I. Quantal effects in biochemical cooperativity and a proposed mechanism for the differentiation of calcium signaling in synaptic plasticity. II. Evolutionary algorithms for the optimization of methods in computational chemistry

In Part 1 of this thesis, we propose that biochemical cooperativity is a fundamentally non-ideal process. We show quantal effects underlying biochemical cooperativity and highlight apparent ergodic breaking at small volumes. The apparent ergodic breaking manifests itself in a divergence of deterministic and stochastic models. We further predict that this divergence of deterministic and stochastic results is a failure of the deterministic methods rather than an issue of stochastic simulations.

Ergodic breaking at small volumes may allow these molecular complexes to function as switches to a greater degree than has previously been shown. We propose that this ergodic breaking is a phenomenon that the synapse might exploit to differentiate Ca$^{2+}$ signaling that would lead to either the strengthening or weakening of a synapse. Techniques such as lattice-based statistics and rule-based modeling are tools that allow us to directly confront this non-ideality. A natural next step to understanding the chemical physics that underlies these processes is to consider \textit{in silico} specifically atomistic simulation methods that might augment our modeling efforts.

In the second part of this thesis, we use evolutionary algorithms to optimize \textit{in silico} methods that might be used to describe biochemical processes at the subcellular and molecular levels. While we have applied evolutionary algorithms to several methods, this thesis will focus on the optimization of charge equilibration methods. Accurate charges are essential to understanding the electrostatic interactions that are involved in ligand binding, as frequently discussed in the first part of this thesis.

In Situ Characterization of Optical Absorption by Carbonaceous Aerosols: Calibration and Measurement

Light absorption by aerosols has a great impact on climate change. A Photoacoustic spectrometer (PA) coupled with aerosol-based classification techniques represents an in situ method that can quantify the light absorption by aerosols in a real time, yet significant differences have been reported using this method versus filter based methods or the so-called difference method based upon light extinction and light scattering measurements. This dissertation focuses on developing calibration techniques for instruments used in measuring the light absorption cross section, including both particle diameter measurements by the differential mobility analyzer (DMA) and light absorption measurements by PA. Appropriate reference materials were explored for the calibration/validation of both measurements. The light absorption of carbonaceous aerosols was also investigated to provide fundamental understanding to the absorption mechanism. The first topic of interest in this dissertation is the development of calibration nanoparticles. In this study, bionanoparticles were confirmed to be a promising reference material for particle diameter as well as ion-mobility. Experimentally, bionanoparticles demonstrated outstanding homogeneity in mobility compared to currently used calibration particles. A numerical method was developed to calculate the true distribution and to explain the broadening of measured distribution. The high stability of bionanoparticles was also confirmed. For PA measurement, three aerosol with spherical or near spherical shapes were investigated as possible candidates for a reference standard: C60, copper and silver. Comparisons were made between experimental photoacoustic absorption data with Mie theory calculations. This resulted in the identification of C60 particles with a mobility diameter of 150 nm to 400 nm as an absorbing standard at wavelengths of 405 nm and 660 nm. Copper particles with a mobility diameter of 80 nm to 300 nm are also shown to be a promising reference candidate at wavelength of 405 nm. The second topic of this dissertation focuses on the investigation of light absorption by carbonaceous particles using PA. Optical absorption spectra of size and mass selected laboratory generated aerosols consisting of black carbon (BC), BC with non-absorbing coating (ammonium sulfate and sodium chloride) and BC with a weakly absorbing coating (brown carbon derived from humic acid) were measured across the visible to near-IR (500 nm to 840 nm). The manner in which BC mixed with each coating material was investigated. The absorption enhancement of BC was determined to be wavelength dependent. Optical absorption spectra were also taken for size and mass selected smoldering smoke produced from six types of commonly seen wood in a laboratory scale apparatus.

Automatic identification of whole-part relations in Portuguese

Dissertação de Mestrado, Ciências da Linguagem, Faculdade de Ciências Humanas e Sociais, Universidade do Algarve, 2014

