Diffusion in polymer systems studied by fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) is a powerful technique to determine the diffusion of fluorescence molecules in various environments. The technique is based on detecting and analyzing the fluctuation of fluorescence light emitted by fluorescence species diffusing through a small and fixed observation volume, formed by a laser focused into the sample. Because of its great potential and high versatility in addressing the diffusion and transport properties in complex systems, FCS has been successfully applied to a great variety of systems. In my thesis, I focused on the application of FCS to study the diffusion of fluorescence molecules in organic environments, especially in polymer melts. In order to examine our FCS setup and a developed measurement protocol, I first utilized FCS to measure tracer diffusion in polystyrene (PS) solutions, for which abundance data exist in the literature. I studied molecular and polymeric tracer diffusion in polystyrene solutions over a broad range of concentrations and different tracer and matrix molecular weights (Mw). Then FCS was further established to study tracer dynamics in polymer melts. In this part I investigated the diffusion of molecular tracers in linear flexible polymer melts [polydimethylsiloxane (PDMS), polyisoprene (PI)], a miscible polymer blend [PI and poly vinyl ethylene (PVE)], and star-shaped polymer [3-arm star polyisoprene (SPI)]. The effects of tracer sizes, polymer Mw, polymer types, and temperature on the diffusion coefficients of small tracers were discussed. The distinct topology of the host polymer, i.e. star polymer melt, revealed the notably different motion of the small tracer, as compared to its linear counterpart. Finally, I emphasized the advantage of the small observation volume which allowed FCS to investigate the tracer diffusions in heterogeneous systems; a swollen cross-linked PS bead and silica inverse opals, where high spatial resolution technique was required.

Finitely coordinated models for low-temperature phases of amorphous systems

We introduce models of heterogeneous systems with finite connectivity defined on random graphs to capture finite-coordination effects on the low-temperature behaviour of finite-dimensional systems. Our models use a description in terms of small deviations of particle coordinates from a set of reference positions, particularly appropriate for the description of low-temperature phenomena. A Born-von Karman-type expansion with random coefficients is used to model effects of frozen heterogeneities. The key quantity appearing in the theoretical description is a full distribution of effective single-site potentials which needs to be determined self-consistently. If microscopic interactions are harmonic, the effective single-site potentials turn out to be harmonic as well, and the distribution of these single-site potentials is equivalent to a distribution of localization lengths used earlier in the description of chemical gels. For structural glasses characterized by frustration and anharmonicities in the microscopic interactions, the distribution of single-site potentials involves anharmonicities of all orders, and both single-well and double-well potentials are observed, the latter with a broad spectrum of barrier heights. The appearance of glassy phases at low temperatures is marked by the appearance of asymmetries in the distribution of single-site potentials, as previously observed for fully connected systems. Double-well potentials with a broad spectrum of barrier heights and asymmetries would give rise to the well-known universal glassy low-temperature anomalies when quantum effects are taken into account. © 2007 IOP Publishing Ltd.

Exploiting Nested Parallelism on Heterogeneous Processors

Heterogeneous computing systems have become common in modern processor architectures. These systems, such as those released by AMD, Intel, and Nvidia, include both CPU and GPU cores on a single die available with reduced communication overhead compared to their discrete predecessors. Currently, discrete CPU/GPU systems are limited, requiring larger, regular, highly-parallel workloads to overcome the communication costs of the system. Without the traditional communication delay assumed between GPUs and CPUs, we believe non-traditional workloads could be targeted for GPU execution. Specifically, this thesis focuses on the execution model of nested parallel workloads on heterogeneous systems. We have designed a simulation flow which utilizes widely used CPU and GPU simulators to model heterogeneous computing architectures. We then applied this simulator to non-traditional GPU workloads using different execution models. We also have proposed a new execution model for nested parallelism allowing users to exploit these heterogeneous systems to reduce execution time.

