Modelling of biochemical systems has received considerable attention over the last decade from bioengineering, biochemistry, computer science, and mathematics. This thesis investigates the applications of computational techniques to computational systems biology, for the construction of biochemical models in terms of topology and kinetic rates. Due to the complexity of biochemical systems, it is natural to construct models representing the biochemical systems incrementally in a piecewise manner. Syntax and semantics of two patterns are defined for the instantiation of components which are extendable, reusable and fundamental building blocks for models composition. We propose and implement a set of genetic operators and composition rules to tackle issues of piecewise composing models from scratch. Quantitative Petri nets are evolved by the genetic operators, and evolutionary process of modelling are guided by the composition rules. Metaheuristic algorithms are widely applied in BioModel Engineering to support intelligent and heuristic analysis of biochemical systems in terms of structure and kinetic rates. We illustrate parameters of biochemical models based on Biochemical Systems Theory, and then the topology and kinetic rates of the models are manipulated by employing evolution strategy and simulated annealing respectively. A new hybrid modelling framework is proposed and implemented for the models construction. Two heuristic algorithms are performed on two embedded layers in the hybrid framework: an outer layer for topology mutation and an inner layer for rates optimization. Moreover, variants of the hybrid piecewise modelling framework are investigated. Regarding flexibility of these variants, various combinations of evolutionary operators, evaluation criteria and design principles can be taken into account. We examine performance of five sets of the variants on specific aspects of modelling. The comparison of variants is not to explicitly show that one variant clearly outperforms the others, but it provides an indication of considering important features for various aspects of the modelling. Because of the very heavy computational demands, the process of modelling is paralleled by employing a grid environment, GridGain. Application of the GridGain and heuristic algorithms to analyze biological processes can support modelling of biochemical systems in a computational manner, which can also benefit mathematical modelling in computer science and bioengineering. We apply our proposed modelling framework to model biochemical systems in a hybrid piecewise manner. Modelling variants of the framework are comparatively studied on specific aims of modelling. Simulation results show that our modelling framework can compose synthetic models exhibiting similar species behaviour, generate models with alternative topologies and obtain general knowledge about key modelling features.

This thesis investigates stray losses in AC machines using the time-stepped finite element technique. Two aspects of this topic are involved in this thesis. The first aspect is to construct a finite element model for AC machine systems and develop an efficient numerical solution for the system equation; as the emphasis of this thesis, the second aspect is use the above model to analyze stray losses in AC machines under a variety of operation, design and manufacturing conditions. The thesis modifies the traditional 2-D finite element technique to account for the variations in electromagnetic field along the machines axis resulting from skewed structures, rotor interbar currents and ventilation ducts. Domain decomposition and parallel computation are incorporated to efficiently give a numerical solution to the system equation. The factors affecting harmonic stray losses in AC machines including pulse width modulation (PWM) supply, interbar resistance and slot shape are investigated using the above efficient analysis tool. Simulations and tests under different load conditions are carried out for an induction motor to investigate the additional harmonic stray loss caused by the PWM supply. For a large synchronous generator, simulations and tests are performed to study the effect of different amortisseur interbar resistances on the slot harmonic contents and the resulting harmonic stray loss in the amorisseur cage. As a factor influential to magnet stray loss in permanent magnet synchronous machines, various slot shape designs are assessed by simulations. An optimization based on an evolutionary strategy is implemented to find the best slot shape design with minimum machine loss. The conclusions in the thesis provide valued information to direct the future design and manufacture of efficient AC machines. / Power Engineering and Power Electronics

No description available.

The following work concerns the study of the evolutionary algorithm, which optimizes freight transport planning. The demand for freight transport is constantly increasing nowadays and with creating, implementing and using proper route planning we are able to significantly reduce transportation costs. However, it is preferably to implement it in companies with large numbers of served customers and with a sufficiently large fleet of vehicles.   The study starts by defining what fright transport planning problem is and by characterizing its existing specifications and variants. My work proceeds to give a background of the possible solutions to the multifaceted aspects of the problem. The specific subproblem I choose to focus on is the Vehicle routing problem with Pickup and Delivery for which I apply the optimization solution. In the main body of my thesis, I will elaborate on the chosen optimization solution which encompasses the genetic algorithm and evolutionary strategy. The aim of the study is to measure the suitability of the algorithms and techniques used, for which reason the final part of my work will deal with the analysis and evaluation of the experiments.

This master's thesis deals with the matter of predicting the effects of aminoacid substitutions on protein stability. The main aim is to design meta-classifier that combines the results of the selected prediction tools. An evolution strategy was used to find the best weights for each of the selected tools with the aim of achieving better prediction performance compared to that achieved by using these tools separately. Five different and obtainable prediction tools were selected and their prediction outputs were weighted. Two different approaches of evolution strategy are investigated and compared: evolution strategy with the 1/5-rule and evolution strategy with the type 2 of control parameters self-adaptation. Two independent datasets of mutations were created for training and evaluating the performance of designed meta-classifier. The performed experiments and obtained results suggest that the evolution strategy could be considered as a~beneficial approach for prediction of protein stability changes. However, the special attention must be paid to careful selection of tools for integration and compilation of training and testing datasets.