A RBES for Generating Automatically Personalized Menus

Food bought at supermarkets in, for instance, North America or the European Union, give comprehensive information about ingredients and allergens. Meanwhile, the menus of restaurants are usually incomplete and cannot be normally completed by the waiter. This is specially important when traveling to countries with a di erent culture. A curious example is "calamares en su tinta" (squid in its own ink), a common dish in Spain. Its brief description would be "squid with boiled rice in its own (black) ink", but an ingredient of its sauce is flour, a fact very important for celiacs. There are constraints based on religious believes, due to food allergies or to illnesses, while others just derive from personal preferences. Another complicated situation arise in hospitals, where the doctors' nutritional recommendations have to be added to the patient's usual constraints. We have therefore designed and developed a Rule Based Expert System (RBES) that can address these problems. The rules derive directly from the recipes of the di fferent dishes and contain the information about the required ingredients and ways of cooking. In fact, we distinguish: ingredients and ways of cooking, intermediate products (like sauces, that aren't always made explicit) and final products (the dishes listed in the menu of the restaurant). For a certain restaurant, customer and instant, the input to the RBES are: actualized stock of ingredients and personal characteristics of that customer. The RBES then prepares a "personalized menu" using set operations and knowledge extraction (thanks to an algebraic inference engine [1]). The RBES has been implemented in the computer algebra system MapleTM2015. A rst version of this work was presented at "Applications of Computer Algebra 2015" (ACA'2015) conference. The corresponding abstract is available at [2].

MODELING AND HARDWARE-IN-THE-LOOP SIMULATION OF POWER-SPLIT HYBRID ELECTRIC VEHICLES

Conventional vehicles are creating pollution problems, global warming and the extinction of high density fuels. To address these problems, automotive companies and universities are researching on hybrid electric vehicles where two different power devices are used to propel a vehicle. This research studies the development and testing of a dynamic model for Prius 2010 Hybrid Synergy Drive (HSD), a power-split device. The device was modeled and integrated with a hybrid vehicle model. To add an electric only mode for vehicle propulsion, the hybrid synergy drive was modified by adding a clutch to carrier 1. The performance of the integrated vehicle model was tested with UDDS drive cycle using rule-based control strategy. The dSPACE Hardware-In-the-Loop (HIL) simulator was used for HIL simulation test. The HIL simulation result shows that the integration of developed HSD dynamic model with a hybrid vehicle model was successful. The HSD model was able to split power and isolate engine speed from vehicle speed in hybrid mode.

Early stage assessment of the inspectability of welded components : A case from the aerospace industry

This paper proposes a method to indicate potential problems when planning dye penetrant and x-ray inspection of welded components. Inspection has been found to be an important part of the manufacturability evaluation made in a large CAD-based parametric environment for making multidisciplinary design simulations in early stages of design at an aircraft component manufacturer. The paper explains how the proposed method is to be included in the design platform at the company. It predicts the expected probability of detection of cracks (POD) in situations where the geometry of the parts is unfavourable for inspection so that potential problems can be discovered and solved in early stages. It is based on automatically extracting information from CAD-models and making a rule-based evaluation. It also provides a scale for how favourable the geometry is for inspection. In the paper it is also shown that the manufacturability evaluation need to take into consideration the expected stresses in the structures, highlighting the importance of multi-disciplinary simulations.

Modelling the generation of customised poetry in Jess

The present paper presents an application that composes formal poetry in Spanish in a semiautomatic interactive fashion. JASPER is a forward reasoning rule-based system that obtains from the user an intended message, the desired metric, a choice of vocabulary, and a corpus of verses; and, by intelligent adaptation of selected examples from this corpus using the given words, carries out a prose-to-poetry translation of the given message. In the composition process, JASPER combines natural language generation and a set of construction heuristics obtained from formal literature on Spanish poetry.

Efectividad del tratamiento de lumbalgia con acupuntura

Se realizó un estudio observacional retrospectivo longitudinal en una Institución prestadora de Servicios de Salud de la ciudad de Bogotá, con el objetivo de evaluar la efectividad en el manejo del dolor de la terapia con acupuntura en el tratamiento de lumbalgia. Se tomaron 150 historias clínicas de pacientes con lumbalgia atendidos de enero de 2014 a mayo de 2016, las cuales fueron sometidas a los criterios de inclusión definidos por los autores, arrojando 48 historias sometidas a la prueba de Friedman con el fin de identificar el impacto sobre el dolor del tratamiento con acupuntura en los pacientes seleccionados. Adicionalmente, bajo un muestreo aleatorio simple de distribución normal sobre las 48 historias clínicas evaluadas, se seleccionaron 25 casos a los cuales se les aplicó una encuesta no estructurada, con el fin de obtener información sobre el estado de la patología después de finalizar el tratamiento e identificar las posibles causas de deserción. Con este estudio se concluye que la terapia con acupuntura es efectiva en el manejo del dolor de pacientes con lumbalgia, y que es necesario realizar más estudios que puedan sustentar la inclusión de la terapéutica en el manejo de esta patología.

