LVB: parsimony and simulated annealing in the search for phylogenetic trees

Summary: The program LVB seeks parsimonious phylogenies from nucleotide alignments, using the simulated annealing heuristic. LVB runs fast and gives high quality results.

Simulated annealing technique for fast learning of SOM networks

The Self-Organizing Map (SOM) is a popular unsupervised neural network able to provide effective clustering and data visualization for multidimensional input datasets. In this paper, we present an application of the simulated annealing procedure to the SOM learning algorithm with the aim to obtain a fast learning and better performances in terms of quantization error. The proposed learning algorithm is called Fast Learning Self-Organized Map, and it does not affect the easiness of the basic learning algorithm of the standard SOM. The proposed learning algorithm also improves the quality of resulting maps by providing better clustering quality and topology preservation of input multi-dimensional data. Several experiments are used to compare the proposed approach with the original algorithm and some of its modification and speed-up techniques.

The effect of annealing on the local structure of glassy polycarbonate

Annealing of polycarbonate glasses at temperatures belowTg leads to an increase in yield stress and a drop in the impact strength. Although such behaviour may be related to the corresponding reduction in free volume upon annealing, variations in the wide-angle X-ray scattering curves indicate some modification to the local structure. The area of an intrachain peak at s ∼ 0.7 Å−1 is monitored with respect to annealing temperature and time. It is proposed that the variations may be described by an increasing level of interlocking or (nesting) between neighbouring chain segments, a process which is a natural consequence of the molecular shape of polycarbonate.

The partial oxidation of methane over Pd/Al2O3 catalyst nanoparticles studied in-situ by near ambient-pressure x-ray photoelectron spectroscopy

Near ambient-pressure X-ray photoelectron spectroscopy (NAP-XPS) is used to study the chemical state of methane oxidation catalysts in-situ. Al2O3{supported Pd catalysts are prepared with different particle sizes ranging from 4 nm to 10 nm. These catalysts were exposed to conditions similar to those used in the partial oxidation of methane (POM) to syn-gas and simultaneously monitored by NAP-XPS and mass spectrometry. NAP-XPS data show changes in the oxidation state of the palladium as the temperature in- creases, from metallic Pd0 to PdO, and back to Pd0. Mass spectrometry shows an increase in CO production whilst the Pd is in the oxide phase, and the metal is reduced back under presence of newly formed H2. A particle size effect is observed, such that CH4 conversion starts at lower temperatures with larger sized particles from 6 nm to 10 nm. We find that all nanoparticles begin CH4 conversion at lower temperatures than polycrystalline Pd foil.

Thermoluminescence properties of natural zoisite mineral under gamma-irradiations and high temperature annealing

Natural silicate mineral of zoisite, Ca(2)Al(3)(SiO(4))(Si(2)O(7))O(OH), has been investigated concerning gamma-radiation, UV-radiation and high temperature annealing effects on thermoluminescence (TL). X-ray diffraction (XRD) measurement confirmed zoisite structure and X-ray fluorescence (XRF) analysis revealed besides Si, Al and Ca that are the main crystal components, other oxides of Fe, Mg, Cr, Na, K, Sr, Ti, Ba and Mn which are present in more than 0.05 wt%. The TL glow curve of natural sample contains (130-150), (340-370) and (435-475)degrees C peaks. Their shapes indicated a possibility that they are result of composition of two or more peaks strongly superposed, a fact confirmed by deconvolution method. Once pre-annealed at 600 degrees C for 1 h, the shape of the glow curves change and the zoisite acquires high sensitivity. Several peaks between 100 and 400 degrees C appear superposed, and the high temperature peak around 435 degrees C cannot be seen. The ultraviolet radiation, on the other hand, produces one TL peak around 130 degrees C and the second one around 200 degrees C and no more. (C) 2010 Elsevier B.V. All rights reserved.

