Governments across the world are implementing legislation for ever more strict limits for vehicle emissions; combined with customer expectations for growing levels of performance and equipment, automotive manufacturers face a significant challenge. With the aim of meeting this challenge, downsizing is an established trend in passenger car engine development. However, since downsizing is commonly achieved through pressure charging (turbocharging, for example), the associated benefits in improved fuel economy and emissions are often obtained at the expense of engine dynamic response, and, consequently, vehicle driveability. This thesis presents predominantly simulation-based research into a novel combined charging system comprising a conventional turbocharger used in conjunction with a declutchable supercharger driven through a CVT. An initial investigation using this system in place of a variable geometry turbocharger on an already downsized passenger car diesel engine demonstrated greatly increased low speed torque as well as improved dynamic response. A downsizing project that involved replacing a naturally aspirated gasoline engine with a highly boosted engine with 40% of the original displacement formed the basis for more extensive investigations. Although it was unable to produce the low speed transient response of the naturally aspirated engine, in tip-in tests the CVT-supercharger system was shown to achieve the target torque much quicker than an equivalent system with a fixed supercharger drive ratio. However, balancing this with good fuel efficiency for the initial part load period was a complex trade-off. In vehicle acceleration simulations the CVT-supercharger system did not outperform the fixed drive ratio configuration, but on the CVT system the boost limit was reached at an early stage during the transients. Thus there may be potential to include an ‘over-boost’ facility, allowing boost pressure to temporarily exceed normal steady state limits in order to improve transient performance and bring it closer to that of the baseline vehicle. It is suggested that the CVT-supercharger provides the best flexibility for calibration and compromise between performance and fuel efficiency, perhaps incorporating different user-selectable modes (such as ‘economy’ and ‘sport’ modes).

In this study, application of computational fluid dynamics to ground vehicle aerodynamics was investigated. Two types of vehicle models namely, Ahmed Body and MIRA Notchback Body and their scaled models were used. A commercial software &quot / Fluent&quot / was used and the effects of implementing different turbulence models with wall functions were observed. As a result, an appropriate turbulence model was selected to use in the study. The drag forces, surface pressure distributions and wake formations were investigated in simulation of various test cases available in the literature. The study was extended to simulate the aerodynamics of the vehicles in close-following situation. The results were then compared with available wind tunnel test data.

The importance of service level management has come to the fore in recent years as computing power becomes more and more of a commodity. In order to present a consistently high quality of service systems must be rigorously analysed, even before implementation, and monitored to ensure these goals can be achieved. The tools and algorithms found in performability analysis offer a potentially ideal method to formally specify and analyse performance and reliability models. This thesis examines Markov reward models, a formalism based on continuous time Markov chains, and it's usage in the generation and analysis of service levels. The particular solution technique we employ in this thesis is model checking, using Continuous Reward Logic as a means to specify requirement and constraints on the model. We survey the current tools available allowing model checking to be performed on Markov reward models. Specifically we extended the Erlangen-Twente Markov Chain Checker to be able to solve Markov reward models by taking advantage of the Duality theorem of Continuous Stochastic Reward Logic, of which Continuous Reward Logic is a sub-logic. We are also concerned with the specification techniques available for Markov reward models, which have in the past merely been extensions to the available specification techniques for continuous time Markov chains. We implement a production rule system using Ruby, a high level language, and show the advantages gained by using it's native interpreter and language features in order to cut down on implementation time and code size. The limitations inherent in Markov reward models are discussed and we focus on the issue of zero reward states. Previous algorithms used to remove zero reward states, while preserving the numerical properties of the model, could potentially alter it's logical properties. We propose algorithms based on analysing the continuous reward logic requirement beforehand to determine whether a zero reward state can be removed safely as well as an approach based on substitution of zero reward states. We also investigate limitations on multiple reward structures and the ability to solve for both time and reward. Finally we perform a case study on a Beowulf parallel computing cluster using Markov reward models and the ETMCC tool, demonstrating their usefulness in the implementation of performability analysis and the determination of the service levels that can be offered by the cluster to it's users.

