Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations.

Maximização da valorização energética em aterros sanitários recorrendo a equipamentos baseados no Ciclo Orgânico de Rankine (ORC)

Atualmente, os aterros sanitários representam uma solução para a gestão e tratamento dos resíduos sólidos urbanos. Da deposição, ocorrem duas formas de emissões ao longo do tempo, a produção de biogás e de lixiviados, que resultam sobretudo da decomposição da matéria orgânica. Um dos principais constituintes do biogás é o metano, o qual tem elevado poder calorífico. O presente trabalho aborda, a maximização da valorização energética em aterros sanitários, recorrendo a equipamentos baseados no Ciclo Orgânico de Rankine (ORC) para a produção de eletricidade. É apresentado como caso de estudo a central de valorização energética da Suldouro, em Sermonde, que produz eletricidade a partir do biogás resultante da decomposição da matéria orgânica depositada em aterro. O biogás é utilizado como combustível para os motogeradores utilizados para o seu aproveitamento energético, sendo que apenas cerca de 40% do potencial energético contido no biogás é transformado em eletricidade, registando-se perdas sobretudo nas emissões dos gases de exaustão e na água de arrefecimento dos motores. Para avaliação do potencial da recuperação energética dos gases de escape é avaliado o desempenho termodinâmico do ciclo ORC. Para tal foi desenvolvida uma ferramenta em MATLAB utilizando como modelo a configuração do ORC com recuperador de calor. O cálculo das propriedades termodinâmicas dos fluidos foi obtido através da criação de uma sub-rotina que chama o programa CoolProp. Este programa restitui propriedades como a entalpia, entropia, pressões e temperaturas em cada ponto do ciclo, permitindo assim ao utilizador otimizar o tempo na obtenção de resultados. A avaliação económica é fundamental na tomada de decisões por parte do investidor e dos financiadores do projeto. É então apresentada a análise económica e efetuada uma análise de sensibilidade, onde foram efetuadas variações nos vetores mais importantes de forma a poder avaliar-se o impacto em termos da sua rentabilidade. A ferramenta desenvolvida permite obter de forma prática, os três indicadores económicos extremamente influentes no que se refere à tomada de decisão. A utilização dos sistemas ORC e os seus benefícios não se esgotam na maximização dos aproveitamentos da valorização energética em aterros sanitários. Também a recuperação de calor para a produção de energia elétrica pode ter um impacto importante em muitos setores intensivos de energia, contribuindo significativamente para a redução do consumo e aumentando a eficiência de todo o processo de produção.

Melhoria da eficiência energética nos ascensores: a recuperação de energia

A presente tese descreve diferentes soluções que permitem a reutilização da energia recuperada em ascensores eléctricos de roda de aderência dotados de conversores electrónicos de frequência e dessa forma contribuir para a melhoria da eficiência energética nos ascensores. Nos ascensores, a energia potencial é constantemente transferida enquanto a cabina está em movimento. Se a cabina se estiver a movimentar em sentido descendente com plena carga, ou em sentido ascendente, mas vazia, o motor estará em modo gerador. Quando a cabina se movimenta em sentido descendente, e o peso na cabina é superior ao peso do contrapeso, então o binário do motor encontra-se em sentido contrário à velocidade, isto é, o motor está a travar, havendo lugar à recuperação de energia. Igualmente, se a cabina subir vazia, também se poderá recuperar energia eléctrica. A energia acumulada em forma de energia potencial nas pessoas e no contrapeso pode ser recuperada, dado que o motor estará a funcionar como um gerador. De modo a estudar a viabilidade técnica e económica das diferentes soluções foram realizadas medições a uma amostra representativa de ascensores eléctricos de roda de aderência. Esta amostra é constituída por 39 ascensores que estão instalados em diferentes tipos de edifícios e que pertencem a diferentes categorias de utilização, de acordo com a norma VDI 4707:2009. Para cada ascensor foi medida a energia consumida e a energia gerada para uma manobra completa – a descida e a subida da cabina sem carga. A partir das medições, e com base na norma VDI 4707:2009 foram calculados os valores anualizados de energia eléctrica consumidos e produzidos por cada ascensor. A partir das 5 hipóteses identificadas para a utilização da energia recuperada (carregamento de bateria para alimentação dos circuitos em stand-by; carregamento de supercondensador para alimentação dos circuitos em stand-by; carregamento de supercondensador para alimentar o barramento DC; reinjecção da energia no barramento DC de um conjunto de ascensores em grupo; reinjecção da energia na rede eléctrica do edifício onde o ascensor está instalado) foi realizada a avaliação técnica e a avaliação económico-financeira para cada um dos ascensores. Por último, foi desenvolvido um simulador que permite definir a solução de recuperação de energia que seja técnica e economicamente mais viável, para um dado ascensor eléctrico de roda de aderência instalado, mediante a introdução dos parâmetros técnicos do ascensor em avaliação.

