Numerical evaluation of the modulus of longitudinal elasticity in structural round timber elements of the Eucalyptus genus

Currently, the standards that deal with the determination of the properties of rigidity and strength for structural round timber elements do not take in consideration in their calculations and mathematical models the influence of the existing irregularities in the geometry of these elements. This study has as objective to determine the effective value of the modulus of longitudinal elasticity for structural round timber pieces of the Eucalyptus citriodora genus by a technique of optimization allied to the Inverse Analysis Method, to the Finite Element Method and the Least Square Method.

Generalized Differential Evolution for Global Multi-Objective Optimization with Constraints

The objective of this thesis work is to develop and study the Differential Evolution Algorithm for multi-objective optimization with constraints. Differential Evolution is an evolutionary algorithm that has gained in popularity because of its simplicity and good observed performance. Multi-objective evolutionary algorithms have become popular since they are able to produce a set of compromise solutions during the search process to approximate the Pareto-optimal front. The starting point for this thesis was an idea how Differential Evolution, with simple changes, could be extended for optimization with multiple constraints and objectives. This approach is implemented, experimentally studied, and further developed in the work. Development and study concentrates on the multi-objective optimization aspect. The main outcomes of the work are versions of a method called Generalized Differential Evolution. The versions aim to improve the performance of the method in multi-objective optimization. A diversity preservation technique that is effective and efficient compared to previous diversity preservation techniques is developed. The thesis also studies the influence of control parameters of Differential Evolution in multi-objective optimization. Proposals for initial control parameter value selection are given. Overall, the work contributes to the diversity preservation of solutions in multi-objective optimization.

Optimization of extrusion process for production of nutritious pellets

A blend of 50% Potato Starch (PS), 35% Quality Protein Maize (QPM), and 15% Soybean Meal (SM) were used in the preparation of expanded pellets utilizing a laboratory extruder with a 1.5 × 20.0 × 100.0 mm die-nozzle. The independent variables analyzed were Barrel Temperature (BT) (75-140 °C) and Feed Moisture (FM) (16-30%). The effect of extrusion variables was investigated in terms of Expansion Index (EI), apparent density (ApD), Penetration Force (PF) and Specific Mechanical Energy (SME), viscosity profiles, DSC, crystallinity by X-ray diffraction, and Scanning Electronic Microscopy (SEM). The PF decreased from 30 to 4 kgf with the increase of both independent variables (BT and FM). SME was affected only by FM, and decreased with the increase in this variable. The optimal region showed that the maximum EI was found for BT in the range of 123-140 °C and 27-31% for FM, respectively. The extruded pellets obtained from the optimal processing region were probably not completely degraded, as shown in the structural characterization. Acceptable expanded pellets could be produced using a blend of PS, QPM, and SM by extrusion cooking.

Optimization of the extraction of carrageenan from Kappaphycus alvarezii using response surface methodology

This study aims to optimize an alternative method of extraction of carrageenan without previous alkaline treatment and ethanol precipitation using Response Surface Methodology (RSM). In order to introduce an innovation in the isolation step, atomization drying was used reducing the time for obtaining dry carrageenan powder. The effects of extraction time and temperature on yield, gel strength, and viscosity were evaluated. Furthermore, the extracted material was submitted to structural analysis, by infrared spectroscopy and nuclear magnetic resonance spectroscopy (¹H-NMR), and chemical composition analysis. Results showed that the generated regression models adequately explained the data variation. Carrageenan yield and gel viscosity were influenced only by the extraction temperature. However, gel strength was influenced by both, extraction time and extraction temperature. Optimal extraction conditions were 74 ºC and 4 hours. In these conditions, the carrageenan extract properties determined by the polynomial model were 31.17%, 158.27 g.cm-2, and 29.5 cP for yield, gel strength, and viscosity, respectively, while under the experimental conditions they were 35.8 ± 4.68%, 112.50 ± 4.96 g.cm-2, and 16.01 ± 1.03 cP, respectively. The chemical composition, nuclear magnetic resonance spectroscopy, and infrared spectroscopy analyses showed that the crude carrageenan extracted is composed mainly of κ-carrageenan.

