The Probabilistic Backbone of Data-Driven Complex Networks: An example in Climate

Correlation Networks (CNs) inherently suffer from redundant information in their network topology. Bayesian Networks (BNs), on the other hand, include only non-redundant information (from a probabilistic perspective) resulting in a sparse topology from which generalizable physical features can be extracted. We advocate the use of BNs to construct data-driven complex networks as they can be regarded as the probabilistic backbone of the underlying complex system. Results are illustrated at the hand of a global climate dataset

Coevolutionary optimization of fuzzy logic intelligence for strategic decision support

©2005 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.We present a description and initial results of a computer code that coevolves fuzzy logic rules to play a two-sided zero-sum competitive game. It is based on the TEMPO Military Planning Game that has been used to teach resource allocation to over 20 000 students over the past 40 years. No feasible algorithm for optimal play is known. The coevolved rules, when pitted against human players, usually win the first few competitions. For reasons not yet understood, the evolved rules (found in a symmetrical competition) place little value on information concerning the play of the opponent.Rodney W. Johnson, Michael E. Melich, Zbigniew Michalewicz, and Martin Schmid

A software tool for network topology analysis under a Metabolic Engineering perspective

In this work, we present a software application that runs as a plug-in over the OptFlux Metabolic Engineering platform allowing the topological analysis of metabolic networks. The major aim of this tool is to allow the interconnection between phenotype simulation tasks (using algorithms such as Flux Balance Analysis) and topological analysis of the same networks. The provided methods include node degree and degree distributions, shortest path analysis, clustering coefficients and several node rankers (betweenness and closeness centrality, hubs and authorities, etc). Also, it allows the creation of sub-networks through severalfilters, including some based on the results of phenotype simulation.(undefined

Modeling and experimental design to characterize permeation and gettering of hydrogen isotopes in fusion materials