A Multiple Criteria Utility-based Approa h for the Unit Commitment with Wind Power and Pumped Storage Hydro

The integration of wind power in eletricity generation brings new challenges to unit commitment due to the random nature of wind speed. For this particular optimisation problem, wind uncertainty has been handled in practice by means of conservative stochastic scenario-based optimisation models, or through additional operating reserve settings. However, generation companies may have different attitudes towards operating costs, load curtailment, or waste of wind energy, when considering the risk caused by wind power variability. Therefore, alternative and possibly more adequate approaches should be explored. This work is divided in two main parts. Firstly we survey the main formulations presented in the literature for the integration of wind power in the unit commitment problem (UCP) and present an alternative model for the wind-thermal unit commitment. We make use of the utility theory concepts to develop a multi-criteria stochastic model. The objectives considered are the minimisation of costs, load curtailment and waste of wind energy. Those are represented by individual utility functions and aggregated in a single additive utility function. This last function is adequately linearised leading to a mixed-integer linear program (MILP) model that can be tackled by general-purpose solvers in order to find the most preferred solution. In the second part we discuss the integration of pumped-storage hydro (PSH) units in the UCP with large wind penetration. Those units can provide extra flexibility by using wind energy to pump and store water in the form of potential energy that can be generated after during peak load periods. PSH units are added to the first model, yielding a MILP model with wind-hydro-thermal coordination. Results showed that the proposed methodology is able to reflect the risk profiles of decision makers for both models. By including PSH units, the results are significantly improved.

Influência dos equipamentos de aquecimento, arrefecimento e AQS na certificação energética de edifícios

Na União Europeia os sectores dos transportes e da indústria são ambos grandes consumidores de energia, mas são os edifícios residenciais e de serviços onde o consumo energético é maior, e em 2005, segundo a EnerBuilding, representavam cerca de 17% dos consumos de energia primária em termos nacionais. A energia gasta com a iluminação, o aquecimento, o arrefecimento e AQS das habitações, locais de trabalho e locais de lazer é superior à consumida pelos sectores dos transportes e da indústria. As habitações representam dois terços do consumo total de energia dos edifícios europeus, o qual aumenta todos os anos com a melhoria da qualidade de vida, traduzindo-se numa maior utilização dos sistemas de climatização. Neste sentido, e de acordo com o decreto-lei que transpõe para a legislação portuguesa a diretiva comunitária relativa ao desempenho energético dos edifícios, todos os Estados da União Europeia devem ter um sistema de certificação energética para informar o cidadão sobre a qualidade térmica dos edifícios, aquando da construção, da venda ou do arrendamento. Assim, entrou em vigor em Portugal, desde 1 de Janeiro de 2009, a obrigatoriedade de apresentação de um certificado de eficiência energética, no ato de compra, venda ou aluguer de edifícios novos e existentes. A certificação energética permite assim aos futuros utilizadores dos edifícios obter informação sobre os potenciais consumos de energia, no caso dos novos edifícios ou no caso de edifícios existentes sujeitos a grandes intervenções de reabilitação, dos seus consumos reais ou aferidos para padrões de utilização típicos, passando o consumo energético a integrar um conjunto dos aspetos importantes para a caracterização de qualquer edifício. Em edifícios de serviços, o certificado energético assegura aos utentes do edifício ou da fração que este reúne condições para garantir a eficiência energética e a adequada qualidade do ar interior. Uma vez que passamos 80% do nosso tempo em edifícios, e que isto se reflete num consumo cada vez mais elevado do sector residencial e dos serviços no consumo total energético do país, este trabalho pretende fazer a comparação dos vários equipamentos de aquecimento, de arrefecimento e de AQS e qual a influência dos mesmos na certificação energética de edifícios, e consequentemente na eficiência dos mesmos, sendo que a eficiência e a certificação energética de um edifício deve ser um aspeto relevante a levar em consideração no momento do planeamento ou da construção, bem como na aquisição de uma nova habitação. Um projeto concebido de modo a tirar proveito das condições climáticas, da orientação solar, dos ventos dominantes e utilizadas técnicas construtivas e os materiais adequados, é possível reduzir os gastos energéticos com a iluminação ou os sistemas de climatização.

