No description available.

In recent years, several interesting biological roles played by RNA have come to light. Apart from their known role in translation of genetic information from DNA to protein, they have been shown to act as enzymes as well as regulators of gene expression. Protein-RNA complexes are involved in regulating cellular processes like cell division, differentiation, growth, cell aging and death. A number of clinically important viruses have RNA as their genetic material. Defective RNA molecules have been linked to a number of human diseases. The ability of RNA to adopt stunningly complex three-dimensional structures aids in diverse functions like catalysis, metabolite sensing and transcriptional control. Several secondary structure motifs are observed in RNA, of which the double-helical RNA motif is ubiquitous and well characterized. Though DNA duplexes have been shown to be present in many polymorphic states, RNA duplexes are believed to exhibit conservatism. Early fibre diffraction analysis on molecular structures of natural and synthetically available oligo- and polynucleotides suggested that the double-helical structures of RNA might exist in two forms: A-form and A′-form. New improved crystallographic methods have contributed to the increased availability of atomic resolution structures of many biologically significant RNA molecules. With the available structural information, it is feasible to try and understand the contribution of the variations at the base pair, base-pair step and backbone torsion angle level to the overall structure of the RNA duplex. Further, the effect of protein binding on RNA structure has not been extensively analysed. These studies have not been investigated in greater detail due to the focus of the research community on understanding conformational changes in proteins when bound to RNA, and due to the lack of a significant number of solved RNA structures in both free and protein-bound state. While studies on the conformation of the DNA double-helical stem have moved beyond the dinucleotide step into tri-, tetra-, hexa- and octanucleotide levels, similar knowledge for RNA even at the dinucleotide step level is lacking. In this thesis, the results of detailed analyses to understand the contribution of the base sequence towards RNA conformational variability as well as the structural changes incurred upon protein binding are reported. Objectives The primary objective of this thesis is to understand the following through detailed analyses of all available high-resolution crystal structures of RNA. 1 Exploring sequence-dependent variations exhibited by dinucleotide steps formed by Watson-Crick (WC) base pairs in RNA duplexes. 2 Identifying sequence-dependent variations exhibited by dinucleotide steps containing non-Watson-Crick (NWC) base pairs in RNA duplexes. 3 Developing a web application for the generation of sequence-dependent non-uniform nucleic acid structures. 4 Investigating the relationship between base sequence and backbone torsion-angle preferences in RNA double helices followed by molecular dynamics simulation using various force fields, to check their ability to reproduce the above experimental findings. Chapter 1 gives an overview of the structural features and polymorphic states of RNA duplexes and the present understanding of the structural architecture of RNA, thereby laying the background to the studies carried out subsequently. The chapter also gives a brief description on the methodologies applied. Relevant methodologies and protocols are dealt with in detail in the respective chapters. Sequence-dependent base-pair step geometries in RNA duplexes A complete understanding of the conformational variability seen in duplex RNA molecules at the dinucleotide step level can aid in the understanding of their function. This work was carried out to derive geometric information using a non-redundant RNA crystal structure dataset and to understand the conformational features (base pair and base-pair step parameters) involving all Watson-Crick (WC) (Chapter 2) and non-Watson-Crick (NWC) base pairs (Chapter 3). The sequence-dependent variations exhibited by the base-pair steps in RNA duplexes are elaborated. Further, potential non-canonical hydrogen bond interactions in the steps are identified and their relationship with dinucleotide step geometry is discussed. Comparison of the features of dinucleotide steps between free and protein-bound RNA datasets suggest variations at the base-pair step level on protein binding, which are more pronounced in non-Watson-Crick base pair containing steps. Chapter 4 describes a web-server NUCGEN-Plus, developed for building and regeneration of curved and non-uniform DNA and RNA duplexes. The main algorithm is a modification of our earlier program NUCGEN that worked mainly for DNA. The WC step parameters and intra-base parameters for RNA were obtained from the work detailed in Chapter 2. The FORTRAN code and input sequence file format was modified. The program has two modules: a) Using the model-building module, the program can build duplex structures for a given input DNA/RNA sequence. Options are available for selecting various derived or user specified base-pair step parameters, and fibre diffraction parameters that can be used in the building process. The program can generate double-helical structures up to 2000 nucleotides in length. In addition, the program can calculate the curvature of the generated duplex at defined length scale. b) Using the regeneration module, double-helical structures of nucleic acids can be rebuilt from the existing solved structures. Further, variants of an existing structure can be generated by varying the input geometric parameters. The web-server has a user-friendly interface and is freely available in the public domain at: http://nucleix.mbu.iisc.ernet.in/nucgenplus/index.html Sequence dependence of backbone torsion angle conformers in RNA duplexes RNA molecules consist of covalently linked nucleotide units. Each of these units has six rigid torsional degrees of freedom (α, β, γ, δ, ε, and ζ) for the backbone and one (χ) around the glycosidic bond connecting the base to the ribose, thereby providing conformational flexibility. An understanding of the relationship between base sequence and structural variations along the backbone can help deduce the rationale for sequence conservation and also their functional importance. Chapter 5 describes in detail the torsion angle-dependent variations seen in dinucleotide steps of RNA duplex. A non-redundant, high resolution (≤2.5Å) crystal structure dataset was created. Base-specific preferences for the backbone and glycosidic torsion angles were observed. Non-A-form torsion angle conformers were found to have a greater prevalence in protein-bound duplexes. Further validation of the above observation was performed by analysing the RNA backbone conformers and the effect of protein binding, in the crystal structure of E. coli 70S ribosome. Chapter 5 further describes the molecular dynamics simulation studies carried out to understand the effect of force fields on the RNA backbone conformer preferences. A 33mer long duplex was simulated using seven different force fields available in AMBER and CHARMM program, each for 100 ns. Trajectory analyses suggest the presence of sequence-dependent torsion angle preferences. Torsion angle conformer distribution closer to that of crystal structures was observed in the system simulated using parmbsc0 force field. Molecular dynamics simulation studies of AU/AU base-pair step A unique geometric feature, unlike that in other purine-pyrimidine (RY) steps in the crystal dataset analysis, was reported for AU/AU step (see Chapter 2). Appendix 1 describes the work carried out to validate these features observed in the crystal structures using simulation studies. Additionally, the effect of nearest-neighbor base pairs on the AU/AU step geometry were examined. General Conclusion Overall, the findings of this thesis work suggest that RNA duplexes exhibit sequence-dependent structural variations and sample a large volume of the double-helical conformational space. Further, protein binding affects the local base-pair step geometry and backbone conformation.

