Database technologies for l-system simulations in virtual plant applications on bioinformatics

One of the most important advantages of database systems is that the underlying mathematics is rich enough to specify very complex operations with a small number of statements in the database language. This research covers an aspect of biological informatics that is the marriage of information technology and biology, involving the study of real-world phenomena using virtual plants derived from L-systems simulation. L-systems were introduced by Aristid Lindenmayer as a mathematical model of multicellular organisms. Not much consideration has been given to the problem of persistent storage for these simulations. Current procedures for querying data generated by L-systems for scientific experiments, simulations and measurements are also inadequate. To address these problems the research in this paper presents a generic process for data-modeling tools (L-DBM) between L-systems and database systems. This paper shows how L-system productions can be generically and automatically represented in database schemas and how a database can be populated from the L-system strings. This paper further describes the idea of pre-computing recursive structures in the data into derived attributes using compiler generation. A method to allow a correspondence between biologists' terms and compiler-generated terms in a biologist computing environment is supplied. Once the L-DBM gets any specific L-systems productions and its declarations, it can generate the specific schema for both simple correspondence terminology and also complex recursive structure data attributes and relationships.

Aplicação de ferramentas de simulação de processos

Este trabalho foi efectuado com o propósito de interpretar, compreender e explicar algumas ferramentas de simulação de processos, em particular o Aspen Energy Analyzer (AEA), o Aspen Economic Evaluation (AEE) e o seu funcionamento integrado com o Aspen Hysys(AH). O AH é uma ferramenta de modelação de processos para a concepção de projectos de engenharia química, o AEA é uma ferramenta de modelação de redes de integração energética. O AEE integrado no AH é uma ferramenta que permite incorporar estudos económicos numa fase preliminar do desenvolvimento de um projecto de engenharia. A abordagem a este trabalho foi efectuada através do estudo de Casos. O Caso I foi baseado na resolução de um problema no AEA através da construção e optimização de uma rede de permutadores de calor. Os Casos II e III foram baseados na construção de um flowsheet de produção de Benzeno e de Cloreto de Vinil, respectivamente, e cada Caso foi dividido em dois cenários diferentes. Para o efeito foram utilizados os softwares AEA para a integração energética dos processos, o AH para construção do fluxograma do processo e o AEE para os estudos económicos dos diferentes cenários. Finalmente, os Casos IV e V dizem respeito à resolução de um problema de integração energética. O Caso IV foi baseado num problema de optimização da rede de permutadores através do aumento da sua área. Já o Caso V foi baseado na informação inicial das correntes do caso anterior e em dois cenários diferentes, nos quais foi estudada a influência dos preços das utilidades na construção da rede de permutadores. A conclusão foi que as ferramentas de modelação, particularmente o AH, o AEA e o AEE são uma mais-valia extraordinária para ajudar o utilizador na tomada de decisões em fases bastante preliminares da engenharia de processos.

Modelação e simulação de sistemas fotovoltaicos

Os sistemas fotovoltaicos produzem energia eléctrica limpa, e inesgotável na nossa escala temporal. A Agência Internacional de Energia encara a tecnologia fotovoltaica como uma das mais promissoras, esperando nas suas previsões mais optimistas, que em 2050 possa representar 20% da produção eléctrica mundial, o equivalente a 18000 TWh. No entanto, e apesar do desenvolvimento notável nas últimas décadas, a principal condicionante a uma maior proliferação destes sistemas é o ainda elevado custo, aliado ao seu fraco desempenho global. Apesar do custo e ineficiência dos módulos fotovoltaicos ter vindo a diminuir, o rendimento dos sistemas contínua dependente de factores externos sujeitos a grande variabilidade, como a temperatura e a irradiância, e às limitações tecnológicas e falta de sinergia dos seus equipamentos constituintes. Neste sentido procurou-se como objectivo na elaboração desta dissertação, avaliar o potencial de optimização dos sistemas fotovoltaicos recorrendo a técnicas de modelação e simulação. Para o efeito, em primeiro lugar foram identificados os principais factores que condicionam o desempenho destes sistemas. Em segundo lugar, e como caso prático de estudo, procedeu-se à modelação de algumas configurações de sistemas fotovoltaicos, e respectivos componentes em ambiente MatlabTM/SimulinkTM. Em seguida procedeu-se à análise das principais vantagens e desvantagens da utilização de diversas ferramentas de modelação na optimização destes sistemas, assim como da incorporação de técnicas de inteligência artificial para responder aos novos desafios que esta tecnologia enfrentará no futuro. Através deste estudo, conclui-se que a modelação é não só um instrumento útil para a optimização dos actuais sistemas PV, como será, certamente uma ferramenta imprescindível para responder aos desafios das novas aplicações desta tecnologia. Neste último ponto as técnicas de modelação com recurso a inteligência artificial (IA) terão seguramente um papel preponderante. O caso prático de modelação realizado permitiu concluir que esta é igualmente uma ferramenta útil no apoio ao ensino e investigação. Contudo, convém não esquecer que um modelo é apenas uma aproximação à realidade, devendo recorrer-se sempre ao sentido crítico na interpretação dos seus resultados.

