I present a study of close white dwarf (WD) and M dwarf (dM) binary systems (WD+dM) to examine the effects that close companions have on the magnetic field generation in dMs. Using the Sloan Digital Sky Survey (SDSS) Data Release 8 spectroscopic database, I construct a sample of 1756 WD+dM high-quality pairs. I show that high-mass dMs (≤M4) in close binary systems are more likely to be magnetically active (as measured by Hα emission) and are able to remain active longer than field dMs. At lower masses (≥M5), where dMs become fully convective, the activity fraction and activity lifetimes of WD+dM binary systems become more comparable to those of the field dMs. The implications of having a close binary companion may include, increased stellar rotation through disk disruption, tidal effects, and/or angular momentum exchange. Thus, the similarity in activity between late-type field dMs and late-type dMs with close companions is likely due to the mechanism generating magnetic fields being less sensitive to the effects caused by a close companion; namely, increased stellar rotation. Using a subset of 181 close WD+dM pairs, matched to the time-domain SDSS Stripe 82 catalog, I show that enhanced magnetic activity extends to the flaring behavior of dMs in close binaries. Specifically, early spectral type dMs (M0-M1), in close WD+dM pairs, are two orders of magnitude more likely to flare than field dMs, whereas mid-type dMs (M2-M3) and late-type dMs (M4-M6) flare as frequently or less than the mid- to late-type field dM sample. To test whether the presence of a close companion leads to star-star interactions, I search for correlations between the WD occultations and flares from the dM member in KOI-256, an eclipsing WD+dM system from Kepler I find no correlations between the flaring activity of the dM and the WD occultations, indicating the there are no obvious signs of star-star interactions at work. In addition, the dM member of KOI-256 flares more than any other dM observed by Kepler and shows evidence for solar-like magnetic activity cycles, a feature not seen in many dMs to date.

This thesis is focused on the problem of growth and integrability in multi-valued dynamics generated by $SL_2 (\mathbb{Z})$ actions. An important example is given by Markov dynamics on the cubic surface $$x^2+ y^2 +z^2 = 3xyz,$$ generating all the integer solutions of this celebrated Diophantine equation, known as Markov triples. To study the growth problem of Markov numbers we use the binary tree representation. This allows us to define the Lyapunov exponents $\Lambda (x)$ as the function of the paths on this tree, labelled by $x \in \mathbb{R}P^1$. We prove that $\Lambda (x)$ is a $PGL_2 (\mathbb{Z})$-invariant function, which is zero almost everywhere but takes all values in $\left[ 0, \ln \varphi \right]$ (where $\varphi$ denotes the golden ratio). We also show that this function is monotonic, and that its restriction to the Markov-Hurwitz set of most irrational numbers is convex in the Farey parametrisation. We also study the growth problem for integer binary quadratic forms using Conway's topograph representation. It is proven that the corresponding Lyapunov exponent $\Lambda_Q(x) = 2 \Lambda(x)$ except for the paths along the Conway river. Finally, we study the tropical version of the Markov dynamics on the tropical version of the Cayley cubic proposed by Adler and Veselov, and show that it is semi-conjugated to the standard action of $SL_2(\mathbb{Z})$ on a torus. This implies the dynamics is ergodic, with the Lyapunov exponent and entropy given by the logarithm of the spectral radius of the corresponding matrix.