Control in distribution networks with demand side management

The way in which electricity networks operate is going through a period of significant change. Renewable generation technologies are having a growing presence and increasing penetrations of generation that are being connected at distribution level. Unfortunately, a renewable energy source is most of the time intermittent and needs to be forecasted. Current trends in Smart grids foresee the accommodation of a variety of distributed generation sources including intermittent renewable sources. It is also expected that smart grids will include demand management resources, widespread communications and control technologies required to use demand response are needed to help the maintenance in supply-demand balance in electricity systems. Consequently, smart household appliances with controllable loads will be likely a common presence in our homes. Thus, new control techniques are requested to manage the loads and achieve all the potential energy present in intermittent energy sources. This thesis is focused on the development of a demand side management control method in a distributed network, aiming the creation of greater flexibility in demand and better ease the integration of renewable technologies. In particular, this work presents a novel multi-agent model-based predictive control method to manage distributed energy systems from the demand side, in presence of limited energy sources with fluctuating output and with energy storage in house-hold or car batteries. Specifically, here is presented a solution for thermal comfort which manages a limited shared energy resource via a demand side management perspective, using an integrated approach which also involves a power price auction and an appliance loads allocation scheme. The control is applied individually to a set of Thermal Control Areas, demand units, where the objective is to minimize the energy usage and not exceed the limited and shared energy resource, while simultaneously indoor temperatures are maintained within a comfort frame. Thermal Control Areas are overall thermodynamically connected in the distributed environment and also coupled by energy related constraints. The energy split is performed based on a fixed sequential order established from a previous completed auction wherein the bids are made by each Thermal Control Area, acting as demand side management agents, based on the daily energy price. The developed solutions are explained with algorithms and are applied to different scenarios, being the results explanatory of the benefits of the proposed approaches.

The financial sustainability of passive house construction in Ireland.

In Ireland the average energy cost for a household in 2006 was estimated to be €1,767, an increase of 4% on 2005 figures. With the state o f the current economic climate, home owners are beginning to realise the potential of energy efficient construction methods. The Passive House Standard offers a cost efficient and sustainable construction solution compared to the Traditional Irish construction methods. This report focuses on the Cost comparison between Passive House construction and traditional construction methods. The report also focuses on barriers that are slowing market penetration of the Passive House standard in the Irish Market. It also identifies potential energy savings that passive house occupants would benefit from. The report also highlights professional opinions on the future development o f the Passive House Standard in Ireland. The conclusions of this report are that the Passive House Standard is a more financially suitable construction solution compared to that o f a traditional dwelling complying with the Irish Building Regulations. The report also concludes that the Passive House Standard won’t be introduced as an Irish Building Regulation in the future but that it will have a big impact on future building regulations. The hypothesis o f this report is supported by data obtained from a literature review, qualitative data analysis and a case study. The report recommends that in order for the Passive House Standard to penetrate further into the Irish construction market, various barriers must be rectified. Local manufactures must start producing suitable components that suit the Passive House specification. The Building Energy Rating system must be altered in order for the Passive House to achieve its potential BER rating.

Rethinking economy-wide rebound measures: an unbiased proposal

In spite of having been first introduced in the last half of the ninetieth century, the debate about the possible rebound effects from energy efficiency improvements is still an open question in the economic literature. This paper contributes to the existing research on this issue proposing an unbiased measure for economy-wide rebound effects. The novelty of this economy-wide rebound measure stems from the fact that not only actual energy savings but also potential energy savings are quantified under general equilibrium conditions. Our findings indicate that the use of engineering savings instead of general equilibrium potential savings downward biases economy-wide rebound effects and upward-biases backfire effects. The discrepancies between the traditional indicator and our proposed measure are analysed in the context of the Spanish economy.

NO rebinding to myoglobin: a reactive molecular dynamics study.

The rebinding of NO to myoglobin after photolysis is studied using the 'reactive molecular dynamics' method. In this approach the energy of the system is evaluated on two potential energy surfaces that include the heme-ligand interactions which change between liganded and unliganded myoglobin. This makes it possible to take into account in a simple way, the high dimensionality of the transition seam connecting the reactant and product states. The dynamics of the dissociated NO molecules are examined, and the geometrical and energetic properties of the transition seam are studied. Analysis of the frequency of recrossing shows that the height of the effective rebinding barrier is dependent on the time after photodissociation. This effect is due mainly to protein relaxation and may contribute to the experimentally observed non-exponential rebinding rate of NO, as has been suggested previously.

An alternative approach to fundamental general physics concepts

An alternative approach to the fundamental general physics concepts has been proposed. We demonstrate that the electrostatic potential energy of a discrete or a continuous system of charges should be stored by the charges and not the field. It is found that there is a possibility that any electric field has no energy density, as well as magnetic field. It is found that there is no direct relation between the electric or magnetic energy and photons. An alternative derivation of the blackbody radiation formula is proposed. It is also found that the zero-point of energy of electromagnetic radiation may not exist.

