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.

Trends Of CPU, GPU and FPGA for high-performance computing

Floating-point computing with more than one TFLOP of peak performance is already a reality in recent Field-Programmable Gate Arrays (FPGA). General-Purpose Graphics Processing Units (GPGPU) and recent many-core CPUs have also taken advantage of the recent technological innovations in integrated circuit (IC) design and had also dramatically improved their peak performances. In this paper, we compare the trends of these computing architectures for high-performance computing and survey these platforms in the execution of algorithms belonging to different scientific application domains. Trends in peak performance, power consumption and sustained performances, for particular applications, show that FPGAs are increasing the gap to GPUs and many-core CPUs moving them away from high-performance computing with intensive floating-point calculations. FPGAs become competitive for custom floating-point or fixed-point representations, for smaller input sizes of certain algorithms, for combinational logic problems and parallel map-reduce problems. © 2014 Technical University of Munich (TUM).

Inverse dynamics based predictive control for unified power flow controllers without DC bus

This paper presents a new predictive digital control method applied to Matrix Converters (MC) operating as Unified Power Flow Controllers (UPFC). This control method, based on the inverse dynamics model equations of the MC operating as UPFC, just needs to compute the optimal control vector once in each control cycle, in contrast to direct dynamics predictive methods that needs 27 vector calculations. The theoretical principles of the inverse dynamics power flow predictive control of the MC based UPFC with input filter are established. The proposed inverse dynamics predictive power control method is tested using Matlab/Simulink Power Systems toolbox and the obtained results show that the designed power controllers guarantees decoupled active and reactive power control, zero error tracking, fast response times and an overall good dynamic and steady-state response.

Interlaminar fracture characterization of a carbon-epoxy composite in pure mode II

The interlaminar fracture toughness in pure mode II (GIIc) of a Carbon-Fibre Reinforced Plastic (CFRP) composite is characterized experimentally and numerically in this work, using the End-Notched Flexure (ENF) fracture characterization test. The value of GIIc was extracted by a new data reduction scheme avoiding the crack length measurement, named Compliance-Based Beam Method (CBBM). This method eliminates the crack measurement errors, which can be non-negligible, and reflect on the accuracy of the fracture energy calculations. Moreover, it accounts for the Fracture Process Zone (FPZ) effects. A numerical study using the Finite Element Method (FEM) and a triangular cohesive damage model, implemented within interface finite elements and based on the indirect use of Fracture Mechanics, was performed to evaluate the suitability of the CBBM to obtain GIIc. This was performed comparing the input values of GIIc in the numerical models with the ones resulting from the application of the CBBM to the numerical load-displacement (P-) curve. In this numerical study, the Compliance Calibration Method (CCM) was also used to extract GIIc, for comparison purposes.

A fluorescente bicyclic Calix[4] Arene-Oxacyclophane with planar chirality: Resolution, chiroptical, properties, and absolute configuration.

A new inherently chiral calix[4]arene ICC 1 has been disclosed. The dissymmetry of 1 is generated from a chirality plane in the quinol moiety of a 1,3-bridged bicyclic calix[4]arene. ICC 1 has been resolved by enantioselective HPLC, and the chiroptical properties of both isolated antipodes (pS)-1 and (pR)-1 confirm their enantiomeric nature. The absolute configuration of the (pS)-1/(pR)-1 enantiomeric pair was established through time-dependent density functional theory (TDDFT) calculations of electronic circular dichroism (CD) spectra. (C) 2014 Elsevier Ltd. All rights reserved.

Inherently chiral calix[4]arenes with planar chirality: two new entries to the family

The synthesis of two new inherently chiral calix[4]arenes (ICCs, 1 and 2), endowed with electron-rich concave surfaces, has been achieved through the desymmetrization of a lower rim distal-bridged oxacyclophane (OCP) macrocycle. The new highly emissive ICCs were resolved by chiral HPLC, and the enantiomeric nature of the isolated antipodes proved by electronic circular dichroism (CD). Using time-dependent density functional calculations of CD spectra, their absolute configurations were established. NMR studies with (S)-Pirkle's alcohol unequivocally showed that the host-guest interactions occur in the chiral pocket comprehending the calix-OCP exo cavities and the carbazole moieties.

Mono(Eta(5)-cyclopentadienyl)metal(II) complexes with thienyl acetylide chromophores: synthesis, electrochemical studies, and first hyperpolarizabilities

A series of mono(eta(5)-cyclopentadienyl)metal-(II) complexes with nitro-substituted thienyl acetylide ligands of general formula [M(eta(5)-C5H5)(L)(C C{C4H2S}(n)NO2)] (M = Fe, L = kappa(2)-DPPE, n = 1,2; M = Ru, L = kappa(2)-DPPE, 2 PPh3, n = 1, 2; M = Ni, L = PPh3, n = 1, 2) has been synthesized and fully characterized by NMR, FT-IR, and UV-Vis spectroscopy. The electrochemical behavior of the complexes was explored by cyclic voltammetry. Quadratic hyperpolarizabilities (beta) of the complexes have been determined by hyper-Rayleigh scattering (HRS) measurements at 1500 nm. The effect of donor abilities of different organometallic fragments on the quadratic hyperpolarizabilities was studied and correlated with spectroscopic and electrochemical data. Density functional theory (DFT) and time-dependent DFT (TDDFT) calculations were employed to get a better understanding of the second-order nonlinear optical properties in these complexes. In this series, the complexity of the push pull systems is revealed; even so, several trends in the second-order hyperpolarizability can still be recognized. In particular, the overall data seem to indicate that the existence of other electronic transitions in addition to the main MLCT clearly controls the effectiveness of the organometallic donor ability on the second-order NLO properties of these push pull systems.