The automated functional and performance analysis of communication systems specified with some Formal Description Technique has long been the goal of telecommunication engineers. In the past SDL and Petri nets have been the most popular FDTs for the purpose. With the growth in popularity of UML the most obvious question to ask is whether one can translate one or more UML diagrams describing a system to a performance model. Until the advent of UML 2.0, that has been an impossible task since the semantics were not clear. Even though the UML semantics are still not clear for the purpose, with UML 2.0 now released and using ITU recommendation Z.109, we describe in this dissertation a methodology and tool called proSPEX (protocol Software Performance Engineering using XMI), for the design and performance analysis of communication protocols specified with UML. Our first consideration in the development of our methodology was to identify the roles of UML 2.0 diagrams in the performance modelling process. In addition, questions regarding the specification of non-functional duration contraints, or temporal aspects, were considered. We developed a semantic time model with which a lack of means of specifying communication delay and processing times in the language are addressed. Environmental characteristics such as channel bandwidth and buffer space can be specified and realistic assumptions are made regarding time and signal transfer. With proSPEX we aimed to integrate a commercial UML 2.0 model editing tool and a discrete-event simulation library. Such an approach has been advocated as being necessary in order to develop a closer integration of performance engineering with formal design and implementation methodologies. In order to realize the integration we firstly identified a suitable simulation library and then extended the library with features required to represent high-level SDL abstractions, such as extended finite state machines (EFSM) and signal addressing. In implementing proSPEX we filtered the XML output of our editor and used text templates for code generation. The filtering of the XML output and the need to extend our simulation library with EFSM abstractions was found to be significant implementation challenges. Lastly, in order to to illustrate the utility of proSPEX we conducted a performance analysis case-study in which the efficient short remote operations (ESRO) protocol is used in a wireless e-commerce scenario.

The Weighted Histogram Analysis Method (WHAM) is a technique used to calculate free energy from molecular simulation data. WHAM recombines biased distributions of samples from multiple Umbrella Sampling simulations to yield an estimate of the global unbiased distribution. The WHAM algorithm iterates two coupled, non-linear, equations, until convergence at an acceptable level of accuracy. The equations have quadratic time complexity for a single reaction coordinate. However, this increases exponentially with the number of reaction coordinates under investigation, which makes multidimensional WHAM a computationally expensive procedure. There is potential to use general purpose graphics processing units (GPGPU) to accelerate the execution of the algorithm. Here we develop and evaluate a multidimensional GPGPU WHAM implementation to investigate the potential speed-up attained over its CPU counterpart. In addition, to avoid the cost of multiple Molecular Dynamics simulations and for validation of the implementations we develop a test system to generate samples analogous to Umbrella Sampling simulations. We observe a maximum problem size dependent speed-up of approximately 19 for the GPGPU optimized WHAM implementation over our single threaded CPU optimized version. We find that the WHAM algorithm is amenable to GPU acceleration, which provides the means to study ever more complex molecular systems in reduced time periods.

The creation of 3D models for games and simulations is generally a time-consuming and labour intensive task. Forested landscapes are an important component of many large virtual environments in games and film. To create the many individual tree models required for forests requires a large numbers of artists and a great deal of time. In order to reduce modelling time procedural methods are often used. Such methods allow tree models to be created automatically and relatively quickly, albeit at potentially reduced quality. Although the process is faster than manual creation, it can still be slow and resource-intensive for large forests. The main contribution of this work is the development of an efficient procedural generation system for creating large forests. Our system uses L-Systems, a grammar based procedural technique, to generate each tree. We explore two approaches to accelerating the creation of large forests. First, we demonstrate performance improvements for the creation of individual trees in the forest, by reducing the computation required by the underlying L-Systems. Second, we reduce the memory overhead by sharing geometry between trees using a novel branch instancing approach. Test results show that our scheme significantly improves the speed of forest generation over naive methods: our system is able to generate over 100, 000 trees in approximately 2 seconds, while using a modest amount of memory. With respect to improving L-System processing, one of our methods achieves a 25% speed up over traditional methods at the cost of a small amount of additional memory, while our second method manages a 99% reduction in memory at the expense of a small amount of extra processing.

