Made available in DSpace on 2014-12-17T15:15:02Z (GMT). No. of bitstreams: 1 FabioFM.pdf: 1459636 bytes, checksum: 4f2bb557c6a5bddb80e46f325bd5b4dd (MD5) Previous issue date: 2004-12-03 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / In this work we study the spectrum (bulk and surface modes) of exciton-polaritons in infinite and semi-infinite binary superlattices (such as, ???ABABA???), where the semiconductor medium (A), whose dielectric function depends on the frequency and the wavevector, alternating with a standard dielectric medium B. Here the medium A will be modeled by a nitride III-V semiconductor whose main characteristic is a wide-direct energy gap Eg. In particular, we consider the numerical values of gallium nitride (GaN) with a crystal structure wurtzite type. The transfer-matrix formalism is used to find the exciton-polariton dispersion relation. The results are obtained for both s (TE mode: transverse electric) and p (TM mode: transverse magnetic) polarizations, using three diferent kind of additional boundary conditions (ABC1, 2 e 3) besides the standard Maxwell's boundary conditions. Moreover, we investigate the behavior of the exciton-polariton modes for diferent ratios of the thickness of the two alternating materials forming the superlattice. The spectrums shows a confinement of the exciton-polariton modes due to the geometry of the superlattice. The method of Attenuated Total Reflection (ATR) and Raman scattering are the most adequate for probing this excitations / Neste trabalho estudamos o espectro (modos de volume e de superf?cie) dos polaritons de exciton em uma super-rede bin?ria infinita e semi-infinita (tal como, ???ABABA???), onde um meio semicondutor (A), cuja fun??o diel?trica depende da frequ?ncia e do vetor de onda, alterna-se com um diel?trico comum (B). Aqui, o meio A ser? modelado por um semicondutor da fam?lia dos nitretos (semicondutor III-V) que tem como caracter?stica principal um gap de energia (Eg) direto e largo. Em particular, consideramos os valores num?ricos para o nitreto de g?lio (GaN) com uma estrutura cristalina tipo wurtzite. A t?cnica da matriz de transfer?ncia ? utilizada para encontrarmos a rela??o de dispers?o do polariton de exciton. Os resultados s?o obtidos para os modos de polariza??o s (ou modo TE: transversal el?trico) e p (ou modo TM: transversal magn?tico), usando tr?s diferentes condi??es de contorno adicionais (ABC1, 2 e 3), mais as condi??es de contorno padr?es de Maxwell. Al?m disso, investigamos o comportamento dos modos do polariton de exciton para diferentes raz?es entre as espessuras das camadas dos dois materiais que comp?em a super-rede Os espectros encontrados evidenciam um comportamento de confinamento dos polaritons de exciton devido ?s geometrias empregadas. As t?cnicas experimentais ATR ("Attenuated Total Reflection") e o espalhamento Raman s?o as mais adequadas para a caracteriza??o dessas excita??es

This essay examines and juxtaposes Mario Jori’s and Frederick Schauer’s ideas on legal formalism. Although developed independently of each other, these ideas show remarkable similarities: both focus on the notion of norm or rule as a tool for clarifying the notion of legal formalism; both defend legal formalism from the criticisms routinely moved against it. The author maintains that Jori’s and Schauer’s theories may contribute to shed light on (and criticize) the controversial notion of defeasibility of legal rules; they may also contribute to scale down, from a legal-theoretical point of view, the novelties of contemporary constitutional orders; finally, it may help to better understand their working machinery. / In questo saggio vengono esaminate e messe a confronto le idee di Mario Jori e di Frederick Schauer in tema di formalismo giuridico. Pur essendo state elaborate l’una indipendentemente dall’altra, presentano notevoli somiglianze, perché entrambe usano la nozione di norma o regola come punto focale per chiarire la nozione di formalismo giuridico, e perché entrambe difendono quest’ultimo dalle critiche usualmente rivolte ad esso. L’autrice ritiene che l’esame delle idee dei due autori possa contribuire a chiarire (e criticare) la controversa nozione di defeasibility delle norme giuridiche e possa altresì, in via generale, contribuire a ridimensionare, dal punto di vista teorico-giuridico, le novità del diritto degli odierni Stati costituzionali, oltre che a comprenderne meglio i meccanismi di funzionamento. / En este trabajo se examina y compara las ideas de Mario Jori y de Frederick Schauer en relación con el formalismo jurídico. A pesar de haber sido desarrolladas de forma independiente unas de las otras, dichas ideas presentan notables semejanzas ya que ambos autores utilizan el concepto de una norma o regla como punto focal para aclarar la noción de formalismo jurídico, y porque ambos lo defienden de las críticas que usualmente se le dirigen. La autora considera que el examen de las ideas de los dos autores puede contribuir a aclarar (y criticar) la controvertida noción de defeasibility (derrotabilidad) de las normas jurídicas y, de modo general, también a redimensionar, desde el punto de vista teórico-jurídico, las novedades que presentan los derechos de los modernos Estados constitucionales, y comprender mejor los mecanismos de su funcionamiento.

