MA160exam00

Exam questions and solutions in LaTex. Diagrams for the questions are all together in the support.zip file, as .eps files

MA160exam01

Exam questions and solutions in LaTex. Diagrams for the questions are all together in the support.zip file, as .eps files

MA160exam01pdf

Exam questions and solutions in PDF

MA160exam00pdf

Exam questions and solutions in PDF

Aldose reductase and the importance of experimental design

Kinetic studies on the AR (aldose reductase) protein have shown that it does not behave as a classical enzyme in relation to ring aldose sugars. As with non-enzymatic glycation reactions, there is probably a free radical element involved derived from monosaccharide autoxidation. in the case of AR, there is free radical oxidation of NADPH by autoxidizing monosaccharides, which is enhanced in the presence of the NADPH-binding protein. Thus any assay for AR based on the oxidation of NADPH in the presence of autoxidizing monosaccharides is invalid, and tissue AR measurements based on this method are also invalid, and should be reassessed. AR exhibits broad specificity for both hydrophilic and hydrophobic aldehydes that suggests that the protein may be involved in detoxification. The last thing we would want to do is to inhibit it. ARIs (AR inhibitors) have a number of actions in the cell which are not specific, and which do not involve them binding to AR. These include peroxy-radical scavenging and effects of metal ion chelation. The AR/ARI story emphasizes the importance of correct experimental design in all biocatalytic experiments. Developing the use of Bayesian utility functions, we have used a systematic method to identify the optimum experimental designs for a number of kinetic model data sets. This has led to the identification of trends between kinetic model types, sets of design rules and the key conclusion that such designs should be based on some prior knowledge of K-m and/or the kinetic model. We suggest an optimal and iterative method for selecting features of the design such as the substrate range, number of measurements and choice of intermediate points. The final design collects data suitable for accurate modelling and analysis and minimizes the error in the parameters estimated, and is suitable for simple or complex steady-state models.

A novel Bayesian approach to drug design with simple and complex enzymes: Use with lens aldehyde dehydrogenase and the glyoxalase pathway

Purpose: Acquiring details of kinetic parameters of enzymes is crucial to biochemical understanding, drug development, and clinical diagnosis in ocular diseases. The correct design of an experiment is critical to collecting data suitable for analysis, modelling and deriving the correct information. As classical design methods are not targeted to the more complex kinetics being frequently studied, attention is needed to estimate parameters of such models with low variance. Methods: We have developed Bayesian utility functions to minimise kinetic parameter variance involving differentiation of model expressions and matrix inversion. These have been applied to the simple kinetics of the enzymes in the glyoxalase pathway (of importance in posttranslational modification of proteins in cataract), and the complex kinetics of lens aldehyde dehydrogenase (also of relevance to cataract). Results: Our successful application of Bayesian statistics has allowed us to identify a set of rules for designing optimum kinetic experiments iteratively. Most importantly, the distribution of points in the range is critical; it is not simply a matter of even or multiple increases. At least 60 % must be below the KM (or plural if more than one dissociation constant) and 40% above. This choice halves the variance found using a simple even spread across the range.With both the glyoxalase system and lens aldehyde dehydrogenase we have significantly improved the variance of kinetic parameter estimation while reducing the number and costs of experiments. Conclusions: We have developed an optimal and iterative method for selecting features of design such as substrate range, number of measurements and choice of intermediate points. Our novel approach minimises parameter error and costs, and maximises experimental efficiency. It is applicable to many areas of ocular drug design, including receptor-ligand binding and immunoglobulin binding, and should be an important tool in ocular drug discovery.

Efficient and accurate experimental design for enzyme kinetics: Bayesian studies reveal a systematic approach

In areas such as drug development, clinical diagnosis and biotechnology research, acquiring details about the kinetic parameters of enzymes is crucial. The correct design of an experiment is critical to collecting data suitable for analysis, modelling and deriving the correct information. As classical design methods are not targeted to the more complex kinetics being frequently studied, attention is needed to estimate parameters of such models with low variance. We demonstrate that a Bayesian approach (the use of prior knowledge) can produce major gains quantifiable in terms of information, productivity and accuracy of each experiment. Developing the use of Bayesian Utility functions, we have used a systematic method to identify the optimum experimental designs for a number of kinetic model data sets. This has enabled the identification of trends between kinetic model types, sets of design rules and the key conclusion that such designs should be based on some prior knowledge of K-M and/or the kinetic model. We suggest an optimal and iterative method for selecting features of the design such as the substrate range, number of measurements and choice of intermediate points. The final design collects data suitable for accurate modelling and analysis and minimises the error in the parameters estimated. (C) 2003 Elsevier Science B.V. All rights reserved.

