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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
31

Efeito Kondo e magnetismo em uma rede Kagome

Silva Junior, José Luiz Ferreira da January 2012 (has links)
Neste trabalho estudamos o modelo da rede de Kondo em uma rede kagome, buscando uma maior compreensão dos efeitos da frustração geométrica em sistemas de férmions pesados. Para tanto, fizemos uma aproximação de campo médio no hamiltoniano do sistema que serve para todas as fases do sistema. Analisamos inicialmente o caso não magnético. Obtemos neste limite as energias eletrônicas e as funções de Green necessárias ao cálculo numérico autoconsistente das ocupações e do parâmetro de Kondo. Os resultados encontrados estão em concordância qualitativa com trabalhos publicados em outras geometrias. A seguir analisamos o caso magnético, onde introduzimos uma aproximação suplementar, a qual é compatível com a de campo médio já considerada e, em princípio, existente apenas em sistemas com frustração geométrica. Realizamos cálculos autoconsistentes através de somas sobre as frequências de Matsubara. Os resultados mostram que não há coexistência entre ordem magnética e efeito Kondo, além de haver a supressão do antiferromagnetismo com o aumento de temperatura e variações no preenchimento de bandas. / In this work we study the Kondo Lattice model for the kagome lattice, in order to understand better the effects of geometrical frustration in heavy-fermion systems. In this context, we consider a mean field scheme valid for all the system’s phases. Firstly, we analyzed the nonmagnetic case. In this approximation the electron energies and spectral functions are reachable, then we use the density of states to calculate the occupations selfconsistently. Our results are qualitatively compared with previous works in other geometries. In the second part we introduce an approximation for magnestism, which takes into account the mean field scheme considered and the presence of geometrical frustration. Self-consistent calculations are done through the frequencies summation method. Our results show that the magnetism is supressed when the temperature is increased or the band filling deviates from half-filling. Besides, the coexistence of magnetic order and Kondo effect is not observable.
32

Efeito Kondo e magnetismo em uma rede Kagome

Silva Junior, José Luiz Ferreira da January 2012 (has links)
Neste trabalho estudamos o modelo da rede de Kondo em uma rede kagome, buscando uma maior compreensão dos efeitos da frustração geométrica em sistemas de férmions pesados. Para tanto, fizemos uma aproximação de campo médio no hamiltoniano do sistema que serve para todas as fases do sistema. Analisamos inicialmente o caso não magnético. Obtemos neste limite as energias eletrônicas e as funções de Green necessárias ao cálculo numérico autoconsistente das ocupações e do parâmetro de Kondo. Os resultados encontrados estão em concordância qualitativa com trabalhos publicados em outras geometrias. A seguir analisamos o caso magnético, onde introduzimos uma aproximação suplementar, a qual é compatível com a de campo médio já considerada e, em princípio, existente apenas em sistemas com frustração geométrica. Realizamos cálculos autoconsistentes através de somas sobre as frequências de Matsubara. Os resultados mostram que não há coexistência entre ordem magnética e efeito Kondo, além de haver a supressão do antiferromagnetismo com o aumento de temperatura e variações no preenchimento de bandas. / In this work we study the Kondo Lattice model for the kagome lattice, in order to understand better the effects of geometrical frustration in heavy-fermion systems. In this context, we consider a mean field scheme valid for all the system’s phases. Firstly, we analyzed the nonmagnetic case. In this approximation the electron energies and spectral functions are reachable, then we use the density of states to calculate the occupations selfconsistently. Our results are qualitatively compared with previous works in other geometries. In the second part we introduce an approximation for magnestism, which takes into account the mean field scheme considered and the presence of geometrical frustration. Self-consistent calculations are done through the frequencies summation method. Our results show that the magnetism is supressed when the temperature is increased or the band filling deviates from half-filling. Besides, the coexistence of magnetic order and Kondo effect is not observable.
33

