Dimensional Stacking is a technique for displaying multivariate data in two dimensional screen space. This technique involves the discretization and recursive embedding of dimensions, each resulting N-dimensional bin occupying a unique position on the screen. This thesis describes the extension of this technique to a three dimensional projection. In addition to the visual enhancements, hashing was used to improve the scalability of records and dimensions. The resulting visualization was evaluated by a usability study.

O presente trabalho tem como objetivo a reconstrução da história evolutiva ao longo do Holoceno da planície costeira de cordões litorâneos estabelecidos sobre o vale fluvial do Rio Itabapoana/ES. A partir desse objetivo, foram realizadas as seguintes etapas metodológicas: Sensoriamento Remoto, Topografia, Geofísica e Geocronologia. Através da análise da imagem de satélite RapidEye, na composição colorida R5-G3-B1, foram discriminadas classes de cobertura vegetal. A relação entre a vegetação e o solo exposto proporcionou a identificação de três padrões distintos na planície costeira de cordões litorâneos. A obtenção de dados contínuos de altimetria através de um sistema global de navegação por satélite (GNSS), concentrado no caminhamento perpendicular à linha de costa, permitiu a elaboração e análise do perfil altimétrico dos cordões litorâneos, identificando-se três principais características: 1) nos primeiros 600 m tem-se um acréscimo na elevação; 2) em seguida, uma longa faixa “estável”, de pouca mudança na elevação; 3) por fim, o decréscimo da elevação nos últimos 500 m. Para caracterizar a arquitetura deposicional em subsuperfície dos cordões litorâneos, utilizou-se um Radar de Penetração no Solo (GPR) O registro obtido com GPR possibilitou a identificação de três padrões, representados pelas unidades retrogradacional e progradacional, onde o padrão de empilhamento compõe uma sequência de barreira regressiva ou progradante. Para a obtenção de uma relação cronoestratigráfica, seis amostras de sedimentos da fração arenosa de deposição eólica foram coletadas para a obtenção de idades absolutas a partir de Luminescência Opticamente Estimulada (LOE). Os cordões datados apresentaram idades holocênicas, com idades inferiores a 5.261 ± 396 anos. A integração dos resultados obtidos através dos métodos aplicados permitiu o reconhecimento de três padrões que levaram à interpretação de três fases decorrentes das variações do nível relativo do mar e do aporte sedimentar na evolução da planície. Essas fases representam os períodos de transgressão, regressão normal e regressão forçada. / The aim of this study is the reconstruction of the evolutionary history along the Holocene of the of beach ridges coastal plain established on the fluvial valley of Itabapoana River/ES. From this objective, the following methodological steps were performed: Remote Sensing, Topography, Geophysics and Geochronology. Through the analysis of the RapidEye satellite image, in the color composition R5-G3-B1, classes of vegetal cover were discriminated. The relationship between vegetation and exposed soil provided the identification of three distinct patterns of the beach ridges coastal plain. Obtaining continuous data of altimetry with a GNSS system, concentrated in the path perpendicular to the coastline, allowed the elaboration and analysis of the altimetric profile of the beach ridges. It was identified three main characteristics: 1) in the first 600 m there is an increase in elevation; 2) then along “stable” stretch, with little change in elevation; 3) lastly, the decrease of the elevation in the last 500 m. A Ground Penetrating Radar (GPR) was used to characterize the depositional architecture in the subsurface of the beach ridges The GPR record allowed the identification of three patterns, represented by the retrogradational and progradational units, in which the stacking pattern consists of a regressive or progradational barrier sequence. Six sediment samples of the sandy fraction of wind deposition were collected to obtain absolute ages from Optically Stimulated Luminescence (OSL). The dated ridges presented Holocene ages, with ages lower than 5,261 ± 396 years. The integration of the results obtained allowed the recognition of three patterns that led to the interpretation of three phases due to the variations of the relative sea level and the sedimentary budget in the evolution of the plain. These phases represent periods of transgression, normal regression and forced regression.