BabeLO : an extensible converter of programming exercises formats

In the last two decades, there was a proliferation of programming exercise formats that hinders interoperability in automatic assessment. In the lack of a widely accepted standard, a pragmatic solution is to convert content among the existing formats. BabeLO is a programming exercise converter providing services to a network of heterogeneous e-learning systems such as contest management systems, programming exercise authoring tools, evaluation engines and repositories of learning objects. Its main feature is the use of a pivotal format to achieve greater extensibility. This approach simplifies the extension to other formats, just requiring the conversion to and from the pivotal format. This paper starts with an analysis of programming exercise formats representative of the existing diversity. This analysis sets the context for the proposed approach to exercise conversion and to the description of the pivotal data format. The abstract service definition is the basis for the design of BabeLO, its components and web service interface. This paper includes a report on the use of BabeLO in two concrete scenarios: to relocate exercises to a different repository, and to use an evaluation engine in a network of heterogeneous systems.

Orchestration of e-learning services for automatic evaluation of programming exercises

Managing programming exercises require several heterogeneous systems such as evaluation engines, learning objects repositories and exercise resolution environments. The coordination of networks of such disparate systems is rather complex. These tools would be too specific to incorporate in an e-Learning platform. Even if they could be provided as pluggable components, the burden of maintaining them would be prohibitive to institutions with few courses in those domains. This work presents a standard based approach for the coordination of a network of e-Learning systems participating on the automatic evaluation of programming exercises. The proposed approach uses a pivot component to orchestrate the interaction among all the systems using communication standards. This approach was validated through its effective use on classroom and we present some preliminary results.

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.

Development of an interface for ontology‐based transformation between features of different types

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

E-learning frameworks: a survey

In recent years the concept of eLearning Framework emerged associated with several initiatives promoted by educational organizations. These initiatives share a common goal: to create flexible learning environments by integrating heterogeneous systems already available in many educational institutions. The paper provides an introductory survey on eLearning Frameworks. It gathers information on these initiatives categorizes them and compares their features regarding a set of predefined criteria such as: architecture, business model, primary user groups, technical implementations, adopted standards, maturity and future development.

Using the learning tools interoperability framework for LMS integration in service oriented architectures

The LMS plays an indisputable role in the majority of the eLearning environments. This eLearning system type is often used for presenting, solving and grading simple exercises. However, exercises from complex domains, such as computer programming, require heterogeneous systems such as evaluation engines, learning objects repositories and exercise resolution environments. The coordination of networks of such disparate systems is rather complex. This work presents a standard approach for the coordination of a network of eLearning systems supporting the resolution of exercises. The proposed approach use a pivot component embedded in the LMS with two roles: provide an exercise resolution environment and coordinate the communication between the LMS and other systems exposing their functions as web services. The integration of the pivot component with the LMS relies on the Learning Tools Interoperability. The validation of this approach is made through the integration of the component with LMSs from two vendors.

PETCHA: a Programming Exercises Teaching Assistant

This paper presents a tool called Petcha that acts as an automated Teaching Assistant in computer programming courses. The ultimate objective of Petcha is to increase the number of programming exercises effectively solved by students. Petcha meets this objective by helping both teachers to author programming exercises and students to solve them. It also coordinates a network of heterogeneous systems, integrating automatic program evaluators, learning management systems, learning object repositories and integrated programming environments. This paper presents the concept and the design of Petcha and sets this tool in a service oriented architecture for managing learning processes based on the automatic evaluation of programming exercises. The paper presents also a case study that validates the use of Petcha and of the proposed architecture.