Computational tools play an important role in the description of biological systems. Scientists describe and study structure, conformational changes and interactions between molecules in silico, often as a cheaper and faster alternative for biosynthesis. The simulated dynamic behavior in time of a molecular system is a straight forward source of information about substrate-enzyme interactions at the atomic level, and a powerful tool for the identification of molecular properties important in enzymatic reactions. Our study is focused on the computational investigation of structure and substrate specificity of hydrolases important in biotransformation. The computational work was performed in close collaboration with biochemists-experimentalists from Charles University and the Microbiological Institute of the Academy of Sciences of the Czech Republic. Hydrolases have great a potential in the chemoenzymatic synthesis of modified carbohydrates with regulated properties. Carbohydrates, as substrates of hydrolases, are important in normal functionality of many organisms. They have a dual role in immune response regulation: some carbohydrates (like GlcNAc and ManNAc) participate in activation and some (like GalNAc) in suppressing immunity; glycosidase deficiency is associated with a number of lysosomal disorders. We used homology modeling, computational docking and molecular dynamics simulation (MD) methods for the complex study of fungal hydrolases: alpha-galactosidase/alpha-N-acetylgalactosaminidase from Aspergillus niger; beta-N-acetylhexosaminidases (HEX) (from Aspergillus oryzae and Penicillium oxalicum); nitrilase from Aspergillus niger. Our structural study unambigously demonstrates that the enzyme encoded by genes variant A (aglA) from A. niger is able to accept alpha-N-acetylgalactosamine as its substrate and explains structural features responsible for its specificity. Homology models of HEXs from P. oxalicum and A. oryzae were built and compared. Homology models were used to study the role of protein glycosylation, disulfide bonds, dimer formation and interaction with natural and modified substrates. Model of nitrilase from Aspergillus niger helped to analyze multimer formation.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / In recent years, several studies have been conducted in order to investigate the problems related to reduced quality of water for public supply, recreation, irrigation, among others, leading to the identification of pollution sources and to develop proposals for its control. Improper use of water has caused serious problems especially in urban centers. The increasing contamination of water resources, caused by several sources, among which stand out the domestic sewage, industrial effluent and urban and agricultural diffuse load, is compromising the use of these resources for their various purposes. The Poxim River is an important source of Sergipe, which supplies a large number of farms and part of the capital Aracaju. Within this context, to understand and try to minimize the problem in a rational manner, we can tell, nowadays, with monitoring of water quality in watersheds and the development and application of tools that consider aspects of quantity and quality. The aim of this study was to monitor and analyze water quality through physical-chemical and microbiological contaminants in the sub-basin of Rio Poxim of different aspects of use and occupation and the possible interference that may cause these water resources, Besides using a computational tool AcquaNet able to simulate critical processes and scenarios for sub-basin, considering the framing parameters of water bodies, in accordance with Resolution 357/2005. To guarantee the water supplyment in amount and quality for agroecosystems and ecosystems associates to the river depends on the planning and management of the water resources that must be thought adopting the hydrographic basins as basic units of planning. / Nos últimos anos vários estudos têm sido realizados com o intuito de investigar os problemas relacionados com a redução da qualidade da água para o abastecimento público, lazer, irrigação, entre outros, levando a identificação das fontes poluidoras, bem como a elaboração de propostas para o seu controle. O uso inadequado da água tem gerado sérios problemas principalmente nos centros urbanos. A crescente contaminação