Ce travail est consacré à l'analyse numérique des milieux poreux saturés, en tenant comptele phénomène d'endommagement sur le squelette solide. Le milieu poreux est pris dans lecadre poro-élastique, dans un état complètement saturé, d'après la théorie de Biot. Unmodèle scalaire d'endommagement est supposé pour cette analyse. Une formulationimplicite de la Méthode des éléments de frontière, basée sur des solutions fondamentalesindépendantes du temps, est développé et implantée numeriquement pour coupler lesproblèmes de l'écoulement de fluide et de l'elasticité endommageable. L'intégration sur deséléments de frontière est realisée en utilisant la méthode numérique de Gauss. Un schémasemi-analytique pour le cas des cellules triangulaires de domaine est suivie pour évaluer lesintégrales de domaine pertinentes. Le systéme non-linéaire est résolu par une procédure deNewton-Raphson. Des exemples numériques sont présentés, afin de valider la formulationimplantée et pour illustrer son efficacité. / This work is devoted to the numerical analysis of saturated porous media, taking into accountthe damage phenomenon on the solid skeleton. The porous media is taken into poroelasticframework, in full-saturated condition, based on the Biot’s Theory. A scalar damage model isassumed for this analysis. An implicit Boundary element Method (BEM) formulation, basedon time-independent fundamental solutions, is developed and implemented to couple thefluid flow and the elasto-damage problems. The integration over boundary elements isevaluated by using a numerical Gauss procedure. A semi-analytical scheme for the case oftriangular domain cells is followed to carry out the relevant domain integrals. The non-linearsystem is solved by a Newton-Raphson procedure. Numerical examples are presented, inorder to validate the implemented formulation and to illustrate its efficiency. / Este trabalho trata da análise numérica de meios porosos saturados, considerandodanificação na matriz sólida. O meio poroso é admitido em regime poroelástico, emcondição saturada, com base na teoria de Biot. Um modelo de dano escalar é empregadonesta análise. Uma formulação implícita do Método dos Elementos de Contorno (MEC),baseada em soluções fundamentais independentes do tempo, é desenvolvida eimplementada de forma a acoplar os problemas de difusão de fluido e de elasto-dano. Aintegração sobre os elementos de contorno é feita através da quadratura de Gauss. Umesquema semi-analítico é aplicado sobre células triangulares para avaliar as integrais dedomínio do problema. A solução do sistema não linear é obtida através de um procedimentodo tipo Newton-Raphson. Apresentam-se exemplos numéricos a fim de validar a formulaçãoimplementada e demonstrar sua eficiência.

Many passerine birds, particularly corvids, are known to express complex cognitive skills comparable to those observed in primates. In order to examine how these similarities are reflected at the cellular level, I counted neurons and nonneuronal cells in passerine brains using the isotropic fractionator method. I show that, in these birds, neuronal numbers scale almost isometrically with telencephalic size, i.e., the average neuron size shows little increase and neuronal density decreases minimally as brains get larger. Neuronal densities in the passerine telencephalon exceed those observed in the primate cerebral cortex by a factor of 3-6. As a result, the number of telencephalic neurons in the Common Raven (Corvus corax) equals those observed in the cerebral cortex of small monkeys. The cerebellum features similar scaling rules. However, because the relative size of the cerebellum is smaller than in mammalian brains, cerebellar neurons make a much smaller proportion of total brain neurons than in mammals. In contrast to the little variation in neuronal densities in telencephalon and cerebellum, the density of neurons rapidly decreases with increasing structure size in the diencephalon, optic tectum and brain stem. For all examined brain structures, the densities of nonneuronal cells remain constant...

