The beta hairpin structure within ribosomal protein S5 mediates interplay between domains II and IV and regulates HCV IRES function

Translation initiation in Hepatitis C Virus (HCV) is mediated by Internal Ribosome Entry Site (IRES), which is independent of cap-structure and uses a limited number of canonical initiation factors. During translation initiation IRES-40S complex formation depends on high affinity interaction of IRES with ribosomal proteins. Earlier, it has been shown that ribosomal protein S5 (RPS5) interacts with HCV IRES. Here, we have extensively characterized the HCV IRES-RPS5 interaction and demonstrated its role in IRES function. Computational modelling and RNA-protein interaction studies demonstrated that the beta hairpin structure within RPS5 is critically required for the binding with domains II and IV. Mutations disrupting IRES-RPS5 interaction drastically reduced the 80S complex formation and the corresponding IRES activity. Computational analysis and UV cross-linking experiments using various IRES-mutants revealed interplay between domains II and IV mediated by RPS5. In addition, present study demonstrated that RPS5 interaction is unique to HCV IRES and is not involved in 40S-3 ` UTR interaction. Further, partial silencing of RPS5 resulted in preferential inhibition of HCV RNA translation. However, global translation was marginally affected by partial silencing of RPS5. Taken together, results provide novel molecular insights into IRES-RPS5 interaction and unravel its functional significance in mediating internal initiation of translation.

Algorithms for colour image processing based on neurological models

373 p. : il., gráf., fot., tablas

Modelagem e avaliação comparativa dos métodos Luus-Jaakola e R2W aplicados na estimativa de parâmetros cinéticos de adsorção

As técnicas inversas têm sido usadas na determinação de parâmetros importantes envolvidos na concepção e desempenho de muitos processos industriais. A aplicação de métodos estocásticos tem aumentado nos últimos anos, demonstrando seu potencial no estudo e análise dos diferentes sistemas em aplicações de engenharia. As rotinas estocásticas são capazes de otimizar a solução em uma ampla gama de variáveis do domínio, sendo possível a determinação dos parâmetros de interesse simultaneamente. Neste trabalho foram adotados os métodos estocásticos Luus-Jaakola (LJ) e Random Restricted Window (R2W) na obtenção dos ótimos dos parâmetros cinéticos de adsorção no sistema de cromatografia em batelada, tendo por objetivo verificar qual método forneceria o melhor ajuste entre os resultados obtidos nas simulações computacionais e os dados experimentais. Este modelo foi resolvido empregando o método de Runge- Kutta de 4 ordem para a solução de equações diferenciais ordinárias.

Análise da resposta dinâmica de passarelas de pedestres considerando-se uma modelagem probabilística do caminhar humano.

Passarelas de pedestres com arquitetura moderna, esbeltas e leves são uma constante nos dias atuais, apresentando grandes vãos e novos materiais. Este arrojo arquitetônico tem gerado inúmeros problemas de vibrações excessivas, especialmente sobre passarelas mistas (aço-concreto). As normas e recomendações de projeto consideram, ainda, que as forças induzidas pelo caminhar humano são determinísticas. Todavia, o caminhar humano e as respectivas forças dinâmicas geradas apresentam comportamento randômico. Deste modo, o presente trabalho de pesquisa objetiva contribuir com os projetistas estruturais, a partir do emprego de uma abordagem probabilística para avaliação do estado limite de utilização deste tipo de estrutura, associado a vibrações excessivas que podem vir a causar desconforto humano. Para tal, utiliza-se como modelo estrutural uma passarela de pedestres mista (aço-concreto) construída no campus do Instituto de Traumatologia e Ortopedia (INTO), na cidade do Rio de Janeiro. Com base na utilização dos métodos probabilísticos, torna-se possível determinar a probabilidade dos valores das acelerações de pico da estrutura ultrapassarem ou não os critérios de conforto humano estabelecidos em normas e recomendações de projeto. Os resultados apontam para o fato de que os valores das acelerações de pico calculadas com base exclusivamente nos métodos determinísticos podem ser superestimados em algumas situações de projeto.

Problemas inversos em engenharia financeira: regularização com critério de entropia