Fractional Dynamics in the Rayleigh's Piston

This paper studies the dynamics of the Rayleigh piston using the modeling tools of Fractional Calculus. Several numerical experiments examine the effect of distinct values of the parameters. The time responses are transformed into the Fourier domain and approximated by means of power law approximations. The description reveals characteristics usual in Fractional Brownian phenomena.

Analysis of urban land use and land cover changes: a case of study in Bahir Dar, Ethiopia

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies

A minimal version of a Protein Tyrosine Phosphatase

Phosphatase and tensin homologue (PTEN) protein belongs to the family of protein tyrosine phos-phatase. Mutations on the phosphatase and tensin homologue (PTEN) protein are highly observed in diverse types of human tumors, being mostly identified on the phosphatase domain of the protein. Although PTEN is a modular protein composed by a phosphatase domain and a C2 domain for mem-brane anchoring, this work aimed at developing a minimal version of PTEN´s phosphatase domain. The minimal version (Small Domain) comprises a 28 residue peptide, with the PTEN 8-mer catalytic peptide accommodated between a α-helix and β-turn as observed in PTEN native structure. Firstly, a de novo prediction of the Small Domain´s secondary structure was carried out by molecular modeling tools. The stability of the predicted structures were then evaluated by Molecular Dynamics. Automated molecular docking of PTEN natural substrate PIP3, its analogue (Inositol) and a PTEN inhibitor (L-tar-tare) were performed with the modeled structure, and PTEN used as a positive control. The gene en-coding for Small Domain was designed and cloned into an expression vector at N-terminal of Green Fluorescence Protein (GFP) encoding gene. The fusion protein was then expressed in Escherichia coli cells. Different expression conditions have been explored for the production of the fusion protein to minimize the formation of inclusion bodies.

Evaluation of the DPMFoam solver

[Extrat] Multiphase flows are relevant in several industrial processes, thus the availability of accurate numerical modeling tools, able to support the design of products and processes, is of much significance. OpenFOAM version 2.3.x comprises a multiphase flow solver able to couple Eulerian and Lagrangian phases using the discrete particles method (DPM), the DPMFoam. In this work the DPMFoam solver is assessed by comparing its predictions with analytical results and experimental and simulated data available in the literature. They are results from Goldschmidt’s [1] and Hoomans’s [2] theses and the analytical Ergun equation. The goal was to define accuracy and performance of DPMFoam in general scientific or commercial applications. Obtained results demonstrate a good agreement with the reference simulation data and is within reasonable deviations from the experimental values. (...)

Avaliação do transporte sedimentar na bacia do rio Lima baseada em ferramentas de modelação