Ácidos graxos são moléculas hidrofóbicas essenciais para a composição da estrutura física celular, para o metabolismo energético dos seres vivos e também para os caminhos de sinalização molecular no proteoma celular. No caso de deficiência no ácido graxo docosahexaenóico (DHA) e do ácido eicosapentaenoico (EPA) temos a depressão e a mudança do comportamento. O transporte destas moléculas hidrofóbicas no citosol celular é realizado por uma família de proteínas capazes de se ligar a esses ácidos graxos de maneira seletiva, com alta afinidade e de forma reversível. Esta família de proteína é conhecida como FABP, ou proteínas ligantes de ácido graxo. Para realizar esta função, as FABP possuem características únicas tanto na sua estrutura tridimensional quanto na dinâmica experimentada pelos vários elementos estruturais. Diversos trabalhos identificaram regiões relevantes e, com mutações realizadas em resíduos específicos, caracterizaram o mecanismo como a proteína interage com ligantes e com a bicamada lipídica para a realização da sua função, identificando um processo multi-estágio na interação com a bicamada lipídica. Contudo, a não realização de mutações em todos os resíduos da proteína pode deixar não-identificados regiões ou resíduos da proteína também envolvidos na sua função. Além disso, nunca foi caracterizado o que ocorre com os resíduos e com a estrutura da FABP quando a proteína está complexada com uma bicamada lipídica. No presente trabalho, escolhemos a B-FABP para estudar a interação com ligantes e o complexo proteína-membrana desta família de proteínas. Para isto, as técnicas de ressonância magnética nuclear 15N-HSQC e eletrônica (RMN e RPE) foram utilizadas para acompanhar mudanças estruturais e dinâmicas ocorridas quanto de interações moleculares. Com a técnica de RPE e o uso de derivados de ácidos graxos marcados com radicais nitróxidos, monitoramos o sítio de ligação da molécula de ácido graxo e suas alterações quando na presença do surfactante SDS. No caso de RMN, foi usada em proteínas marcadas isotopicamente com 15N na presença de bicelas isotrópicas de DMPC: DHPC na razão igual a um (q = 1), em uma concentração lipídica (CL) de 4%. Nossos resultados além de identificar os mesmos resíduos já conhecidos na interação da FABP com modelos de membrana, também encontrou novos resíduos nunca antes associados à superfície de contato da FABP com a bicamada lipídica. / Fatty acids are hydrophobic molecules essential to the cell structure, to the energetic metabolism of living organisms and to the molecular signaling pathways in the cell proteome. Depression and behavior alteations are two common consequences of deficiencies in docosahexanoic (DHA) and eicosapentaenoic (EPA) acids. The transport of such hydrophobic molecules in the cytosol is the main function of a family of proteins capable of making a selective, high affinity, and reversible binding of fatty acids. This family of proteins is known as FABPs (fatty acid binding proteins). To perform their function, FABPs have unique features in both their tridimensional structure and in the dynamics experienced by the several structural elements. Many reports have identified regions that are relevant to function and, through point mutations of specific residues, have characterized the mechanism used by the protein to bind its ligand and also to interact with lipid bilayers. However, the point mutation strategy relies heavily on the choice of residues such that missing residues can lead to the lack of identification of important elements involved in protein function. Moreover, the characterization of the protein-bilayer complex still deserves a more detailed investigation. In this work, we study the B-FABP protein in terms of its interaction with ligands as well as a membrane model system. We made use of magnetic resonance techniques, nuclear (NMR) and electronic (EPR), to probe structural and dynamical changes occurring upon intermolecular interaction. EPR and spin labeled fatty acids allowed us to monitor the ligand binding site in the protein structure and also its alterations in the presence of the surfactant SDS. NMR HSQC was used to gain information on the conformational changes of isotopically labeled protein in the presence of biceles made of DMPC:DHPC (q = 1 and lipid concentration CL of 4%). Our results confirmed relevant functional residues that had been previously identified and also pointed to new residues that had not been implicated as part of the contact surface before, thus widening our understanding of FABP-bilayer interaction.

