There are two general ways to introduce functionalities into a polymeric structure: functionalization of the monomeric units before polymerization and postfunctionalization of the preformed polymer. Building libraries of polymers with different functionalities can be completed with significantly less effort by the second method, as each postfunctionalization of a single batch of polymeric backbone can involve as little as one synthetic step. One method of building a polymeric backbone for postfunctionalization involves the synthesis of hyperbranched conjugated polymers (HCPs) from AB2 monomeric units. A polymer formed from n AB2 monomeric units should contain n reactive B groups, which act as sites of functionalization. Utilizing this principle, two different hyperbranched poly(phenylene vinylene-phenylene ethynylene) scaffolds were synthesized and studied in both their inherent properties and functionalization. The first HCP synthesized was compared against a monomeric cruciform model and a linear polymer with a similar structure. The hyperbranched polymer has red-shifted absorption and emission in comparison to the cruciform model and linear polymer. The HCP quenches paraquat more efficiently than the linear polymer by a factor of about two, suggesting a greater rate of energy transfer. The functionalization of HCPs was studied; iodine groups decorating the HCPs were replaced with terminal alkynes by Pd-catalyzed coupling, providing a library of 24 differently functionalized HCPs. Elemental analyses of the postfunctionalized polymers show nearly complete substitution of the iodine groups. The postfunctionalized polymers show increased fluorescence compared to the original iodine decorated polymers, due to the loss of the heavy atom effect inducing iodine groups. The emissions of the postfunctionalized polymers in solution show a strong dependence on the groups attached to the conjugated structures, with emission maxima ranging from 505 nm to 602 nm; quantum yields range from 0.7% to 25%. Solid-state emission studies show stronger and more red-shifted spectra compared to emissions observed in solution.

The purpose of the author is to present a geological survey of the Backbone Ridge area in Burnet and Llano counties, Texas. During the summer of 1947 while enrolled in a geologic field course in McCullough County, it was noted that a new classification of the Cambrian and Ordovician formations In central Texas had been presented In the literature. It was noted at the same time that the Paleozoic rocks of the Llano uplift are more highly faulted than had been shown on previous geologic maps of the region. The writer concluded from field observations that the Backbone Ridge area was more complexly faulted then had been previously shown, and it was decided to test this conclusion by making a detailed geologic map of the area using the stratigraphic subdivisions recently established by Bridge, Barnes, and Cloud. A detailed study was made of these subdivisions and a large number of the type sections were visited. It was necessary to study the complete geologic history of the region in order that the events which involved the complex structural pattern and the present physiographic forms might be properly understood. The material contained in this report consists of data obtained from the literature and from field observations which were made in the area during the months of June and July of 1948. / text

This communication reports a unique ultra-large sheet formation through hierarchical self-assembly of a rod–coil graft copolymer containing a rigid polyphenylene backbone and flexible poly(ethylene oxide) (PEO) side chains. The hierarchical self-assembly process involved a distinctive morphological transition of 1D helical to 2D superstructures. The graft copolymer offers a new chance for the challenging bottom-up fabrication of ultra-large self-assembled nanosheets in solution, as well as a novel system for fundamental studies on 2D self-assembly of polymers.

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.

This communication reports a unique ultra-large sheet formation through hierarchical self-assembly of a rod–coil graft copolymer containing a rigid polyphenylene backbone and flexible poly(ethylene oxide) (PEO) side chains. The hierarchical self-assembly process involved a distinctive morphological transition of 1D helical to 2D superstructures. The graft copolymer offers a new chance for the challenging bottom-up fabrication of ultra-large self-assembled nanosheets in solution, as well as a novel system for fundamental studies on 2D self-assembly of polymers.

The main goal of this diploma thesis is to design of high-speed optical network. The first part deals with theoretical knowledge in the field of optical transmissions, especially principle of wavelength division multiplexing. Generally speaking, this part is dedicated to optical connections over long distances. It will concentrate on different types of wavelength division multiplexing, optical fiber amplifiers and other basic optical components. Then it discusses influence of negative effects acting on optical transmission and discusses how to reduce or suppress their influence. Subsequently, there is designed backbone network in the Czech Republic in OptiSystem 7.0 software and are verified some mentioned theoretical knowledge. One of chapters also presents results of measurements of real optical routes in our state. The second part of the diploma thesis moves its attention on that part of optical network, which provides data connectivity to end users, that means it is focused on optical access network. There are described the most common topologies, standards and components. Based on these findings, in the last chapter, there is worked out design of optical access network FTTH (more precisely FTTD) in the selected location. Afterwards, the design is transferred to the OptiSystem 7.0 software, where is verified its functionality.

The thesis is focused on the technical issues removal on the backbone of internet service provider, MX-NET Telekomunikace Ltd. After marketing research of impacts on client there will be determined the best alternative of solution, ensured the appropriate funding and organized the installation.