Investigation of ultra wideband multi-channel dichroic beamsplitters from 0.3 to 52µm

The development of a set of multi-channel dichroics which includes a 6 channel dichroic operating over the wavelength region from 0.3 to 52µm is described. In order to achieve the optimum performance, the optical constants of PbTe, Ge and CdTe coatings in the strongly absorptive region have been determined by use of a new iterative method using normal incidence reflectance measurement of the multilayer together with initial values of energy gap Eg and infinite refractive index n for the semiconductor model. The design and manufacture of the dichroics is discussed and the final results are presented.

Wave trapping in a two-dimensional sound-soft or sound-hard acoustic waveguide of slowly-varying width

In this paper we derive novel approximations to trapped waves in a two-dimensional acoustic waveguide whose walls vary slowly along the guide, and at which either Dirichlet (sound-soft) or Neumann (sound-hard) conditions are imposed. The guide contains a single smoothly bulging region of arbitrary amplitude, but is otherwise straight, and the modes are trapped within this localised increase in width. Using a similar approach to that in Rienstra (2003), a WKBJ-type expansion yields an approximate expression for the modes which can be present, which display either propagating or evanescent behaviour; matched asymptotic expansions are then used to derive connection formulae which bridge the gap across the cut-off between propagating and evanescent solutions in a tapering waveguide. A uniform expansion is then determined, and it is shown that appropriate zeros of this expansion correspond to trapped mode wavenumbers; the trapped modes themselves are then approximated by the uniform expansion. Numerical results determined via a standard iterative method are then compared to results of the full linear problem calculated using a spectral method, and the two are shown to be in excellent agreement, even when $\epsilon$, the parameter characterising the slow variations of the guide’s walls, is relatively large.

Optimal linearization trajectories for tangent linear models

We examine differential equations where nonlinearity is a result of the advection part of the total derivative or the use of quadratic algebraic constraints between state variables (such as the ideal gas law). We show that these types of nonlinearity can be accounted for in the tangent linear model by a suitable choice of the linearization trajectory. Using this optimal linearization trajectory, we show that the tangent linear model can be used to reproduce the exact nonlinear error growth of perturbations for more than 200 days in a quasi-geostrophic model and more than (the equivalent of) 150 days in the Lorenz 96 model. We introduce an iterative method, purely based on tangent linear integrations, that converges to this optimal linearization trajectory. The main conclusion from this article is that this iterative method can be used to account for nonlinearity in estimation problems without using the nonlinear model. We demonstrate this by performing forecast sensitivity experiments in the Lorenz 96 model and show that we are able to estimate analysis increments that improve the two-day forecast using only four backward integrations with the tangent linear model. Copyright © 2011 Royal Meteorological Society

Digital predistorter design using B-Spline neural network and inverse of De Boor algorithm

This contribution introduces a new digital predistorter to compensate serious distortions caused by memory high power amplifiers (HPAs) which exhibit output saturation characteristics. The proposed design is based on direct learning using a data-driven B-spline Wiener system modeling approach. The nonlinear HPA with memory is first identified based on the B-spline neural network model using the Gauss-Newton algorithm, which incorporates the efficient De Boor algorithm with both B-spline curve and first derivative recursions. The estimated Wiener HPA model is then used to design the Hammerstein predistorter. In particular, the inverse of the amplitude distortion of the HPA's static nonlinearity can be calculated effectively using the Newton-Raphson formula based on the inverse of De Boor algorithm. A major advantage of this approach is that both the Wiener HPA identification and the Hammerstein predistorter inverse can be achieved very efficiently and accurately. Simulation results obtained are presented to demonstrate the effectiveness of this novel digital predistorter design.