[pt] O objetivo deste trabalho é desenvolver dentro do programa FTOOL uma ferramenta para obtenção de envoltórias de esforços internos devido a cargas móveis. Envoltórias geralmente são obtidas através de interpolação de valores limites de seções pré-selecionadas ao longo da estrutura. Estes valores são obtidos com base no posicionamento da carga móvel em relação às linhas de influência dos esforços internos. A determinação de valores limites de um esforço em uma seção constitui um problema de otimização cujo objetivo é minimizar ou maximizar os valores dos esforços em relação à posição do tremtipo que percorre a estrutura. Porém, não existe uma expressão analítica que defina os valores limites de um esforço em uma seção para um dado trem-tipo, o que impossibilita o uso da maioria dos métodos clássicos de otimização para resolver o problema, porque esses métodos requerem, na maioria das vezes, o uso de pelo menos a primeira derivada da função objetivo em relação às variáveis de projeto. Portanto, este trabalho adotou algoritmos da Estratégia Evolutiva ( EE ) para determinar os valores limites devidos a cargas móveis. Foram feitas duas implementação distintas de Estratégia Evolutiva, conhecidas como EE − + ) 1 ( (lambda) e EE − + ) ( (lambda) (mi) . Além de utilizar algoritmos de EE para resolver o problema de envoltórias, foi desenvolvido um outro processo de solução denominado Força Bruta, que consiste em percorrer com o trem-tipo toda estrutura por passos pré-estabelecidos e calcular os valores dos esforços mínimos e máximos. Para a grande maioria dos casos, os resultados obtidos com a Estratégia Evolutiva foram corretos, porém, em alguns casos mais críticos, o valor exato da envoltória não é encontrado em algumas seções da estrutura, embora encontre um valor muito próximo a ele. Observou-se que os resultados da EE podem ser melhorados quando se enriquece a solução com uma estratégia econômica de posicionamento de cargas concentradas em cima de picos da linha de influência. / [en] The objective of this work is to develop a tool for obtaining envelopes of internal forces due to load-trains in the FTOOL software. Usually, envelopes are obtained through interpolation of limiting values on pre- selected sections along the structure. These values are obtained based on the positioning of the loadtrain in relation to influence lines of internal forces. The determination of limiting values of an effect at a section represents an optimization problem whose objective is to minimize or maximize the values of that effect in relation to the position of a load-train that passes along the structure. However, there is no analytical expression that defines a limiting value of an effect on a section for a specific load-train. Therefore, classical optimization methods cannot be used to solve this problem. Rather, the solution requires a method that does not require derivatives of the objective function. For this reason, this work adopts algorithms of the Evolution Strategy (ES) to achieve the limiting values due to load-trains. Two distinct algorithms of the ES, known as ES − + ) 1 ( (lambda) and ES − + ) ( (lambda) (mi) , were implemented. In addition to the ES algorithms to trace the envelopes, another process of solution called Force Brute was developed. It consists of moving the load-train in pre-determined steps along the structure and calculating minimum e maximum values. In general, the ES method converges to the correct solution. However, there are cases, depending on the complexity of the load-train, that the algorithms do not find the exact limiting value (although usually very close to it). It was observed that the ES results could be complemented and improved with results from an inexpensive solution in which concentrated loads are positioned on peak values of the influence lines.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2016-08-12T12:19:01Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) TESE_LEANDRO WILLER P COIMBRA.pdf: 1061880 bytes, checksum: 11f8b239ae17788ee3e063586ea2e919 (MD5) / Made available in DSpace on 2016-08-12T12:19:01Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) TESE_LEANDRO WILLER P COIMBRA.pdf: 1061880 bytes, checksum: 11f8b239ae17788ee3e063586ea2e919 (MD5) Previous issue date: 2015-11-30 / FACEPE / Este trabalho foi dividido em trˆes ensaios que se complementam na mesma tem´atica: a discriminac¸ ˜ao salarial. O objetivo ´e a constatac¸ ˜ao do comportamento discriminat´orio no mercado de trabalho brasileiro e a compreens˜ao das motivac¸ ˜oes e efeitos deste comportamento a partir de uma perspectiva econˆomica. Primeiramente, ´e utilizado o m´etodo de Propensity Score Matching para comparar trabalhadores com mesmos n´ıveis de esforc¸os, ocupac¸ ˜ao social, background familiar e outras vari´aveis de circunstˆancias, de forma a evidenciar a discriminac¸ ˜ao salarial baseada na cor da pele. A an´alise aponta para uma remunerac¸ ˜ao por hora trabalhada cerca de 14% menor para os trabalhadores “n˜ao brancos”. Al´em disso, ´e observado uma tendˆencia “elitista”da discriminac¸ ˜ao. Na segunda parte, ´e proposta a modelagem do mercado de trabalho baseada no Modelo de Search de Dale Mortensen, caracterizado por uma distribuic¸ ˜ao de ofertas de sal´ario cont´ınua. Este modelo ´e modificado de forma a introduzir trabalhadores heterogˆeneos quanto a habilidade produtiva e um grau de assimetria informacional entre os agentes. Observou-se que o n´ıvel de assimetria de informac¸ ˜ao de um mercado n˜ao ´e apenas precursor da discriminac¸ ˜ao mas definidor da magnitude desta. Por fim, foca-se na evoluc¸ ˜ao e sobrevivˆencia do comportamento discriminat´orio. Para isto, utilizou-se de um modelo com equil´ıbrio dinˆamico evolutivo, dividido em dois casos diferentes, de forma a endogeneizar o n´ıvel de assimetria de informac¸ ˜ao e da capacidade produtiva dos trabalhadores. Observou-se que o mercado possui possibilidades diferentes de equil´ıbrio, enquanto no primeiro caso, o percentual de trabalhadores de alta habilidade est´a ligado ao maior interesse das firmas selecionarem, no outro, o elevado percentual de trabalhadores de alta habilidade no mercado indica menor necessidade de selec¸ ˜ao. Na realidade, a diferenc¸a entre os dois casos se resume aos prˆemios e punic¸ ˜oes relativos a detenc¸ ˜ao de informac¸ ˜ao por parte dos trabalhadores de baixa habilidade. / This thesis was divided into three works that complement each other with the same theme: wage discrimination. The objective of this study is investigate the discriminatory behavior in the Brazilian labor market and understand the motivations and effects from an economic perspective. First, it is used the method of Propensity Score Matching to compare workers with the same level of effort, social occupation, family background and others variables of circumstances, it highlights wage discrimination based on skin color. The analysis found a wage per hour worked about 14% lower for workers “non-white”. Moreover, a tendency “elite”discrimination is observed. Next, it is proposed to model the labor market based on the Search Model of Dale Mortensen, characterized by a continuous distribution of wage offers. This model is modified to introduce heterogeneous productive ability and a degree of information asymmetry between agents. It was observed that the asymmetric information level of a market is not only the precursor of discrimination but defining the magnitude. Finally, focuses on the evolution and survival of discriminatory behavior. For this, we used a model with evolutionary dynamic equilibrium, divided into two different cases, in order to endogenize the level of asymmetric information and the productive capacity of workers. It was observed that the market has different possibilities to balance, in the first case, the percentage of high-skill labor is linked to higher interest selecting firms, on the other, the high percentage of high-skill labor market indicates less need for selection. In fact, the difference between the two cases comes down to rewards and punishments for the possession of information on the part of low-skill workers.