Au niveau moléculaire, les fonctions des motifs hélicoïdaux sont souvent associées à la stabilité de cesarchitectures. Par exemple, lorsqu’une hélice α est isolée de la structure tertiaire des protéines, celle-cidevient alors flexible et perd son activité. Afin de contrôler la rigidité de ces architectures, différentesapproches ont été proposées dont la construction d’édifices moléculaires repliés de façon contrôlée : lesfoldamères. Notre équipe s’intéresse aux foldamères d’oligoamide aromatique hélicoïdaux et à l’heureactuelle plusieurs études ont déjà été menées afin de comprendre les facteurs influant la stabilité de telleshélices: la longueur de l’oligomère, le solvant et l’effet de l’introduction d’un espaceur aliphatique dans laséquence. Lors de ce travail nous nous sommes tout d’abord intéressés à la capacité de repliement de cinqmonomères aromatiques couramment utilisés pour la préparation de foldamères. Leur contribution dans lastabilité hélicoïdale du système a été évaluée par RMN, diffraction des rayons-X et HPLC chirale dynamique.Inspirés par le rôle des ponts disulfure dans les protéines, nous avons décidé d’explorer l’effet d’une telleliaison sur la stabilité des hélices d’oligoamide aromatique. Deux composés contenant une liaison disulfureintramoléculaire ou deux liaisons intermoléculaires ont été synthétisés et leur stabilité étudiée par RMN, HPLCChiral et Dichroïsme circulaire.Enfin, la synthèse d’hélices moléculaires de grandes dimensions (assimilables à celles de polymèresmonodisperses) a été réalisée par une approche convergente de triplement de longueur de segment via laformation de liaisons anhydrides entre blocs oligomériques. / At the molecular level, the functions of helical patterns are often directly associated with the stability of thesearchitectures, (in α-helices). For example, upon removal of such an entity from the protein’s tertiary structure,the peptidic helix becomes flexible and thus inactive. In order to control the rigidity of these architectures,several strategies have been used and the construction of completely artificial well folded molecules known asfoldamers is one them. Our group mainly focuses on helical aromatic oligoamide foldamers and to dateseveral studies have been carried out to investigate factors affecting the helical stability; the influence ofoligomer length, solvent effects and the effect of aliphatic linkers within a helical aromatic sequence.In the present study we investigate the helical propensity of five commonly used aromatic monomers infoldamer synthesis and by using NMR spectroscopy, X-ray crystallography and dynamic chiral HPLC weevaluate their contribution in helical stability. Additionally, inspired by the role of disulfide bonds in proteins wedecided to explore their effect on helical stability. For this reason intra- and inter-molecularly disulfide bondedcompounds were designed and synthesized. Their stability was studied using NMR spectroscopy, chiral HPLCand CD experiments.Finally, the synthesis of mono-disperse helical strings of polymeric dimensions through a convergent, segmenttripling strategy has been developed. This protection/deprotection free synthesis was carried out byconnecting oligomeric blocks via a labile anhydride functionality.

