In this thesis, theoretical and computer simulation studies of vibrational phase relaxation in various molecular liquids are presented. That includes liquid nitrogen, both along the coexistence line and the critical isochore, binary liquid mixture and liquid water. The focus of the thesis is to understand the dependence of the vibrational relaxation on the density, temperature, composition and the role of different interactions among the molecules. The density fluctuation of the solute particles in a solvent is studied systematically, where the computer simulation results are compared with the mode coupling theory (MCT). The classical density functional theory (DFT) is used to study the vibrational relaxation dynamics in molecular liquids with an aim to understand the heterogeneous nature of the dynamics commonly observed in experiments. Chapter 1 contains a brief overview of the earlier relevant theories, their successes and shortcomings in the light of the problems discussed in this thesis. This chapter discusses mainly the basic features of the vibrational dynamics of molecular liquids and portrays some of the theoretical frameworks and formalisms which are widely recognized to have contributed to our present understanding. Vibrational dephasing of nitrogen molecules is known to show highly interesting anomalies near its gas–liquid critical point. In Chapter 2, we present the results of extensive computer simulation studies and theoretical analysis of the vibrational phase relaxation of nitrogen molecules both along the critical isochore and the gas–liquid coexistence line. The simulation includes the different contributions (density (ρ), vibration–rotation (VR), and resonant transfer (Rs)) and their cross–correlations. Following Everitt and Skinner, we have included the vibrational coordinate (q) dependence of the inter–atomic potential, which is found to have an important contribution. The simulated results are in good agreement with the experiments. The linewidth (directly proportional to the rate of the vibrational phase relaxation) is found to have a lambda shaped temperature dependence near the critical point. As observed in the experimental studies, the calculated lineshape becomes Gaussian–like as the critical temperature (Tc) is approached while being Lorentzian–like at the temperatures away from Tc. Both the present simulation and a mode coupling theory (MCT) analysis show that the slow decay of the enhanced density fluctuations near the critical point (CP), probed at the sub–picosecond timescales by the vibrational frequency modulation, and an enhanced vibration–rotation coupling, are the main causes of the observed anomalies. Dephasing time (тv) and the root mean square frequency fluctuation (Δ) in the supercritical region are calculated. The principal results are: 1. a crossover from a Lorentzian–like to a Gaussian–like lineshape is observed as the critical point is approached along the critical isochore, 2. the root mean square frequency fluctuation shows a non–monotonic dependence on the temperature along the critical isochore, 3. the temperature dependent linewidth shows a divergence–like (λ–shaped) behavior along the coexistence line and the critical isochore. It is found that the linewidth calculated from the time integral of the normal coordinate time correlation function (CQ(t)) is in good agreement with the known experimental results. The origin of the anomalous temperature dependence of linewidth can be traced to simultaneous effects of several factors, (i) the enhancement of the negative cross–correlations of ρ with VR and Rs and (ii) the large density fluctuations as the critical point (CP) is approached. Due to the negative cross–correlations of ρ with VR and Rs the total decay becomes faster (correlation times are in the femtosecond scale). The reason for the negative cross–correlation between ρ and VR is explored in detail. A mode coupling theory (MCT) analysis shows a slow decay of the enhanced density fluctuations near the critical point. The MCT analysis demonstrates that the large enhancement of VR–coupling near CP may arise from a non–Gaussian behavior of the equilibrium density fluctuations. This enters through a non–zero value of the triplet direct correlation function. Many of the complex systems found in nature and used routinely in industry are multi–component systems. In particular, binary mixtures are highly non–ideal and play an important role in the industry. The dynamic properties are strongly influenced