Optimization of image analysis techniques for quality assessment of whole-wheat breads made with fat replacer

The cellular structure of healthy food products, with added dietary fiber and low in calories, is an important factor that contributes to the assessment of quality, which can be quantified by image analysis of visual texture. This study seeks to compare image analysis techniques (binarization using Otsu’s method and the default ImageJ algorithm, a variation of the iterative intermeans method) for quantification of differences in the crumb structure of breads made with different percentages of whole-wheat flour and fat replacer, and discuss the behavior of the parameters number of cells, mean cell area, cell density, and circularity using response surface methodology. Comparative analysis of the results achieved with the Otsu and default ImageJ algorithms showed a significant difference between the studied parameters. The Otsu method demonstrated the crumb structure of the analyzed breads more reliably than the default ImageJ algorithm, and is thus the most suitable in terms of structural representation of the crumb texture.

The Role of Structural Imperfections in Sr2FeMoO6 Thin Films

In this work, Sr2FeMoO6 (SFMO) thin films were studied with the main focus on their magnetic and magneto-transport properties. The fabrication process of pulsed laser deposited SFMO films was first optimized. Then the effects of strain, film thickness and substrate were thoroughly investigated. In addition to these external factors, the effect of intrinsic defects on the magnetic properties of SFMO were also clarified. Secondly, the magnetoresistivity mechanims of SFMO films were studied and a semiempirical model of the temperature dependence of resistivity was introduced. The films were grown on single crystal substrates using a ceramic target made with sol-gel method. The structural characterization of the films were carried out with X-ray diffraction, atomic force microscopy, transmission electron microscopy and high kinetic energy photoelectron spectroscopy. The magnetic properties were measured with SQUID magnetometer and the magneto-transport properties by magnetometer with a resistivity option. SFMO films with the best combination of structural and magnetic properties were grown in Ar atmosphere at 1050 °C . Their magnetic properties could not be improved by the ex situ post-annealing treatments aside from the treatments in ultra-high vacuum conditions. The optimal film thickness was found to be around 150 nm and only small improvement in the magnetic properties with decreasing strain was observed. Instead, the magnetic properties were observed to be highly dependent on the choice of the substrate due to the lattice mismatch induced defects, which are best avoided by using the SrTiO3 substrate. The large difference in the Curie temperature and the saturation magnetization between the SFMO thin film and polycrystalline bulk samples was connected to the antisite disorder and oxygen vacancies. Thus, the Curie temperature of SFMO thin films could be improved by increasing the amount of oxygen vacancies for example with ultra-high vacuum treatments or improving the B-site ordering by further optimization of the deposition parameters. The magneto-transport properties of SFMO thin films do not follow any conventional models, but the temperature dependence of resistivity was succesfully described with a model of two spin channel system. Also, evidences that the resistivity-temperature behaviour of SFMO thin films is dominated by the structural defects, which reduce the band gap in the majority spin band were found. Moreover, the magnetic field response of the resistivity in SFMO thin films were found to be superposition of different mechanisms that seems to be related to the structural changes in the film.

VAP-1 as drug target in inflammation : structural features determining ligand interactions