Orientador: Fábio Roberto Chavarette / Resumo: Este trabalho é dedicado ao desenvolvimento de uma metodologia baseada no monitoramento da integridade estrutural em aeronaves com foco em técnicas de computação inteligente, tendo como intuito detectar, localizar e quantificar falhas estruturais utilizando os sistemas imunológicos artificiais (SIA). Este conceito permite compor o sistema de diagnóstico apto a aprender continuamente, contemplando distintas situações de danos, sem a necessidade de reiniciar o processo de aprendizado. Neste cenário, foi empregado dois algoritmos imunológicos artificiais, sendo o algoritmo de seleção negativa, responsável pelo processo de reconhecimento de padrões, e o algoritmo de seleção clonal responsável pelo processo de aprendizado continuado. Também foi possível quantificar o grau de influência do dano para as cinco situações de danos. Para avaliar a metodologia foi montada uma bancada experimental com transdutores piezelétricos que funcionam como sensor e atuador em configurações experimentais, que podem ser anexadas à estrutura para produzir ou coletar ondas numa placa de alumínio (representando a asa do avião), sendo coletados sinais na situação normal e em cinco situações distintas de danos. Os resultados demonstraram robustez e precisão da nova metodologia proposta. / Abstract: This work is dedicated to the development of a methodology based on the monitoring of structural integrity in aircraft with a focus on intelligent computing techniques, aiming to detect structural failures using the artificial immune systems (AIS). This concept allows to compose the diagnostic system capable of learning continuously, contemplating different situations of damages, without the need to restart the learning process. In this scenario, two artificial immunological algorithms were employed, the negative selection algorithm, responsible for the pattern recognition process, and the clonal selection algorithm responsible for the continuous learning process. It was also possible to quantify the degree of influence of the damage for the five damage situations. To assess the methodology, an experimental bench was mounted with piezoelectric transducers that act as sensors and actuators in experimental configurations, which can be attached to the structure to produce or collect waves on an aluminum plate (representing the wing of the airplane), being collected signals in the normal situation and in five different situations of damages. The results demonstrate the robustness and accuracy of the proposed new methodology. / Doutor

[pt] Este trabalho propõe uma técnica do tipo rotação de fase para migração em profundidade de dados sísmicos para meios com simetria polar local (localmente transversalmente isotrópicos, LTI), nos quais a direção do eixo de simetria varia continuamente ao longo das camadas. São testadas, através de simulações numéricas de levantamentos sísmicos, a precisão e a estabilidade do método, em função da variação do eixo de simetria. Para a realização das simulações, desenvolveu-se um método a partir da solução da equação elástica da onda usando-se a técnica das diferenças finitas, que possibilita a modelagem em meios LTI, onde cada ponto da malha tem suas características definidas pelas velocidades de fase P e SV, parâmetros de Thomsen, densidade e inclinação do eixo de simetria. Na separação dos modos de onda qP e qSV dos sismogramas, implementou-se um algoritmo baseado na solução da equação de Christoffel para determinar os operadores de separação. A migração para cada família de tiro comum é realizada por soluções da equação da onda usando somente técnicas de rotações de fase. De fato, tanto a depropagação do campo registrado quanto a geração das matrizes de tempo utilizadas na condição de imageamento, são realizadas por soluções que envolvem rotações de fase para cada conjunto de parâmetros, em cada nível de profundidade. Nos resultados das migrações usando reflexões dos tipos qP-qP, e qP-qSV, os horizontes foram localizados precisamente e verificou-se que o processo é estável em relação à variação do eixo de simetria. Vale ressaltar que o método não está restrito a aquisições sísmicas multicomponentes, podendo ser aplicado em dados sísmicos marítimos convencionais, como também em dados provenientes de aquisições do tipo OBC (Ocean Bottom Cable) e com cabo vertical. Como o método proposto se baseia em algoritmos que utilizam técnicas de rotação de fase, a sua implementação conta com o beneficio de ser altamente paralelizável. / [en] This work proposes a technique based on the phase-shift method to implement pre-stack depth migration on locally transverse isotropic media (LTI), in which the direction of the symmetry axis varies continually along the layers. Through numerical seismic data simulations the methods robustness and stability were tested in relation to the axis symmetry variations. For seismic modeling, a generalization of the finite differences method for the solution of the elastic wave equation was used. With this procedure, it was possible to accommodate seismic modeling on LTI media defined by six parameters at each grid point, i.e., density, P and S wave propagation velocities along the local symmetry axis, Thomsen parameters and, the direction of the local symmetry axis itself. In order to separate from the seismograms the qP and qSV wavefields, an algorithm based on the Christoffel equation was implemented. The migration for each common shot gather is implemented solely by phase-shift based algorithms, which means that not only the depropagation of the registered wavefield, but also the generation of the time matrices involved in the imaging condition were obtained in this manner for each set of parameters at each depth level. The migration results using qP-qP and qP-qSV reflections show that the horizons were located precisely, and that the process is stable in relation to the symmetry axis variations. The proposed method is not restricted to multicomponent seismic acquisitions, but it can be applied to marine seismic data using streamers, or Ocean Bottom Cables or vertical cables. Since the proposed method uses phaseshift algorithms, its parallel implementation can be highly efficient.