Atualmente, a adição de uma nova função implementada em hardware em um processador não deve impor nenhuma mudança no conjunto de instruções (ISA – Instruction Set Architecture) suportado para atingir melhorias em seu desempenho. O objetivo é manter a compatibilidade retroativa e futura de programas já compilados. Todavia, este fato se torna, muitas vezes, um fator impeditivo para o aprimoramento ou desenvolvimento de uma nova arquitetura. Desta maneira, a utilização de mecanismos de Tradução Binária abre novas oportunidades aos projetistas, já que estes mecanismos permitem a execução de programas já compilados em arquiteturas que suportam conjuntos de instruções diferentes do previsto inicialmente. Assim, para eliminar o custo adicional apresentado por estes sistemas de tradução, será proposto um novo mecanismo de tradução binária dinâmico de dois níveis. Enquanto o primeiro nível é responsável pela tradução de facto das instruções do conjunto nativo para instruções de uma linguagem de máquina intermediária, o segundo nível otimiza estas instruções já traduzidas para serem executadas na arquitetura alvo. O sistema é totalmente flexível, pois pode suportar a tradução de conjuntos de instruções completamente diferentes; assim como a utilização de arquiteturas de hardware com as mais diversas características. Este trabalho apresenta o primeiro esforço nesta direção: um estudo de caso onde ocorre a tradução de código x86 para MIPS (linguagem intermediária), que será otimizado para ser executado em uma arquitetura que realiza reconfiguração dinâmica. Resta demonstrado que é possível manter a compatibilidade binária, com melhoria no desempenho em torno de 45% em média e consumo de energia semelhante ao da execução nativa. / In these days, every new added hardware feature must not change the underlying instruction set architecture (ISA), in order to avoid adaptation or recompilation of existing code. Therefore, Binary Translation (BT) opens new possibilities for designers, previously tied to a specific ISA and all its legacy hardware issues, since it allows the execution of already compiled applications on different architectures. To overcome the BT inherent performance penalty, we propose a new mechanism based on a dynamic two-level binary translation system. While the first level is responsible for the BT de facto to an intermediate machine language, the second level optimizes the already translated instructions to be executed on the target architecture. The system is totally flexible, supporting the porting of radically different ISAs and the employment of different target architectures. This work presents the first effort towards this direction: it translates code implemented in the x86 ISA to MIPS assembly (the intermediate language), which will be optimized by the target architecture: a dynamically reconfigurable architecture. In this work is showed that is possible to maintain binary compatibility with performance improvements on average 45% and similar energy consumption when compared to native execution.

As limitações resultantes do avanço das tecnologias de integração, como o crescente aumento da densidade de potência, levando à necessidade de redução da frequência de operação dos circuitos somados à necessidade de redução do consumo energético, sejam por motivos ecológicos ou para melhor suprir dispositivos portáteis, trazem a necessidade de maior intervenção e personalização do hardware em relação às exigências do software. Em diversos níveis estas intervenções podem ser aplicadas, onde a granularidade pode variar desde elementos de processamento sendo completamente desativados até processadores tendo apenas unidades funcionais sendo desativadas, memórias cache reconfiguradas em tamanho e associatividade, etc. Entretanto, a reconfiguração do hardware deve atingir todas as etapas destes sistemas para que seja possível atingir redução satisfatória em termos de potência e consumo de energia. Além da integração acelerada de elementos de processamento em um mesmo circuito integrado, a crescente concentração de heterogêneas tarefas em um mesmo dispositivo, leva à integração de elementos de processamento também heterogêneos, e por consequência diferentes comportamentos variando de acordo com a aplicação. Para justificar esta reconfigurabilidade e heterogeneidade dos elementos de processamento este trabalho apresenta um estudo que possibilita a observação da execução de diferentes aplicações em elementos de processamento amplamente reconfiguráveis. Para que a reconfigurabilidade e heterogeneidade possam ser aplicáveis, foi inserida uma ferramenta capaz de manter a compatibilidade entre o elemento de processamento mestre e os elementos de processamento aceleradores reconfiguráveis disponíveis. Os experimentos apresentados baseiam-se na necessidade de manter a menor quantidade de silício ativa, acelerando o código fonte enquanto reduz-se o consumo de energia. Somada a redução de energia, a compatibilidade binária é levada em consideração buscando a manutenção da produtividade quando da utilização de sistemas heterogêneos reconfiguráveis. / The limitations resulting from the advancement of integration technologies, such as the increasing power density, leading to the need to reduce the operating frequency of the circuits added to the need to reduce energy consumption, whether for environmental reasons or to better serve mobile devices, bring the need for greater intervention and hardware customization to the demands of the software. To varying degrees these interventions can be applied where the granularity can range from processing elements being completely disabled until processors having only functional units being disabled, reset cache memories in size and associativity, etc. However, the reconfiguration of hardware should reach all stages of these systems so that you can achieve satisfactory reduction in power and energy consumption. In addition to the accelerated integration of processing elements on a single integrated circuit, the increasing concentration of heterogeneous tasks in a same device, also leads to the integration of heterogeneous processing elements, and therefore different behavior varies according to the application. To justify this reconfigurability and variety of processing elements this work presents a study that allows the observation of the implementation of different applications in widely reconfigurable processing elements. For reconfigurability and heterogeneity may be applicable, a tool to maintain compatibility between the master processing element and accelerators reconfigurable processing elements available was inserted. The experiments presented are based on the need to maintain the lowest amount of active silicon, accelerating the source code while reducing power consumption. Added to energy reduction, binary compatibility is taken into consideration seeking to maintain productivity when using reconfigurable heterogeneous systems.