Carbohydrate-binding proteins play vital roles in many vital biological processes and study of these interactions, at residue level, are useful in treating many critical diseases. Analyzing the local sequential environments of the binding and non-binding regions to predict the protein-carbohydrate binding sites is one of the challenging problems in molecular and computational biology. Prediction of such binding sites, directly from sequences, using computational methods, can be useful to fast annotate the binding sites and guide the experimental process. Because the number of carbohydrate-binding residues is significantly lower than non-carbohydrate-binding residues, most of the methods developed are biased towards over predicting the non-carbohydrate-binding residues. Here, we propose a balanced predictor, called StackCBPred, which utilizes features, extracted from evolution-driven sequence profile, called the position-specific scoring matrix (PSSM) and several predicted structural properties of amino acids to effectively train a stacking-based machine learning method for the accurate prediction of protein-carbohydrate binding sites.

<p>This thesis is based on ten publications (Papers I-X). The phosphodiester backbone makes DNA or RNA to behave as polyelectrolyte, the pentose sugar gives the flexibility, and the aglycones promote the self-assembly or the ligand-binding process. The hydrogen bonding, stacking, stereoelectronics and hydration are few of the important non-covalent forces dictating the self-assembly of DNA/RNA. The pH-dependent thermodynamics clearly show (Papers I and II) that a change of the electronic character of aglycone modulates the conformation of the sugar moiety by the tunable interplay of stereoelectronic anomeric and <i>gauche</i> effects, which are further transmitted to steer the sugar-phosphate backbone conformation in a cooperative manner. 3'<i>-</i>anthraniloyl<b> </b>adenosine<b> </b>(a mimic of 3'-teminal CC<u>A</u>_OH of the aminoacyl-tRNA^Phe) binds to EF-Tu*GTP in preference over 2'<i>-</i>anthraniloyl<b> </b>adenosine<b>, </b>thereby showing (Paper III) that the 2’-<i>endo</i> sugar conformation is a more suitable mimic of the transition state geometry than the 3’<i>-endo</i> conformation in discriminating between correctly and incorrectly charged aminoacyl-tRNA^Phe by EF-Tu during protein synthesis. The presence of 2'-OH in RNA distinguishesit from DNA both functionallyas well as structurally. This work (Paper IV) provides straightforward NMR evidence to show that the 2'-OH is intramolecularly hydrogen bonded with the vicinal 3'-oxygen, and the exposure of the 3'<i>-</i>phosphate of the ribonucleotides to the bulk water determines the availability of the bound water around the vicinal 2'-OH, which then can play various functional role through inter- or intramolecular interactions. The pH-dependent ¹H NMR study with nicotinamide derivatives demonstrates (Paper V) that the cascade of intramolecular cation (pyridinium)-π(phenyl)-CH(methyl) interaction in edge-to-face geometry is responsible for perturbing the p<i>K</i>_a of the pyridine-nitrogen as well as for the modulation of the aromatic character of the neighboring phenyl moiety, which is also supported by the T₁ relaxation studies and <i>ab initio</i> calculations. It has been found (Papers VI-IX) that the variable intramolecular electrostatic interaction between electronically coupled nearest neighbor nucleobases (steered by their respective microenvironments) can modulate their respective pseudoaromatic characters. The net result of this pseudoaromatic cross-modulation is the creation of a unique set of aglycones in an oligo or polynucleotide, whose physico-chemical properties are completely dependent upon the propensity and geometry of the nearest neighbor interactions (extended genetic code). The propagation of the interplay of these electrostatic interactions across the hexameric ssDNA chain is considerably less favoured (effectively up to the fourth nucleobase) compared to that of the isosequential ssRNA (up to the sixth nucleobase). The dissection of the relative strength of basepairing and stacking in a duplex shows that stability of DNA-DNA duplex weakens over the corresponding RNA-RNA duplexes with the increasing content of A-T/U base pairs, while the strength of stacking of A-T rich DNA-DNA duplex increases in comparison with A-U rich sequence in RNA-RNA duplexes (Paper X).</p>