Dissertação de mestrado integrado em Engenharia Civil

Todennäköisyyspohjaisen paloanalyysimenetelmän kehittäminen ydinvoimalaitoksella

Diplomityössä on tutustuttu ydinvoimalaitosten paloriskejä käsittelevään todennäköisyyspohjaiseen turvallisuusanalyysiin. Tavoitteena on ollut Olkiluoto 1 ja 2 laitosyksiköiden paloanalyysimenetelmän kehittäminen. Työssä esitetään paloanalyysin pääpiirteet, kaksi erilaista palotaajuuksien estimointimenetelmää sekä palojen leviämisen arviointimenetelmiä. Palotaajuuksien estimointimenetelmistä keskitytään Berryn menetelmän sekä NUREG/CR-6850-palotaajuuslaskentamenetelmän tarkasteluun. Palon leviämisen arvioinnissa on esitetty kolmen erilaisen virtausteknisen laskentatyökalun perusteet sekä palon leviämistodennäköisyyksiä arvioivan Probabilistic Fire Simulator (PFS) -ohjelman käyttöä. Työn aikana on laskettu molemmilla palotaajuuden estimointimenetelmillä palotaajuuksia eri tyyppisille huonetiloille. Berryn menetelmän palotaajuudet olivat pääosin alhaisempia kuin NUREG/CR-6850-menetelmällä lasketut palotaajuudet. Palon leviämistarkastelussa on tutkittu ydinvoimalaitoksen relehuoneen tulipaloa. PFS:n avulla laskettujen leviämistodennäköisyyksien arvoja on vertailtu TVO:n paloanalyysissa käytettyihin kvalitatiivisiin peittokertoimiin. Palon leviämistodennäköisyys eri osajärjestelmien välillä todettiin suuresti riippuvan analyysissaoletetuista vaurioitumislämpötiloista. Tutkittuja menetelmiä hyödyntäen diplomityössä kehitettiin paloanalyysimenetelmäkuvaus. Menetelmäkuvauksessa huonetilojen paloriskit kartoitetaan aluksi Berryn menetelmällä. Näin kaikille laitoksen huonetiloille saadaan arvioitua palotaajuus sekä paloalkutapahtumaluokkien sydänvauriotaajuus. Seuraavaksi suoritetaan valintamenettely, jossa valitut kriteerit täyttäville huonetiloille tehdään tarkentava palotaajuuslaskenta. Tarkentava palotaajuuslaskenta perustuu NUREG/CR-6850-menetelmän mukaisesti huonetilojen realistisiin syttymislähteisiin. Kriittisimpien huonetilojen osalta palon leviämisen arviointiin on tarkoitus hyödyntää numeerista simulointia.

Logging residues from regeneration fellings for biofuel production - a GIS-based availability and supply cost analysis

Finland has large forest fuel resources. However, the use of forest fuels for energy production has been low, except for small-scale use in heating. According to national action plans and programs related to wood energy promotion, the utilization of such resources will be multiplied over the next few years. The most significant part of this growth will be based on the utilization of forest fuels, produced from logging residues of regeneration fellings, in industrial and municipal power and heating plants. Availability of logging residues was analyzed by means of resource and demand approaches in order to identify the most suitable regions with focus on increasing the forest fuel usage. The analysis included availability and supply cost comparisons between power plant sites and resource allocation in a least cost manner, and between a predefined power plant structure under demand and supply constraints. Spatial analysis of worksite factors and regional geographies were carried out using the GIS-model environment via geoprocessing and cartographic modeling tools. According to the results of analyses, the cost competitiveness of forest fuel supply should be improved in order to achieve the designed objectives in the near future. Availability and supply costs of forest fuels varied spatially and were very sensitive to worksite factors and transport distances. According to the site-specific analysis the supply potential between differentlocations can be multifold. However, due to technical and economical reasons ofthe fuel supply and dense power plant infrastructure, the supply potential is limited at plant level. Therefore, the potential and supply cost calculations aredepending on site-specific matters, where regional characteristics of resourcesand infrastructure should be taken into consideration, for example by using a GIS-modeling approach constructed in this study.

Simulações computacionais e ferramentas de modelização em educação química: uma revisão de literatura publicada

This article presents a review of published literature concerning the use of computer simulations and modeling tools in Chemical Education. The findings about the possibilities of their application in the Chemistry curriculum, their effective implementation, the teaching methods involved, the research methodology and also the instruments of evaluation that were used and their results were described and analyzed. The need to develop adequate theory support to educators who want to start using this new technology in their Chemistry classes became evident along the research, as well as the lack of development of model perception among Chemistry educators and learners.

A Development and Application of a Three-Dimensional Model for a CFB Gasifier

The developing energy markets and rising energy system costs have sparked the need to find new forms of energy production and increase the self-sufficiency of energy production. One alternative is gasification, whose principles have been known for decades, but it is only recently when the technology has become a true alternative. However, in order to meet the requirements of modern energy production methods, it is necessary to study the phenomenon thoroughly. In order to understand the gasification process better and optimize it from the viewpoint of ecology and energy efficiency, it is necessary to develop effective and reliable modeling tools for gasifiers. The main aims of this work have been to understand gasification as a process and furthermore to develop an existing three-dimensional circulating fluidized bed modeling tool for modeling of gasification. The model is applied to two gasification processes of 12 and 50 MWth. The results of modeling and measurements have been compared and subsequently reviewed. The work was done in co-operation with Lappeenranta University of Technology and Foster Wheeler Energia Oy.