La Physique des Hautes Densités d’Énergies (HEDP) est caractérisée par desécoulements multi-matériaux fortement compressibles. Le domaine contenant l’écoulementsubit de grandes variations de taille et est le siège d’ondes de chocs et dedétente intenses. La représentation Lagrangienne est bien adaptée à la descriptionde ce type d’écoulements. Elle permet en effet une très bonne description deschocs ainsi qu’un suivit naturel des interfaces multi-matériaux et des surfaces libres.En particulier, les schémas Volumes Finis centrés Lagrangiens GLACE (GodunovtypeLAgrangian scheme Conservative for total Energy) et EUCCLHYD (ExplicitUnstructured Cell-Centered Lagrangian HYDrodynamics) ont prouvé leur efficacitépour la modélisation des équations de la dynamique des gaz ainsi que de l’élastoplasticité.Le travail de cette thèse s’inscrit dans la continuité des travaux de Maireet Nkonga [JCP, 2009] pour la modélisation de l’hydrodynamique et des travauxde Kluth et Després [JCP, 2010] pour l’hyperelasticité. Plus précisément, cettethèse propose le développement de méthodes robustes et précises pour l’extension3D du schéma EUCCLHYD avec une extension d’ordre deux basée sur les méthodesMUSCL (Monotonic Upstream-centered Scheme for Conservation Laws) et GRP(Generalized Riemann Problem). Une attention particulière est portée sur la préservationdes symétries et la monotonie des solutions. La robustesse et la précision duschéma seront validées sur de nombreux cas tests Lagrangiens dont l’extension 3Dest particulièrement difficile. / High Energy Density Physics (HEDP) flows are multi-material flows characterizedby strong shock waves and large changes in the domain shape due to rarefactionwaves. Numerical schemes based on the Lagrangian formalism are good candidatesto model this kind of flows since the computational grid follows the fluid motion.This provides accurate results around the shocks as well as a natural tracking ofmulti-material interfaces and free-surfaces. In particular, cell-centered Finite VolumeLagrangian schemes such as GLACE (Godunov-type LAgrangian scheme Conservativefor total Energy) and EUCCLHYD (Explicit Unstructured Cell-CenteredLagrangian HYDrodynamics) provide good results on both the modeling of gas dynamicsand elastic-plastic equations. The work produced during this PhD thesisis in continuity with the work of Maire and Nkonga [JCP, 2009] for the hydrodynamicpart and the work of Kluth and Després [JCP, 2010] for the hyperelasticitypart. More precisely, the aim of this thesis is to develop robust and accurate methodsfor the 3D extension of the EUCCLHYD scheme with a second-order extensionbased on MUSCL (Monotonic Upstream-centered Scheme for Conservation Laws)and GRP (Generalized Riemann Problem) procedures. A particular care is taken onthe preservation of symmetries and the monotonicity of the solutions. The schemerobustness and accuracy are assessed on numerous Lagrangian test cases for whichthe 3D extensions are very challenging.