New RuII(arene) complexes with halogen-substituted bis- and tris(pyrazol-1-YL)borate ligands

[RuCl(arene)(-Cl)](2) dimers were treated in a 1:2 molar ratio with sodium or thallium salts of bis- and tris(pyrazolyl)borate ligands [Na(BpBr3)], [Tl(TpBr3)], and [Tl(Tp(iPr,4Br))]. Mononuclear neutral complexes [RuCl(arene)((2)-BpBr3)] (1: arene=p-cymene (cym); 2: arene=hexamethylbenzene (hmb); 3: arene=benzene (bz)), [RuCl(arene)((2)-TpBr3)] (4: arene=cym; 6: arene=bz), and [RuCl(arene)((2)-Tp(iPr,4Br))] (7: arene=cym, 8: arene=hmb, 9: arene=bz) have been always obtained with the exception of the ionic [Ru-2(hmb)(2)(-Cl)(3)][TpBr3] (5), which formed independently of the ratio of reactants and reaction conditions employed. The ionic [Ru(CH3OH)(cym)((2)-BpBr3)][X] (10: X=PF6, 12: X=O3SCF3) and the neutral [Ru(O2CCF3)(cym)((2)-BpBr3)] (11) have been obtained by a metathesis reaction with corresponding silver salts. All complexes 1-12 have been characterized by analytical and spectroscopic data (IR, ESI-MS, H-1 and (CNMR)-C-13 spectroscopy). The structures of the thallium and calcium derivatives of ligand TpBr3, [Tl(TpBr3)] and [Ca(dmso)(6)][TpBr3](2)2DMSO, of the complexes 1, 4, 5, 6, 11, and of the decomposition product [RuCl(cym)(Hpz(iPr,4Br))(2)][Cl] (7) have been confirmed by using single-crystal X-ray diffraction. Electrochemical studies showed that 1-9 and 11 undergo a single-electron (RuRuIII)-Ru-II oxidation at a potential, measured by cyclic voltammetry, which allows comparison of the electron-donor characters of the bis- and tris(pyrazol-1-yl)borate and arene ligands, and to estimate, for the first time, the values of the Lever E-L ligand parameter for BpBr3, TpBr3, and Tp(iPr,4Br). Theoretical calculations at the DFT level indicated that both oxidation and reduction of the Ru complexes under study are mostly metal-centered with some involvement of the chloride ligand in the former case, and also demonstrated that the experimental isolation of the (3)-binuclear complex 5 (instead of the mononuclear 5) is accounted for by the low thermodynamic stability of the latter species due to steric reasons.

Functional disability of adults in Brazil: prevalence and associated factors

ABSTRACT OBJECTIVE To estimate the prevalence and factors associated with functional disability in adults in Brazil. METHODS We used information from the health supplement of the National Household Sample Survey in 2008. The dependent variable was the functional disability among adults of 18 to 65 years, measured by the difficulty of walking about 100 meters; independent variables were: health plan membership, region of residence, state of domicile, education level, household income, economic activity, self-perception of health, hospitalization, chronic diseases, age group, sex, and color. We calculated the gross odds ratios (OR), and their respective confidence intervals (95%), and adjusted them for variables of study by ordinal logistic regression, following hierarchical model. Sample weights were considered in all calculations. RESULTS We included 18,745 subjects, 74.0% of whom were women. More than a third of adults reported having functional disability. The disability was significantly higher among men (OR = 1.17; 95%CI 1.09;1.27), people from 35 to 49 years (OR = 1.30; 95%CI 1.17;1.45) and 50 to 65 years (OR = 1.38; 95%CI 1.24;1.54); economically inactive individuals (OR = 2.21; 95%CI 1.65;2.96); adults who reported heart disease (OR = 1.13; 95%CI 1.03;1.24), diabetes mellitus (OR = 1.16; 95%CI 1.05;1.29), arterial systemic hypertension (OR = 1.10; 95%CI 1.02;1.18), and arthritis/rheumatism (OR = 1.24; 95%CI 1.15;1.34); and participants who were admitted in the last 12 months (OR = 2.35; 95%CI 1.73;3.2). CONCLUSIONS Functional disability is common among Brazilian adults. Hospitalization is the most strongly associated factor, followed by economic activity, and chronic diseases. Sex, age, education, and income are also associated. Results indicate specific targets for actions that address the main factors associated with functional disabilities and contribute to the projection of interventions for the improvement of the well-being and promotion of adults' quality of life.