by composition fluctuations which are absent in the one component liquids. In Chapter 3, isothermal–isobaric (NPT) ensemble molecular dynamics simulation studies of vibrational phase relaxation (VPR) in a model system are presented. The model considers strong attractive interaction between the dissimilar species to prevent phase separation. The model reproduces the experimentally observed non–monotonic, nearly symmetric, composition dependence of the dephasing rate. In addition, several other experimentally observed features, such as the maximum of the frequency modulation correlation time (т c) at a mole fraction near 0.5 and the maximum rate enhancement by a factor of about 3 above the pure component value, are also reproduced. The product of the mean square frequency modulation ((Δω2(0))) with тc indicates that the present model is in the intermediate regime of the inhomogeneous broadening. The non–monotonic composition (χ) dependence of тv is found to be primarily due to the non–monotonic χ dependence of тc, rather than due to a similar dependence in the amplitude of (Δω2(0)). The probability distribution of Δω shows a markedly non–Gaussian behavior at intermediate composition (χ - 0.5). We have also calculated the composition dependence of the viscosity (η∗) in order to explore the correlation between the viscosity with that of тv and тc. It is found that both the correlation times essentially follow the nature of the composition dependence of the viscosity. A mode coupling theory (MCT) analysis is presented to include the effects of the composition fluctuations in binary mixture. Water is an interesting and attractive object for research, not only because of its great importance in life processes but also due to its unusual and intriguing properties. Most of the anomalous properties of water are related to the presence of a three–dimensional network of hydrogen bonds, which is constantly changing at ultrafast, sub–picosecond timescales. Vibrational spectroscopy provides the means to study the dynamics of processes involving only certain chemical bonds. The dynamics of hydrogen bonding can be probed via its reflection on molecular vibrations, e.g., the stretching vibrational mode of the O–H bond. Recently developed femtosecond infrared vibrational spectroscopy has proved to be valuable to study water dynamics because of its unique temporal resolution. Recent studies have shown that the vibrational relaxation of the O–H stretch of HDO occurs at an extremely fast timescale with time constant being less than 100 femtosecond. Here, in Chapter 4, we investigate the origin of this ultrafast vibrational dephasing using computer simulation and appropriate theoretical analysis. In addition to the usual fast vibrational dynamics due to the hydrogen bonding excitations, we find two additional reasons: (a) the large amplitude of angular jumps of the water molecules (with 30–40 fs time intervals) provide large contribution to the mean square vibrational frequency and (b) the projected force along the O–H bond due to the solvent molecules, on the oxygen (FO(t)) and hydrogen (FH (t)) atoms of the O–H bond exhibit a large negative cross–correlation (NCC) between FO(t) and FH (t). This NCC is shown to be partly responsible for a weak, non–Arrhenius temperature dependence of the relaxation rate. In the concluding note, Chapter 5 starts with a brief summary of the outcome of this thesis and ends up with suggestions of a few relevant problems that may prove worthwhile to be addressed in the future.

Rheumatoid arthritis (RA) is an autoimmune inflammatory disease that leads to degradation of cartilage and bone mainly in peripheral joints. In collagen-induced arthritis (CIA), a mouse model for RA, activation of autoimmune CD4+ T cells depends on a molecular recognition system where T-cell receptors (TCRs) recognize a complex between the class II MHC Aq protein and CII259-273, a glycopeptide epitope from type II collagen (CII). Interestingly, vaccination with the Aq/CII259-273 complex can relieve symptoms and cause disease regression in mice. This thesis describes the use of modified glycopeptides to explore interactions important for binding to the Aq protein and recognition by autoimmune T-cell hybridomas obtained from mice with CIA. The CII259-273 glycopeptide was modified by replacement of backbone amides with different amide bond isosteres, as well as substitution of two residues that anchor the glycopeptide in prominent pockets in the Aq binding site. A