Le thème de cette thèse est les différents aspects de la théorie de Borel-Moore dans le monde motivique. Classiquement, sur le corps des nombres complexes, l’homologie de Borel-Moore, aussi appelée “homologie à support compact”, possède des propriétés assez différentes comparée avec l’homologie singulière. Dans cette thèse on étudiera quelques généralisations et applications de cette théorie dans les catégories triangulées de motifs.La thèse est composée de deux parties. Dans la première partie on définit l'homologie motivique de Borel-Moore dans les catégories triangulées de motifs mixtes définies par Cisinski et Déglise et étudie ses diverses propriétés fonctorielles, tout particulièrement une fonctorialité analogue au morphisme de Gysin raffiné défini par Fulton. Ces résultats nous serviront ensuite à identifier le coeur de la structure de poids de Chow définie par Hébert et Bondarko: il se trouve que le coeur, autrement dit la catégorie des éléments de poids zéro, est équivalente à une version relative des motifs purs de Chow sur une base définie par Corti et Hanamura.Dans la deuxième partie on démontre la représentabilité de la G-théorie de Quillen, sous la reformulation de Thomason, dans un premier temps dans la catégorie A1-homotopique des schémas de Morel-Voevodsky, mais aussi dans la catégorie homotopique stable construite par Jardine. On établit une identification de celle-ci comme la théorie de Borel-Moore associée à la K-théorie algébrique, en utilisant le formalisme des six foncteurs établi par Ayoub et Cisinski-Déglise. / The theme of this thesis is different aspects of Borel-Moore theory in the world of motives. Classically, over the field of complex numbers, Borel-Moore homology, also called “homology with compact support”, has some properties quite different from singular homology. In this thesis we study some generalizations and applications of this theory in triangulated categories of motives.The thesis is composed of two parts. In the first part we define Borel-Moore motivic homology in the triangulated categories of mixed motives defined by Cisinski and Déglise and study its various functorial properties, especially a functoriality similar to the refined Gysin morphism defined by Fulton. These results are then used to identify the heart of the Chow weight structure defined by Hébert and Bondarko: it turns out that the heart, namely the category of elements of weight zero, is equivalent to a relative version of pure Chow motives over a base defined by Corti and Hanamura.In the second part we show the representability of Quillen’s G-theory, reformulated by Thomason, firstly in the A1-homotopy category of schemes of Morel-Voevodsky, but also in the stable homotopy category constructed by Jardine. We establish an identification of G-theory as the Borel-Moore theory associated to algebraic K-theory, by using the six functors formalism settled by Ayoub and Cisinski-Déglise.

This study aims to defend value formalism, like the formalism useful to the procedure as a means of achieving a fair process. For both historical analysis is made of the jurisdiction under the focus of the power conferred on the Judge from the Roman State to the present day. Takes the postwar constitutionalism as a starting point to treat the state as insurer of the fundamental rights of the citizen and as a provider of public policies. The process no longer seen as a mere tool in the service of the right stuff and will be recognized as a fundamental constitutional guarantee, as applied constitutional law. To do so, we start a process permeated by formalism-excessive in search of a value formalism emptying into the necessary balance or balance between the principles of effectiveness and legal certainty. Shows the need and possibility to change the paradigm of legal positivism to the model of principles and rules, as well as the possibility of dialogue in the countries of civil law institutes the common law. Search on the judicial activism the means to achieve the necessary flexibility procedural, either by technical management of litigation, the principle of elasticity, the use of axiological and ontological gaps as well as the principle of proportionality. All analysis aims to find solutions to reach decisions fairer and according with the democratic rule of law. / O presente estudo tem por objetivo defender o formalismo-valorativo, ou seja, o formalismo útil ao procedimento, como meio de se alcançar um processo justo. Para tanto é feita a análise histórica da jurisdição sob o enfoque do poder conferido ao Juiz desde o Estado Romano até os dias atuais. Toma-se o constitucionalismo do pósguerra como ponto de partida para tratar do Estado como assegurador dos direitos fundamentais do cidadão e como provedor das políticas públicas. O processo deixa de ser visto como mero instrumento a serviço do direito material e passa a ser reconhecido como uma garantia constitucional fundamental, como direito constitucional aplicado. Para tanto, parte-se de um processo permeado por um formalismo-excessivo em busca de um formalismo-valorativo a desaguar no necessário equilíbrio ou ponderação entre os princípios da efetividade e segurança jurídica. Mostra-se a necessidade e possibilidade de mudança do paradigma do positivismo jurídico para o modelo de princípios e regras, como também a possibilidade de diálogo nos países da civil law de institutos da common law. Buscase no ativismo judicial o meio de concretizar a necessária flexibilização procedimental, seja pela técnica de gerenciamento de processos judiciais, pela aplicação do princípio da elasticidade, do uso das lacunas axiológicas e ontológicas, bem como do princípio da proporcionalidade. Toda a análise visa buscar soluções para o alcance de decisões mais justas e consetâneas com o Estado Democrático de Direito.