Some Studies On Numerical Models For Fracture Of Concrete

Rao, T V R L 01 1900 (has links) (PDF)
Concrete has established itself as the most widely used structural material. There is hardly any place where human life and concrete structure do not exist together. It's use is seen in wide variety of structures like buildings, bridges, dams, nuclear structures, floating and submerged structures and so on. Hence, in view of safety, serviceability and economy, proper understanding of the behaviour of concrete is imperative in designing these complex structures. Current reinforced concrete codes are based on strength and serviceability concepts. The tensile strength of concrete is totally neglected in the limit state method of analysis. The concrete in tension is assumed to be fully cracked and conservative method of design is adopted. The crack causes a considerable degradation of stiffness of overall structure and gives rise to regions of stress concentration, which are not accounted for, in the present design methods. Besides, it is found that the size of the structural component significantly influences the stress at failure. It has been fairly well established that large specimens fail by catastrophic crack propagation while small specimens tend to fail in a ductile manner with considerable amount of slow crack growth preceding fracture. Initial attempts to understand the cracking of concrete through the principles of fracture mechanics was made in 1960's. It was concluded that the LEFM and small scale yielding fracture mechanics which are developed for metals are inapplicable to concrete structures except for certain limiting situations such as the behaviour at extremely large sizes. The reasons for the inapplicability of LEFM principles to concrete structures are attributed to slow crack growth, formation of nonlinear fracture process zone, and softening behaviour of concrete in tension. Several analytical and numerical models have been proposed to characterize the fracture behaviour of concrete. In the present work a simple numerical method is proposed to analyse the Mode-I fracture behaviour of concrete structures, using finite element method. The stiffness matrices calculated at the beginning of the analysis are used till the end without any modification. For this reason, the method is named as Initial Stiffness Method (ISM). An attempt has also been made to modify the lattice model existing in literature. The contents of the thesis are organised in six chapters. In chapter 1, a brief introduction to basic principles of fracture mechanics theory is presented. This is included mainly for the completeness of the thesis. In chapter 2, a brief review of literature regarding the application of principles of fracture mechanics to concrete structures is presented. The need for the introduction of fracture mechanics to concrete is presented. Early work, applying LEFM principles to concrete structures is discussed. The reasons for the inapplicability of linear elastic fracture mechanics principles to concrete structures are discussed. Necessities for nonlinear fracture mechanics principles are pointed out. Attention is focused on the influence of the factors like slow crack growth, formation of nonlinear fracture process zone and softening behaviour of concrete in tension on the fracture behaviour. Besides a possible use of fracture energy as an alternative fracture criterion for concrete is contemplated. Several analytical and numerical models (assuming concrete as homogeneous continuum), proposed so far to characterize the fracture behaviour of concrete, are presented and discussed in detail. Different heterogeneous models presented so far are also discussed. In chapter 3, a simple numerical method to analyse the fracture of concrete (strain softening material) in Mode-I, using FEM is proposed. The stiffness matrices are generated only once and are used till the end of the analysis. This feature makes the model simple and computationally efficient. A new parameter namely, strain softening parameter α has been introduced. It is found that this strain softening parameter ‘α’ is a structural property. The results obtained from the present method are found to converge with increasing number of elements thus making the method mesh independent, and thus objective. The method was validated by analysing the beams tested and reported by various researchers. The predicted values of maximum load by the present method are found to agree well with the experimental values. Initially, all the beams are analysed using uniform meshes and load-deflection diagrams are plotted. All the beams are again analysed using graded meshes. The load-deflection, load-CMOD diagrams are plotted from the results obtained from the analysis using graded meshes. In chapter 4, the results obtained in chapter 3 are analysed for size effect. Literature regarding size effect of concrete structures has been reviewed. In addition to the size effect on nominal stress at failure which exists in literature, two new parameters namely, post peak slope and softening slope parameter α have been used to confirm the size effect. This does not exist in the literature. In chapter 5, an attempt is made to modify the lattice model existing in literature. This is done with a view to model concrete as a heterogeneous medium, which would be nearer to reality. The softening property of concrete has been incorporated. The model was validated against some of the experimental results existing in literature. The results are found to be encouraging. The results from this model show the post peak softening similar to the experimentally observed ones. The effects of different probabilistic distributions to the properties of mortar on the maximum load of the beam are studied. It is found that normal distribution of properties to mortar gives the best results. A study is made regarding the sensitivity of various properties of mortar on the maximum load of the beam. It is concluded that load carrying capacity of the beam can be increased by using a mortar of higher tensile strength. Finally in chapter 6, general conclusions and suggestions for further investigations are discussed.
34