three-dimensional structure of the Aq/glycopeptide complex was modeled to provide a structural basis for interpretation of the modified glycopeptide’s immunological activities. Overall, it was found that the amide bond isosteres affected Aq binding more than could be explained by the static model of the Aq/glycopeptide complex. Molecular dynamics (MD) simulations, however, revealed that the introduced amide bond isosteres substantially altered the hydrogen-bonding network formed between the N-terminal 259-265 backbone sequence of CII259-273 and Aq. These results indicated that the N-terminal hydrogen-bonding interactions follow a cooperative model, where the strength and presence of individual hydrogen bonds depended on the neighboring interactions. The two important anchor residues Ile260 and Phe263 were investigated using a designed library of CII259-273 based glycopeptides with substitutions by different (non-)natural amino acids at positions 260 and 263. Evaluation of binding to the Aq protein showed that there was scope for improvement in position 263 while Ile was preferred in position 260. The obtained SAR understanding provided a valuable basis for future development of modified glycopeptides with improved Aq binding. Furthermore, the modified glycopeptides elicited varying T-cell responses that generally could be correlated to their ability to bind to Aq. However, in several cases, there was a lack of correlation between Aq binding and T-cell recognition, which indicated that the interactions with the TCRs were determined by other factors, such as presentation of altered epitopes and changes in the kinetics of the TCR’s interaction with the Aq/glycopeptide complex. Several of the modified glycopeptides were also found to bind well to the human RA-associated DR4 protein and elicit strong responses with T-cell hybridomas obtained from transgenic mice expressing DR4 and the human CD4 co-receptor. This encourages future investigations of modified glycopeptides that can be used to further probe the MHC/glycopeptide/TCR recognition system and that also constitute potential therapeutic vaccines for treatment of RA. As a step towards this goal, three modified glycopeptides presented in this thesis have been identified as candidates for vaccination studies using the CIA mouse model.

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Orientador: Milton Dias Júnior / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Mecânica / Made available in DSpace on 2018-08-17T17:39:07Z (GMT). No. of bitstreams: 1 Simionatto_ViniciusGabrielSegala_M.pdf: 5623305 bytes, checksum: 1fa9e5b17f2a168dfa754ee947f53417 (MD5) Previous issue date: 2011 / Resumo: O desenvolvimento de novas tecnologias na área automotiva e as restrições cada vez mais apertadas com relação a emissões culminaram em veículos cada vez mais leves, silenciosos e potentes. Por este motivo, os trens de potência atuais são cada vez mais susceptíveis a fenômenos de NVH. Além disso, pelo fato de os motores atuais emitirem menor nível de ruído, alguns destes fenômenos tornam-se mais perceptíveis. Neste contexto se encaixa o trabalho atual. Sabe-se que muitos problemas desta área são solucionados realizando alterações no disco de embreagem, e por isto, neste trabalho estuda-se a influência dos parâmetros de seu pré amortecedor nos fenômenos de shuffle e clunk. São feitas análises do trem de potência linearizado, por este ser um procedimento muito comum na área de desenvolvimento deste sistema. Após isso, analisa-se o mesmo sistema, através de simulações numéricas, porém considerando não linearidades no disco de embreagem e nos engrenamentos, onde foi considerado o impact damping. Identifica-se os pares engrenados que mais contribuem para o surgimento do fenômeno de clunk, e a influência dos parâmetros do pré-amortecedor sobre ambos os fenômenos / Abstract: The development of new technologies on automotive engineering and the toughening emissions laws led to the design of lighter, more silent and more powerful vehicles. For this reason, today's powertrains are more prone to NVH phenomena. Furthermore, the noticeability of those phenomena is increased since newer engines produce lower noise levels. This is the subject in which this work fits into. It is known that many of the NVH phenomena can be attenuated by performing changes on the parameters of the clutch disc, and because of it, the influence of the parameters of the clutch damper on shuffle and clonk is studied in this work. For being a widely used procedure on the development of drivelines, a inear analysis is performed on a linearized model of a powertrain. After that, using umerical integration methods, further analyses are performed on a nonlinear model of the driveline, considering that the clutch disc and the gear meshes are nonlinearities. The latter's energy loss is modeled used impact damping. The geared pairs that contribute most for the clunk phenomenon are identified, and finally the influence of the parameters of the clutch damper on both phenomena are stated / Mestrado / Mecanica dos Sólidos e Projeto Mecanico / Mestre em Engenharia Mecânica