Molecular Dynamics (MD) simulation methods were used to perform simulations of the adsorption of multilayer films of three fluoromethane compounds -- nonpolar CF4 and its polar relatives, CF3Cl and CF3Br -- onto two chemically and structurally different substrates: graphite and hydroxylated α-quartz (a form of silica). The purpose of the simulations was to determine how differences in polarity and substrate type affect the structure of film layers at the adsorption surface, as well as to compare how these factors affect the mobility of molecules near the surface as they move along or away from the surface, to see how each of these factors affects the substrate affinity for the adsorbed compound. Simulations were performed for pure fluoromethane films as well as films created from binary mixtures of the above fluoromethanes adsorbed on each substrate over a range of temperatures from 80 K to 280 K. Analysis suggests a strong influence of substrate characteristics on both the structure and mobility of molecules in adsorbed layers, an effect that is partially temperature dependent but only weakly suggestive of effects due to the differences in polarity of the adsorbed molecules.

OLIVEIRA, Paulo William Simão de. Estudo das propriedades estruturais e dinâmicas de um sistema binário quasi-unidimensional. 2007. 105 f. Dissertação (Mestrado em Física) - Programa de Pós-Graduação em Física, Departamento de Física, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2007. / Submitted by Edvander Pires (edvanderpires@gmail.com) on 2015-05-22T19:35:48Z No. of bitstreams: 1 2007_dis_pwsoliveira.pdf: 2259918 bytes, checksum: 48074a559be7bed99a345a92c3c2a969 (MD5) / Approved for entry into archive by Edvander Pires(edvanderpires@gmail.com) on 2015-05-22T20:06:53Z (GMT) No. of bitstreams: 1 2007_dis_pwsoliveira.pdf: 2259918 bytes, checksum: 48074a559be7bed99a345a92c3c2a969 (MD5) / Made available in DSpace on 2015-05-22T20:06:53Z (GMT). No. of bitstreams: 1 2007_dis_pwsoliveira.pdf: 2259918 bytes, checksum: 48074a559be7bed99a345a92c3c2a969 (MD5) Previous issue date: 2007 / The aim of this work is to study the structural and dynamical properties of a classical binary system of charged particles confined in a two dimensional channel. Such a system is described in the literature as quasi-unidimensional, and its relevance is supported by the possibility of technological applications, shown recently in the scientific literature, and also the interest and understanding of properties in condensed matter physics. Although the theoretical and numerical character of the present work, several experimental systems can be described by the present model. The summary of the contents of this work is presented in each chapter. In chapter 1, a general overview is given. The concept of Wigner crystallization is introduced, and examples of experimental systems, which exhibit such an ordered phase under proper conditions are given. We discuss the physics of complex plasmas, colloidal suspensions and applications in biological systems. A description of the simulation method is given in chapter 2. Scale transformations are introduced in order to construct a general model, i.e. no longer depending on particular features of the system, but only on relevant parameters of a general model. The Molecular Dynamics simulation technique (MD) is presented, focusing on the Langevin Dynamics. The competition between the inter-particle interaction, in the form of the electrostatic repulsion, and the external confinement, which is assumed to be parabolic and act only in one direction, generates a chain-like strutural pattern. A description of the model, the harmonic approach used in the analytical calculations of the normal modes spectrum, and the analytical calculation of the energy per particle of the different chain-configutations are given in chapter 3. The ground state configurations, the structural phase transitions and normal modes of the present chain-like binary system are presented in Chapter 4. In the low density regime particles crystallize in a single chain. When the density is increased a zig-zag transition occurs and the single chain splits into two chains. Such a transition is characterized by a spontaneous symmetry breaking. With the increase of the density the system changes to the four-chains configuration (case 1) (particles not aligned vertically), where the two -> four chains (case 1) transition occurs through a zig-zag transition accompanied by a shift along the chain direction. A further increase of the density will lead the system to a new ground state configuration with four chains (case 2) (particles aligned vertically). The dynamical properties are related to the phonon spectrum, in which the number of normal modes is two times the number particle in the unit cell. The conclusions and perspectives are presented in chapter 5. / O objetivo deste trabalho é estudar as propriedades estruturais e dinâmicas de um sistema binário clássico consistindo de partículas carregadas