Flussgleichungen zur Beschreibung statischer und dynamischer Eigenschaften des eindimensionalen Kondo-Gitter-Modells

Sommer, Torsten 15 March 2005 (has links)
In dieser Arbeit wird das eindimensionale Kondo-Gitter-Modell untersucht, das die Wechselwirkung eines Gitters lokaler magnetischer Momente mit unkorrelierten Leitungselektronen beschreibt. Mit Hilfe der Methode der kontinuierlichen unitären Transformationen (Flussgleichungen) wird das Modell im Parameterbereich schwacher Wechselwirkungsstärke betrachtet. In diesem Bereich zeigt das Modell so genanntes Luttinger-Flüssigkeitsverhalten. Im Rahmen der Flussgleichungsmethode wird der Hamilton-Operator auf ein effektives Modell abgebildet, in dem Elektronen und Spinmomente vollständig entkoppelt sind. Das Resultat dieses Prozesses ist ein Modell, das ein nichtwechselwirkendes Elektronengas und eine Heisenberg-Spinkette beschreibt. Das Eigenwertproblem der Heisenberg-Kette wird im Rahmen einer Schwinger-Boson-Molekularfeld-Theorie beschrieben. Zur Charakterisierung der Grundzustandseigenschaften des eindimensionalen Kondo-Gitter-Modells wurden verschiedene Erwartungswerte und Korrelationsfunktionen betrachtet. Neben statischen Größen, wie der Ladungskorrelationsfunktion der Elektronen oder der Spinkorrelationsfunktion der lokalen Spinmomente, werden dynamische Größen, wie die elektronische Zustandsdichte oder die dynamischen Spinstrukturfaktoren der Elektronen und der lokalen Spinmomente, berechnet. / The one-dimensional Kondo lattice model is investigated. This model describes the interaction between a lattice of local magnetic moments and uncorrelated conduction electrons. It is studied by means of the continuous unitary transformation's method (flow equations) within the parameter regime of weak interaction strength. Here the model shows so called Luttinger liquid behaviour. Within the framework of the flow equation's method the original Hamiltonian is mapped on an effective model, where electrons and local moments are completely decoupled. The result of this process is a model describing a non-interacting electron gas and a Heisenberg spin chain. The eigenvalue problem of the Heisenberg chain is described within a Schwinger bosons molecular field theory. In order to characterise the ground state properties of the one-dimensional Kondo lattice model different expectation values and correlation functions are investigated. Beside static properties like the charge correlation function of the electrons or the local moment's spin correlation function, dynamic properties are determined, like the electronic density of states or the dynamic spin structure factor of both the electrons and the local moments.
35