Vascular adhesion protein-1 (VAP-1), which belongs to the copper amine oxidases (CAOs), is a validated drug target in inflammatory diseases. Inhibition of VAP-1 blocks the leukocyte trafficking to sites of inflammation and alleviates inflammatory reactions. In this study, a novel set of potent pyridazinone inhibitors is presented together with their X-ray structure complexes with VAP-1. The crystal structure of serum VAP-1 (sVAP-1) revealed an imidazole binding site in the active site channel and, analogously, the pyridazinone inhibitors were designed to bind into the channel. This is the first time human VAP-1 has been crystallized with a reversible inhibitor and the structures reveal detailed information of the binding mode on the atomic level. Similarly to some earlier studied inhibitors of human VAP-1, the designed pyridazinone inhibitors bind rodent VAP-1 with a lower affinity than human VAP-1. Therefore, we made homology models of rodent VAP-1 and compared human and rodent enzymes to determine differences that might affect the inhibitor binding. The comparison of the crystal structures of the human VAP-1 and the mouse VAP-1 homology model revealed key differences important for the species specific binding properties. In general, the channel in mouse VAP-1 is more narrow and polar than the channel in human VAP-1, which is wider and more hydrophobic. The differences are located in the channel leading to the active site, as well as, in the entrance to the active site channel. The information obtained from these studies is of great importance for the development and design of drugs blocking the activity of human VAP-1, as rodents are often used for in vivo testing of candidate drugs. In order to gain more insight into the selective binding properties of the different CAOs in one species a comprehensive evolutionary study of mammalian CAOs was performed. We found that CAOs can be classified into sub-families according to the residues X1 and X2 of the Thr/Ser-X1-X2-Asn-Tyr-Asp active site motif. In the phylogenetic tree, CAOs group into diamine oxidase, retina specific amine oxidase and VAP-1/serum amine oxidase clades based on the residue in the position X2. We also found that VAP-1 and SAO can be further differentiated based on the residue in the position X1. This is the first large-scale comparison of CAO sequences, which explains some of the reasons for the unique substrate specificities within the CAO family.

Statistical potentials for evolutionary studies

Les séquences protéiques naturelles sont le résultat net de l’interaction entre les mécanismes de mutation, de sélection naturelle et de dérive stochastique au cours des temps évolutifs. Les modèles probabilistes d’évolution moléculaire qui tiennent compte de ces différents facteurs ont été substantiellement améliorés au cours des dernières années. En particulier, ont été proposés des modèles incorporant explicitement la structure des protéines et les interdépendances entre sites, ainsi que les outils statistiques pour évaluer la performance de ces modèles. Toutefois, en dépit des avancées significatives dans cette direction, seules des représentations très simplifiées de la structure protéique ont été utilisées jusqu’à présent. Dans ce contexte, le sujet général de cette thèse est la modélisation de la structure tridimensionnelle des protéines, en tenant compte des limitations pratiques imposées par l’utilisation de méthodes phylogénétiques très gourmandes en temps de calcul. Dans un premier temps, une méthode statistique générale est présentée, visant à optimiser les paramètres d’un potentiel statistique (qui est une pseudo-énergie mesurant la compatibilité séquence-structure). La forme fonctionnelle du potentiel est par la suite raffinée, en augmentant le niveau de détails dans la description structurale sans alourdir les coûts computationnels. Plusieurs éléments structuraux sont explorés : interactions entre pairs de résidus, accessibilité au solvant, conformation de la chaîne principale et flexibilité. Les potentiels sont ensuite inclus dans un modèle d’évolution et leur performance est évaluée en termes d’ajustement statistique à des données réelles, et contrastée avec des modèles d’évolution standards. Finalement, le nouveau modèle structurellement contraint ainsi obtenu est utilisé pour mieux comprendre les relations entre niveau d’expression des gènes et sélection et conservation de leur séquence protéique.

Structural aspects of the ribosome evolution and function

Les résultats ont été obtenus avec le logiciel "Insight-2" de Accelris (San Diego, CA)

Optimization of Two Stage Process for the Growth of In2S3 , CuInSe2 and CuIn (Sel-xSx)2Thin Films for Solar Cell Application