Master's thesis deals with the design of an antenna system for wireless sound transmission used mainly in professional sound reinforcement. The introductory part deals generally with wireless microphones, frequency bands used and proven antenna types. Next, this work deals with signal distribution that is realized using the antenna splitter. The antenna parts is focused on easy production and real usage, therefore were selected antennas with appropriate properties suitable for small series production. This thesis includes simulation of each device, their real construction design and measurements of built prototypes and final products. All three produced devices – the rack splitter, /4 antenna and Helix antenna are fully working, achieve good parameters and are ready for further manufacturing and easy modifications in case of frequency band change requirement. The conclusion includes an overall assessment of the results achieved.

This master’s thesis is focused on the compilation of a computational modelling of gear mesh engagement dynamics of a spur gear by MBS approach. The user input is the specific geometry of gears, the operating speed, and the load torque. The output are the forces in the gear engagement and the reaction of the forces in the wheel bearings depending on the change in the stiffness of the gear due to the changing number of teeth in the engagement and the change in the axial distance. This model is characterized by a fast and relatively accurate calculation in the time domain. This means that it can react to changes in parameters during simulation such as axial distance, speed, and torque.

The purpose of this work was to make a proposal for input parts of receiver for band 430 to 440 MHz. A model of chosen semiconductor triode BFP540 was created in simulation software. Possibilities how to decrease consumption of this semiconductor triode, keeping the profit, were investigated through the simulation.In compromise consumption, keeping the profit of the amplifier - an optimal operating point for this semiconductor triode UCE = 1,2 V and IC = 2 mA was found. It was tested through the testing wiring with noise microstrips conformity. Ascertained knowledge was used for construction of tuner for UHF receiver. An operating point of input amplifier of UHF receiver was owing to power supply amplifier forced for bigger effectiveness to UCE = 2,65 V and IC = 2,0 mA. Suppression of mirror frequency is provided with Helix filter of the third order, because of intermediate frequency 10,7 MHz. Mixing on intermediate frequency is made again by semiconductor triode BFP540. Selectivity of receiver is provided with intermediate frequency crystal filter 10,7 MHz with bandwidth 15 kHz. Designed input part enables reception of SSB, FM and digital types of modulation.Bandwidth intermediate frequency exit is adapted to this request To receive particular modulation , it is necessary to complete intermediate frequency signal way with appropriate intermediate frequency filter.

The thesis is draft a multi-storey parking garage in the area of University Hospital in Brno Bohunice to insufficient capacity of the parking spaces. The aim of thesis is to create a sufficient number of parking spaces, which would solve the deficit of parking spaces and connecting the street Jihlavská. The parking garage is located on the south side of the University Hospital and ensures pedestrian connections to the hospital. The parking garage should serve for patient, visitors and hospital staff. This thesis takes into consideration the solution of terminal of public transport in Bohunice’s hospital and for patients and visitors to the hospital is also designed park.

Buildings account for up to 32% of the total energy use in different countries. Directives from the European Union have pointed out the importance of increasing energy efficiency in buildings. New regulation in countries like Sweden establishes that new buildings should fulfill regulations of Nearly Zero Energy Buildings (NZEB), opening an opportunity for new technologies to achieve these goals. Almost 80-90% of the energy in domestic hot water use is wasted from different applications with almost no use and with a lot of potential energy to be recovered. The present work studied the characteristics of greywater heat exchanger as a solution to recuperate heat from greywater to increase efficiency in buildings. This study explored the fluid mechanics involved in the vertical greywater heat exchangers, analyzing the falling film effect present in drain pipes and the effects of the secondary flow generated in the external helical coil. A heat transfer model from a theoretical approach was proposed and validated. In addition, this study explored the different variables influencing the economic feasibility of the technology and an economic analysis was performed. A theoretical comparison between a greywater heat exchanger application and a reference case without it was evaluated highlighting the importance of all the variables involved in the potential of implementation of the technology. The technology shows big potential in households with high water consumptions, especially with electric boilers.

No description available.

No description available.