<p>This thesis is based on nine research publications (<b>I – IX</b>) on structure and reactivity of RNA vis-à-vis DNA. The DNA and RNA are made of flexible pentose sugar units, polyelectrolytic phosphodiester backbone, and heterocyclic nucleobases. DNA stores our genetic code, whereas RNA is involved both in protein biosynthesis and catalysis. Various ligand-binding and recognition properties of DNA/RNA are mediated through inter- and intra-molecular H-bonding and stacking interactions, beside hydration, van der Waal and London dispersion forces. In this work the pH dependant chemical shift, p<i>K</i>_a values of 2'-OH group as well as those the nucleobases in different sequence context, alkaline hydrolysis of the internucleotidic phosphodiester bonds and analysis of NOESY footprints along with NMR constrained molecular dynamics simulation were used as tools to explore and understand the physico-chemical behavior of various nucleic acid sequences, and the forces involved in their self-assembly process. <b>Papers I – II</b> showed that the ionization of 2'-OH group is nucleobase-dependant. <b>Paper III</b> showed that the chemical characters of internucleotidic phosphate are non-identical in RNA compared to that of DNA. <b>Papers IV – VI</b> show that variable intramolecular electrostatic interactions between electronically coupled nearest neighbor nucleobases in a ssRNA can modulate their respective pseudoaromatic character, and result in creation of a unique set of aglycons with unique properties depending on propensity and geometry of nearest neighbor interaction. <b>Paper VII</b> showed that the cross-modulation of the pseudoaromatic character of nucleobases by the nearest neighbor is sequence-dependant in nature in oligonucleotides. <b>Paper VIII</b> showed that the purine-rich hexameric ssDNA and ssRNA retain the right-handed helical structure (B-type in ssDNA and A-type in ssRNA) in the single-stranded form even in absence of intermolecular hydrogen bonding. The directionality of stacking geometry however differs in ssDNA compared to ssRNA. In ssDNA the relatively electron-rich imidazole stacks above the electron-deficient pyrimidine in the 5' to 3' direction, in contradistinction, the pyrimidine stacks above the imidazole in the 5' to 3' direction in ssRNA. <b>Paper IX</b> showed that the p<i>K</i>_a values of the nucleobases in monomeric nucleotides can be used to show that a RNA-RNA duplex is more stable than a DNA-DNA duplex. The dissection of the relative strength of base-pairing and stacking showed that the relative contribution of former compared to that of the latter in an RNA-RNA over the corresponding DNA-DNA duplexes decreases with the increasing content of A-T/U base pairs in a sequence.</p>

This thesis is based on ten publications (Papers I-X). The phosphodiester backbone makes DNA or RNA to behave as polyelectrolyte, the pentose sugar gives the flexibility, and the aglycones promote the self-assembly or the ligand-binding process. The hydrogen bonding, stacking, stereoelectronics and hydration are few of the important non-covalent forces dictating the self-assembly of DNA/RNA. The pH-dependent thermodynamics clearly show (Papers I and II) that a change of the electronic character of aglycone modulates the conformation of the sugar moiety by the tunable interplay of stereoelectronic anomeric and gauche effects, which are further transmitted to steer the sugar-phosphate backbone conformation in a cooperative manner. 3'-anthraniloyl<b> </b>adenosine<b> </b>(a mimic of 3'-teminal CC<u>A</u>OH of the aminoacyl-tRNAPhe) binds to EF-Tu*GTP in preference over 2'-anthraniloyl<b> </b>adenosine<b>, </b>thereby showing (Paper III) that the 2’-endo sugar conformation is a more suitable mimic of the transition state geometry than the 3’-endo conformation in discriminating between correctly and incorrectly charged aminoacyl-tRNAPhe by EF-Tu during protein synthesis. The presence of 2'-OH in RNA distinguishes it from DNA both functionally as well as structurally. This work (Paper IV) provides straightforward NMR evidence to show that the 2'-OH is intramolecularly hydrogen bonded with the vicinal 3'-oxygen, and the exposure of the 3'-phosphate of the ribonucleotides to the bulk water determines the availability of the bound water around the vicinal 2'-OH, which then can play various functional role through inter- or intramolecular interactions. The pH-dependent 1H NMR study with nicotinamide derivatives demonstrates (Paper V) that the cascade of intramolecular cation (pyridinium)-π(phenyl)-CH(methyl) interaction in edge-to-face geometry is responsible for perturbing the pKa of the pyridine-nitrogen as well as for the modulation of the aromatic character of the neighboring phenyl moiety, which is also supported by the T1 relaxation studies and ab initio calculations. It has been found (Papers VI-IX) that the variable intramolecular electrostatic interaction between electronically coupled nearest neighbor nucleobases (steered by their respective microenvironments) can modulate their respective pseudoaromatic characters. The net result of this pseudoaromatic cross-modulation is the creation of a unique set of aglycones in an oligo or polynucleotide, whose physico-chemical properties are completely dependent upon the propensity and geometry of the nearest neighbor interactions (extended genetic code). The propagation of the interplay of these electrostatic interactions across the hexameric ssDNA chain is considerably less favoured (effectively up to the fourth nucleobase) compared to that of the isosequential ssRNA (up to the sixth nucleobase). The dissection of the relative strength of basepairing and stacking in a duplex shows that stability of DNA-DNA duplex weakens over the corresponding RNA-RNA duplexes with the increasing content of A-T/U base pairs, while the strength of stacking of A-T rich DNA-DNA duplex increases in comparison with A-U rich sequence in RNA-RNA duplexes (Paper X).