que estão confinadas em um canal bidimensional. Tal sistema é descrito na literatura como quasi-unidimensional, e esta relevância apoia-se na possibilidade de aplicações tecnológicas, como tem sido mostrado recentemente na literatura científica, bem como no interesse e entendimento em propriedades da Física da matéria condensada. Apesar do caráter teórico do presente estudo, diversos sistemas experimentais podem ser descritos pelo modelo aqui considerado. O resumo do conteúdo deste trabalho é apresentado em cada capítulo. No capítulo 1, é dada uma visão geral do presente trabalho. O conceito da cristalização de Wigner é introduzido e são dados exemplos de sistemas experimentais, que exibem uma fase ordenada sob circunstâncias apropriadas. Discute-se a Física dos plasmas complexos, das suspensões coloidais e aplicações em sistemas biológicos. Uma descrição do método de simulação é dada no capítulo 2. As transformações de escalas são introduzidas a fim de construir um modelo geral, isto é, não dependente das características particulares do sistema, mas somente das quantidades relevantes gerais. Apresenta-se a técnica de simulação por Dinâmica Molecular (DM), focalizando também a Dinâmica de Langevin. A competição entre a interação entre partícula, na forma de repulsão eletrostática, e o confinamento externo, que é suposto parabólico e age somente em uma direção, gera uma estrutura de cadeias no sistema. Uma descrição do modelo, bem como a aproximação harmônica utilizada para o cálculo dos modos normais e o cálculo da energia por partícula das várias estruturas de cadeias são dadas no capítulo 3. A configuração do estado fundamental, as transições estruturais de fase e modos normais para o sistema binário de cadeias são examinadas no capítulo 4. Para baixas densidades as partículas cristalizam-se em uma única cadeia; com o aumento da densidade uma transição zig − zag ocorre e a única cadeia se parte em duas. Observa-se que esta transição estrutural é caracterizada por uma quebra espontânea de simetria. Com o aumento da densidade, o sistema passa para quatro cadeias (caso 1) (partículas não alinhadas na vertical), onde a transição de duas para quatro cadeias (caso 1) ocorre com uma transição zig − zag, em cada uma das cadeias, acompanhadas por um deslocamento ao longo da direção da cadeia. Então com um aumento da densidade conduzirá a uma nova estrutura de quatro cadeias (caso 2) (partículas alinhadas na vertical). As propriedades dinâmicas aqui consideradas resumem-se ao espectro de fônons, no qual o número de modos normais é igual ao dobro do número de partículas na célula unitária. As conclusões e perspectivas são apresentadas no capítulo 5.

DELFINO, Jair. Ifá e Odús: interdisciplinaridade, lógica binária, cultura e filosofia africana. 2016. 106f. – Dissertação (Mestrado) – Universidade Federal do Ceará, Programa de Pós-graduação em Educação Brasileira, Fortaleza (CE), 2016. / Submitted by Márcia Araújo (marcia_m_bezerra@yahoo.com.br) on 2016-04-26T11:27:11Z No. of bitstreams: 1 2016_dis_jdelfino.pdf: 4763014 bytes, checksum: 4dd053fbbc1d1fc95331c06e51401d3b (MD5) / Approved for entry into archive by Márcia Araújo (marcia_m_bezerra@yahoo.com.br) on 2016-04-26T16:57:00Z (GMT) No. of bitstreams: 1 2016_dis_jdelfino.pdf: 4763014 bytes, checksum: 4dd053fbbc1d1fc95331c06e51401d3b (MD5) / Made available in DSpace on 2016-04-26T16:57:00Z (GMT). No. of bitstreams: 1 2016_dis_jdelfino.pdf: 4763014 bytes, checksum: 4dd053fbbc1d1fc95331c06e51401d3b (MD5) Previous issue date: 2016 / Within the history of studies and African culture and afrodescendencia this dissertation is an innovative integration within the Ifa tradition. Ifa is a literary and philosophical body, which descends from a deity between two worlds understood as the physical and the spiritual. The systematization of Ifa representations work questions on binary algebra and organization of Ifa meanings was the purpose of the idealized research. The importance of this issue is to examine specific knowledge of a culture and tradition that has the educational process orality and the preservation of interdisciplinary culture. We add our proposal for the systematic examination of the concepts and propositions of life that includes developing the collectivity and individuality in learning and understanding through the exercise of philosophical virtues, specific thinking Yoruba, starting from the design of nature and divine genealogy of creation within the African tradition inherited from Ancient Egypt. Ifa is cultural diversity that can be science, religion and sociability. We bring to this body of work beyond what has already been explained geometry, aesthetics and medicine within the inter-relational aspect to show as is the absorption of knowledge. We intend to stay away from the universalistic, Eurocentric theoretical basis seeking the deepening of African philosophy and interdisciplinarity to contemplate the cultural and ethnic-Brazilian aspects as well as being in accordance with Law No. 