Orientador: Milton Dias Junior / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Mecânica / Made available in DSpace on 2018-08-22T19:22:01Z (GMT). No. of bitstreams: 1 RoldaoPerestrelo_LeandroTadeu_M.pdf: 15158370 bytes, checksum: 84a10bb14b3381b619db8ff9bb97be9c (MD5) Previous issue date: 2013 / Resumo: O resumo poderá ser visualizado no texto completo da tese digital / Abstract: The abstract is available with the full electronic document / Mestrado / Mecanica dos Sólidos e Projeto Mecanico / Mestre em Engenharia Mecânica

De nombreux processus biologiques liés aux membranes cellulaires lipidiques sont encore très mal connus. La présence d'eau et d'ions à l'interface influence les propriétés structurelles et dynamiques de la bicouche lipidique. Les techniques de fluorescence sont très utiles pour étudier les membranes en raison de la grande sensibilité des sondes à leur environnement. Nous avons utilisé la technique de relaxation de solvant (SR) pour explorer l'hydratation et la mobilité de l'eau. Nous avons également réalisé des calculs quantiques (QM) et des dynamiques moléculaires (DM) pour étayer nos expériences. Les résultats SR montrent qu'un petit cation (Na+) est très attiré par la membrane et augmente sa rigidité à l'opposé des cations (NH4+, Cs+) plus gros. Les anions (CI04-, SCN-) s'adsorbent à l'interface plus facilement que Cl-. Ces anions changent la mobilité et l'hydratation des têtes polaires des lipides de la bicouche. Les études SR de la zone hydrophobe de la membrane montrent que les processus de relaxation sont ici très complexes. lis reflètent des processus rapides intramoléculaire (relaxation de torsion, transferts de charge) et des processus intermoléculaires lents. Les calculs QM ont permis de créer les champs de force de trois sondes fluorescentes (Prodan, Laurdan et C-laurdan). Les simulations DM ont permis de déterminer les positions des sondes dans une membrane DOPC. La modélisation reproduit correctement les résultats SR, en particulier les temps de relaxation : de l'ordre de la ps en solvant aqueux et de la ns dans la membrane. Les simulations MD sont complémentaires des méthodes SR et permettent de surveiller le comportement de molécules uniques. / Many biologically important processes and phcnomena in lipid membranes are still not fully understood. The presence of ions and water molœules has a significant influence on the structural and dynamical properties of lipid bilayers. Fluorescent techniques are versatile tools for studying the lipid membranes, because the fluorescence emission is strongly sensitive to dye environment. We have conducted fluorescent solvent relaxation (SR) experiments to explore the hydration and mobility properties in lipid membranes in the presence of different chaotropic ions. We have also carried out Quantum Mechanical (QM) calculations and Molecular Dynamics (MD) simulations for supporting the SR experiments. SR experiments show that small cation (Na+) is attracted to the membrane and increases rigidity ofbilayer, while larger cations (NH/, Cs+) should not. Large anions (CI04·, SCN') adsorl, at the membrane interface more easily than smaller ones (Cl') and significantly change tl!e mobility and hydration of the headgroup region oflipid bilayer. SR study ofhydrophobic part of the membrane show that SR processes are complex there and reflect botl!: faster, intramolecular (torsional relaxation or fonnation of charge transfer state) and slower, intermolecular (SR) relaxation processes. QM calculatiom were used to create force-field for three fluorescent dyes (Prodan, Laurdan and C-laurdan). MD simulations allow detennining position of the dye in the lipid membrane in the ground state and after excitation and reproduce correctly SR timescale- ps in water and ns in the membrane. MD simulations extend the capabilities of SR method and allow observing the behaviour of individual molecules.