Two stage processes consisting of precursor preparation by thermal evaporation followed by chalcogenisation in the required atmosphere is found to be a feasible technique for the PV materials such as n-Beta In2S3, p-CulnSe2, p-CulnS2 and p-CuIn(Sel_xSx)2. The growth parameters such as chalcogenisation temperature and duration of chalcogenisation etc have been optimised in the present study.Single phase Beta-In2S3 thin films can be obtained by sulfurising the indium films above 300°C for 45 minutes. Low sulfurisation temperatures required prolonged annealing after the sulfurisation to obtain single phase Beta-1n2S3, which resulted in high material loss. The maximum band gap of 2.58 eV was obtained for the nearly stoichiometric Beta-In2S3 film which was sulfurised at 350°C. This wider band gap, n type Beta-In2S3 can be used as an alternative to toxic CdS as window layer in photovoltaics .The systematic study on the structural optical and electrical properties of CuInSe2 films by varying the process parameters such as the duration of selenization and the selenization temperature led to the conclusion that for the growth of single-phase CuInSe2, the optimum selenization temperature is 350°C and duration is 3 hours. The presence of some binary phases in films for shorter selenization period and lower selenization temperature may be due to the incomplete reaction and indium loss. Optical band gap energy of 1.05 eV obtained for the films under the optimum condition.In order to obtain a closer match to the solar spectrum it is desirable to increase the band gap of the CulnSe2 by a few meV . Further research works were carried out to produce graded band gap CuIn(Se,S)2 absorber films by incorporation of sulfur into CuInSe2. It was observed that when the CulnSe2 prepared by two stage process were post annealed in sulfur atmosphere, the sulfur may be occupying the interstitial positions or forming a CuInS2 phase along with CuInSe2 phase. The sulfur treatment during the selenization process OfCu11 ln9 precursors resulted in Culn (Se,S)2 thin films. A band gap of 1.38 eV was obtained for the CuIn(Se,S)2.The optimised thin films n-beta 1n2S3, p-CulnSe2 and p-Culn(Sel-xSx)2 can be used for fabrication of polycrystalline solar cells.

Optimization of parameters of chemical spray pyrolysis technique to get n and p-type layers of SnS

SnS thin films were prepared using automated chemical spray pyrolysis (CSP) technique. Single-phase, p-type, stoichiometric, SnS films with direct band gap of 1.33 eV and having very high absorption coefficient (N105/cm) were deposited at substrate temperature of 375 °C. The role of substrate temperature in determining the optoelectronic and structural properties of SnS films was established and concentration ratios of anionic and cationic precursor solutions were optimized. n-type SnS samples were also prepared using CSP technique at the same substrate temperature of 375 °C, which facilitates sequential deposition of SnS homojunction. A comprehensive analysis of both types of films was done using x-ray diffraction, energy dispersive x-ray analysis, scanning electron microscopy, atomic force microscopy, optical absorption and electrical measurements. Deposition temperatures required for growth of other binary sulfide phases of tin such as SnS2, Sn2S3 were also determined

Global Optimization Algorithms and their Application to Distributed Systems

In this report, we discuss the application of global optimization and Evolutionary Computation to distributed systems. We therefore selected and classified many publications, giving an insight into the wide variety of optimization problems which arise in distributed systems. Some interesting approaches from different areas will be discussed in greater detail with the use of illustrative examples.

Improvement of strategies for the management of fire blight (Erwinia amylovora). Evaluation and optimization of physical and chemical control methods, and use of decision support systems