Thickness and Annealing Temperature Effects on the Optical Properties and Surface Morphology of Layer-by-Layer Poly(p-phenyline vinylene) plus Dodecylbenzenesulfonate Films

The fabrication of controlled molecular architectures is essential for organic devices, as is the case of emission of polarized light for the information industry. In this study, we show that optimized conditions can be established to allow layer-by-layer (LbL) films of poly(p-phenylene vinylene) (PPV)+dodecylbenzenesulfonate (DBS) to be obtained with anisotropic properties. Films with five layers and converted at 110 degrees C had a dichroic ratio delta = 2.3 and order parameter r = 34%, as indicated in optical spectroscopy and emission ellipsometry data. This anisotropy was decreased with the number of layers deposited, with delta = 1.0 for a 75-layer LbL PPV + DBS film. The analysis with atomic force microscopy showed the formation of polymer clusters in a random growth process with the normalized height distribution being represented by a Gaussian function. In spite of this randomness in film growth, the self-covariance function pointed to a correlation between clusters, especially for thick films. In summary, the LbL method may be exploited to obtain both anisotropic films with polarized emission and regular, nanostructured surfaces. (c) 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 206-213, 2011

Synthesis of L1(0) Fe-Pd films by electrodeposition and thermal annealing

Fe-Pd alloy films have been prepared by electrochemical deposition from an alkaline electrolyte containing Fe sulfate, Pd chloride and 5-sulfosalicylic acid onto polycrystalline titanium substrates. The as-deposited films were nanocrystalline and magnetically soft (coercivity similar to 25 Oe). L1(0) Fe-Pd films with a (111) preferred orientation were obtained by post-deposition thermal annealing of films with composition about 37 at% Fe in an (Ar + 5% H-2) gas flow at 500 degrees C. Such films exhibit hard magnetic properties, with a coercivity up to 1880 Oe, and a slightly anisotropic magnetic response, with a larger in-plane remanence. Preliminary magnetic investigations support magnetization switching through pinning of domain walls. (c) 2008 Elsevier B.V. All rights reserved.

Co/Al2O3 catalysts promoted with noble metals for production of hydrogen by methane steam reforming

The effect of noble metal addition on the catalytic properties of Co/Al2O3 was evaluated for the steam reforming of methane. Co/Al2O3 catalysts were prepared with addition of different noble metals (Pt, Pd, Ru and Ir 0.3 wt.%) by a wetness impregnation method and characterized by UV-vis spectroscopy, temperature programmed reduction (TPR) and temperature programmed oxidation (TPO) of the reduced catalysts. The UV-vis spectra of the samples indicate that, most likely, large amounts of the supported cobalt form Co species in which cobalt is in octahedral and tetrahedral symmetries. No peaks assigned to cobalt species from aluminate were found for the promoted and unpromoted cobalt catalysts. TPO analyses showed that the addition of the noble metals on the Co/Al2O3 catalyst leads to a more stable metallic state and less susceptible to the deactivation process during the reforming reaction. The Co/Al2O3 promoted with Pt showed higher stability and selectivity for H(2)production during the methane steam reforming. (C) 2007 Elsevier Ltd. All rights reserved.

Production of hydrogen by ethanol steam reforming on Co/Al2O3 catalysts: Effect of addition of small quantities of noble metals

The catalytic performance of Co/Al2O3 catalysts promoted with small amounts noble metals (Pt, Pd, Ru, Ir) for steam reforming of ethanol (SRE) has been investigated. The catalysts were characterized by the energy dispersive X-ray, X-ray diffraction, BET surface area, X-ray absorption fine structure and temperature reduction programmed techniques. The results showed that the promoting effect of noble metals included a marked decrease of the reduction temperatures of both Co3O4 and cobalt surface species interacting with the support due to the hydrogen spillover effect, leading to a significant increase of the reducibilities of the promoted catalysts. The better catalytic performance for the ethanol steam reforming at 400 degrees C was obtained for the CoRu/Al2O3 catalyst, which presented an effluent gaseous mixture with the highest H, selectivity and the reasonable low CO formation. (C) 2007 Published by Elsevier B.V.

Solving the Vehicle Routing Problem with Genetic ALgorithm and Simulated Annealing