10,639 / 03. Thus, based on orality present in religions of African origin, and through the literary body of Ifá, embark on the complexity of reason and metaphysics and timeless logic to understand cognition in the aspect of institutiva worldview values and principles. / Dentro dos estudos de história e cultura africana e afrodescendente a presente dissertação faz uma inserção inovadora dentro da tradição do Ifá. O Ifá é um corpo literário e filosófico, que descende de uma divindade entre dois mundos entendidos como o físico e o espiritual. As sistematizações das representações do Ifá trabalham as questões sobre álgebra binária e a organização dos significados do Ifá foi o objetivo da pesquisa idealizada. A importância deste tema está em examinar conhecimentos específicos de uma cultura e tradição que tem como processo educativo a oralidade e a preservação da cultura interdisciplinar. Adicionamos à nossa proposta o exame sistemático dos conceitos e proposições de vida que abrange desenvolver a coletividade e individualidade, no aprender e entender através do exercício das virtudes filosóficas, específicas do pensar yorubá, partindo da concepção da natureza e da genealogia divina da criação dentro da tradição africana herdada do Antigo Egito. Ifá é pluralidade cultural que pode ser ciência, religião e sociabilidade. Além do que já foi explanado, trazemos para este corpo de trabalho a geometria, estética e medicina dentro do aspecto inter-relacional, a fim de mostrar como acontece a absorção de conhecimentos. Pretendemos ficar distantes da base teórica universalista e eurocentrista buscando o aprofundamento da filosofia africana e a interdisciplinaridade para contemplar os aspectos culturais e étnico-brasileiros bem como estar de acordo com a Lei n° 10.639/03. Assim, com base na oralidade presente nas religiões de matriz africana e, através do corpo literário do Ifá, embarcaremos na complexidade da razão e da lógica metafísica e atemporal para entendermos a cognição no aspecto da cosmovisão institutiva de valores e princípios.

Made available in DSpace on 2014-06-11T19:25:29Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-08-29Bitstream added on 2014-06-13T19:53:17Z : No. of bitstreams: 1 gaspar_hs_me_guara.pdf: 5532943 bytes, checksum: 36914104bcf66e5c6eede927677242df (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A existência de satélites irregulares é um tema de interesse científico há muito tempo devido às suas características peculiares, isto é, órbitas bem excêntricas, distantes do planeta e geralmente com altas inclinações em relação ao plano equatorial de seu planeta, chegando a ser em grande parte retrógradas. A existência de famílias de satélites irregulares, caracterizadas pela semelhança dos elementos orbitais dos satélites que as compõem é, ainda hoje, um fato não explicado. Tais características sugerem que os satélites irregulares não tenham sido formados juntamente com os planetas que estes orbitam, como se acredita ser o caso dos satélites regulares. Deste modo, uma explicação coerente para a existência dos mesmos é a captura gravitacional de corpos, formados em outras regiões, a partir de órbitas heliocêntricas após a ocorrência de um encontro próximo com o planeta. Entretanto, sob a dinâmica do Problema Circular Restrito de Três Corpos - PCR3C - capturas gravitacionais têm carater temporário, o que torna necessária a existência de um mecanismo de captura auxiliar. Isto tem incentivado, por anos, à proposição de vários modelos para explicar a existência dos satélites irregulares através da captura gravitacional, dentre os quais três se destacam na literatura: Dissipação por arrasto em gás, Pull-down capture – captura por puxão, interação colisional ou por encontros próximos com satélites pré-existentes, capturas de planetesimais durante encontros planetários e captura de asteróides binários. Considerando a dinâmica de 4-Corpos, investigamos numericamente a viabilidade de um modelo no qual um ente de um asteróide binário é capturado após sofrer um encontro próximo com um Júpiter, avaliando as condições que propiciam a captura de cada um dos membros, realizando um mapeamento dos parâmetros de modo... / The existence of irregular satellites has been the focus of scientific interest for many years. That is due to their peculiar orbital features, i.e., highly eccentric orbits, large distance from the planet and, usually, with high inclination and many of them are retrograde. There are very well characterized families of irregular satellites, whose origin were not explained yet. These features suggest that irregular satellites were not formed together with the planet, during its formation stage, as were the regular ones. Therefore, an explanation for their existence is the gravitational capture of asteroids, originally in heliocentric orbits, that had a close encounter with the planet. However, considering only the Restrict Three Body Problem dynamics, it is not possible to accomplish permanent captures, being necessary