Bridging between programming exercises formats with BabeLO

Assessment plays a vital role in learning. This is certainly the case with assessment of computer programs, both in curricular and competitive learning. The lack of a standard – or at least a widely used format – creates a modern Ba- bel tower made of Learning Objects, of assessment items that cannot be shared among automatic assessment systems. These systems whose interoperability is hindered by the lack of a common format include contest management systems, evaluation engines, repositories of learning objects and authoring tools. A prag- matical approach to remedy this problem is to create a service to convert among existing formats. A kind of translation service specialized in programming prob- lems formats. To convert programming exercises on-the-fly among the most used formats is the purpose of the BabeLO – a service to cope with the existing Babel of Learning Object formats for programming exercises. BabeLO was designed as a service to act as a middleware in a network of systems typically used in auto- matic assessment of programs. It provides support for multiple exercise formats and can be used by: evaluation engines to assess exercises regardless of its format; repositories to import exercises from various sources; authoring systems to create exercises in multiple formats or based on exercises from other sources. This paper analyses several of existing formats to highlight both their differ- ences and their similar features. Based on this analysis it presents an approach to extensible format conversion. It presents also the features of PExIL, the pivotal format in which the conversion is based; and the function definitions of the proposed service – BabeLO. Details on the design and implementation of BabeLO, including the service API and the interfaces required to extend the conversion to a new format, are also provided. To evaluate the effectiveness and efficiency of this approach this paper reports on two actual uses of BabeLO: to relocate exercises to a different repository; and to use an evaluation engine in a network of heterogeneous systems.

Implementação ESB numa unidade hospitalar. Uso normalizado de mensagens HL7

Atualmente, os sistemas de informação hospitalares têm de possibilitar uma utilização diferenciada pelos diferentes intervenientes, num cenário de constante adaptação e evolução. Para tal, é essencial a interoperabilidade entre os sistemas de informação do hospital e os diversos fornecedores de serviços, assim como dispositivos hospitalares. Apesar da necessidade de suportar uma heterogeneidade entre sistemas ser fundamental, o acesso/troca de informação deve ser feito de uma forma protocolada, segura e transparente. A infraestrutura de informação médica moderna consiste em muitos sistemas heterogéneos, com diversos mecanismos para controlar os dados subjacentes. Informações relativas a um único paciente podem estar dispersas por vários sistemas (ex: transferência de pacientes, readmissão, múltiplos tratamentos, etc.). Torna-se evidente a necessidade aceder a dados do paciente de forma consolidada a partir de diferentes locais. Desta forma, é fundamental utilizar uma arquitetura que promova a interoperabilidade entre sistemas. Para conseguir esta interoperabilidade, podem-se implementar camadas de “middleware” que façam a adaptação das trocas de informação entre os sistemas. Todavia, não resolvemos o problema subjacente, ou seja, a necessidade de utilização de um standard para garantir uma interacção fiável entre cliente/fornecedor. Para tal, é proposto uma solução que passa por um ESB dedicado para a área da saúde, denominada por HSB (Healthcare Service Bus). Entre as normas mais usuais nesta área devem-se salientar o HL7 e DICOM, esta última mais especificamente para dispositivos de imagem hospitalar, sendo a primeira utilizada para gestão e trocas de informação médica entre sistemas. O caso de estudo que serviu de base a esta dissertação é o de um hospital de média dimensão cujo sistema de informação começou por ser uma solução monolítica, de um só fornecedor. Com o passar dos anos, o fornecedor único desagregou-se em vários, independentes e concorrentes, dando lugar a um cenário extremamente preocupante em termos de manutenção e evolução futura do sistema de informação existente. Como resultado do trabalho efetuado, foi proposta uma arquitetura que permite a evolução do sistema atual de forma progressiva para um HSB puro.

Geometry based visualization with OpenCL

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Multi-GPU support on the marrow algorithmic skeleton framework

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Sistemas heterogéneos adaptativos basados en el contexto

Delivery context-aware adaptative heterogenous systems. Currently, many types of devices that have gained access to the network is large and diverse. The different capabilities and characteristics of them, in addition to the different characteristics and preferences of users, have generated a new goal to overcome: how to adapt the contents taking into account this heterogeneity, known as the “delivery context.” The concepts of adaptation and accessibility have been widely discussed and have resulted in many proposals, standards and techniques designed to solve the problem, making it necessary to refine the analysis of the issue to be considered in the process of adaptation. We present a tour of the various proposals and standards that have marked the area of heterogeneous systems works, and others who have worked since the real-time interaction through agents based platforms. All targeted to solve a common goal: the delivery context