Genetic Programming meets Model-Driven Development

Genetic programming is known to provide good solutions for many problems like the evolution of network protocols and distributed algorithms. In such cases it is most likely a hardwired module of a design framework that assists the engineer to optimize specific aspects of the system to be developed. It provides its results in a fixed format through an internal interface. In this paper we show how the utility of genetic programming can be increased remarkably by isolating it as a component and integrating it into the model-driven software development process. Our genetic programming framework produces XMI-encoded UML models that can easily be loaded into widely available modeling tools which in turn posses code generation as well as additional analysis and test capabilities. We use the evolution of a distributed election algorithm as an example to illustrate how genetic programming can be combined with model-driven development. This example clearly illustrates the advantages of our approach – the generation of source code in different programming languages.

Gestión de la cadena de suministros desde la dinámica de sistemas. Aproximación al mejoramiento de la toma de decisiones

El objetivo de este trabajo es hacer un estudio sobre la cadena de suministros en organizaciones empresariales desde la Dinámica de Sistemas y como esta puede aportar al desempeño y el control de las cadenas de suministros. Se buscará Abordar el cocimiento sobre tres perspectivas de Supply Chain y su relación con la dinámica de sistemas. También se buscará identificar los tipos de integración en las actividades de la gestión en la cadena de suministros y sus horizontes de planeación. Por último, se pretende analizar las aplicaciones de Supply Chain Management que se han basado en el uso de la metodología de dinámica de sistemas. Para esto, la investigación empezará por definir la problemática alrededor de unir estas dos áreas y definirá el marco teórico que fundan estas dos disciplinas. Luego se abordará la metodología usada por la Dinámica de Sistemas y los diferentes aspectos de la cadena de suministros. Se Ahondará en el acercamiento de las dos disciplinas y como convergen ayudando la SD a la SCM (Supply Chain Management). En este punto también se describirán los trabajos en los diferentes enfoques que se han hecho a partir de uso de la dinámica de sistemas. Por último, presentaremos las correspondientes conclusiones y comentarios acerca de este campo de investigación y su pertinencia en el campo de la Supply Chain. Esta investigación abarca dos grandes corrientes de pensamiento, una sistémica, a través de la metodología de dinámica de sistemas y la otra, lógico analítica la cual es usada en Supply Chain. Se realizó una revisión de la literatura sobre las aplicaciones de dinámica de sistemas (SD) en el área de Supply Chain, sus puntos en común y se documentaron importantes empleos de esta metodología que se han hecho en la gestión de la cadena de suministros.

Stratospheric temperature trends: our evolving understanding

We review the scientific literature since the 1960s to examine the evolution of modeling tools and observations that have advanced understanding of global stratospheric temperature changes. Observations show overall cooling of the stratosphere during the period for which they are available (since the late 1950s and late 1970s from radiosondes and satellites, respectively), interrupted by episodes of warming associated with volcanic eruptions, and superimposed on variations associated with the solar cycle. There has been little global mean temperature change since about 1995. The temporal and vertical structure of these variations are reasonably well explained bymodels that include changes in greenhouse gases, ozone, volcanic aerosols, and solar output, although there are significant uncertainties in the temperature observations and regarding the nature and influence of past changes in stratospheric water vapor. As a companion to a recent WIREs review of tropospheric temperature trends, this article identifies areas of commonality and contrast between the tropospheric and stratospheric trend literature. For example, the increased attention over time to radiosonde and satellite data quality has contributed to better characterization of uncertainty in observed trends both in the troposphere and in the lower stratosphere, and has highlighted the relative deficiency of attention to observations in the middle and upper stratosphere. In contrast to the relatively unchanging expectations of surface and tropospheric warming primarily induced by greenhouse gas increases, stratospheric temperature change expectations have arisen from experiments with a wider variety of model types, showingmore complex trend patterns associated with a greater diversity of forcing agents.