the existence of an auxiliary mechanism. Then, several models were proposed in order to generate a permanent capture. Among the most important we found Gas drag dissipation, Pull-down capture, collisional and close encounters interactions with regular satellites, capture during planetary encounters and capture of binary asteroids. The current research had assessed how viable is a 4-body mechanism in which a member body of a binary asteroid remain captured after a close encounter with Jupiter. In order to accomplish that, we have mapped a set o parameters in order to find the proper conditions to yield the capture of one member. From the main results it is shown a very well permanent capture probability of the minor member when the primordial binary asteroid disrupts at a suitable “quadrature” configuration. Finally, it is also shown that this capture mechanism is well explained through energy exchanges.

The thesis presents detailed results of theoretical analyses based on extensive computer simulation studies with an aim to explore, quantify whenever possible, and understand structure and dynamics of polymers and proteins in several complex solvents. In order to make the Thesis coherent, we also study certain aspects of binary mixtures. Based on the phenomena studied, the thesis has been divided into four major parts: I. Dynamics of biological water: Distance dependent variation of dielectric constants in aqueous protein solutions II. Temperature dependent study of structural transformations in aqueous binary mixtures III. Conformation and dynamics of polymers in solution: Role of aqueous binary mixtures IV. Conformational change and unfolding dynamics of proteins: Role of sol-vent environment The above mentioned four parts have further been divided into thirteen chapters. In the following we provide a brief chapter-wise outline of the thesis. Part I consists of two chapters, where we focus on the study of dynamics of biological water and distance dependent variation of static and dynamic proper-ties (including dielectric constant) of water near different proteins. To start with, chapter 1 provides an introduction to the structure and dynamics of biological water. Here we discuss different experimental studies; including dielectric relaxation, NMR and salvation dynamics those explore the bimolecular hydration dynamics in great detail. We also discuss the wide range of computer simulation and theoretical studies that have been carried out to understand the dynamical behaviour of biological water. In chapter 2, we present our molecular dynamics simulation study to ex-plore the distance dependent static and dynamic behaviour of biological water near four different protein surfaces. Proteins are known to have large permanent dipole moments that can influence structure and dynamics of even distant water molecules. Therefore, distance dependence of polarization punctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different char-acteristics and varying sizes. We find that the calculated dielectric constants of the systems show a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water is found to be sensitive to the nature of the protein. We also define and calculate the effective dielectric constant of successive layers and find that the layer adjacent to protein always has significantly lower value (∼ 50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4–5 layers away. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in this chapter. Part II deals with the temperature dependent study of aqueous DMSO and ethanol solutions and consists of three chapters. Chapter 3 provides a general introduction to the non-ideality (deviation from Raoult’s law) encountered in different binary mixtures. We discuss different theoretical models for treatment of binary mixtures. Finally we provide a systematic study about the non-ideality observed in aqueous binary mixtures. Here we discuss the anomalies observed in such systems and carry out a brief survey on the existing ideas of structural transformations associated with the solvation of a foreign molecule in water. In chapter 4, we discuss the results of temperature dependent study of struc-tural and dynamic properties of aqueous dimethyl sulfoxide (DMSO) mixture. It is now well-known that aqueous DMSO mixture exhibits signature of perco-lation driven structural aggregation at a mole fraction range xDMSO ≈ 0.15. We study the structural and dynamical change in this binary mixture below and above the percolation threshold along with decreasing temperature. Significant change in the molecular structure of DMSO as well as that of water is observed above the percolation threshold at a lower temperature, particularly at 200K. The structural arrangement of the DMSO molecules is found to be progressively more ordered with increasing DMSO concentration and decreasing temperature. On the other hand, water structure is found to be significantly deviated from tetrahedral arrangement in presence of DMSO clusters even