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-10-11T14:36:57Z No. of bitstreams: 1 rafaelleitefernandes.pdf: 279997 bytes, checksum: 10717a2d36ac106c7c879c22dcad130e (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-10-16T13:49:39Z (GMT) No. of bitstreams: 1 rafaelleitefernandes.pdf: 279997 bytes, checksum: 10717a2d36ac106c7c879c22dcad130e (MD5) / Made available in DSpace on 2017-10-16T13:49:39Z (GMT). No. of bitstreams: 1 rafaelleitefernandes.pdf: 279997 bytes, checksum: 10717a2d36ac106c7c879c22dcad130e (MD5) Previous issue date: 2017-03-08 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Neste trabalho vamos analisar as contribuições da não-comutatividade nos modelos eletrodinâmicos de Proca e Podolsky. O modelo de Proca não-comutativo (NC) é originalmente não invariante perante transformações de calibre. Neste trabalho obteremos, através do método chamado "gauge unfixing" (GU), uma hamiltoniana invariante por transformações de calibre. Em seguida, vamos estudar a versão NC do modelo eletro-dinâmico de Podolsky. Utilizando o produto Moyal e o mapeamento de Seiberg-Witten, encontraremos uma lagrangeana para o modelo de Podolsky no espaço-tempo NC e, a partir daí, analisaremos as contribuições da não-comutatividade para tal modelo. O primeiro aspecto importante é a invariância de calibre. O modelo de Podolsky é originalmente invariante de calibre porém, no espaço-tempo NC, a lagrangeana não é invariante perante as mesmas tranformações. Utilizando o método de Noether, encontraremos uma ação dual invariante de calibre e as simetrias serão calculadas. Em seguida é feita a quantização do modelo de Podolsky NC através de dois métodos, o método de Dirac e o método de Faddev-Jackiw. Uma comparação será feita entre os dois métodos. / In this work we will analyse the contributions of non-commutative (NC) to the Proca electrodynamics and also Podolsky's electrodynamics. The NC Proca model is originally not gauge invariant. Here we find, through the gauge unfixing method, a gauge invariant Hamiltonian. With respect to the Podolsky model, we used de Moyal product and the Seiberg-Witten map to analyze the NC contributions to this model. The first important aspect is the gauge invariance. The Podolky model is originally gauge invariant, however, in NC space the Lagrangian in not gauge invariant through the same transformations. Using the Noether method, we find a dual action gauge invariant and we calculate the symmetries. Then, we make the quantization for the NC Podolsky model through two formalism: the Dirac and the Faddev-Jackiw. A comparison is make between this two methods.

Une idée particulière de littérature est née au cours des XVIIIe et XIXe siècles, période qui coïncide avec la naissance du genre romanesque moderne. L’idée de roman moderne issue de ces transformations à cette époque-là configure un champ virtuel de caractéristiques qui a marqué aussi bien la théorie littéraire du XXe siècle que la production de textes. Cette recherche pose la question de la vitalité de cette idée de roman moderne et, par voie de conséquence, de la notion de littérature qu’elle suppose. Nous proposons donc une étude de l’idée de roman au sein des poétiques de trois auteurs hispano-américains contemporains : Juan José Saer, Ricardo Piglia et Roberto Bolaño. Cette étude tient compte autant d’aspects théoriques que formels et se concentre sur les essais et les entretiens des auteurs, ainsi que sur trois romans : La grande, La ciudad ausente et 2666. Nous postulons ainsi une lecture comparée à partir de l’indétermination, du rapport à l’expérience et de la réflexivité, considérés comme traits principaux de l’idée de roman moderne, ainsi qu’une analyse des trois romans à partir de leurs formes narratives, réflexives et hybrides. / A particular idea of literature was born during the 18th and 19th centuries, a period that corresponds with the rise of the modern novel genre. The idea of the modern novel, which came about during this time period, constitutes a virtual field of characteristics that has left its mark on both 20th century literary theory and on textual production. This research questions the vitality of this particular idea of the modern novel and, therefore, of the notion of literature it withholds. Our aim then, is to study the idea of the novel as it is expressed in the poetics of three contemporary Latin American writers: Juan José Saer, Ricardo Piglia and Roberto Bolaño. This study considers theoretical aspects as well as formal ones, focusing on essays and interviews of the three authors, as well as on three novels: La grande, La ciudad ausente and 2666.It presents a comparative reading of these poetics according to three main concepts: indetermination, relation to experience and reflexivity, which we think to be central to the idea of the modern novel. In addition, this study analyzes the three novels in terms of their narrative, reflexive and hybrid forms.