El foc bacterià és una malaltia que afecta a plantes de la família de la rosàcies, causada pel bacteri Erwinia amylovora. El seu rang d'hostes inclou arbres fruiters, com la perera, la pomera o el codonyer, i plantes ornamentals de gran interès comercial i econòmic. Actualment, la malaltia s'ha dispersat i es troba àmpliament distribuïda en totes les zones de clima temperat del món. A Espanya, on la malaltia no és endèmica, el foc bacterià es va detectar per primer cop al 1995 al nord del país (Euskadi) i posteriorment, han aparegut varis focus en altres localitzacions, que han estat convenientment eradicats. El control del foc bacterià, és molt poc efectiu en plantes afectades per la malaltia, de manera que es basa en mesures encaminades a evitar la dispersió del patogen, i la introducció de la malaltia en regions no endèmiques. En aquest treball, la termoteràpia ha estat avaluada com a mètode d'eradicació d'E. amylovora de material vegetal de propagació asimptomàtic. S'ha demostrat que la termoteràpia és un mètode viable d'eradicar E. amylovora de material de propagació. Gairebé totes les espècies i varietats de rosàcies mantingudes en condicions d'humitat sobrevivien 7 hores a 45 ºC i més de 3 hores a 50 ºC, mentre que més d'1 hora d'exposició a 50 ºC amb calor seca produïa danys en el material vegetal i reduïa la brotació. Tractaments de 60 min a 45 ºC o 30 min a 50 ºC van ser suficients per reduir la població epífita d'E. amylovora a nivells no detectables (5 x 102 ufc g-1 p.f.) en branques de perera. Els derivats dels fosfonats i el benzotiadiazol són efectius en el control del foc bacterià en perera i pomera, tant en condicions de laboratori, com d'hivernacle i camp. Els inductors de defensa de les plantes redueixen els nivells de malaltia fins al 40-60%. Els intervals de temps mínims per aconseguir el millor control de la malaltia van ser 5 dies pel fosetil-Al, i 7 dies per l'etefon i el benzotiadiazol, i les dosis òptimes pel fosetil-Al i el benzotiadiazol van ser 3.72 g HPO32- L-1 i 150 mg i.a. L-1, respectivament. Es millora l'eficàcia del fosetil-Al i del benzotiadiazol en el control del foc bacterià, quan es combinen amb els antibiòtics a la meitat de la dosi d'aquests últims. Tot i que l'estratègia de barrejar productes és més pràctica i fàcil de dur a terme a camp, que l'estratègia de combinar productes, el millor nivell de control de la malaltia s'aconsegueix amb l'estratègia de combinar productes. Es va analitzar a nivell histològic i ultrastructural l'efecte del benzotiadiazol i dels fosfonats en la interacció Erwinia amylovora-perera. Ni el benzotiadiazol, ni el fosetil-Al, ni l'etefon van induir canvis estructurals en els teixits de perera 7 dies després de la seva aplicació. No obstant, després de la inoculació d'E. amylovora es va observar en plantes tractades amb fosetil-Al i etefon una desorganització estructural cel·lular, mentre que en les plantes tractades amb benzotiadiazol aquestes alteracions tissulars van ser retardades. S'han avaluat dos models (Maryblyt, Cougarblight) en un camp a Espanya afectat per la malaltia, per determinar la precisió de les prediccions. Es van utilitzar dos models per elaborar el mapa de risc, el BRS-Powell combinat i el BIS95 modificat. Els resultats van mostrar dos zones amb elevat i baix risc de la malaltia. Maryblyt i Cougarblight són dos models de fàcil ús, tot i que la seva implementació en programes de maneig de la malaltia requereix que siguin avaluats i validats per un període de temps més llarg i en àrees on la malaltia hi estigui present.