Recent research interests in studying the performance of different seismic force resisting systems (SFRS) have been shifting from component- (individual walls) to system-level (complete building) studies. Although there is wealth of knowledge on component-level performance of reinforced masonry shear walls (RMSW) under seismic loading, a gap still exists in understanding the response of these components within a complete system. Consequently, this study’s main objective is to investigate the influence of the diaphragm’s out-of-plane stiffness on the seismic response of RMSW buildings. In addition, the study aims to synthesize how this influence can be implemented in different seismic design approaches and assessment frameworks. To meet these objectives a two-story scaled asymmetrical RMSW building was tested under quasi-static cyclic loading. The analysis of the test results showed that the floor diaphragms’ out-of-plane stiffness played an important role in flexurally coupling the RMSW aligned along the loading direction with those walls orthogonal to it. This system-level aspect affected not only the different wall strength and displacement demands but also the failure mechanism sequence and the building twist response. The results of the study also showed that neglecting diaphragm flexural coupling influence on the RMSW at the system-level may result in unconservative designs and possibly undesirable failure modes. To address these findings, an analytical model was developed that can account for the aforementioned influences, in which, simplified load-displacement relationships were developed to predict RMSW component- and system-level responses under lateral seismic loads. This model is expected to give better predictions of the system response which can be implemented, within the model limitations, in forced- and displacement-based seismic design approaches. In addition, and in order to adapt to the increasing interest in more resilient buildings, this study presents an approach to calculate the system robustness based on the experimental data. Finally, literature shows that the vast majority of the loss models available for RMSW systems were based on individual component testing and/or engineering judgment. Consequently, this study proposes system damage states in lieu of component damage states in order to enhance the prediction capabilities of such models. The current dissertation highlights the significant influence of the diaphragm out-of-plane stiffness on the system-level response that may alter the RMSW response to seismic events; an issue that need to be addressed in design codes and standards. / Dissertation / Doctor of Philosophy (PhD)

Peptide-bound methionine may transfer oxidative damage from the thioether side chain to the peptide backbone, catalyzing decomposition in general and α-amidation in particular. In the present study, we focused on the reactivity and reaction pathways of peptides. We synthesized model peptides comprising methionine or not and investigated their overall tendency towards decomposition and formation of specific products under conditions mimicking the cooking process at 100°C in buffered solution (pH 6.0) in the presence of redox-active substances such as transition metal ions and reductones. Peptides containing methionine were more susceptible to α-amidation under all oxidative conditions, and the products of N-terminus-directed α-amidation were quantified. Exemplarily, after incubation in the presence of cupric sulfate, about 2.0 mol-% of the overall decomposition of Z-glycylmethionylglycine accounted for the formation of Z-glycinamide, whereas it was below 0.1 mol-% for Z-glycylalanylglycine. Surprisingly and different from previous observations, C-terminus-directed α-amidation was observed for the first time. From Z-glycylmethionylglycine, the respective products were formed in higher amounts than the N-terminus-directed α-amidation product Z-glycinamide under all applied oxidation conditions. The preference of electron transfer from the amino nitrogen bound in the peptide bond directed to the C-terminus may be ascribed to a sterically less demanding hexagonal 3-electron-2-center intermediate during methionine-catalyzed α-amidation.

The involvement of dynamical fluctuations in driving enzymatic processes is widely accepted. With respect to NQM tunnelling enzymes, the role of promoting motions in facilitating hydrogenic transfers is well studied. Few studies have however, specifically attributed, dedicated dynamical fluctuations characterised by their timescales and magnitudes, as a function of a reaction coordinate, to specific groups in a protein system. An effectively full suite of backbone resonance assignments were obtained for PETNR and on relevant ligand complexes. This provided an essential platform on which residue specific, backbone amide fluctuations were assessed. This thesis documents the application of pressure up to 1500 bar, in tandem with high resolution TROSY based NMR analysis, as a means of studying residue specific, conformer exchange perturbations. Residue specific amide compression profiles of the PETNR:FMN free enzyme system, and complexes with progesterone and tetrahydropyridine dinucleotides have been obtained. The binding of progesterone appears to induce conformational tightening of residues within the active site vicinity. The complexation of PETNR:FMN with tetrahydropyridine dinucleotides, appears to stimulate conformational shifts towards intermediate, and in some cases, slow exchange regimes in multiple residues about the active site vicinity. This is evidenced by extensive intensity attenuation of 1H-15N TROSY resonances, on the binding of tetrahydropyridine dinucleotides at 1 bar pressure, and on going from 1 bar to 1500 bar pressure. Multiple regions of sequence, spatially clustering about the active site vicinity within a 10 Å sphere of the FMN binding pocket, display appreciable sensitivity to ligand binding. Differential responses of residues to the application of high pressure between complexes was noted within segments of these regions. A region of sequence, named the β-hairpin flap displays significant differential compression profiles between the PETNR:FMN free enzyme system, and associated progesterone and tetrahydropyridine dinucleotide complexes. A role in mediating ligand engagement is proposed for R130 and R142 in the β-hairpin flap. A central hydrogen bonding network, perhaps constituting a putative proton wire in the active site of the PETNR:FMN:Progesterone complex, has been identified that could enable the shuttling of protons following catalytic protonation of oxidative substrate. The resonance response behaviour of G185 acts as a sensitive reporter on the formation of these interactions, revealed by an interrogation of the differences in chemical shift changes on progesterone binding, and in response to high pressure. The recruitment of high resolution crystallographic data sets readily supported a structural and dynamical interpretation of the observed chemical shift responses to ligand binding at 1 bar pressure, and on the application high pressure. A definitive atomistic identification of fast motion contribution to activation barrier compression was not obtained. Nevertheless, detailed, residue specific amide compression profiles, and shifts in backbone amide conformational exchange regimes in response to ground state ligand binding, and at high pressure, have been catalogued in the PETNR:FMN free enzyme system. These dynamical profiles in the free enzyme are contrasted against comparative, residue specific observations in analogue complexes of the oxidative and reductive half reactions of PETNR.