This Thesis Work will concentrate on a very interesting problem, the Vehicle Routing Problem (VRP). In this problem, customers or cities have to be visited and packages have to be transported to each of them, starting from a basis point on the map. The goal is to solve the transportation problem, to be able to deliver the packages-on time for the customers,-enough package for each Customer,-using the available resources- and – of course - to be so effective as it is possible.Although this problem seems to be very easy to solve with a small number of cities or customers, it is not. In this problem the algorithm have to face with several constraints, for example opening hours, package delivery times, truck capacities, etc. This makes this problem a so called Multi Constraint Optimization Problem (MCOP). What’s more, this problem is intractable with current amount of computational power which is available for most of us. As the number of customers grow, the calculations to be done grows exponential fast, because all constraints have to be solved for each customers and it should not be forgotten that the goal is to find a solution, what is best enough, before the time for the calculation is up. This problem is introduced in the first chapter: form its basics, the Traveling Salesman Problem, using some theoretical and mathematical background it is shown, why is it so hard to optimize this problem, and although it is so hard, and there is no best algorithm known for huge number of customers, why is it a worth to deal with it. Just think about a huge transportation company with ten thousands of trucks, millions of customers: how much money could be saved if we would know the optimal path for all our packages.Although there is no best algorithm is known for this kind of optimization problems, we are trying to give an acceptable solution for it in the second and third chapter, where two algorithms are described: the Genetic Algorithm and the Simulated Annealing. Both of them are based on obtaining the processes of nature and material science. These algorithms will hardly ever be able to find the best solution for the problem, but they are able to give a very good solution in special cases within acceptable calculation time.In these chapters (2nd and 3rd) the Genetic Algorithm and Simulated Annealing is described in details, from their basis in the “real world” through their terminology and finally the basic implementation of them. The work will put a stress on the limits of these algorithms, their advantages and disadvantages, and also the comparison of them to each other.Finally, after all of these theories are shown, a simulation will be executed on an artificial environment of the VRP, with both Simulated Annealing and Genetic Algorithm. They will both solve the same problem in the same environment and are going to be compared to each other. The environment and the implementation are also described here, so as the test results obtained.Finally the possible improvements of these algorithms are discussed, and the work will try to answer the “big” question, “Which algorithm is better?”, if this question even exists.

Uma Proposta de especificação formal e fundamentação teórica para simulated annealing

Os algoritmos baseados no paradigma Simulated Annealing e suas variações são atualmente usados de forma ampla na resolução de problemas de otimização de larga escala. Esta popularidade é resultado da estrutura extremamente simples e aparentemente universal dos algoritmos, da aplicabilidade geral e da habilidade de fornecer soluções bastante próximas da ótima. No início da década de 80, Kirkpatrick e outros apresentaram uma proposta de utilização dos conceitos de annealing (resfriamento lento e controlado de sólidos) em otimização combinatória. Esta proposta considera a forte analogia entre o processo físico de annealing e a resolução de problemas grandes de otimização combinatória. Simulated Annealing (SA) é um denominação genérica para os algoritmos desenvolvidos com base nesta proposta. Estes algoritmos combinam técnicas de busca local e de randomização. O objetivo do presente trabalho é proporcionar um entendimento das características do Simulated Annealing e facilitar o desenvolvimento de algoritmos com estas características. Assim, é apresentado como Simulated Annealing e suas variações estão sendo utilizados na resolução de problemas de otimização combinatória, proposta uma formalização através de um método de desenvolvimento de algoritmos e analisados aspectos de complexidade. O método de desenvolvimento especifica um programa abstrato para um algoritmo Simulated Annealing seqüencial, identifica funções e predicados que constituem os procedimentos deste programa abstrato e estabelece axiomas que permitem a visualização das propriedades que estes procedimentos devem satisfazer. A complexidade do Simulated Annealing é analisada a partir do programa abstrato desenvolvido e de seus principais procedimentos, permitindo o estabelecimento de uma equação genérica para a complexidade. Esta equação genérica é aplicável aos algoritmos desenvolvidos com base no método proposto. Uma prova de correção é apresentada para o programa abstrato e um código exemplo é analisado com relação aos axiomas estabelecidos. O estabelecimento de axiomas tem como propósito definir uma semântica para o algoritmo, o que permite a um desenvolvedor analisar a correção do código especificado para um algoritmo levando em consideração estes axiomas. O trabalho foi realizado a partir de um estudo introdutório de otimização combinatória, de técnicas de resolução de problemas, de um levantamento histórico do uso do Simulated Annealing, das variações em torno do modelo e de embasamentos matemáticos documentados. Isto permitiu identificar as características essenciais dos algoritmos baseados no paradigma, analisar os aspectos relacionados com estas características, como as diferentes formas de realizar uma prescrição de resfriamento e percorrer um espaço de soluções, e construir a fundamentação teórica genérica proposta.