dos recursos hídricos, causada por diversas fontes, dentre as quais destacam-se os efluentes domésticos; os efluentes industriais e a carga difusa urbana e agrícola, vem comprometendo o uso destes recursos para os seus diversos fins. O Rio Poxim é um importante manancial do estado de Sergipe, que abastece um grande número de propriedades rurais e parte da capital Aracaju. Dentro desse contexto, para compreender e tentar minimizar o problema de maneira racional pode-se contar, atualmente, com o monitoramento da qualidade da água em bacias hidrográficas e o desenvolvimento e aplicação de ferramentas que consideram aspectos de quantidade e qualidade. O objetivo deste estudo foi monitorar e analisar a qualidade da água através de parâmetros físico-químicos e microbiológico na sub-bacia hidrográfica do Rio Poxim quanto a diferentes aspectos de uso e ocupação do solo e as possíveis interferências que estes pode provocar nos recursos hídricos, além de usar uma ferramenta computacional AcquaNet capaz de simular processos e cenários críticos para a sub-bacia, considerando os parâmetros de enquadramento dos corpos d água, de acordo com a resolução CONAMA 357/2005. Garantir o suprimento de água em quantidade e qualidade para os agroecossistemas e ecossistemas associados ao rio depende do planejamento e gestão dos recursos hídricos que devem ser pensados, adotando-se as bacias hidrográficas como unidades básicas de planejamento.

[EN] Heart failure (HF) constitutes a major public health problem worldwide. Operationally it is defined as a clinical syndrome characterized by the marked and progressive inability of the ventricles to fill and generate adequate cardiac output to meet the demands of cellular metabolism that may have significant variability in its etiology and it is the final common pathway of various cardiac pathologies. Much attention has been paid to the understanding of the arrhythmogenic mechanisms induced by the structural, electrical, and metabolic remodeling of the failing heart. Due to the complexity of the electrophysiological changes that may occur during heart failure, the scientific literature is complex and sometimes equivocal. Nevertheless, a number of common features of failing hearts have been documented. At the cellular level, prolongation of the action potential (AP) involving ion channel remodeling and alterations in calcium handling have been established as the hallmark characteristics of myocytes isolated from failing hearts. At the tissue level, intercellular uncoupling and fibrosis are identified as major arrhythmogenic factors. In this Thesis a computational model for cellular heart failure was proposed using a modified version of Grandi et al. model for human ventricular action potential that incorporates the formulation of the late sodium current (INaL) in order to study the arrhythmogenic processes due to failing phenotype. Experimental data from several sources were used to validate the model. Due to extensive literature in the subject a sensitivity analysis was performed to assess the influence of main ionic currents and parameters upon most related biomarkers. In addition, multiscale simulations were carried out to characterize this pathology (transmural cardiac fibres and tissues). The proposed model for the human INaL and the electrophysiological remodeling of myocytes from failing hearts accurately reproduce experimental observations. An enhanced INaL appears to be an important contributor to the electrophysiological phenotype and to the dysregulation of calcium homeostasis of failing myocytes. Our strand simulation results illustrate how the presence of M cells and heterogeneous electrophysiological remodeling in the human failing ventricle modulate the dispersion of action potential duration (APD) and repolarization time (RT). Conduction velocity (CV) and the safety factor for conduction (SF) were also reduced by the progressive structural remodeling during heart failure. In our transmural ventricular tissue simulations, no reentry was observed in normal conditions or in the presence of HF ionic remodeling. However, defined amount of fibrosis and/or cellular uncoupling were sufficient to elicit reentrant activity. Under conditions where reentry was generated, HF electrophysiological remodeling did not alter the width of the vulnerable window (VW). However, intermediate fibrosis