at low temperature. The dynamics of water is also found to be considerably affected with increase of concentration and lowering of temperature. Similar phenomenon is observed for another amphiphilic molecule, ethanol, and has been discussed in chapter 5. Aqueous ethanol mixture is a widely studied solvent, both experimentally and using computer simulations. All the studies indicate several distinct salvation regimes. In recent molecular dynamics simulation studies, the reason for formation of micro-aggregates of ethanol is again attributed to percolation driven structural transformation. We carry out a temperature dependent study of water-ethanol binary mixture, particularly at low ethanol concentration to understand the molecular origin of such structural transformation. We find that the structural arrangement of ethanol as well as water molecules is similarly affected as that of DMSO with lowering of temperature. However, dynamics of water molecules in aqueous ethanol solution is found to be marginally affected, unlike the case of aqueous DMSO solution. We discuss the microscopic reason for such behaviour in a detailed manner. In Part III, we discuss the dynamics of linear polymer chains in different aqueous binary mixtures. Here we have three chapters. In chapter 6, we carry out a brief survey of the existing theories of polymers in solution. We discuss the quality of solvents depending on the preferred interactions between the polymer and the solvent or the polymer with its own. We also discuss the celebrated Flory-Huggins theory. We derive the expression of free energy of the Flory-Huggins theory in terms of the volume fraction of monomer and solvent molecules. In chapter 7, we discuss the results of our study of polymer dynamics in aqueous DMSO solution. We find that at a mole fraction 0.05 of DMSO (xDMSO ≈ 0.05) in aqueous solution, a linear polymer chain of intermediate length (n=30) adopts collapsed conformation as the most stable conformational state. The same chain exhibits an intermittent oscillation between the collapsed and the extended coiled conformations in neat water. Even when the mole fraction of DMSO in the bulk is 0.05, the concentration of the same in the first hydration layer around the polymer is found to be as large as 17 %. Formation of such hydrophobic environment around the hydrocarbon chain may be viewed as the reason for the collapsed conformation gaining additional stability. We find a second anomalous behaviour to emerge near xDMSO ≈ 0.15 that is attributed to the percolation driven structural aggregation of DMSO that lowers the relative concentration of the DMSO molecules in the hydration layer. In chapter 8, we carry out similar study of linear polymer chain in water– ethanol binary mixture. In this case also, we find a sudden collapse of the poly-merat xEtOH ≈ 0.05. Since ethanol molecules are known to form micro-aggregates in this concentration range, stability of collapsed state of polymer at this con-centration is anticipated to be correlated to this phenomenon. In fact, a purely hydrophobic polymer chain, in its collapsed form is anticipated to assist in the formation of spanning cluster comprised of hydrophobic ethyl groups at this concentration range thereby facilitating the percolation transition. We discuss these prospects in this chapter. Part IV deals with the solvent sensitivity to the conformational change and unfolding dynamics of protein. Part IV consists of five chapters. In chapter 9, we develop an understanding of protein folding and unfolding dynamics by discussing the fundamental theories developed in the last few decades. We also discuss the major role of solvents in stabilizing or destabilizing the native, ordered state. In chapter 10, we present a detailed study of unfolding of a small protein, chicken villin headpiece (HP36) in water-ethanol binary mixture, using molecular dynamics simulations. The prime objective of this work is to explore the sensitivity of protein dynamics towards increasing concentration of the cosolvent and unravel essential features of intermediates formed in the unfolding path-way. In water–ethanol binary mixtures, HP36 is found to unfold partially, under ambient conditions, that otherwise requires temperature as high as ∼ 600K to denature in pure aqueous solvent. The study unravels certain interesting aspects about the pathway of unfolding, guided by the formation of unique intermediates. Unfolding is initiated by the separation of hydrophoic core comprising three phenylalanine residues (Phe7, Phe11, Phe18). This separation initiates the melting of the helix2 of the protein. However, with an increase of cosolvent concentration different partially unfolded intermediates are found to be formed. We attribute the emergence of such partially unfolded states to the preferential solvation of hydrophobic residues by the ethyl groups of ethanol. We explore and subsequently quantify the detailed dynamics of unfolding in water-ethanol that appear to be more complex and