No description available.

This thesis is focused on predicting the impact of amino acid substitution on protein stability. The main goal is to create a consensual predictor that uses the outputs of chosen existing tools in order to improve accuracy of prediction. The optimal consensus of theese tools was designed using evolution strategies in three variants: 1/5 success rule, self-adaptation variant and the CMA-ES method. Then, the quality of calculated weight vectors was tested on the independent dataset. Although the highest prediction performance was attained by self-adaptation method, the differences between all three variants were not significant. Compared to the individual tools, the predictions provided by consensual methods were generally more accurate - the self-adaptation variant imporved the Pearson's corelation coeficient of the predictions by 0,057 on the training dataset. On the testing dataset, the improvement of designed method was smaller (0,040). Relatively low improvement of prediction performance (both on the training and the testing dataset) were caused by the fact, that for some records of testing dataset, some individual tools vere not able to provide their results. When omitting these records, consensual method improved the Pearson's corelations coeficient by 0,118.

Diplomová práce se zabývá optimalizací systému pro sledování letadel, využívaného pro řízení letového provozu. Je popsána metodika vyhodnocování přesnosti sledovacího systému a přehled relevantních algoritmů pro sledování objektů. Dále jsou navrženy tři přístupy k řešení problému. První se pokouší identifikovat parametry filtrovacích algoritmů pomocí algoritmu Expectation-Maximisation, implementací metody maximální věrohodnosti. Druhý přístup je založen na prostých odhadech parametrů normálního rozložení z naměřených a referenčních dat. Nakonec je zkoumána možnost řešení pomocí optimalizačního algoritmu Evoluční strategie. Závěrečné vyhodnocení ukazuje, že třetí přístup je pro daný problém nejvhodnější.