and cellular uncoupling significantly widened the VW. In conclusion, enhanced fibrosis in failing hearts, as well as reduced intercellular coupling, combine to increase electrophysiological gradients and reduce electrical propagation. In that sense, structural remodeling is a key factor in the genesis of vulnerability to reentry, mainly at intermediates levels of fibrosis and intercellular uncoupling. / [ES] La insuficiencia cardíaca (IC) constituye un importante problema de salud pública en todo el mundo. Operacionalmente se define como un síndrome clínico caracterizado por la incapacidad marcada y progresiva de los ventrículos para llenar y generar gasto cardíaco adecuado para satisfacer las demandas del metabolismo celular, que puede tener una variabilidad significativa en su etiología y es la vía final común de varias patologías cardíacas. Se ha prestado mucha atención a la comprensión de los mecanismos arritmogénicos inducidos por la remodelación estructural, eléctrica, y metabólica del corazón afectado de IC. Debido a la complejidad de los cambios electrofisiológicos que pueden ocurrir durante la IC, la literatura científica es compleja y, a veces equívoca. Sin embargo, se han documentado una serie de características comunes en corazones afectados de IC. A nivel celular, se han establecido como las características distintivas de los miocitos aislados de corazones afectados de IC la prolongación del potencial de acción (PA), que implica la remodelación de los canales iónicos y las alteraciones en la dinámica del calcio. A nivel de los tejidos, el desacoplamiento intercelular y la fibrosis se identifican como los principales factores arritmogénicos. En esta tesis se propuso un modelo celular computacional para la insuficiencia cardíaca utilizando una versión modificada del modelo de potencial de acción ventricular humano de Grandi y colaboradores que incorpora la formulación de la corriente tardía de sodio (INaL) con el fin de estudiar los procesos arritmogénicas debido al fenotipo de la IC. Los datos experimentales de varias fuentes se utilizaron para validar el modelo. Debido a la extensa literatura en la temática se realizó un análisis de sensibilidad para evaluar la influencia de las principales corrientes iónicas y los parámetros sobre los biomarcadores relacionados. Además, se llevaron a cabo simulaciones multiescala para caracterizar esta patología (en fibras y tejidos transmurales). El modelo propuesto para la corriente tardía de sodio y la remodelación electrofisiológica de los miocitos de corazones afectados de IC reprodujeron con precisión las observaciones experimentales. Una INaL incrementada parece ser un importante contribuyente al fenotipo electrofisiológico y la desregulación de la homeostasis del calcio de los miocitos afectados de IC. Nuestros resultados de la simulaciones en fibra ilustran cómo la presencia de células M y el remodelado electrofisiológico heterogéneo en el ventrículo humano afectado de IC modulan la dispersión de la duración potencial de acción (DPA) y el tiempo de repolarización (TR). La velocidad de conducción (VC) y el factor de seguridad para la conducción (FS) también se redujeron en la remodelación estructural progresiva durante la insuficiencia cardíaca. En nuestras simulaciones transmurales de tejido ventricular, no se observó reentrada en condiciones normales o en presencia de la remodelación iónica de la IC. Sin embargo, determinadas cantidades de fibrosis y / o desacoplamiento celular eran suficientes para provocar la actividad reentrante. En condiciones donde se había generado la reentrada, el remodelado electrofisiológico de la IC no alteró la anchura de la ventana vulnerable (VV). Sin embargo, niveles intermedios de fibrosis y el desacoplamiento celular ampliaron significativamente la VV. En conclusión, niveles elevados de fibrosis en corazones afectados de IC, así como la reducción de acoplamiento intercelular, se combinan para aumentar los gradientes electrofisiológicos y reducir la propagación eléctrica. En ese sentido, la remodelación estructural es un factor clave en la génesis de la vulnerabilidad a las reentradas, principalmente en niveles intermedios de fibrosis y desacoplamiento intercelular. El remodelado electrofisiológico promueve la arritmogénesis y puede ser alterado dependi / [CAT] La insuficiència cardíaca (IC) constitueix un important problema de