sensitive to solvent composition. With an aim to develop a general understanding of the role of water–ethanol binary mixture in facilitating anomalous conformational dynamics of proteins, we carry out combined theoretical and experimental studies to explore detailed structural change of a larger protein, Myoglobin with increasing ethanol concentration. These studies are described in chapter 11. In agreement with our pre-vious observations, we identify in this case two well-defined structural regimes, one at xEtOH ≈ 0.05 and the other at xEtOH ≈ 0.25, characterized by formation of distinct partially folded conformations and separated by a unique partially unfolded intermediate state at xEtOH ≈ 0.15. We also find non-monotonic com-position dependence of (i) radius of gyration (ii) long range contact order (iii) residue specific solvent accessible surface area of tryptophan (iv) circular dichro-ism spectra and UV-absorption peaks. Multiple structural transformations, well-known in water-ethanol binary mixture, appear to have considerably stronger effects on the conformation and dynamics of protein Myoglobin. In chapter 12, we explore the free energy surface of unfolding pathway through umbrella sampling, for the small globular alpha-helical protein chicken-villin headpiece (HP36) in three different solvent conditions (water, xDMSO ≈ 0.15 and xDMSO ≈ 0.3). Recently established as a facilitator of helix melting, DMSO is found to be a good denaturant for HP36 and at a mole fraction of xDMSO ≈ 0.3, complete melting of the protein is ensured. The unfolding proceeds through initial separation or melting of the same aggregated hydrophobic core that com-prises three phenylalanine residues (Phe7, Phe11 and Phe18) accompanied by simultaneous melting of the helix2. Unfolding is found to be a multistage process involving crossing of three consecutive minima and two barriers at the initial stage. At a molecular level, Phe18 is observed to reorient itself towards other hy-drophobic grooves to stabilize the intermediate states. We identify the configuration of intermediates in all the solvent conditions which are found to be unique for the corresponding minima with similar structural arrangement. Consider-able softening of the barriers is observed with increasing DMSO concentration. Higher concentration of DMSO tunes the unfolding pathway by destabilizing the third minimum and stabilizing the second one, indicating the development of solvent modified, less rugged pathway. Chapter 13 provides a detailed microscopic mechanism of DMSO induced unfolding of HP36. We analyze the free energy contours of the protein HP36, obtained from molecular dynamics simulation in xDMSO ≈ 0.15 and xDMSO ≈ 0.3. The most probable intermediates obtained from the free energy contours are found to be similar to those obtained from umbrella sampling which again sup-ports the fact that the melting proceeds through formation of a series of unique intermediates. We characterize the preferential hydrophobic salvation of the hydrophobic core that drives the melting of secondary structure, by calculating time dependent radial distribution function and identifying the formation of strong orientation order between methyl groups of DMSO and phenyl alanine residues. Finally we employ Kramer’s rate equation to calculate the rate of bar-rier crossing that reveals significantly faster rate of unfolding with increasing DMSO concentration that is in agreement with simulation results. Whenever possible, we have discussed the scope of future work at the end of each chapter.

abstract: Image segmentation is of great importance and value in many applications. In computer vision, image segmentation is the tool and process of locating objects and boundaries within images. The segmentation result may provide more meaningful image data. Generally, there are two fundamental image segmentation algorithms: discontinuity and similarity. The idea behind discontinuity is locating the abrupt changes in intensity of images, as are often seen in edges or boundaries. Similarity subdivides an image into regions that fit the pre-defined criteria. The algorithm utilized in this thesis is the second category. This study addresses the problem of particle image segmentation by measuring the similarity between a sampled region and an adjacent region, based on Bhattacharyya distance and an image feature extraction technique that uses distribution of local binary patterns and pattern contrasts. A boundary smoothing process is developed to improve the accuracy of the segmentation. The novel particle image segmentation algorithm is tested using four different cases of particle image velocimetry (PIV) images. The obtained experimental results of segmentations provide partitioning of the objects within 10 percent error rate. Ground-truth segmentation data, which are manually segmented image from each case, are used to calculate the error rate of the segmentations. / Dissertation/Thesis / Masters Thesis Electrical Engineering 2015