Electrochemical detection of metals can be done at polycrystalline gold ultramicroelectrodes using repetitive cyclic voltammetry (RCV), a detection method sharing some similarities with anodic stripping voltammetry (ASV). Each cycle of the potential waveform for RCV involves application of a negative preconcentration potential (for 50 to 300 ms) followed by a cyclic voltammetry (CV) scan at 20 to 1000 V/s. The response due to the metals is evident at potentials negative of the region for oxide formation in the resulting CVs. Metals are deposited at the Au surface by underpotential deposition (UPD) processes. Any metal that can be analyzed by RCV could potentially be quantified using UPD-ASV at Au (rather than by ASV at Hg). The UPD kinetics of Pb and Cu at polycrystalline Au were examined by setting kinetic parameters (rate constant, symmetry factor, and electrosorption valency) within a simulation program used to generate simulated CVs. Reasonably good agreement between experimental and simulated CVs was possible using the simulation, with the same kinetic parameters used to generate simulated CVs to match experimental CVs over a range of sweep rates for each system. Using this method, the following rate constants (k) were estimated: for UPD of Cu in H2SO4 and HClO4, ks ~ 36000 s−1 and 11000 s−1, respectively, and for UPD of Pb in H2SO4, ks ~ 400000 s−1. <p> Repetitive cyclic voltammetry was applied to the detection of metals separated by capillary electrophoresis. Separation of Tl+, Cd2+, Cu2+, Pb2+, Zn2+, Ni2+, Co2+ and Mn2+ was demonstrated in 0.01 mol/L acetic acid and 0.01 mol/L ammonium acetate(pH ~ 4.6) using RCV. While stacking is commonly exploited for sensitivity enhancement during injection, it was shown that detection-end stacking is also useful. A novel technique named electrophoretic extraction (EE) was developed for analysis of particle-containing solutions (e.g. soil extracts or other colloidal suspensions). EE involves application of backpressure during CE to prevent particles from entering the separation capillary: the applied pressure is regulated so analyte ions enter the capillary and migrate to the detector, whereas other particles are prevented from entering the capillary. The feasibility of this approach was demonstrated.