This thesis presents the work done on electronic transport in various interacting and non-interacting systems in one and two dimensions. The systems under study are: an interacting quantum dot [1], a non-interacting quantum wire and a ring in which time-dependent potentials are applied [2], an interacting quantum wire and networks of multiple quantum wires with resistive regions [3, 4], one-dimensional edge stages of a two-dimensional topological insulator [5], and a hybrid system of two-dimensional surface states of a three-dimensional topological insulator and a superconductor [6]. In the first chapter, we introduce a number of concepts which are used in the rest of the thesis, such as scattering theory, Landauer conductance formula, quantum wires, bosonization, topological insulators and superconductor. In the second chapter, we study transport through a quantum dot with interacting electrons which is connected to two reservoirs. The quantum dot is modeled by two sites within a tight-binding model with spinless electrons. Using the Lippman-Schwinger method, we write down an exact two-particle wave function for the dot-reservoir system with the interaction localized in the region of the dot. We discuss the phenomena of two-particle resonance and rectification. In the third chapter, we study pumping in two kinds of one-dimensional systems: (i) an infinite line connected to reservoirs at the two ends, and (ii) an isolated ring. The infinite line is modeled by the Dirac equation with two time-independent point-like backscatterers that create a resonant barrier. We demonstrate that even if the reservoirs are at the same chemical potential, a net current can be driven through the channel by the application of one or more time-dependent point-like potentials. When the left-right symmetry is broken, a net current can be pumped from one reservoir to the other by applying a time-varying potential at only one site. For a finite ring, we model the system by a tight-binding model. The ring is isolated in the sense that it is not connected to any reservoir or environment. The system is driven by one or more time-varying on-site potentials. We develop an exact method to calculate the current averaged over an infinite amount of time by converting it to the calculation of the current carried by certain states averaged over just one time period. Using this method, we demonstrate that an oscillating potential at only one site cannot pump charge, and oscillating potentials at two or more sites are necessary to pump charge. Further we study the dependence of the pumped current on the phases and the amplitudes of the oscillating potentials at two sites. In the fourth chapter, we study the effect of resistances present in an extended region in a one-dimensional quantum wire described by a Tomonaga-Luttinger liquid model. We combine the concept of a Rayleigh dissipation function with the technique of bosonization to model the dissipative region. In the DC limit, we find that the resistance of the dissipative patch adds in series to the contact resistance. Using a current splitting matrix M to describe junctions, we study in detail the conductances of: a three-wire junction with resistances and a parallel combination of resistances. The conductance and power dissipated in these networks depend in general on the resistances and the current splitting matrices that make up the network. We also show that the idea of a Rayleigh dissipation function can be extended to couple two wires; this gives rise to a finite transconductance analogous to the Coulomb drag. In the fifth chapter, we study the effect of a Zeeman field coupled to the edge states of a two-dimensional topological insulator. These edge states form two one-dimensional channels with spin-momentum locking which are protected by time-reversal symmetry. We study what happens when time-reversal symmetry is broken by a magnetic field which is Zeeman-coupled to the edge states. We show that a magnetic field over a finite region leads to Fabry-P´erot type resonances and the conductance can be controlled by changing the direction of the magnetic field. We also study the effect of a static impurity in the patch that can backscatter electrons in the presence of a magnetic field. In the sixth chapter, we use the Blonder-Tinkham-Klapwijk formalism to study trans-port across a line junction lying between two orthogonal topological insulator surfaces and a superconductor (which can have either s-wave or p-wave pairing). The charge and spin conductances across such a junction and their behaviors as a function of the bias voltage applied across the junction and various junction parameters are studied. Our study reveals that in addition to the zero conductance bias peak, there is a non-zero spin conductance for some particular spin states of the triplet Cooper pairs. We also find an unusual satellite peak (in addition to the usual zero bias peak) in the spin conductance for a p-wave symmetry of the superconductor order parameter.