The roadmap towards fusion electricity includes the construction of an experimental fusion reactor called DEMO (DEMOnstration power plant). A critical element of DEMO is the tritium breeding blanket. Amongst others, two breeding blanket designs are currently under investigation: the HCPB (helium-cooled pebble bed) and the WCLL (watercooled lithium-lead) breeding blanket. In an HCPB breeding blanket, tritium is bred in lithium-containing ceramic pebble beds rinsed by a helium purge gas flowing past helium coolant channels. In a WCLL breeding blanket, a flowing lithium-lead breeder fluid is penetrated by water coolant pipes. In both designs, it is inevitable that radioactive tritium permeates from the breeder zone through Eurofer’97 steel walls into the adjacent coolant. To ensure a safe operation of DEMO, finding methods that mitigate tritium contamination of the coolant is essential. Previous experimental observations suggest that the addition of protium to the breeder fluid or coolant of the breeding blankets might, under certain conditions, reduce the tritium permeation flux. However, there is insufficient information in the literature that would allow the evaluation of this technique as a suitable tritium mitigation method. For this purpose, in the first part of this thesis, a theoretical study of multi-isotopic hydrogen gas-to-gas (relevant to an HCPB breeding blanket) and liquid metal-to-water (relevant to a WCLL breeding blanket) co- and counter-permeation is conducted in which the cause of the permeation flux altering effect of multi-isotopic permeation is revealed. Algebraic formulas are derived that allow expressing the tritium permeation flux as a function of the concentration of simultaneously co- or counter-permeating protium. Numerical system-level hydrogen transport models of the HCPB and WCLL breeding zones are developed which allow simulation of the occurring tritium permeation fluxes for different protium concentrations in the respective breeder fluid and the coolant. According to the simulations, an addition of protium to the coolant of an HCPB breeding blanket only leads to a reduction in tritium permeation when the protium concentration is too high to be technically feasible. However, adding protium to the HCPB purge gas is found to indeed result in a significant reduction in tritium permeation flux at still relatively low protium concentrations and should therefore be considered as a tritium mitigation method for HCPB breeding blankets. It is found that an increased concentration of protium in the lithium-lead or water coolant of a WCLL breeding blanket can only lead to an increase in tritium permeation and should hence be avoided. The numerical model and derived algebraic formulas describing gas-to-gas counter-permeation are experimentally validated by reproducing experimental data. To enable additional on-site experimental verification of gas-to-gas co- and counter permeation effects with Eurofer’97 as membrane material a new experimental facility is developed from scratch, called COOPER (CO- and cOunter-permeation) experiment. This thesis presents the experimental design and commissioning of the COOPER facility as well as preliminary mono-isotopic permeation measurements in which hydrogen transport coefficients such as the diffusivity, permeability and Sieverts’ constant of deuterium in Eurofer’97 are determined. Moreover, detailed experimental procedures for performing co- and counter-permeation flux measurements with the COOPER experiment are presented. The described procedures are supported by numerical simulations of multiisotopic permeation measurements taking into account the geometry and experimental conditions of the COOPER device. Another key research facility to be built on the path to fusion power is DONES (DEMO-Oriented Neutron Source), an experimental neutron irradiation facility for fusionrelevant materials. It consists of a deuterium beam colliding with a liquid lithium target that is part of a lithium loop system. Nuclear stripping reactions occur between the deuterons and the lithium, producing neutrons, but also protium, deuterium and tritium, which accumulate in the lithium. To comply with hydrogen concentration limits in lithium, an yttrium-based hydrogen getter trap will be installed. However, the physical processes that determine the absorption dynamics and the getter capacity of such a trap have not yet been sufficiently studied to allow a reliable trap design. For this reason, the second part of this thesis is devoted to the numerical and experimental investigation of hydrogen capture in DONES with the objective of defining trap design conditions that ensure meeting DONES safety limits. A numerical tool is developed from scratch capable of simulating multi-isotopic hydrogen transport in the DONES lithium loop connected to an arbitrary yttrium pebble bed. It includes the physical mechanisms of lithium and yttrium hydride formation, which is a novelty in system-level hydrogen transport modeling. A thermodynamic analysis of the lithium-yttrium-hydrogen system is carried out which reveals the solubility of hydrogen in different yttrium hydride phases exposed to hydrogen-loaded lithium. Moreover, an approximate concentrationdependent relationship of hydrogen diffusivity in yttrium is derived and incorporated into the model. Simulations are performed to analyze the dynamics of hydrogen purification processes during different operating phases of DONES by varying design parameters of the trap. It is found that yttrium dihydride formation greatly increases the gettering capacity of the trap and prevents the concentration in the lithium to increase above a critical value. Moreover, algebraic formulas are derived that allow calculating the required yttrium pebble bed mass and trap replacement period at any given temperature to comply with DONES safety requirements. Finally, the model is validated by a numerical reproduction of experimental results. To allow future experimental validation of the developed model, a new experimental lithium system is developed and put into operation. It is called the LYDER (Lithium system for Yttrium-based DEeuterium Retention) experiment, the design and construction of which are presented in this thesis. The LYDER system is designed to allow the loading of 100mL of molten lithium with a controlled concentration of deuterium. The design foresees creating a pressure differential in two argon-filled tanks which moves the deuterium-loaded lithium through a thin pipe system connected to an yttrium-based deuterium trap. The LYDER system is equipped with a lithium sample extraction system and a thermal desorption spectroscopy branch with the purpose of analyzing the extracted samples for their deuterium content. Numerical hydrogen transport models of the developed lithium system and the deuterium injection system are created and simulation results are discussed in this thesis.El camino hacia la energía de fusión incluye la construcción de un reactor de fusión experimental denominado DEMO (DEMOnstration power plant). Un elemento crítico de DEMO es la envoltura reproductora de tritio (de ahora en adelante breeding blanket) donde se produce el combustible tritio. Entre otros, se están investigando intensamente dos diseños de breeding blankts: el HCPB (helium-cooled pebble bed) y el WCLL (watercooled lithium-lead) breding blanket. En el