Cette thèse est constituée de quatre chapitres. Le premier contient les notions de base qui permettent d'aborder les divers thèmes qui y sont étudiés. Le second est consacré à l'étude des sous-variétés lagrangiennes d'une variété presque kählérienne. J'y présente les résultats obtenus en collaboration avec Burcu Bektas, Joeri Van der Veken et Luc Vrancken. Dans le troisième, je m'intéresse à un problème de géométrie différentielle affine et je donne une classification des hypersphères affines qui sont isotropiques. Ce résultat a été obtenu en collaboration avec Luc Vrancken. Et enfin dans le dernier chapitre, je présente quelques résultats sur les surfaces de translation et les surfaces homothétiques, objet d'un travail en commun avec Rafael López. / Abstract in English not available

The influence of several hardwoods and softwoods pulp fibre on the free shrinkage of isotropic paper sheets was investigated. The effect of properties such as density, grammage, Fractional Contact Area (FCA), Water Retention Value (WRV), fines content and fibre morphology were also investigated on the free shrinkage of isotropic paper sheets. Further, the influence of Lyocell fibre and glycerol on the free shrinkage of isotropic paper sheets is reported. Experimental results showed that in general the free shrinkage of hardwood pulps is a few percent higher than that of softwood pulps at the same density. It was found that although free shrinkage increases with fines content, a high fines content does not imply high shrinkage, and some pulp samples with higher amount of fines, exhibited lower free shrinkage. For all pulps at low densities there is little influence of grammage on free shrinkage, though as density increases a significant dependence is observed. The results showed that the free shrinkage of isotropic paper sheets formed from hardwood pulps is more sensitive to grammage compared to that of softwood pulps. Interestingly, it was shown that some pulp samples with the same intrinsic density, WRV and FCA exhibited different free shrinkage over the range of grammages. In addition, some pulp samples with stiffer fibres but higher amount of fines exhibited higher free shrinkage. Experimental results showed that longitudinal shrinkage of a fibre is an important parameter and pulp samples with higher microfibril angle (MFA) exhibited higher longitudinal shrinkage. Finally, the free shrinkage of isotropic paper sheets was reduced by applying Lyocell fibre and glycerol. Interestingly, by adding a small amount of Lyocell fibre, 2%, an increase in tensile index, tensile energy absorption (TEA) and modulus is observed, while the free shrinkage reduced up to 2%. In addition, adding glycerol to the pulp samples not only reduced the free shrinkage of isotropic paper sheets up to 1.5%, but also mechanical properties, such as tensile index and stretch slightly improved.

Aplicamos a teoria de representação de funções isotrópicas para determinar o número mínimo de invariantes independentes necessários para caracterizar completamente a densidade de energia de deformação de sólido hiperelástico com duas direções de simetria material. Expressamos a densidade de energia em termos de dezoito invariantes e extraímos um conjunto de dez invariantes para analisar dois casos de simetria material. No caso de direções ortogonais, recuperamos o resultado clássico de sete invariantes e oferecemos uma justificativa para a escolha dos invariantes encontrados na literatura. Se as direções não são ortogonais, descobrimos que o número mínimo também é sete e corrigimos um erro em fórmula encontrada na literatura. Uma densidade de energia deste tipo é usada para modelar, na escala macroscópica, materiais de engenharia, tais como compósitos reforçados com fibras, e tecidos biológicos, tais como ossos. / We determine the minimum number of independent invariants that are needed to characterize completely the strain energy density of a hyperelastic solid having two distinct material symmetry directions. We use a theory of representation of isotropic functions to express this energy density in terms of eighteen invariants and extract a set of ten invariants to analyze two cases of material symmetry. In the case of orthogonal directions, we recover the classical result of seven invariants and offer a justification for the choice of invariants found in the literature. If the directions are not orthogonal, we find that the minimum number is also seven and correct a mistake in a formula found in the literature. An energy density of this type is used to model, on the macroscopic scale, engineering materials, such as fiber-reinforced composites, and biological tissues, such as bones.