QED and relativistic corrections in superheavy elements

In this paper we review the different relativistic and QED contributions to energies, ionic radii, transition probabilities and Landé g-factors in super-heavy elements, with the help of the MultiConfiguration Dirac-Fock method (MCDF). The effects of taking into account the Breit interaction to all orders by including it in the self-consistent field process are demonstrated. State of the art radiative corrections are included in the calculation and discussed. We also study the non-relativistic limit of MCDF calculation and find that the non-relativistic offset can be unexpectedly large.

Health care costs of domestic violence against women – evidence from Portugal

Our main objective is to estimate the additional health care costs to the Portuguese National Health Service (NHS) due to domestic violence against women. We collected information through a survey addressed to health care centres’ female users. Both victims and non-victims of violence were inquired. We estimate costs according to five different groups – consultation costs, health care treatment and therapeutic costs, costs of complementary and diagnostic exams, drugs costs and transport costs. The estimations have been split into two perspectives – the NHS perspective (public perspective) and private perspective of inquired women (out of pocket payments). The timeframe of our calculations is one year, referring to all costs generated by domestic violence situations in the last twelve months. Essentially costs were estimated through the product of total number of episodes by the average estimated price per episode. Additionally, for the private costs, we also considered the costs originated by income losses, the opportunity cost of time spent on health care treatments and the work inability caused by sickness. The results suggest that the victims of domestic violence’s additional demand for health care is valued €140 per annum, that is about 22% higher than health care costs of non-victims. These results match those of similar studies for the United States, taking account of per capita differences in health care spending. A large proportion (90%) of the additional costs associated with domestic violence is supported by the NHS, where consultations and drugs are the most important contributors of such costs. Health consequences of domestic violence result from losses in quality of life and worst health status of victims and correspond to additional permanent economic costs of domestic violence episodes.

Synthesis of organometallic Ruthenium(II) complexes with strong activity against several human canceer cell lines

A new family of "RuCp" (Cp=eta(5)-C5H5) derivatives with bidentate N,O and N,N'-heteroaromatic ligands revealed outstanding cytotoxic properties against several human cell lines namely, A2780, A2780CisR, HT29, MCF7, MDAMB231, and PD. IC50 values were much lower than those found for cisplatin. Crystal structure of compound 4 was determined by X-ray diffraction studies. Density functional theory (DFT) calculations performed for compound 1 showed electronic flow from the ruthenium center to the coordinated bidentate ligand, in agreement with the electrochemical studies and the existence of a metal-to-ligand charge-transfer (MLCT) band evidenced by spectroscopic data.

Produção centralizada a biogás - análise do impacto a nível cooperativo

A utilização de energia renovável é hoje tema abordado em todo o mundo, devido à preocupação com a preservação do meio ambiente. Entre as energias renováveis, a biomassa destaca-se pela excelente disponibilidade que possui. Os dejetos bovinos são uma das mais abundantes, o qual tem grande potencial energético, se fermentado corretamente em biodigestores, obtendo como um dos produtos finais, o biogás. Esse gás é constituído na sua maior parte por gás metano (CH4) que é altamente inflamável. Neste trabalho pretende-se fazer a avaliação do potencial energético das propriedades de produção de leite na região do concelho de BRAGA aplicando uma tecnologia de queima de biogás e de produção de eletricidade utilizando um sistema de cogeração convencional e uma tecnologia mais recente, o Organic Rankine Cycle (ORC) e explicitando a respetiva análise económica. As opções por um sistema ORC na central em análise foram justificadas ponderando as vantagens e desvantagens deste ciclo em relação ao ciclo de vapor de água. O objetivo é a obtenção de energia elétrica e térmica e o aumento do rendimento global da instalação com o aproveitamento de todas as energias disponíveis, assim como a eliminação da toxidade dos dejetos para aproveitamento como biomassa. Partindo do levantamento bibliográfico e caraterização das diversas propriedades existentes no concelho, utilizando a tecnologia mais indicada e atual para este tipo de instalação. A biomassa utilizada foi uma mistura de dejetos bovinos com água. O biogás produzido foi convertido em energia elétrica e térmica, através da sua queima. Tem-se assim uma central que além de dar destino adequado aos dejetos animais, diminui a contaminação ambiental, evita a emissão de gás metano para a atmosfera e produz biogás. Efetua-se os cálculos económicos para dois cenários distintos, implementação de uma central de valorização de biogás em cada um dos oito maiores produtores de leite do núcleo de Penso e o aproveitamento dos dejetos produzidos pelos mesmos para implementação de uma central global de recolha dos mesmos, onde é feito o tratamento dos mesmos e a consequente produção de biogás. Na análise económica foram utilizados os seguintes critérios: o VAL (valor atual líquido), a TIR (taxa interna de rendibilidade) e o Período de Retorno Financeiro do Projeto.

The influence of geometric factors on the wall shear stress distribution in realistic human coronary arteries

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia Biomédica. A presente dissertação foi desenvolvida no Erasmus Medical Center em Roterdão, Holanda

Transformador diferencial de variação linear: condicionamento de sinal e desmodulação síncrona

Dissertação para obtenção do grau de Mestre em Engenharia Eletrotécnica Ramo de Automação e eletrónica Industrial