A model study for Eu-rich EuO

Sinjukow, Peter 20 August 2004 (has links)
In dieser Arbeit wird ein Modell für das Eu-reiche EuO formuliert. Es besteht in einer Erweiterung des Kondo-Gitter-Modells (KGM). Für das KGM existieren nur einige exakte Aussagen. In dieser Arbeit kommt eine neue hinzu, nämlich die exakte Abbildung des periodischen Anderson-Modells auf das antiferromagnetische KGM für beliebige Kopplungsstärke J. Reines EuO ist ein ferromagnetischer Halbleiter. Eu-reiches EuO zeigt einen gewaltigen Metall-Isolator-Übergang in der Nähe der Curie-Temperatur mit einem Sprung im Widerstand von bis zu 13 Größenordnungen. Das ist der größte Sprung im Widerstand, der jemals in der Natur beobachtet wurde. Wir reproduzieren diesen Sprung theoretisch mit der Kubo-Formel. Wir erzielen sehr gute Fits bereits in einer nicht vollständig selbstkonsistenten Theorie, bei der die Magnetisierung der Eu-Spins einer Brillouin-Funktion entnommen ist. In einer vollständig selbstkonsistenten Theorie bestimmen wir die Magnetisierung, die Curie-Temperatur, den spezifischen Widerstand und andere Transporteigenschaften. Wir berechnen Größen wie die elektronische Wärmeleitfähigkeit und die Thermokraft, für die weniger experimentelle Daten zum Vergleich vorhanden sind. Nichtsdestoweniger erscheinen z.B. die Rechnungen für die thermische Leitfähigkeit vertrauenswürdig, da das Wiedemann-Franz-Verhältnis mit der elektrischen Leitfähigkeit einen vernünftigen Wert liefert. Die Leitungselektronenzahl des Eu-reichen EuO kommt aus der Theorie unabhängig von der Leitfähigkeit heraus. Daher können wir aus der Leitfähigkeit und der Leitungselektronenzahl die durchschnittliche Drude-Mobilität (oder Streuzeit) berechnen. Diese Größe hat für höhere Impurity-(Sauerstoff-Leerstellen)-Konzentrationen einen Sprung in der Nähe der Curie-Temperatur von bis zu zwei Größenordnungen in Übereinstimmung mit dem Experiment. / In this thesis a model is formulated for Eu-rich EuO. It consists in an extension of the Kondo lattice model (KLM). For the KLM only a few exact statements exist. To those we add a new one, namely the exact mapping of the periodic Anderson model on the antiferromagnetic KLM for arbitrary coupling constant J. Pure EuO is a ferromagnetic semiconductor. Eu-rich EuO exhibits a huge metal--insulator transition near the Curie temperature with a jump in resistivity of up to 13 orders of magnitude. It is the biggest jump in resistivity ever observed in nature. We theoretically reproduce this jump. We achieve very good fits already within a not fully self-consistent theory where the magnetization of the Eu spins is taken from a Brillouin function. In a fully self-consistent theory we determine the magnetization, the Curie temperature, the resistivity and other transport properties. We calculate quantities like the electronic thermal conductivity and the thermopower, for which there are less experimental data to compare with. Nevertheless, e.g. the calculations for the thermal conductivity seem reliable since the Wiedemann-Franz ratio with the electrical conductivity gives a reasonable result. The conduction-electron number of Eu-rich EuO comes out of the theory independently of the conductivity. So we can calculate from the conductivity and the conduction-electron number the average Drude mobility (or scattering time). This quantitiy has a jump near the Curie temperature of up to two orders of magnitude for higher impurity (oxygen vacancy) concentrations in agreement with the experiment.
36