The present thesis reports computer simulation studies of several phase transition related phenomena in a range of soft-condensed matter systems. A coherent unifying theme of the thesis is the understanding of dynamics of phase transitions through free energy calculations using recently developed efficient non-Boltzmann sampling methods. Based on the system/phenomena of interest, the thesis has been classified into four major parts: I. Isotropic-nematic (IN) phase transition in liquid crystals. II. Nucleation phenomena in gas-liquid transition with particular emphasis on the systems close to the spinodal curve. III. Collapse transition in linear hydrocarbon (n-alkane) chains for a varying range of length, solvent and temperature. IV. Crystallization of unbranched polymer chains in dilute solution, with particular emphasis on the temperature dependent crossover between the rod-like crystalline state and spherical molten globule state. The thesis has been further divided into ten chapters running through the four parts mentioned before. In the following we provide a brief chapter-wise outline of the thesis. Part I deals with the power law relaxation and glassy dynamics in thermotropic liquid crystals close to the IN transition and consists of two chapters. To start with, Chapter I.1 provides an introduction to thermotropic liquid crystals. Here we briefly introduce various liquid crystalline phases, the order parameter used to characterize the IN transition, a few well established theoretical models, and we conclude with describing the recent experimental and computer simulation studies that have motivated the work described in the next chapter. In Chapter I.2, we present our molecular dynamics simulation studies on single particle and collective orientational dynamics across the IN transition for Lebwohl Lasher model, which is a well-known lattice model for thermotropic liquid crystals. Even this simplified model without any translational degrees of freedom successfully captures the short-tointermediate time power law decay recently observed in optical heterodyne detected optical Kerr effect (OHDOKE) measurements near the IN transition. The angular velocity time correlation function also exhibits a rather pronounced power law decay near the IN boundary. In the mean squared angular displacement at comparable time scales, we observe the emergence of a sub-diffusive regime which is followed by a super-diffusive regime before the onset of the longtime diffusive behavior. We observe signature of dynamical heterogeneity through pronounced non-Gaussian behavior in the orientational motion particularly at lower temperatures. Interestingly, this behavior closely resembles what is usually observed in supercooled liquids. We obtain the free energy as a function of orientational order parameter by the use of recently developed transition matrix Monte Carlo (TMMC) method. The free energy surface is flat for the system considered here and the barrier between isotropic and nematic phases is vanishingly small for this weakly first-order transition, hence allowing for large scale, collective, and correlated orientational density fluctuations. We attribute this large scale fluctuations as the reason for the observed power law decay of the orientational time correlation functions. Part II consists of three chapters, where we focus on the age old problem of nucleation and growth, both from the perspective of thermodynamics and kinetics. We account for the rich history of the problem in the introductory Chapter II.1. In this chapter we describe various types and examples of the nucleation phenomena, and a brief account of the major theoretical approaches used so far. We begin with the most successful Classical Nucleation Theory (CNT), and then move on to more recent applications of Density Functional Theory (DFT) and other mean-field types of models. We conclude with a comparison between the experiments, theories and computational studies. In the next chapter (Chapter II.2) we attempt to elucidate the mechanism of nucleation near the gas-liquid spinodal from a microscopic point of view. Here we construct a multidimensional free energy surface of nucleation of the liquid phase from the parent supercooled and supersaturated vapor phase near the gas-liquid spinodal. In particular, we remove the Becker-Doring constraint of having only one growing cluster in the system. The free energy, as a function of the size of the largest cluster, develops a pronounced minimum at a subcritical cluster size close to the spinodal. This signifies a two step nature of the process of nucleation, where the rapid formation of subcritical nuclei is followed by further growth by slower density fluctuations on an uphill free energy surface. An alternative free energy pathway involving the participation of many subcritical clusters is envisaged near the spinodal where the growth of the