A systematic and feasible method for computing nuclear contributions to electrical properties of polyatomic molecules

An analytic method to evaluate nuclear contributions to electrical properties of polyatomic molecules is presented. Such contributions control changes induced by an electric field on equilibrium geometry (nuclear relaxation contribution) and vibrational motion (vibrational contribution) of a molecular system. Expressions to compute the nuclear contributions have been derived from a power series expansion of the potential energy. These contributions to the electrical properties are given in terms of energy derivatives with respect to normal coordinates, electric field intensity or both. Only one calculation of such derivatives at the field-free equilibrium geometry is required. To show the useful efficiency of the analytical evaluation of electrical properties (the so-called AEEP method), results for calculations on water and pyridine at the SCF/TZ2P and the MP2/TZ2P levels of theory are reported. The results obtained are compared with previous theoretical calculations and with experimental values

Autosuficiència energètica. Estudi pilot a Alinyà (Alt Urgell)

A aquest estudi s'ha analitzat si és viable l'autosuficiència energètica en base a un estudi pilot al nucli rural d'Alinyà aprofitant els recursos naturals de la zona. S'ha realitzat un estudi del consum energètic de la població i s'ha comparat amb el potencial de producció energètica dels recursos renovables locals incloent energia provinent de la biomassa i aprofitada en calderes individuals per a cada habitatge, energia solar en teulades i energia hidroelèctrica a partir de centrals minihidràuliques restaurades ja existents. També s’ha realitzat un anàlisi per detectar possibles factors d’ineficiència energètica i a partir d’aquí, proposar una sèrie de mesures per corregir aquesta. S'han comptabilitzat les emissions de CO2 derivades del consum energètic i les proporcions que representa cada tipus de font energètica sobre el total del nucli. També s'ha establert una comparativa del consum mitjà per habitant i any entre la població i Catalunya; el consum a Alinyà és d'1,46 Tep's, mentre que el de Catalunya és d'1,7 Tep's, el nostre estudi no contempla la mobilitat, si se li resta aquest vector a la mitjana de Catalunya veiem que és de 0,9 Tep's, per tant, hi observem un major consum energètic. El 76% del consum d'Alinyà prové dels combustibles fòssils, concretament del gasoil, el nucli té una forta dependència respecte a aquesta energia, que a més a més representa el 86% (56T CO2 eq.) de les emissions totals de CO2. Per finalitzar, s'ha demostrat que és possible assolir l'autosuficiència energètica mitjançant l'implantació d'una combinació d'estratègies, viables en tots els aspectes; tant tècnics com socioeconòmics. Abastint el poble d'energia a un menor cost econòmic i amb un estil de vida més respectuós amb el medi ambient.

Simple finite field method for calculation of static and dynamic vibrational hyperpolarizabilities: curvature contributions

In the static field limit, the vibrational hyperpolarizability consists of two contributions due to: (1) the shift in the equilibrium geometry (known as nuclear relaxation), and (2) the change in the shape of the potential energy surface (known as curvature). Simple finite field methods have previously been developed for evaluating these static field contributions and also for determining the effect of nuclear relaxation on dynamic vibrational hyperpolarizabilities in the infinite frequency approximation. In this paper the finite field approach is extended to include, within the infinite frequency approximation, the effect of curvature on the major dynamic nonlinear optical processes

Variational calculation of static and dynamic vibrational nonlinear optical properties

The vibrational configuration interaction method used to obtain static vibrational (hyper)polarizabilities is extended to dynamic nonlinear optical properties in the infinite optical frequency approximation. Illustrative calculations are carried out on H2 O and N H3. The former molecule is weakly anharmonic while the latter contains a strongly anharmonic umbrella mode. The effect on vibrational (hyper)polarizabilities due to various truncations of the potential energy and property surfaces involved in the calculation are examined

The curvature of the conical intersection seam: an approximate second-order analysis

We present a method for analyzing the curvature (second derivatives) of the conical intersection hyperline at an optimized critical point. Our method uses the projected Hessians of the degenerate states after elimination of the two branching space coordinates, and is equivalent to a frequency calculation on a single Born-Oppenheimer potential-energy surface. Based on the projected Hessians, we develop an equation for the energy as a function of a set of curvilinear coordinates where the degeneracy is preserved to second order (i.e., the conical intersection hyperline). The curvature of the potential-energy surface in these coordinates is the curvature of the conical intersection hyperline itself, and thus determines whether one has a minimum or saddle point on the hyperline. The equation used to classify optimized conical intersection points depends in a simple way on the first- and second-order degeneracy splittings calculated at these points. As an example, for fulvene, we show that the two optimized conical intersection points of C2v symmetry are saddle points on the intersection hyperline. Accordingly, there are further intersection points of lower energy, and one of C2 symmetry - presented here for the first time - is found to be the global minimum in the intersection space