HCPB breeding blanket, el tritio se genera en lechos de pebbles cerámicos antes de ser arrastrado por un gas de purga de helio que fluye a lo largo de canales de refrigeración de helio. En el WCLL breeding blanket el tritio se produce en litio-plomo líquido que fluye a través de tubos refrigerados por agua. En ambos diseños, es inevitable que el tritio radiactivo generado permea desde la zona de su producción, a través de las paredes de acero de Eurofer’97, hacia el refrigerante. Para garantizar un funcionamiento seguro de DEMO, es esencial encontrar métodos que mitiguen la contaminación del refrigerante por tritio. Resultados experimentales previos sugieren que, en determinadas condiciones, la inyección de protio a la zona de producción de tritio o al refrigerante podría reducir el flujo de permeación de tritio al refrigerante. Sin embargo, hoy en día no existe suficiente información en la literatura que permita evaluar esta técnica como método de mitigación de tritio. Con este fin, en la primera parte de esta disertación se lleva a cabo un estudio teórico de la co- y contra-permeación multi-isotópica de gas-a-gas (relevante para un breeding blanket HCPB) y de metal líquido-a-agua (relevante para un breeding blanket WCLL). De esta manera se revela la causa de la alteración del flujo de permeación por efectos multi-isotópicas. Se derivan fórmulas algebraicas que permiten expresar el flujo de permeación de tritio en función de la concentración de protio que simultáneamente co- o contra-permea. Además, en esta tesis, se presenta el desarollo de modelos numéricos del transporte de hidrógeno a nivel de sistema de las zonas de producción de tritio en los breeding blankets HCPB y WCLL que permiten simular los flujos de permeación de tritio para diferentes concentraciones de protio añadido. De acuerdo con las simulaciones, la inyección de protio al refrigerante de un breeding blanket HCPB solamente resulta en una reducción de la permeación de tritio cuando la concentración de protio es demasiado alta para ser técnicamente viable. Sin embargo, se ha comprobado que la adición de protio al gas de purga del HCPB produce una reducción significativa a concentraciones de protio relativamente bajas, por lo cual se debería considerar como un posible método de mitigación de tritio, eficaz y barato. Se ha descubierto que una mayor concentración de protio en el refrigerante de litio-plomo o agua de un breeding blanket WCLL sólo puede resultar en un aumento de la permeación de tritio y, por lo tanto, debe evitarse. El modelo numérico y las fórmulas algebraicas derivadas que describen la contra-permeación gas-a-gas se validan mediante datos experimentales. Para permitir una verificación experimental adicional in situ de los efectos predichos tanto de la co-permeación gas-a-gas como de la contra-permeación gas-a-gas con Eurofer’ 97 como material de membrana, se desarrolla una nueva instalación experimental desde cero, denominada experimento COOPER (CO- and cOunter-PERmeation). Esta tesis presenta el diseño experimental y la puesta en marcha de la instalación COOPER, así como mediciones preliminares de permeación mono-isotópica en las que se determinan coeficientes de transporte de hidrógeno como la difusividad, la permeabilidad y la constante de Sievert de deuterio en Eurofer’97. Además, se presentan procedimientos experimentales detallados para realizar mediciones de flujo de co-permeación y contrapermeación con el experimento COOPER. Los procedimientos descritos están respaldados por simulaciones numéricas, teniendo en cuenta la geometría característica y las condiciones experimentales del experimento COOPER. Otra instalación de investigación clave que se construirá en el camino hacia la energía de fusión es DONES (DEMO-Oriented Neutron Source), una instalación experimental de irradiación neutrónica de materiales para la fusión. DONES consiste en un haz de deuterio que colisiona con un blanco de litio líquido que forma parte de un lazo de litio. Reacciones nucleares entre los deuterones y el litio producen neutrones, pero también protio, deuterio y tritio, que se acumulan en el litio. Para respetar los límites de concentración de isotopos de hidrógeno en el litio, se instalará una trampa captadora de hidrógeno a base de itrio. Hasta ahora, los procesos físicos que determinan la dinámica de absorción y la capacidad de captación de una trampa de este tipo no se han investigado lo suficiente como para poder diseñar una trampa fiable. Por esta razón, la segunda parte de esta tesis se dedica a la investigación numérica y experimental de los mecanismos físicos implicados con el objetivo de definir los parámetros de diseño de la trampa apropiados para DONES. Se desarrolla desde cero una herramienta numérica capaz de simular el transporte de hidrógeno que se produce en el lazo de litio de DONES conectado a un lecho de pebbles de itrio. El modelo incluye los mecanismos físicos de la formación de hidruros de litio e itrio, lo que constituye una novedad en la modelado del transporte de hidrógeno a nivel de sistema. Se lleva a cabo un análisis termodinámico del sistema litio-itrio-hidrógeno que revela la solubilidad de los isótopos de hidrógeno en diferentes fases de hidruro de itrio expuesto a litio cargado de hidrógeno. Además, se deriva una relación aproximada de la difusividad de hidrógeno en itrio dependiente de la concentración de hidrógeno que está incorporado en el modelo. Se realizan simulaciones para analizar la dinámica de los procesos de purificación de isótopos de hidrógeno durante diferentes fases de operación de DONES variando los parámetros de diseño de la trampa. Se observa que la formación de dihidruro de itrio aumenta en gran medida la capacidad de absorción de la trampa y evita que la concentración en el litio aumente por encima de un valor crítico. Además, se derivan fórmulas algebraicas que permiten calcular la masa necesaria del lecho de pebbles de itrio y el periodo de sustitución de la trampa para cumplir los requisitos de seguridad de DONES. El modelo se valida mediante una reproducción numérica de resultados experimentales. Para facilitar la futura validación experimental del modelo creado, se ha desarrollado y puesto en funcionamiento un nuevo sistema experimental de litio en el marco de esta tesis. Se trata del experimento LYDER (Lithium system for Yttrium-based DEeuterium Retention), cuyo diseño y construcción se presentan en esta tesis. El sistema LYDER está diseñado para permitir la carga de 100mL de litio fundido con una concentración controlada de deuterio. El diseño prevé la creación de un diferencial de presión entre dos tanques presurizados con argón que mueve el litio cargado de deuterio a través de una linea de tuberías que pasa por una trampa experimental de deuterio. El sistema LYDER está equipado con un sistema de extracción de muestras de litio y una rama de espectroscopia de desorción térmica con el objetivo de analizar las muestras extraídas para determinar su contenido de deuterio. Además, se presentan modelos numéricos del transporte de deuterio en el sistema de litio y del sistema de inyección de deuterio de LYDER. Los resultados de las simulaciones están analizados en esta disertación.Programa de Doctorado en Ciencia e Ingeniería de Materiales por la Universidad Carlos III de MadridPresidente: Ángel Ibarra Sánchez.- Secretario: Manuel José Pérez Mendoza.- Vocal: Igor Peñalva Bengo