Modelling and Optimization of Energy Management Strategies for Hybrid Vehicles

In the last decades the automotive sector has seen a technological revolution, due mainly to the more restrictive regulation, the newly introduced technologies and, as last, to the poor resources of fossil fuels remaining on Earth. Promising solution in vehicles’ propulsion are represented by alternative architectures and energy sources, for example fuel-cells and pure electric vehicles. The automotive transition to new and green vehicles is passing through the development of hybrid vehicles, that usually combine positive aspects of each technology. To fully exploit the powerful of hybrid vehicles, however, it is important to manage the powertrain’s degrees of freedom in the smartest way possible, otherwise hybridization would be worthless. To this aim, this dissertation is focused on the development of energy management strategies and predictive control functions. Such algorithms have the goal of increasing the powertrain overall efficiency and contextually increasing the driver safety. Such control algorithms have been applied to an axle-split Plug-in Hybrid Electric Vehicle with a complex architecture that allows more than one driving modes, including the pure electric one. The different energy management strategies investigated are mainly three: the vehicle baseline heuristic controller, in the following mentioned as rule-based controller, a sub-optimal controller that can include also predictive functionalities, referred to as Equivalent Consumption Minimization Strategy, and a vehicle global optimum control technique, called Dynamic Programming, also including the high-voltage battery thermal management. During this project, different modelling approaches have been applied to the powertrain, including Hardware-in-the-loop, and diverse powertrain high-level controllers have been developed and implemented, increasing at each step their complexity. It has been proven the potential of using sophisticated powertrain control techniques, and that the gainable benefits in terms of fuel economy are largely influenced by the chose energy management strategy, even considering the powerful vehicle investigated.

Development of Optimal Energy Management Strategies for a Hybrid Boat

The present work proposes different approaches to extend the mathematical methods of supervisory energy management used in terrestrial environments to the maritime sector, that diverges in constraints, variables and disturbances. The aim is to find the optimal real-time solution that includes the minimization of a defined track time, while maintaining the classical energetic approach. Starting from analyzing and modelling the powertrain and boat dynamics, the energy economy problem formulation is done, following the mathematical principles behind the optimal control theory. Then, an adaptation aimed in finding a winning strategy for the Monaco Energy Boat Challenge endurance trial is performed via ECMS and A-ECMS control strategies, which lead to a more accurate knowledge of energy sources and boat’s behaviour. The simulations show that the algorithm accomplishes fuel economy and time optimization targets, but the latter adds huge tuning and calculation complexity. In order to assess a practical implementation on real hardware, the knowledge of the previous approaches has been translated into a rule-based algorithm, that let it be run on an embedded CPU. Finally, the algorithm has been tuned and tested in a real-world race scenario, showing promising results.

Development of a Predictive Control Function for a Plug-in Hybrid Electric Vehicle with Electrically-heated Catalyst

This master thesis work is focused on the development of a predictive EHC control function for a diesel plug-in hybrid electric vehicle equipped with a EURO 7 compliant exhaust aftertreatment system (EATS), with the purpose of showing the advantages provided by the implementation of a predictive control strategy with respect to a rule-based one. A preliminary step will be the definition of an accurate powertrain and EATS physical model, starting from already existing and validated applications. Then, a rule-based control strategy managing the torque split between the electric motor (EM) and the internal combustion engine (ICE) will be developed and calibrated, with the main target of limiting tailpipe NOx emission by taking into account EM and ICE operating conditions together with EATS conversion efficiency. The information available from vehicle connectivity will be used to reconstruct the future driving scenario, also referred to as electronic horizon (eHorizon), and in particular to predict ICE first start. Based on this knowledge, an EATS pre-heating phase can be planned to avoid low pollutant conversion efficiencies, thus preventing high NOx emission due to engine cold start. Consequently, the final NOx emission over the complete driving cycle will be strongly reduced, allowing to comply with the limits potentially set by the incoming EURO 7 regulation. Moreover, given the same NOx emission target, the gain achieved thanks to the implementation of an EHC predictive control function will allow to consider a simplified EATS layout, thus reducing the related manufacturing cost. The promising results achieved in terms of NOx emission reduction show the effectiveness of the application of a predictive control strategy focused on EATS thermal management and highlight the potential of a complete integration and parallel development of involved vehicle physical systems, control software and connectivity data management.