Multi-objective optimization scheme for static and dynamic multicast flows

Muchas de las nuevas aplicaciones emergentes de Internet tales como TV sobre Internet, Radio sobre Internet,Video Streamming multi-punto, entre otras, necesitan los siguientes requerimientos de recursos: ancho de banda consumido, retardo extremo-a-extremo, tasa de paquetes perdidos, etc. Por lo anterior, es necesario formular una propuesta que especifique y provea para este tipo de aplicaciones los recursos necesarios para su buen funcionamiento. En esta tesis, proponemos un esquema de ingeniería de tráfico multi-objetivo a través del uso de diferentes árboles de distribución para muchos flujos multicast. En este caso, estamos usando la aproximación de múltiples caminos para cada nodo egreso y de esta forma obtener la aproximación de múltiples árboles y a través de esta forma crear diferentes árboles multicast. Sin embargo, nuestra propuesta resuelve la fracción de la división del tráfico a través de múltiples árboles. La propuesta puede ser aplicada en redes MPLS estableciendo rutas explícitas en eventos multicast. En primera instancia, el objetivo es combinar los siguientes objetivos ponderados dentro de una métrica agregada: máxima utilización de los enlaces, cantidad de saltos, el ancho de banda total consumido y el retardo total extremo-a-extremo. Nosotros hemos formulado esta función multi-objetivo (modelo MHDB-S) y los resultados obtenidos muestran que varios objetivos ponderados son reducidos y la máxima utilización de los enlaces es minimizada. El problema es NP-duro, por lo tanto, un algoritmo es propuesto para optimizar los diferentes objetivos. El comportamiento que obtuvimos usando este algoritmo es similar al que obtuvimos con el modelo. Normalmente, durante la transmisión multicast los nodos egresos pueden salir o entrar del árbol y por esta razón en esta tesis proponemos un esquema de ingeniería de tráfico multi-objetivo usando diferentes árboles para grupos multicast dinámicos. (en el cual los nodos egresos pueden cambiar durante el tiempo de vida de la conexión). Si un árbol multicast es recomputado desde el principio, esto podría consumir un tiempo considerable de CPU y además todas las comuicaciones que están usando el árbol multicast serán temporalmente interrumpida. Para aliviar estos inconvenientes, proponemos un modelo de optimización (modelo dinámico MHDB-D) que utilice los árboles multicast previamente computados (modelo estático MHDB-S) adicionando nuevos nodos egreso. Usando el método de la suma ponderada para resolver el modelo analítico, no necesariamente es correcto, porque es posible tener un espacio de solución no convexo y por esta razón algunas soluciones pueden no ser encontradas. Adicionalmente, otros tipos de objetivos fueron encontrados en diferentes trabajos de investigación. Por las razones mencionadas anteriormente, un nuevo modelo llamado GMM es propuesto y para dar solución a este problema un nuevo algoritmo usando Algoritmos Evolutivos Multi-Objetivos es propuesto. Este algoritmo esta inspirado por el algoritmo Strength Pareto Evolutionary Algorithm (SPEA). Para dar una solución al caso dinámico con este modelo generalizado, nosotros hemos propuesto un nuevo modelo dinámico y una solución computacional usando Breadth First Search (BFS) probabilístico. Finalmente, para evaluar nuestro esquema de optimización propuesto, ejecutamos diferentes pruebas y simulaciones. Las principales contribuciones de esta tesis son la taxonomía, los modelos de optimización multi-objetivo para los casos estático y dinámico en transmisiones multicast (MHDB-S y MHDB-D), los algoritmos para dar solución computacional a los modelos. Finalmente, los modelos generalizados también para los casos estático y dinámico (GMM y GMM Dinámico) y las propuestas computacionales para dar slución usando MOEA y BFS probabilístico.

The life history legacy of evolutionary body size change in carnivores

We estimate the body sizes of direct ancestors of extant carnivores, and examine selected aspects of life history as a function not only of species' current size, but also of recent changes in size. Carnivore species that have undergone marked recent evolutionary size change show life history characteristics typically associated with species closer to the ancestral body size. Thus, phyletic giants tend to mature earlier and have larger litters of smaller offspring at shorter intervals than do species of the same body size that are not phyletic giants. Phyletic dwarfs, by contrast, have slower life histories than nondwarf species of the same body size. We discuss two possible mechanisms for the legacy of recent size change: lag (in which life history variables cannot evolve as quickly as body size, leading to species having the 'wrong' life history for their body size) and body size optimization (in which life history and hence body size evolve in response to changes in energy availability); at present, we cannot distinguish between these alternatives. Our finding that recent body size changes help explain residual variation around life history allometries shows that a more dynamic view of character change enables comparative studies to make more precise predictions about species traits in the context of their evolutionary background.