La composition interne de notre planète est un vaste sujet d’étude auquel participent de nombreuses disciplines scientifiques. Les conditions extrêmes de pression et de température qui règnent à l’intérieur du noyau (constitué principalement de fer et de nickel) et du manteau terrestre (à base de pérovskites) rendent très difficile la détermination de leur compositions exactes. Ce projet de thèse contribue aux études récentes dont l’enjeu est de déterminer plus précisément le chimisme des minéraux présents. Il a pour objet le développement d’un outil de calcul des vitesses de propagation des ondes sismiques a l’aide d’une méthode fondée sur les simulations ab initio. Ces vitesses sont déduites du tenseur élastique complet, incluant la relaxation atomique et les modifications induites du champ cristallin. Nous utilisons l’approche de la théorie de perturbation de la fonctionnelle de la densité (DFPT) qui permet de s'affranchir des incertitudes numériques qu’impliquent les méthodes classiques basées sur des différences finies. Nous combinons cette approche avec le formalisme « Projector Augmented-Wave » (PAW) qui permet, avec un coût de calcul faible, de prendre en compte tous les électrons du système. Nous avons appliqué la méthode sur des matériaux du noyau et du manteau terrestre. Nous avons déterminé les effets de différents éléments légers (Si, S, C, O et H) sur les vitesses de propagation des ondes sismiques dans le fer pur ainsi que celui de l’aluminium dans la pérovskite MgSiO3. / The internal composition of our planet is a large topic of study and involves many scientific disciplines. The extreme conditions of pressure and temperature prevailing inside the core (consisting primarily of iron and nickel) and the mantle (consisting mainly of perovskites) make the determination of the exact compositions very difficult. This thesis contributes to recent studies whose aim is to determine more accurately the chemistry of these minerals. Its purpose is the development of a tool for the calculation of seismic wave velocities within methods based on ab-initio simulations. These velocities are calculated from the full elastic tensor, including the atomic relaxation and induced changes in the crystal field. We use the approach of the density functional perturbation theory (DFPT) to eliminate numerical uncertainties induced by conventional methods based on finite differences. We combine this approach with the « Projector Augmented-Wave » (PAW) formalism that takes into account all the electrons of the system with a low computational cost. We apply the method on core and mantle materials and we determine the effects of various lights elements (Si, S, C, O and H) on the seismic wave velocities of pure iron, as well as the effect of aluminum in the perovskite MgSiO3.

The fidelity of biological processes and reactions, inspite of the widespread diversity, is programmed by highly specific physico-chemical principles. This underlines our basic understanding of different interesting phenomena of biological relevance, ranging from enzyme specificity to allosteric communication, from selection of fold to structural organization / states of oligomerization, from half-sites-reactivity to reshuffling of the conformational free energy landscape, encompassing the dogma of sequence-structure dynamics-function of macromolecules. The role of striking an optimal balance between rigidity and flexibility in macromolecular 3D structural organisation is yet another concept that needs attention from the functional perspective. Needless to say that the variety of protein structures and conformations naturally leads to the diversity of their function and consequently many other biological functions in general. Classical models of allostery like the ‘MWC model’ or the ‘KNF model’ and the more recently proposed ‘population shift model’ have advanced our understanding of the underlying principles of long range signal transfer in macromolecules. Extensive studies have also reported the importance of the fold selection and 3D structural organisation in the context of macromolecular function. Also ligand induced conformational changes in macromolecules, both subtle and drastic, forms the basis for controlling several biological processes in an ordered manner by re-organizing the free energy landscape. The above mentioned biological phenomena have been observed from several different biochemical and biophysical approaches. Although these processes may often seem independent of each other and are associated with regulation of specialized functions in macromolecules, it is worthwhile to investigate if they share any commonality or interdependence at the detailed atomic level of the 3D structural organisation. So the nagging question is, do these diverse biological processes have a unifying theme, when probed at a level that takes into account even subtle re-orchestrations of the interactions and energetics at the protein/nucleic acid side-chain level. This is a complex problem to address and here we have made attempts to examine this problem using computational tools. Two methods have been extensively applied: Molecular Dynamics (MD) simulations and network theory and related parameters. Network theory has been extensively used in the past in several studies, ranging from analysis of social networks to systems level networks in biology (e.g., metabolic networks) and have