nucleus is found to be promoted by a coalescence mechanism in contrast to the single particle addition assumption within CNT. The growth of the stable phase becomes progressively collective and spatially diffuse, and the significance of a “critical nucleus” is lost for deeper quenches. In this chapter we present our studies both in 3dimensional Lennard-Jones (LJ) system and Ising model (both 2and 3dimensions). Our general findings seem to be independent of the model chosen. While the previous chapter focuses on relatively well-studied 3-dimensional (3D) LJ system, in Chapter II.3 we present our studies on the characteristics of the nucleation phenomena in 2dimensional (2D) Lennard-Jones fluid. To the best of our knowledge this is the first extensive computer simulation study to check the accuracy of CNT in 2D. Using various Monte Carlo methods, we calculate the free energy barrier for nucleation, line tension, and bulk densities of equilibrium liquid and vapor phases, and also investigate the size and shape of the critical nucleus. The study is carried out at an intermediate level of supersaturation (away from the spinoidal limit). In 2D, a surprisingly large cutoff (rc ≥ 7.0σ where σ is the diameter of LJ particles) in the truncation of the LJ potential is required to obtain converged results. A lower cutoff leads to a substantial error in the values of the line tension, nucleation barrier, and characteristics of the critical cluster. Note that typically 2.5σ is sufficient for 3D LJ fluids. We observe that in 2D system CNT fails to provide a reliable estimate of the free energy barrier. While it is known to slightly overestimate the nucleation barrier in 3D, it underestimates the barrier by as much as 50% at the saturation ratio S = 1.1(defined as S = P/Pc, where Pc is the coexistence pressure) and at the reduced temperature T* = 0.427(defined as T* = KBT/ ε, where ε is the depth of the potential well). The reason for the marked inadequacy of the CNT in 2D can be attributed to the non-circular nature of the critical clusters. Although the shape becomes increasingly circular and the clusters become more compact with increase in cutoff radius, an appreciable non-circular nature remains even without any cutoff to make the simple CNT inaccurate. Part III again consists of three chapters and focuses on the conformational equilibria. Collapse transition and self-organized structures of n-alkanes in solution. In Chapter III.1 we carry out a brief survey of the existing theories of polymer in solution, with particular emphasis on the collapse process in poor solvents. We also introduce the concept of “hydrophobicity” and “hydrophobic collapse”, which is now a subject enormous interest, partly because it my help in understanding the initial processes involved in protein folding. We briefly discuss the subject of formation of beautiful self-organized structures by block copolymers, and also simple homopolymers which is essentially the focus of the work embodied in the next two chapters. In Chapter III.2 we demonstrated a chain length dependent crossover in the structural properties of linear hydrocarbon (n-alkane) chains using detailed atomistic simulations in explicit water. We identify a number of exotic structures o the polymer chain through energy minimization of representative snapshots collected from molecular dynamics trajectory. While the collapsed state is ring-like(circular) for small chains(CnH2n+2; n ≤ 20) and spherical for very long ones( n = 100), we find the emergence of ordered helical structures at intermediate lengths (n ~ 40). We find different types of disordered helices and toroid-like structures at n = 60. We also report a sharp transition in the stability of the collapsed state as a function of the chain length through relevant free energy calculations. While the collapsed state is only marginally metastable for C20H42, a clear bistable free energy surface emerges only when the chain is about 30 monomers long. For n = 30, the polymer exhibits an intermittent oscillation(characterized by well-developed 1/f noise, where f is the frequency ) between the collapsed and the coil structures, characteristic of two stable states separated by a small barrier. This appears to support a weakly first order phase transition between the extended and the collapsed states. Chapter III.3 extends the study of previous chapter to much longer chains (n ≥ 100), which irreversibly collapse in water into globular forms. Even though the collapsed form has a nearly spherical shape, close inspection shows a propensity towards local ordering in the alignment of the polymer segments. This tendency to maintain alignment in order to maximize the number of contacts leads to a core-shell like structure, where the shell is often characterized by a bent rod-like shape consisting of two adjacent segments running in parallel. A key event associated with the