salut pública arreu del món. A efectes pràctics, es defineix com una síndrome clínica caracteritzada per la incapacitat marcada i progressiva dels ventricles per omplir i generar el cabal cardíac adequat, per tal de satisfer les demandes del metabolisme cel·lular, el qual pot tenir una variabilitat significativa en la seua etiologia i és la via final comuna de diverses patologies cardíaques. S'ha prestat molta atenció a la comprensió dels mecanismes aritmogènics induïts per la remodelació estructural, elèctrica, i metabòlica del cor afectat d'IC. A causa de la complexitat dels canvis electrofisiològics que poden ocórrer durant la IC, trobem que la literatura científica és complexa i, de vegades, equívoca. No obstant això, s'han documentat una sèrie de característiques comunes en cors afectats d'IC. A nivell cel·lular, com característiques distintives dels miòcits aïllats de cors afectats d'IC, s'han establert la prolongació del potencial d'acció (PA), que implica la remodelació dels canals iònics, i les alteracions en la dinàmica del calci. A nivell dels teixits, el desacoblament intercel·lular i la fibrosi s'identifiquen com els principals factors aritmogènics. Per tal d'estudiar els processos aritmogènics a causa del fenotip de la IC, es va proposar un model cel·lular computacional d'IC utilitzant una versió modificada del model de potencial d'acció ventricular humà de Grandi i els seus col·laboradors, el qual incorpora la formulació del corrent de sodi tardà (INaL). Amb l'objectiu de validar el model es van utilitzar dades experimentals de diverses fonts. A causa de l'extensa literatura en la temàtica, es va realitzar una anàlisi de sensibilitat per tal d'avaluar la influència de les principals corrents iòniques i els paràmetres sobre els biomarcadors relacionats. A més, es van dur a terme simulacions multiescala per a la caracterització d'aquesta patología (fibres i teixits transmurals). El model proposat per al corrent de sodi tardà i la remodelació electrofisiològica dels miòcits de cors afectats d'IC van reproduir amb precisió les observacions experimentals. Una INaL incrementada sembla contribuir de manera important al fenotip electrofisiològic i a la desregulació de l'homeòstasi del calci dels miòcits afectats d'IC. Els resultats de les nostres simulacions en fibra indiquen que la presència de cèl·lules M i el remodelat electrofisiològic heterogeni en el ventricle humà afectat d'IC modulen la dispersió de la durada del potencial d'acció (DPA) i el temps de repolarització (TR). La velocitat de conducció (VC) i el factor de seguretat per a la conducció (FS) també es van reduir en la remodelació estructural progressiva durant la IC. A les nostres simulacions transmurals de teixit ventricular, no s'observà cap reentrada ni en condicions normals ni en presència de la remodelació iònica de la IC. No obstant això, amb determinades quantitats de fibrosi i/o desacoblament cel·lular sí que es provocà l'activitat reentrant. I amb les condicions que produïren la reentrada, el remodelat electrofisiològic de la IC no va alterar l'amplada de la finestra vulnerable (FV). Tanmateix, nivells intermedis de fibrosi i el desacoblament cel·lular sí que ampliaren significativament la FV. En conclusió, nivells elevats de fibrosi en cors afectats d'IC, així com la reducció d'acoblament intercel·lular, es combinen per augmentar els gradients electrofisiològics i reduir la propagació elèctrica. Per tant, la remodelació estructural és un factor clau en la gènesi de la vulnerabilitat a les reentrades, principalment en nivells intermedis de fibrosi i desacoblament intercel·lular. / Gómez García, JF. (2015). Multiscale Modeling and Simulation of Human Heart Failure [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/52389 / TESIS

The aim of this paper is to acquaint the readers with basic classification of wind turbine configuration by used electric generator, with speed and power control used in power plants and with mathematical model of wind and parts of power plant. Procedure of making model in applications Mathematica and MathModelica is described in the other part of this paper. There were made models of power plants with squirrel cage asynchronous generator, one with pitch control, the other with stall control. In the last part of the thesis comparison of model behavior of both models with the same input conditions was made.