Ferromagnetism and interlayer exchange coupling in then metallic films

Kienert, Jochen 20 October 2008 (has links)
Die vorliegende Arbeit befasst sich mit dem ferromagnetischen Kondo-Gitter-Modell (s-d-, s-f-Modell) für Filmstrukturen. Die Spin-Fermion-Wechselwirkung des Modells kommt in Materialien vor, in denen lokalisierte Spins mit beweglichen Ladungsträgern wechselwirken, wie etwa in (verdünnten) magnetischen Halbleitern, Manganaten, oder Seltene-Erd-Verbindungen. Die durch die Ladungsträger vermittelte, indirekte Wechselwirkung zwischen den lokalisierten Spins reicht von der langreichweitigen, oszillierenden RKKY-Austauschwechselwirkung im Falle schwacher Kopplung bis zur kurzreichweitigen Doppelaustausch-Wechselwirkung bei starker Spin-Fermion-Kopplung. Beide Grenzfälle werden in dieser Arbeit durch die Abbildung des Problems auf ein effektives Heisenberg-Modell erfasst. Der Einfluss von reduzierter Translationssymmetrie auf die effektive Austauschwechselwirkung und auf die magnetischen Eigenschaften des ferromagnetischen Kondo-Gitter-Modells wird untersucht. Curie-Temperaturen werden für verschiedene Parameterkonstellationen berechnet. Die Auswirkungen von Ladungstransfer und von Gitter-Relaxation auf die magnetische Oberflächenstabilität werden betrachtet. Die Diskussion bezieht sich auf die Modifizierungen der Zustandsdichte und der kinetischen Energie im dimensionsreduzierten Fall, da die effektiven Austauschintegrale eng mit diesen Größen verknüpft sind. Die Bedeutung von Spinwellen für den Magnetismus dünner Filme und an der Oberfläche wird gezeigt. Die Interlagen-Austauschkopplung stellt ein besonders interessantes und wichtiges Beispiel der indirekten Wechselwirkung zwischen lokalisierten Momenten dar. Im Rahmen einer RKKY-Behandlung wird die Kopplung zwischen Monolagen in dünnen Filmen untersucht. Sie wird entscheidend durch die Art der ebenen und senkrechten Ladungsträgerdispersion bestimmt und ist jenseits eines kritischen Wertes der Fermi-Energie stark unterdrückt. Schließlich wird die temperaturabhängige magnetische Stabilität von interlagen-gekoppelten dünnen Filmen behandelt und die Bedingungen für einen temperaturgetriebenen magnetischen Reorientierungsübergang werden diskutiert. / This thesis is concerned with the ferromagnetic Kondo lattice (s-d, s-f) model for film geometry. The spin-fermion interaction of this model refers to materials in which localized spins interact with mobile charge carriers like in (dilute) magnetic semiconductors, manganites, or rare-earth compounds. The carrier-mediated, indirect interaction between the localized spins comprises the long-range, oscillatory RKKY exchange interaction in the weak-coupling case and the short-range double-exchange interaction for strong spin-fermion coupling. Both limits are recovered in this work by mapping the problem onto an effective Heisenberg model. The influence of reduced translational symmetry on the effective exchange interaction and on the magnetic properties of the ferromagnetic Kondo lattice model is investigated. Curie temperatures are obtained for different parameter constellations. The consequences of charge transfer and of lattice relaxation on the magnetic stability at the surface are considered. Since the effective exchange integrals are closely related to the electronic structure in terms of the density of states and of the kinetic energy, the discussion is based on the modifications of these quantities in the dimensionally-reduced case. The important role of spin waves for thin film and surface magnetism is demonstrated. Interlayer exchange coupling represents a particularly interesting and important manifestation of the indirect interaction among localized magnetic moments. The coupling between monatomic layers in thin films is studied in the framework of an RKKY approach. It is decisively determined by the type of in-plane and perpendicular dispersion of the charge carriers and is strongly suppressed above a critical value of the Fermi energy. Finally, the temperature-dependent magnetic stability of thin interlayer-coupled films is addressed and the conditions for a temperature-driven magnetic reorientation transition are discussed.
37

"Potencial estéreo-hidrofóbico e propriedades topológicas no enovelamento de proteínas". / Stereo-hydrophobic potential and topological properties in the protein folding

Tarragó, Maria Eulália Pinto 26 February 2003 (has links)
O entendimento dos princípios básicos do enovelamento proteico pode conduzir a muitas aplicações importantes. Embora não se conheçam todos os aspectos significativos envolvidos neste problema, experimentos e aproximações teóricas têm produzido avanços relevantes na sua compreensão, como, por exemplo, o papel dominante das forças hidrofóbicas. Com o propósito de contribuir para a identificação de alguns parâmetros determinantes no processo de folding, o objetivo deste trabalho consiste em estudar o potencial estéreo-hidrofóbico (isto é, o potencial hidrofóbico e um conjunto de especificidades estéricas adequadas) relacionado ao processo de enovelamento de proteínas globulares, evidenciando o papel das restrições estéricas e as características topológicas do estado nativo. Para tanto, empregou-se um modelo simplificado em rede cúbica, estudando-se, através de simulações Monte Carlo, o comportamento de mais de 40 cadeias tipo-proteínas, que apresentam estados nativos caracterizados pelos seguintes parâmetros topológicos: ordem de contato, χ, ordem de longo alcance e número φ de estruturas tipo grande manivela. Claramente, os resultados das simulações para as cadeias com configurações nativas, caracterizadas por baixo valor de χ e elevado valor de φ, são bastante diferenciados daqueles obtidos para as cadeias que apresentam configurações nativas com χ elevado e φ pequeno, evidenciando que o potencial estéreo-hidrofóbico, adotado neste trabalho, permite relacionar os comportamentos termodinâmico e cinético da cadeia tipo-proteína com os atributos topológicos da configuração nativa correspondente. Adicionalmente, mostrou-se que as restrições estéricas consideradas introduzem fortes mudanças na atividade configuracional, aumentando a estabilidade do estado nativo, bem como alterando, drasticamente, a curva da capacidade térmica, em função da temperatura, em comparação com os resultados das simulações obtidos com o potencial hidrofóbico (sem restrições estéricas). / The understanding of the basic principles of the protein folding process may lead to very important applications. Although all significant aspects of this problem are not yet known, experimental and theoretical results have given important contribution on the subject, as, for instance, about the dominant role of the hydrophobic forces. In order to contribute to the identification of significant ingredients for the folding process, the main goal of this work consists in studying the stereo-hydrophobic potential (that is, the hydrophobic potential and a set of steric specificities) related to the folding process of globular proteins, revealing the importance of the steric constraints and the role of the native structure. A minimalist lattice model was employed for this purpose, and more than forty distinct protein-like chains were studied. These chains were designed based on native structures characterized by topological parameters as contact order, χ, long range order and number φ of crankshaft-like structures. The Monte Carlo simulation results show clearly that the folding process depends strongly on the topological attributes of the native structure: thermodynamical and kinetic behavior for chains designed from native structures, presenting smaller χ and higher φ, are very distinguishable from those with higher χ and lower φ. Additionally it was shown that the steric constraints significantly modify the configurational activity, increasing the general conditions for the globule stability, as well changing drastically the shape of the thermal capacity behavior, as a function of the temperature, in comparison with the corresponding results obtained using the hydrophobic potential only, i.e., without the steric specificities.
38