initial stage of collapse seems to be the formation of a skewed ring (or loop) that serves as a “nucleation center” for rest of the chain to collapse into. Time evolution of the radial distribution function of water surrounding the polymer, shows that the density of neighboring water decreases by only about 15-20% from that of bulk water. Even though interior of the ting-like structures is fully devoid of water, solvent accessible surface representation shows that these regions are geometrically/spatially inaccessible to water molecules. We suggest that the role of water is to stabilize such ring-like structures once formed by natural conformational fluctuations of the polymer chain. This view is confirmed by observation of spontaneous formation and melting away of such ring-like entities in a polar aprotic solvent(DMSO). We also comment on the role of the flexibility of polymer chains in determining the collapse kinetics. The last part(Part IV) of the thesis consists of two chapters that deal with the crystallization of linear polymer chains from dilute solution. The way long chain polymers crystallize is drastically different from their small molecule counterparts due to their topological connectivity. Linear polymers often crystallize from dilute solution in the form of thin lamellae with well-defined crystallographic features. In Chapter IV.1 we briefly survey the current theoretical understanding and confusions associated with the highly debated field of polymer crystallization. While the last few decades have seen the development of many successful phenomenological theories, the molecular mechanism of formation of such self-organized lamellae is extremely complex and very poorly understood. There are clearly two distinct steps in polymer crystallization. Firstly, the individual linear polymers must self-organize into bundles of somewhat regular structures. These structures then further aggregate to lamellar form and crystallize into a lattice. In this respect , it has marked similarity to the problem of protein crystallization. In chapter IV.2 we present Brownian dynamics simulation studies of a single polythelene chain of length 500. Such systems can reasonably mimic the process of crystallization from dilute solutions. Our simulations could successfully reproduce some of the interesting phenomena observed in experiments and very recent computer simulation studies, including multi-center nucleation of rod-like structures within a single polymer chain, an inverse relation between lamellar thickness and temperature etc. But our primary focus has been to understand the nature of the phase transition as one traverses along the melting temperature and the underlying free energy surface. Near the melting temperature we observe a very intriguing fluctuation between the disordered molten globule state and the ordered rod-like crystalline, where these two forms have highly different shape and structure. These fluctuations have strong signature of 1/f noise or intermittency. This clearly indicates the existence of a weakly first order transition, where two widely different states with large difference in values of order parameter are separated by a rather small free energy barrier. This can be related to the experimentally observed density fluctuations that resemble spinodal decomposition. It is important to note that very similar fluctuations have been observed in our previous studies on liquid crystals (Chapter 1.2) and intermediate sized alkalines in water(Chapter III.2) that signifies a universal underlying energy landscape for these systems. We have discussed the scope of future work at the end of each chapter whenever appropriate.

ABSTRACT DEVELOPMENT OF A MICRO-FABRICATION PROCESS SIMULATOR FOR MICRO-ELECTRO-MECHANICAL SYSTEMS (MEMS) Yildirim, Alper M.S, Department of Mechanical Engineering Supervisor: Asst. Prof. Dr. Melik D&ouml / len December 2005, 140 pages The aim of this study is to devise a computer simulation tool, which will speed-up the design of Micro-Electro-Mechanical Systems by providing the results of the micro-fabrication processes in advance. Anisotropic etching along with isotropic etching of silicon wafers are to be simulated in this environment. Similarly, additive processes like doping and material deposition could be simulated by means of a Cellular Automata based algorithm along with the use of OpenGL library functions. Equipped with an integrated mask design editor, complex mask patterns can be created by the software and the results are displayed by the Cellular Automata cells based on their spatial location and plane. The resultant etched shapes are in agreement with the experimental results both qualitatively and quantitatively. Keywords: Wet Etching, Anisotropic Etching, Doping, Cellular Automata, Micro-fabrication simulation, Material Deposition, Isotropic Etching, Dry Etching, Deep Reactive Ion Etching