Esta dissertação aplica a regularização por entropia máxima no problema inverso de apreçamento de opções, sugerido pelo trabalho de Neri e Schneider em 2012. Eles observaram que a densidade de probabilidade que resolve este problema, no caso de dados provenientes de opções de compra e opções digitais, pode ser descrito como exponenciais nos diferentes intervalos da semireta positiva. Estes intervalos são limitados pelos preços de exercício. O critério de entropia máxima é uma ferramenta poderosa para regularizar este problema mal posto. A família de exponencial do conjunto solução, é calculado usando o algoritmo de Newton-Raphson, com limites específicos para as opções digitais. Estes limites são resultados do princípio de ausência de arbitragem. A metodologia foi usada em dados do índice de ação da Bolsa de Valores de São Paulo com seus preços de opções de compra em diferentes preços de exercício. A análise paramétrica da entropia em função do preços de opções digitais sínteticas (construídas a partir de limites respeitando a ausência de arbitragem) mostraram valores onde as digitais maximizaram a entropia. O exemplo de extração de dados do IBOVESPA de 24 de janeiro de 2013, mostrou um desvio do princípio de ausência de arbitragem para as opções de compra in the money. Este princípio é uma condição necessária para aplicar a regularização por entropia máxima a fim de obter a densidade e os preços. Nossos resultados mostraram que, uma vez preenchida a condição de convexidade na ausência de arbitragem, é possível ter uma forma de smile na curva de volatilidade, com preços calculados a partir da densidade exponencial do modelo. Isto coloca o modelo consistente com os dados do mercado. Do ponto de vista computacional, esta dissertação permitiu de implementar, um modelo de apreçamento que utiliza o princípio de entropia máxima. Três algoritmos clássicos foram usados: primeiramente a bisseção padrão, e depois uma combinação de metodo de bisseção com Newton-Raphson para achar a volatilidade implícita proveniente dos dados de mercado. Depois, o metodo de Newton-Raphson unidimensional para o cálculo dos coeficientes das densidades exponenciais: este é objetivo do estudo. Enfim, o algoritmo de Simpson foi usado para o calculo integral das distribuições cumulativas bem como os preços do modelo obtido através da esperança matemática.

Verificação à fadiga estrutural de ponte em concreto armado.

As pontes rodoviárias de concreto armado estão sujeitas à ações dinâmicas variáveis devido ao tráfego de veículos sobre o tabuleiro. Estas ações dinâmicas nem sempre são corretamente consideradas pelos projetistas. Deste modo, a correta consideração destes aspectos mostra-se de fundamental importância, de forma a se avaliar os esforços dinâmicos oriundos do tráfego de veículos sobre o tabuleiro. De acordo com este contexto, a ponte rodoviária investigada nesta dissertação é constituída por duas vigas longitudinais, três transversinas, sendo uma central e duas sobre os apoios, e por um tabuleiro em concreto armado. O modelo computacional, desenvolvido para a análise dinâmica da ponte, foi concebido com base no emprego de técnicas usuais de discretização através do método dos elementos finitos. Os veículos são representados a partir de sistemas do tipo "massa-mola-amortecedor". O tráfego destes veículos é considerado mediante a simulação de comboios semi-infinitos, deslocando-se com velocidade constante sobre a ponte. As técnicas para a contagem de ciclos de tensões e a aplicação das regras de dano acumulado foram analisadas através das curvas S-N de diversas normas e recomendações internacionais vigentes que versam sobre o tema. As conclusões deste trabalho de pesquisa se referem à análise da resposta dinâmica bem como da vida útil de serviço da obra de arte rodoviária de concreto armado investigada, quando submetida às ações dinâmicas provenientes do tráfego de veículos pesados sobre o tabuleiro.

Properties of molecules in tunnel junctions

Molecular tunnel junctions involve studying the behaviour of a single molecule sandwiched between metal leads. When a molecule makes contact with electrodes, it becomes open to the environment which can heavily influence its properties, such as electronegativity and electron transport. While the most common computational approaches remain to be single particle approximations, in this thesis it is shown that a more explicit treatment of electron interactions can be required. By studying an open atomic chain junction, it is found that including electron correlations corrects the strong lead-molecule interaction seen by the ΔSCF approximation, and has an impact on junction I − V properties. The need for an accurate description of electronegativity is highlighted by studying a correlated model of hexatriene-di-thiol with a systematically varied correlation parameter and comparing the results to various electronic structure treatments. The results indicating an overestimation of the band gap and underestimation of charge transfer in the Hartree-Fock regime is equivalent to not treating electron-electron correlations. While in the opposite limit, over-compensating for electron-electron interaction leads to underestimated band gap and too high an electron current as seen in DFT/LDA treatment. It is emphasised in this thesis that correcting electronegativity is equivalent to maximising the overlap of the approximate density matrix to the exact reduced density matrix found at the exact many-body solution. In this work, the complex absorbing potential (CAP) formalism which allows for the inclusion metal electrodes into explicit wavefunction many-body formalisms is further developed. The CAP methodology is applied to study the electron state lifetimes and shifts as the junction is made open.

A finite volume unstructured mesh approach to dynamic fluid-structure interaction: an assessment of the challenge of flutter analysis

Computational modelling of dynamic fluid-structure interaction (DFSI) is problematical since conventionally computational fluid dynamics (CFD) is solved using finite volume (FV) methods and computational structural mechanics (CSM) is based entirely on finite element (FE) methods. Hence, progress in modelling the emerging multi-physics problem of dynamic fluid-structure interaction in a consistent manner is frustrated and significant problems in computation convergence may be encountered in transferring and filtering data from one mesh and solution procedure to another, unless the fluid-structure coupling is either one way, very weak or both. This paper sets out the solution procedure for modelling the multi-physics dynamic fluid-structure interaction problem within a single software framework PHYSICA, using finite volume, unstructured mesh (FV-UM) procedures and will focus upon some of the problems and issues that have to be resolved for time accurate closely coupled dynamic fluid-structure flutter analysis.