Interchain interactions between π-systems have a strong effect on the properties of conjugated organic materials that find application in devices such as light emitting diodes (OLEDs), organic photovoltaics (OPVs), and field effect transistors (FETs). We have prepared covalently-stacked oligo(1,4-phenylene ethynylene)s and oligo(1,4-phenylene vinylene)s to study the influence of chain-chain interactions on the electronic structure of closely packed conjugated units. These serve as models for segments of conjugated materials in thin film devices. Extension of this concept has allowed us to prepare multi-tiered systems that display the influence of pi-stacking. The stacked architectures were prepared by multi-step synthesis of the scaffolds, followed by metal-catalyzed cross coupling reactions (Sonogashira, Heck, Suzuki couplings) to incorporate the conjugated oligomers. The optical and electrochemical properties of these stacked compounds and polymers were compared to their unstacked linear counterparts. These studies provide a platform for the exploration of the nature of charge carriers and excitons in a broad class of materials that have significant potential in addressing challenges in power generation, lighting and electronics.

This thesis consists of seven research publications concerning (i) pKa studies of nucleobases in model nucleotides to understand why RNA duplexes are more stable than DNA duplexes (Paper I), (ii) the role of Me(T)-π interactions in the relative stability of DNA-RNA heteroduplexes (Paper II), (iii) pKa measurements in nucleotides with different 2′-substituents (paper III), (iv) a conformation study of constrained sugars and a pKa study of 1-thyminyl to reveal effect of sugar constraints on the pKa of the nucleobase (paper IV), (v) NMR and MD studies of 1′, 2′-oxetane constrained thymidine incorporated Dickerson Drew dodecamer (paper V), (vi) the sequence dependent pKa perturbation of 9-guaninyl moeity in single stranded (ss) DNA and RNA (paper VI), (vii) the non identical chemical nature of internucleotidic phosphates in (ss) RNA using 31P NMR (paper VI), and an alkaline hydrolysis study of phosphodiesters in ssRNAs (paper VII). The architecture of DNA and RNA molecules is determined by (a) hydrogen bonding (b) base stacking (c) a variety of additional non-covalent interactions. In paper (I) we showed that A-U and G-C base pairings in RNA are more stable than A-T and G-C base pairings in DNA by 4.3 and 1 kJ mol-1 respectively. Me(T)-π interaction plays a dominant role in the relative stability of DNA-RNA duplexes (paper II). In paper III and IV, we have shown that 1′ , 2′- oxetane and azetidine rings have strong inductive effect on pyrimidine bases, and that the H2′-sugar proton can be the marker to understand the pseudoaromaticity of pyrimidine bases, as well as increasing constraints in sugar reducing the basicity of nucleobases. A 1′, 2′-oxetane locked thymidine (T) moiety deforms the local structure of Dickerson-Drew dodecamer, d(CGCGAATTCGCG)2- investigated by High resolution NMR and MD study, as is discussed in the paper V. In papers VI and VII, we showed sequence context dependent pKa (N1) of 9-guaninyl perturbation in (ss) DNAs and RNAs and the non identical chemical nature of inter-nucleotidic phosphate groups in single stranded RNAs.

Global increase in energy consumption and global warming require more energy production but less CO2emission. Increase in efficiency of energy production is an effective way for this purpose. This can be reached by increasing boiler temperature and pressure in a biomass power plant. By increasing material temperature 50°C, the efficiency in biomass power plants can be increased significantly and the CO2emission can be greatly reduced. However, the materials used for future biomass power plants with higher temperature require improved properties. Austenitic stainless steels are used in most biomass power plants. In austenitic stainless steels a phenomenon called dynamic strain aging (DSA), can occur in the operating temperature range for biomass power plants. DSA is an effect of interaction between moving dislocations and solute atoms and occurs during deformation at certain temperatures. An investigation of DSA influences on ductility in austenitic stainless steels and nickel base alloys have been done. Tensile tests at room temperature up to 700°C and scanning electron microscope investigations have been used. Tensile tests revealed that ductility increases with increased temperature for some materials when for others the ductility decreases. This is, probably due to formation of twins. Increased stacking fault energy (SFE) gives increased amount of twins and high nickel content gives a higher SFE. Deformation mechanisms observed in the microstructure are glide bands (or deformations band), twins, dislocation cells and shear bands. Damage due to DSA can probably be related to intersection between glide bands or twins, see figure 6 a). Broken particles and voids are damage mechanisms observed in the microstructure.