Flussgleichungen für das Anderson-Gitter zur Beschreibung von Schwer-Fermion-Systemen

Meyer, Karsten 22 February 2004 (has links) (PDF)
In der vorliegenden Arbeit wird die Physik von Schwer-Fermion-Systemen, die durch Lanthanid- und Aktinid-Übergangsmetallverbindungen realisiert werden, untersucht. Die Basis für eine theoretische Beschreibung bildet das Anderson-Gitter, welches das Wechselspiel freier Leitungselektronen und stark korrelierter Elektronen aus lokalisierten f-Orbitalen charakterisiert. Als Zugang zu diesem Modell wird die von Wegner vorgeschlagene Flussgleichungsmethode verwendet, ein analytisches Verfahren, welches auf der Konstruktion eines effektiven Hamilton-Operators basiert. Ein zentrales Thema dieser Arbeit ist die Beschreibung der elektronischen Struktur von Schwer-Fermion-Systemen. Insbesondere wird die Abhängigkeit statischer Größen vom Einfluss verschiedener Systemparameter betrachtet. Die Dynamik kollektiver Anregungen in Schwer-Fermion-Systemen wird an Hand der elektronischen Zustandsdichten und dynamischen magnetischen Suszeptibilitäten untersucht. / The physical properties of heavy-fermion systems are examined. These systems are mainly formed by rare earth or actinide compounds. Their essential physics can be characterized by the periodic Anderson model which describes the interplay of itinerant metal electrons and localized, but strongly correlated f-electrons. The present calculations are based on the flow equations approach proposed by Wegner. This method uses a continuous unitary transformation to derive an effective Hamiltonian of an easy to treat structure. Within this framework the electronic structure of heavy-fermion systems is calculated and the influence of external parameters is studied. Beside the derivation of static properties the density of states and dynamic magnetic susceptibilities are investigated in order to characterize the nature of collective excitations.
39

"Potencial estéreo-hidrofóbico e propriedades topológicas no enovelamento de proteínas". / Stereo-hydrophobic potential and topological properties in the protein folding