Formulação LTSn para problemas de transporte sem simetria azimutal e problemas dependentes do tempo

Neste trabalho, estendemos, de forma analítica, a formulação LTSN à problemas de transporte unidimensionais sem simetria azimutal. Para este problema, também apresentamos a solução com dependência contínua na variável angular, a partir da qual é estabelecido um método iterativo de solução da equação de transporte unidimensional. Também discutimos como a formulação LTSN é aplicada na resolução de problemas de transporte unidimensionais dependentes do tempo, tanto de forma aproximada pela inversão numérica do fluxo transformado na variável tempo, bem como analiticamente, pela aplicação do método LTSNnas equações nodais. Simulações numéricas e comparações com resultados disponíveis na literatura são apresentadas.

O modelo de Gurson para dano dúctil : estratégia computacional e aplicações

Este trabalho trata do emprego do modelo de dano dúctil de Gurson e de alguns aspectos relativos a sua implementação computacional. Emprega-se como ponto de partida o programa Metafor, código de elementos finitos voltado para a simulação de problemas de conformação mecânica, contemplando portanto grandes deformações plásticas. Estudam-se alguns casos simples procurando identificar a influência de cada parâmetro do modelo de Gurson na resposta. É discutida a aplicação dos modelos de nucleação de vazios usualmente empregados em conjunto com a superfície de escoamento de Gurson em situações onde há reversão de solicitação. São propostas alterações nos modelos usuais de nucleação de forma a minorar resultados incoerentes verificados. Apresenta-se um algoritmo alternativo ao método de Newton-Raphson para a solução do sistema de equações associado à forma fraca das equações de equilíbrio, em situações onde a rigidez fica muito pequena. Tal algoritmo é implementado e testado. Um algoritmo de integração de tensões é apresentado e implementado, mostrando-se sua vantagem do ponto de vista de robustez, ou seja, obtenção da resposta correta a despeito do tamanho de incremento empregado. Também é discutido um procedimento para desconsiderar elementos que apresentem ruptura local Estudam-se problemas envolvendo geração de calor por deformação plástica em conjunto com a formulação do modelo de Gurson, mostrando que a consideração de acoplamento termo-mecânico com dano traz vantagens em algumas simulações. É discutida a implementação do modelo de Gurson sobre a versão tridimensional do Metafor, que contempla a formulação lagrangiana-euleriana arbitrária (LEA). Ao final, é feita uma simulação inicial do comportamento de espumas metálicas.

Desenvolvimento de circuitos planares sobre substratos têxteis

The use of flexible materials for the development of planar circuits is one of the most desired and studied characteristics, lately, by researchers. This happens because the flexibility of the substrate can provide previously impracticable applications, due to the rigidity of the substrates normally used that makes it difficult to fit into the circuits in irregular surfaces. The constant interest in recent years for more lighter devices, increasingly more compacts, flexible and with low cost, led to a new line of research of great interest from both academic and technological views, that is the study and development of textile substrates that can be applied in the development of planar circuits, for applications in the areas of security, biomedical and telecommunications. This paper proposes the development of planar circuits, such as antennas , frequency selective surfaces (FSS) and planar filters, using textile (cotton ticking, jeans and brim santista) as the dielectric substrate and the Pure Copper Polyester Taffeta Fabric, a textile of pure copper, highly conductive, lightweight and flexible, commercially sold as a conductive material. The electrical characteristics of textiles (electric permittivity and loss tangent) were characterized using the transmission line method (rectangular waveguide) and compared with those found in the literature. The structures were analyzed using commercial software Ansoft Designer and Ansoft HFSS, both from the company Ansys and for comparison we used the Iterative Method of Waves (WCIP). For the purpose of validation were built and measured several prototypes of antennas, planar filters and FSS, being possible to confirm an excellent agreement between simulated and measured results

Caracterização de circuitos planares de micro-ondas pelo método iterativo das ondas

The planar circuits are structures that increasingly attracting the attention of researchers, due the good performance and capacity to integrate with other devices, in the prototyping of systems for transmitting and receiving signals in the microwave range. In this context, the study and development of new techniques for analysis of these devices have significantly contributed in the design of structures with excellent performance and high reliability. In this work, the full-wave method based on the concept of electromagnetic waves and the principle of reflection and transmission of waves at an interface, Wave Concept Iterative Procedure (WCIP), or iterative method of waves is described as a tool with high precision study microwave planar circuits. The proposed method is applied to the characterization of planar filters, microstrip antennas and frequency selective surfaces. Prototype devices were built and the experimental results confirmed the proposed mathematical model. The results were also compared with simulated results by Ansoft HFSS, observing a good agreement between them.