Concevoir un composant automobile et s’assurer que celui-ci atteindra un niveau de fiabilité cible requière une connaissance précise de la variabilité des chargements que ce composant est susceptible de rencontrer dans son environnement d’utilisation. La grande diversité des chargements appliqués à différents véhicules par différents clients, ou à un même véhicule tout au long de son historique d’utilisation, représente un défi statistique majeur. Généralement, l’acquisition d’information relative à la variabilité des chargements imposés aux composants des véhicules, repose sur la réalisation de campagnes de mesures. La complexité, la durée et le coût de telles campagnes limite naturellement la taille des échantillons statistiques constitués et les chargements enregistrés sont inévitablement dépendants du véhicule utilisé pour la mesure.Le travail présenté dans ce manuscrit explore la possibilité de changer fondamentalement d’approche, en se basant sur la simulation plutôt que sur la mesure et en concentrant l’effort d’analyse statistique non pas directement sur la variabilité des chargements mais sur la variabilité des facteurs qui les déterminent. Dans ce but, des modèles stochastiques sont proposés pour décrire l’évolution de la géométrie des surfaces de routes rencontrées par les véhicules ainsi que l’évolution de la vitesse à laquelle les conducteurs les parcourent. La caractérisation de la variabilité de ces facteurs est couplée à la notion de situations de vie. Ces dernières permettent de segmenter l’historique d’utilisation des véhicules, afin de faciliter l’analyse statistique de leur évolution au sein d’une population de clients. Pour finir, la réponse dynamique du véhicule à l’excitation générée par la route est déduite par la simulation.Des données statistiques relatives à la variabilité des facteurs de route et de vitesse sont évidemment nécessaires. L’information sur les routes parcourues peut par exemple être acquise à moindre coût au moyen d’une méthode d’estimation des profils de route proposée dans ce manuscrit. Cette information peut ensuite être exploitée afin de constituer, par la simulation, à un coût très faible et pour n’importe quel véhicule dont les caractéristiques sont connues, un échantillon d’historiques de chargements aussi important que souhaité. Cette méthodologie basée sur la simulation offre la possibilité d’analyser plus largement la variabilité des chargements de fatigue provenant de la route, l’influence des différents facteurs qui les déterminent ainsi que l’effet sur la fiabilité des composants du véhicule étudié. / In order to design vehicle components that will achieve a prescribed reliability target, it is imperative to possess a precise description of the variability of the loads to which such components may be subjected within the environment in which they are used. The strong diversity of the loads imposed on different vehicles by different customers, or on a particular vehicle throughout its life, constitutes a formidable statistical challenge. Generally, the acquisition of information about the load variability experienced by vehicle components is based on the use of load measurement campaigns. The complexity, duration and cost of such campaigns naturally limit the size of the statistical samples that may be collected. Moreover, the recorded load histories are inevitably dependent on the vehicle used for the measurements.The work presented within this manuscript explores the possibility of a fundamental change in the approach to load characterisation. The objective is to make use of simulation rather than measurements and focus statistical analysis efforts not directly on load variability itself but on the variability of the factors that determine such loads. Stochastic models are proposed to describe the evolution of the geometry of road surfaces covered by vehicles, as well as the evolution of vehicles’ speed on those road surfaces. The characterisation of the variability of such factors is performed in combination with the use of life situations. The latter may be employed to divide the load histories associated to different vehicles, within a population of customers, and analyse their variation more easily. Eventually, the dynamic response of the vehicle to the excitation imposed by the road can bederived through simulation.Statistical data on the variation of the road and speed factors obviously have to be acquired in order to apply the methodology. For example, road-related information may be obtained through the use of a road profile estimation algorithm proposed within the framework of this manuscript. Such information may then be exploited to constitute, through simulation, an arbitrarily large set of load histories at a very low cost and for any vehicle whose mechanical characteristics are known.The proposed methodology based on simulation enables us to study more extensively the variability of road-induced fatigue loads, the influence of the different factors that determine such loads, as well as the effect they have on the reliability of any considered vehicle component.

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.