Two fluid approach to high speed impact interaction amongst solid structures

The issues surrounding collision of projectiles with structures has gained a high profile since the events of 11th September 2001. In such collision problems, the projectile penetrates the stucture so that tracking the interface between one material and another becomes very complex, especially if the projectile is essentially a vessel containing a fluid, e.g. fuel load. The subsequent combustion, heat transfer and melting and re-solidification process in the structure render this a very challenging computational modelling problem. The conventional approaches to the analysis of collision processes involves a Lagrangian-Lagrangian contact driven methodology. This approach suffers from a number of disadvantages in its implementation, most of which are associated with the challenges of the contact analysis component of the calculations. This paper describes a 'two fluid' approach to high speed impact between solid structures, where the objective is to overcome the problems of penetration and re-meshing. The work has been carried out using the finite volume, unstructured mesh multi-physics code PHYSICA+, where the three dimensional fluid flow, free surface, heat transfer, combustion, melting and re-solidification algorithms are approximated using cell-centred finite volume, unstructured mesh techniques on a collocated mesh. The basic procedure is illustrated for two cases of Newtonian and non-Newtonian flow to test various of its component capabilities in the analysis of problems of industrial interest.

A finite volume unstructured mesh approach to dynamic fluid–structure interaction: an assessment of the challenge of predicting the onset of flutter

Computational modelling of dynamic fluid–structure interaction (DFSI) is a considerable challenge. Our approach to this class of problems involves the use of a single software framework for all the phenomena involved, employing finite volume methods on unstructured meshes in three dimensions. This method enables time and space accurate calculations in a consistent manner. One key application of DFSI simulation is the analysis of the onset of flutter in aircraft wings, where the work of Yates et al. [Measured and Calculated Subsonic and Transonic Flutter Characteristics of a 45° degree Sweptback Wing Planform in Air and Freon-12 in the Langley Transonic Dynamic Tunnel. NASA Technical Note D-1616, 1963] on the AGARD 445.6 wing planform still provides the most comprehensive benchmark data available. This paper presents the results of a significant effort to model the onset of flutter for the AGARD 445.6 wing planform geometry. A series of key issues needs to be addressed for this computational approach. • The advantage of using a single mesh, in order to eliminate numerical problems when applying boundary conditions at the fluid-structure interface, is counteracted by the challenge of generating a suitably high quality mesh in both the fluid and structural domains. • The computational effort for this DFSI procedure, in terms of run time and memory requirements, is very significant. Practical simulations require even finer meshes and shorter time steps, requiring parallel implementation for operation on large, high performance parallel systems. • The consistency and completeness of the AGARD data in the public domain is inadequate for use in the validation of DFSI codes when predicting the onset of flutter.

A generic time and space accurate numerical approach to closely coupled fluid-structure interaction problems

Fluid structure interaction, as applied to flexible structures, has wide application in diverse areas such as flutter in aircraft, flow in elastic pipes and blood vessels and extrusion of metals through dies. However a comprehensive computational model of these multi-physics phenomena is a considerable challenge. Until recently work in this area focused on one phenomenon and represented the behaviour of the other more simply even to the extent in metal forming, for example, that the deformation of the die is totally ignored. More recently, strategies for solving the full coupling between the fluid and soild mechanics behaviour have developed. Conventionally, the computational modelling of fluid structure interaction is problematical since computational fluid dynamics (CFD) is solved using finite volume (FV) methods and computational structural mechanics (CSM) is based entirely on finite element (FE) methods. In the past the concurrent, but rather disparate, development paths for the finite element and finite volume methods have resulted in numerical software tools for CFD and CSM that are different in almost every respect. Hence, progress is frustrated in modelling the emerging multi-physics problem of fluid structure interaction in a consistent manner. Unless the fluid-structure coupling is either one way, very weak or both, transferring and filtering data from one mesh and solution procedure to another may lead to significant problems in computational convergence. Using a novel three phase technique the full interaction between the fluid and the dynamic structural response are represented. The procedure is demonstrated on some challenging applications in complex three dimensional geometries involving aircraft flutter, metal forming and blood flow in arteries.

Using computer models to identify optimal conditions for flip-chip assembly and reliability

Flip-chip assembly, developed in the early 1960s, is now being positioned as a key joining technology to achieve high-density mounting of electronic components on to printed circuit boards for high-volume, low-cost products. Computer models are now being used early within the product design stage to ensure that optimal process conditions are used. These models capture the governing physics taking place during the assembly process and they can also predict relevant defects that may occur. Describes the application of computational modelling techniques that have the ability to predict a range of interacting physical phenomena associated with the manufacturing process. For example, in the flip-chip assembly process we have solder paste deposition, solder joint shape formation, heat transfer, solidification and thermal stress. Illustrates the application of modelling technology being used as part of a larger UK study aiming to establish a process route for high-volume, low-cost, sub-100-micron pitch flip-chip assembly.