also found applications in the varied fields of physics, economics, cartography and psychology. More recently, this concept has been applied to study the intricate details of the structural organisation in proteins, providing a local view of molecular interactions from a global perspective. On the other hand, MD simulations capture the dynamics of interactions and the conformational space associated with a given state (e.g., different ligand-bound states) of the macromolecule. The unison of these two methods enables the detection and investigation of the energetic and geometric re-arrangements of the 3D structural organisation of macromolecule/macromolecular complexes from a dynamical or ensemble perspective and this has been one of the thrust areas of the current study. So we not only correlate structure and functions in terms of subtle changes in interactions but also bring in conformational dynamics into the picture by studying such changes along the MD ensemble. The focus was to identify the subtle rearrangements of interactions between non-covalently interacting partners in proteins and the interacting nucleic acids. We propose that these rearrangements in interactions between residues (amino acids in proteins, nucleic acids in RNA/DNA) form the common basis for different biological phenomena which regulates several apparently unrelated processes in biology. Broadly, the major goal of this work is to elucidate the physico-chemical principles underlying some of the important biological phenomena, such as allosteric communication, ligand induced modulation of rigidity/flexibility, half-sites-reactivity and so on, in molecular details. We have investigated several proteins, protein-RNA/DNA complexes to formulate general methodologies to address these questions from a molecular perspective. In the process we have also specifically illuminated upon the mechanistic aspects of the aminoacylation reaction by aminoacyl-tRNA synthetases like tryptophanyl and pyrrolysyl tRNA synthetase, structural details related to an enzyme catalyzed reaction that influences the process of quorum sensing in bacteria. Further, we have also examined the ‘dynamic allosterism’ that manipulates the activity of MutS, a prominent component of the DNA bp ‘mismatch repair’ machinery. Additionally, our protein structure network (PSN) based studies on a dataset of Rossmann fold containing proteins have provided insights into the structural signatures that drive the adoption of a fold from a repertoire of diverse sequences. Ligand induced percolations distant from the active sites, which may be of functional relevance have also been probed, in the context of the S1A family of serine proteases. In the course of our investigation, we have borrowed several concepts of network parameters from social network analysis and have developed new concepts. The Introduction (Chapter-1) summarizes the relevant literature and lays down a suitable background for the subsequent chapters in the thesis. The major questions addressed and the main goal of this thesis are described to set an appropriate stage for the detailed discussions. The methodologies involved are discussed in Chapter-2. Chapter-3 deals with a protein, LuxS that is involved in the bacterial quorum sensing; the first part of the chapter describes the application of network analysis on the static structures of several LuxS proteins from different organisms and the second part of this chapter describes the application of a dynamic network approach to analyze the MD trajectories of H.pylori LuxS. Chapter-4 focuses on the investigation of human tryptophanyl-tRNA synthetase (hTrpRS), with an emphasis to identify ligand induced subtle conformational changes in terms of the alternation of rigidity/flexibility at different sites and the re-organisation of the free energy landscape. Chapter-5 presents a novel application of a quantum clustering (QC) technique, popular in the fields of pattern recognition, to objectively cluster the conformations, sampled by molecular dynamics simulations performed on different ligand bound structures of the protein. The protein structure network (PSN) in the earlier studies were constituted on the basis of geometric interactions. In Chapters 6 and 7, we describe the networks (proteins+nucleic acids) using interaction energy as edges, thus incorporating the detailed chemistry in terms of an energy-weighted complex network. Chapter-6 describes an application of the energy weighted network formalism to probe allosteric communication in D.hafniense pyrrolysyl-tRNA synthetase. The methodology developed for in-depth study of ligand induced changes in DhPylRS has been adopted to the protein MutS, the first ‘check-point protein’ for DNA base pair (bp) mismatch repair. In Chapter-7, we describe the network analysis and the biological insights derived from this study (the work is done in collaboration with Prof. David Beveridge and Dr. Susan Pieniazek). Chapter-8 describes the application of a network approach to capture the ligand-induced subtle global changes in protein structures, using a dataset of high resolution structures from the S1A family of serine proteases. Chapter-9 deals with probing the structural rationale behind diverse sequences adopting the same fold with the NAD(P)-binding Rossmann fold as a case study. Future directions are discussed in the final chapter of the thesis (Chapter-10).