as hubs. Crucial topological changes take place in the transition region (–10 to –20 kJ/mol), where the smaller clusters aggregate, through low energy van der Waals interactions, to form a single large cluster in the post–transition region (energies>–10 kJ/mol). These behaviors reinforce the concept that hydrophobic interactions hold together local clusters of highly interacting residues, keeping the protein topology intact (Vijayabaskar and Vishveshwara 2010). The applications of PENs in studying protein organization, allosteric communication, thermophilic stability and the structural relation of remote homologues of TIM barrel families have been outlined in Chapter 6. In the first case, the weighted networks were used to identify stabilization regions in protein structures and hierarchical organization in the folded proteins, which may provide some insights into the general mechanism of protein folding and stabilization (Vijayabaskar and Vishveshwara 2010). In the second case the features of communication paths in proteins were elucidated from PENs, and specific paths have been extensively discussed in the case of PDZ domain, which is known to bring together protein partners, mediating various cellular processes. Changes in PEN upon ligand binding, resulting in alterations of the shortest paths (energetically most favorable paths) for a small fraction of residues, indicated that allosteric communication is anisotropic in PDZ. The observations also establish that the shortest paths between functionally important sites traverse through key residues in PDZ2 domain. Furthermore, shortest paths in PENs provide us the exact pathways of communication between residues. Although the communication in PDZ has been extensively investigated, detailed information of pathways at the energy level has emerged for the first time from the present study from PEN analysis (Vijayabaskar and Vishveshwara 2010). In the third case, a set of thermophilic and mesophilic proteins were compared to determine the factors responsible for their thermal stability from a network perspective using PENs. The sub– graph parameters such as cluster population, hubs and cliques were the prominent contributing factors for thermal stability. Also, the thermophilic proteins have a better–packed hydrophobic core. The property of thermophilic protein to increase stability by increasing the connectivity but retain conformational flexibility is discussed from a cliques and communities (higher order inter–connection of residues) perspective (Vijayabaskar and Vishveshwara 2010). Finally, the remote homologues from the TIM barrel fold have been analyzed using PENs to identify the interactions responsible for the maintenance of the fold despite low sequence similarity. A study of conserved Synopsis interactions in family specific PENs reveals that the formation of the central beta barrel is vital for the TIM barrel formation. The beta barrel is being formed by either conserved long range electrostatic interactions or by tandem arrangement of low energy hydrophobic interactions. The contributions of helix–sheet and helix–helix interactions are not conserved in the families. This study suggests that the sequentially near residues forming the helix–sheet interactions are common in many folds and hence formed despite non– conservation, whereas formation of beta barrel requires long range interactions, thus more conserved within the families. The thesis also consists of an appendix in which a web–tool, developed to express proteins as networks and analyze these networks using different network parameters is discussed. The web based program–GraProStr allows us to represent proteins as structure graphs/networks by considering the amino acid residues as nodes and representing non–covalent interactions among them as edges. The different networks (classified based on edge definition) which can be obtained using GraProStr are Protein Side–chain Networks (PScNs), Cα/Cβ distance based networks (PcNs) and Protein– Ligand Networks (PLNs). The parameters which can be generated include clusters, hubs, cliques (rigid regions in proteins) and communities (group of cliques). It is also possible to differentiate the above mentioned parameters for monomers and interfaces in multimeric proteins. The well tested tool is now made available to the scientific community for the first time. GraProStr is available online and can be accessed from http://vishgraph.mbu.iisc.ernet.in/GraProStr/index.html. With a variety of structure networks, and a set of easily interpretable network parameters GraProStr can be useful is analyzing protein structures from a global paradigm (Vijayabaskar, Vidya et al. 2010). In summary, we have extensively studied DNA binding proteins using side– chain based protein structure networks and by integrating the DNA molecule into the network. Also, we have upgraded the existing methodology of generating structure networks, by representing both the geometry and the chemistry of residues as interaction energies among them. Using this energy based network we have studied diverse problems like protein structure formation, stabilization, and allosteric communication in detail. The above mentioned methodologies are a considerable advancement over existing structure network representations and have been shown in this thesis to shed more light on the structural features of proteins.

The DNA binding proteins under starvation (Dps) from M. smegmatis are cage-like structures which internalize iron and bind DNA. They provide resistance to the cells from free radical damage, and physically protect the DNA from the harmful effects of reactive oxygen species by DNA compaction. The work compiled in this thesis has been an effort to study oligomerization and dynamics of iron metabolism by these nano-protein compartments. Chapter 1 gives a general introduction on stress, especially oxidative stress, and the ways bacteria fight back the host resistance systems. This has been elaborated from the point of view of the Dps proteins which is the focus of our work. Also, the competition for iron among the host and pathogens, and the modes of iron trafficking of the pathogens from host organisms has been summarized. Finally, the structural aspects of ferritin family proteins to which Dps belongs, has been discussed. Chapter 2 elaborates on the oligomerization pathways of the first M. smegmatis Dps MsDps1, which exists in vitro as two oligomeric forms. The GFP-tagging has been used to locate the Dps1 proteins by live cell imaging and the over-expression of these proteins during nutrient limiting conditions has been studied. The crystal structure of a point mutant F47E in the background of MsDps1, which shows no dodecamerization in vitro, has been solved. The possible ways of dodecamerization of MsDps1 has been concluded by analyzing the intermediates via glutaraldehyde cross-linking and native electrospray mass spectrometry. Chapter 3 documents the gating machinery of iron in MsDps2 protein, the second M. smegmatis Dps protein. Through graph theoretical approaches, a tight histidine-aspartate cluster was identified at the ferritin-like trimeric pore which harbors the channel for the entry and exit of iron. Sitespecific variants of MsDps2 were generated to disrupt this ionic knot, and the mutants were further assayed for ferroxidation, iron uptake and iron release properties. Our studies in MsDps2 show the importance of counter-acting positive and negatively charged residues for efficient assimilation and dispersion of iron. Chapter 4 describes crystallization studies of MsDps2 pore variants, done in an attempt to connect the changes in functional properties described in chapter 3, with structural alterations of the point mutants. We show here that the gating mechanism happens by alterations in side chain configuration at the pore and does not alter the over-all stability of the proteins. Chapter 5 is the final section where we have employed site specific mutations and cocrystallization studies to elucidate the behaviour of MsDps2 proteins upon the addition of iron. By studying the effect of substitutions at conserved sites near ferroxidation center, we attempt to arrive at a pathway which iron atoms take to reach the ferroxidation site. Also, by crystallization of proteins loaded with varying amounts of iron we tried to map the changes in the protein structure in the presence of its ligand. Chapter 6 concludes briefly the work that has been documented in this thesis. Appendix I relates the role of N-terminal tail for DNA binding in MsDp2. Appendix II gives the technical details of a modified protein preparation and oligomerization process for his-tagged MsDps1 protein. Appendix III gives the maps of the plasmids used in this study.