A cDNA microarray approach to decipher sunflower (Helianthus annuus) responses to the necrotrophic fungus Phoma macdonaldii

To identify the genes involved in the partial resistance of sunflower (Helianthus annuus) to the necrotrophic fungus Phoma macdonaldii, we developed a 1000‐element cDNA microarray containing carefully chosen genes putatively involved in primary metabolic pathways, signal transduction and biotic stress responses. A two‐pass general linear model was used to normalize the data and then to detect differentially expressed genes. This method allowed us to identify 38 genes differentially expressed among genotypes, treatments and times, mainly belonging to plant defense, signaling pathways and amino acid metabolism. Based on a set of genes whose differential expression was highly significant, we propose a model in which negative regulation of a dual‐specificity MAPK phosphatase could be implicated in sunflower defense mechanisms against the pathogen. The resulting activation of the MAP kinase cascade could subsequently trigger defense responses (e.g. thaumatin biosynthesis and phenylalanine ammonia lyase activation), under the control of transcription factors belonging to MYB and WRKY families. Concurrently, the activation of protein phosphatase 2A (PP2A), which is implicated in cell death inhibition, could limit pathogen development. The results reported here provide a valuable first step towards the understanding and analysis of the P. macdonaldii–sunflower interaction

Development of a data integration pipeline for human metabolic models and databases