Performance assessment of vehicular connectivity in hybrid electric vehicles for fuel and emissions reduction

Nowadays, the spreading of the air pollution crisis enhanced by greenhouse gases emission is leading to the worsening of global warming. Recently, several metropolitan cities introduced Zero-Emissions Zones where the use of the Internal Combustion Engine is forbidden to reduce localized pollutants emissions. This is particularly problematic for Plug-in Hybrid Electric Vehicles, which usually work in depleting mode. In order to address these issues, the present thesis presents a viable solution by exploiting vehicular connectivity to retrieve navigation data of the urban event along a selected route. The battery energy needed, in the form of a minimum State of Charge (SoC), is calculated by a Speed Profile Prediction algorithm and a Backward Vehicle Model. That value is then fed to both a Rule-Based Strategy, developed specifically for this application, and an Adaptive Equivalent Consumption Minimization Strategy (A-ECMS). The effectiveness of this approach has been tested with a Connected Hardware-in-the-Loop (C-HiL) on a driving cycle measured on-road, stimulating the predictions with multiple re-routings. However, even if hybrid electric vehicles have been recognized as a valid solution in response to increasingly tight regulations, the reduced engine load and the repeated engine starts and stops may reduce substantially the temperature of the exhaust after-treatment system (EATS), leading to relevant issues related to pollutant emission control. In this context, electrically heated catalysts (EHCs) represent a promising solution to ensure high pollutant conversion efficiency without affecting engine efficiency and performance. This work aims at studying the advantages provided by the introduction of a predictive EHC control function for a light-duty Diesel plug-in hybrid electric vehicle (PHEV) equipped with a Euro 7-oriented EATS. Based on the knowledge of future driving scenarios provided by vehicular connectivity, engine first start can be predicted and therefore an EATS pre-heating phase can be planned.

Neural networks and statistical analysis for classification of corneal videokeratography maps based on Zernike coefficients: a quantitative comparison

PURPOSE: The main goal of this study was to develop and compare two different techniques for classification of specific types of corneal shapes when Zernike coefficients are used as inputs. A feed-forward artificial Neural Network (NN) and discriminant analysis (DA) techniques were used. METHODS: The inputs both for the NN and DA were the first 15 standard Zernike coefficients for 80 previously classified corneal elevation data files from an Eyesys System 2000 Videokeratograph (VK), installed at the Departamento de Oftalmologia of the Escola Paulista de Medicina, São Paulo. The NN had 5 output neurons which were associated with 5 typical corneal shapes: keratoconus, with-the-rule astigmatism, against-the-rule astigmatism, "regular" or "normal" shape and post-PRK. RESULTS: The NN and DA responses were statistically analyzed in terms of precision ([true positive+true negative]/total number of cases). Mean overall results for all cases for the NN and DA techniques were, respectively, 94% and 84.8%. CONCLUSION: Although we used a relatively small database, results obtained in the present study indicate that Zernike polynomials as descriptors of corneal shape may be a reliable parameter as input data for diagnostic automation of VK maps, using either NN or DA.

P-Prism: a computationally efficient approach to scaling up classification rule induction

Top Down Induction of Decision Trees (TDIDT) is the most commonly used method of constructing a model from a dataset in the form of classification rules to classify previously unseen data. Alternative algorithms have been developed such as the Prism algorithm. Prism constructs modular rules which produce qualitatively better rules than rules induced by TDIDT. However, along with the increasing size of databases, many existing rule learning algorithms have proved to be computational expensive on large datasets. To tackle the problem of scalability, parallel classification rule induction algorithms have been introduced. As TDIDT is the most popular classifier, even though there are strongly competitive alternative algorithms, most parallel approaches to inducing classification rules are based on TDIDT. In this paper we describe work on a distributed classifier that induces classification rules in a parallel manner based on Prism.

J-measure based hybrid pruning for complexity reduction in classification rules

Prism is a modular classification rule generation method based on the ‘separate and conquer’ approach that is alternative to the rule induction approach using decision trees also known as ‘divide and conquer’. Prism often achieves a similar level of classification accuracy compared with decision trees, but tends to produce a more compact noise tolerant set of classification rules. As with other classification rule generation methods, a principle problem arising with Prism is that of overfitting due to over-specialised rules. In addition, over-specialised rules increase the associated computational complexity. These problems can be solved by pruning methods. For the Prism method, two pruning algorithms have been introduced recently for reducing overfitting of classification rules - J-pruning and Jmax-pruning. Both algorithms are based on the J-measure, an information theoretic means for quantifying the theoretical information content of a rule. Jmax-pruning attempts to exploit the J-measure to its full potential because J-pruning does not actually achieve this and may even lead to underfitting. A series of experiments have proved that Jmax-pruning may outperform J-pruning in reducing overfitting. However, Jmax-pruning is computationally relatively expensive and may also lead to underfitting. This paper reviews the Prism method and the two existing pruning algorithms above. It also proposes a novel pruning algorithm called Jmid-pruning. The latter is based on the J-measure and it reduces overfitting to a similar level as the other two algorithms but is better in avoiding underfitting and unnecessary computational effort. The authors conduct an experimental study on the performance of the Jmid-pruning algorithm in terms of classification accuracy and computational efficiency. The algorithm is also evaluated comparatively with the J-pruning and Jmax-pruning algorithms.