Maria Eulália Pinto Tarragó 26 February 2003 (has links)
O entendimento dos princípios básicos do enovelamento proteico pode conduzir a muitas aplicações importantes. Embora não se conheçam todos os aspectos significativos envolvidos neste problema, experimentos e aproximações teóricas têm produzido avanços relevantes na sua compreensão, como, por exemplo, o papel dominante das forças hidrofóbicas. Com o propósito de contribuir para a identificação de alguns parâmetros determinantes no processo de folding, o objetivo deste trabalho consiste em estudar o potencial estéreo-hidrofóbico (isto é, o potencial hidrofóbico e um conjunto de especificidades estéricas adequadas) relacionado ao processo de enovelamento de proteínas globulares, evidenciando o papel das restrições estéricas e as características topológicas do estado nativo. Para tanto, empregou-se um modelo simplificado em rede cúbica, estudando-se, através de simulações Monte Carlo, o comportamento de mais de 40 cadeias tipo-proteínas, que apresentam estados nativos caracterizados pelos seguintes parâmetros topológicos: ordem de contato, χ, ordem de longo alcance e número φ de estruturas tipo grande manivela. Claramente, os resultados das simulações para as cadeias com configurações nativas, caracterizadas por baixo valor de χ e elevado valor de φ, são bastante diferenciados daqueles obtidos para as cadeias que apresentam configurações nativas com χ elevado e φ pequeno, evidenciando que o potencial estéreo-hidrofóbico, adotado neste trabalho, permite relacionar os comportamentos termodinâmico e cinético da cadeia tipo-proteína com os atributos topológicos da configuração nativa correspondente. Adicionalmente, mostrou-se que as restrições estéricas consideradas introduzem fortes mudanças na atividade configuracional, aumentando a estabilidade do estado nativo, bem como alterando, drasticamente, a curva da capacidade térmica, em função da temperatura, em comparação com os resultados das simulações obtidos com o potencial hidrofóbico (sem restrições estéricas). / The understanding of the basic principles of the protein folding process may lead to very important applications. Although all significant aspects of this problem are not yet known, experimental and theoretical results have given important contribution on the subject, as, for instance, about the dominant role of the hydrophobic forces. In order to contribute to the identification of significant ingredients for the folding process, the main goal of this work consists in studying the stereo-hydrophobic potential (that is, the hydrophobic potential and a set of steric specificities) related to the folding process of globular proteins, revealing the importance of the steric constraints and the role of the native structure. A minimalist lattice model was employed for this purpose, and more than forty distinct protein-like chains were studied. These chains were designed based on native structures characterized by topological parameters as contact order, χ, long range order and number φ of crankshaft-like structures. The Monte Carlo simulation results show clearly that the folding process depends strongly on the topological attributes of the native structure: thermodynamical and kinetic behavior for chains designed from native structures, presenting smaller χ and higher φ, are very distinguishable from those with higher χ and lower φ. Additionally it was shown that the steric constraints significantly modify the configurational activity, increasing the general conditions for the globule stability, as well changing drastically the shape of the thermal capacity behavior, as a function of the temperature, in comparison with the corresponding results obtained using the hydrophobic potential only, i.e., without the steric specificities.
40

Nonlinear reactive processes in constrained media

Bullara, Domenico 27 March 2015 (has links)
In this thesis we show how reactive processes can be affected by the presence of different types of spatial constraints, so much so that their nonlinear dynamics can be qualitatively altered or that new and unexpected behaviors can be produced. To understand how this interplay can occur in general terms, we theoretically investigate four very different examples of this situation. <p><p>The first system we study is a reversible trimolecular chemical reaction which is taking place in closed one-dimensional lattices. We show that the low dimensionality may or may not prevent the reaction from reaching its equilibrium state, depending on the microscopic properties of the molecular reactive mechanism. <p><p>The second reactive process we consider is a network of biological interactions between pigment cells on the skin of zebrafish. We show that the combination of short-range and long-range contact-mediated feedbacks can promote a Turing instability which gives rise to stationary patterns in space with intrinsic wavelength, without the need of any kind of motion.<p><p>Then we investigate the behavior of a typical chemical oscillator (the Brusselator) when it is constrained in a finite space. We show that molecular crowding can in such cases promote new nonlinear dynamical behaviors, affect the usual ones or even destroy them. <p><p>Finally we look at the situation where the constraint is given by the presence of a solid porous matrix that can react with a perfect gas in an exothermic way. We show on one hand that the interplay between reaction, heat flux and mass transport can give rise to the propagation of adsorption waves, and on the other hand that the coupling between the chemical reaction and the changes in the structural properties of the matrix can produce sustained chemomechanical oscillations. <p><p>These results show that spatial constraints can affect the kinetics of reactions, and are able to produce otherwise absent nonlinear dynamical behaviors. As a consequence of this, the usual understanding of the nonlinear dynamics of reactive systems can be put into question or even disproved. In order to have a better understanding of these systems we must acknowledge that mechanical and structural feedbacks can be important components of many reactive systems, and that they can be the very source of complex and fascinating phenomena.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

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