Dissertação de mestrado em BioinformaticsSystems Biology aims to integrate experimental and computational approaches with the purpose of explaining and predicting the organisms' behavior. The development of mathematical models in silico gives us a better in-depth knowledge of their biological mechanism. Bioinformatics tools enabled the integration of a large amount of complex biological data into computer models, but also capable to perform computational simulations with these models, that can predict the organisms' phenotypic behavior in different conditions. Up to date, genome-scale metabolic models (GSMMs) include several metabolic components of an organism. These are related to the metabolic capabilities encoded in the genome. In recent years, multiple GSMMs have been built by several research groups. With the increase in number, of these models, important issues regarding the standardization have arisen, a common problem is the different nomenclatures used by each of the research groups. In this work, the major focus is to address these problems, specifically for the human GSSMs. Therefore, the two most recent human GSMMs were selected to go through a data integration process. Integration strategies of these models most important entities (metabolites and reactions), were defined based on an exhaustive analysis of the models. The broad knowledge of their attributes enabled the creation of effective and efficient integration methods, supported by a core database developed in the local research group. The final result of this work, is a unified repository of the human metabolism. It contains all the metabolites and reactions that were automatically integrated along with some manual curation.A Biologia de Sistemas pretende integrar abordagens experimentais e computacionais com o objetivo de explicar e prever o comportamento dos organismos. O desenvolvimento in silico de modelos matemáticos permite atingir um conhecimento mais aprofundado dos seus mecanismos biológicos. Através de ferramentas Bioinformáticas é possível integrar uma grande quantidade de dados complexos nestes modelos computadorizados, assim como, realizar simulações computacionais que permitem prever o comportamento fenotípico dos organismos em diferentes condições ambientais. Até à data, os Modelos Metabólicos à Escala Genómica (MMEGs) incluem muitos componentes metabólicos de um organismo, relacionando a codificação do seu genoma com as suas capacidades metabólicas. Nos últimos anos, têm sido construídos vários MMEGs, por diferentes grupos de investigação. Com o crescente surgimento destes, tem-se denotado grandes falhas ao nível da padronização, uma vez que são utilizadas diferentes nomenclaturas por cada grupo de investigação. Neste trabalho, pretende-se colmatar essas falhas especificamente para os MMEGs humanos. Deste modo, foram selecionados os dois MMEGs humanos mais recentes, para passarem por um processo de integração de dados. As estratégias de integração das entidades mais importantes destes modelos (os metabolitos e as reações) foram definidas com base numa análise exaustiva dos modelos. O conhecimento dos atributos destes permitiu construir métodos eficientes e eficazes, tendo como núcleo uma base de dados desenvolvida no grupo de acolhimento. O resultado final deste trabalho é um repositório unificado do metabolismo humano. Neste, estão contidos todos os metabolitos e reações que foram integrados automaticamente, com alguma verificação manual

Ontology-based methodology for error detection in software design

Improving the quality of a software design with the goal of producing a high quality software product continues to grow in importance due to the costs that result from poorly designed software. It is commonly accepted that multiple design views are required in order to clearly specify the required functionality of software. There is universal agreement as to the importance of identifying inconsistencies early in the software design process, but the challenge is how to reconcile the representations of the diverse views to ensure consistency. To address the problem of inconsistencies that occur across multiple design views, this research introduces the Methodology for Objects to Agents (MOA). MOA utilizes a new ontology, the Ontology for Software Specification and Design (OSSD), as a common information model to integrate specification knowledge and design knowledge in order to facilitate the interoperability of formal requirements modeling tools and design tools, with the end goal of detecting inconsistency errors in a design. The methodology, which transforms designs represented using the Unified Modeling Language (UML) into representations written in formal agent-oriented modeling languages, integrates object-oriented concepts and agent-oriented concepts in order to take advantage of the benefits that both approaches can provide. The OSSD model is a hierarchical decomposition of software development concepts, including ontological constructs of objects, attributes, behavior, relations, states, transitions, goals, constraints, and plans. The methodology includes a consistency checking process that defines a consistency framework and an Inter-View Inconsistency Detection technique. MOA enhances software design quality by integrating multiple software design views, integrating object-oriented and agent-oriented concepts, and defining an error detection method that associates rules with ontological properties

In-situ absorption and fluorescence studies of electrogenerated species

Imperial Users onl