Funcions densitat i semblança molecular quàntica: nous desenvolupaments i aplicacions

La present tesi, tot i que emmarcada dins de la teoria de les Mesures Semblança Molecular Quántica (MQSM), es deriva en tres àmbits clarament definits: - La creació de Contorns Moleculars de IsoDensitat Electrònica (MIDCOs, de l'anglès Molecular IsoDensity COntours) a partir de densitats electròniques ajustades. - El desenvolupament d'un mètode de sobreposició molecular, alternatiu a la regla de la màxima semblança. - Relacions Quantitatives Estructura-Activitat (QSAR, de l'anglès Quantitative Structure-Activity Relationships). L'objectiu en el camp dels MIDCOs és l'aplicació de funcions densitat ajustades, ideades inicialment per a abaratir els càlculs de MQSM, per a l'obtenció de MIDCOs. Així, es realitza un estudi gràfic comparatiu entre diferents funcions densitat ajustades a diferents bases amb densitats obtingudes de càlculs duts a terme a nivells ab initio. D'aquesta manera, l'analogia visual entre les funcions ajustades i les ab initio obtinguda en el ventall de representacions de densitat obtingudes, i juntament amb els valors de les mesures de semblança obtinguts prèviament, totalment comparables, fonamenta l'ús d'aquestes funcions ajustades. Més enllà del propòsit inicial, es van realitzar dos estudis complementaris a la simple representació de densitats, i són l'anàlisi de curvatura i l'extensió a macromolècules. La primera observació correspon a comprovar no només la semblança dels MIDCOs, sinó la coherència del seu comportament a nivell de curvatura, podent-se així observar punts d'inflexió en la representació de densitats i veure gràficament aquelles zones on la densitat és còncava o convexa. Aquest primer estudi revela que tant les densitats ajustades com les calculades a nivell ab initio es comporten de manera totalment anàloga. En la segona part d'aquest treball es va poder estendre el mètode a molècules més grans, de fins uns 2500 àtoms. Finalment, s'aplica part de la filosofia del MEDLA. Sabent que la densitat electrònica decau ràpidament al allunyar-se dels nuclis, el càlcul d'aquesta pot ser obviat a distàncies grans d'aquests. D'aquesta manera es va proposar particionar l'espai, i calcular tan sols les funcions ajustades de cada àtom tan sols en una regió petita, envoltant l'àtom en qüestió. Duent a terme aquest procés, es disminueix el temps de càlcul i el procés esdevé lineal amb nombre d'àtoms presents en la molècula tractada. En el tema dedicat a la sobreposició molecular es tracta la creació d'un algorisme, així com la seva implementació en forma de programa, batejat Topo-Geometrical Superposition Algorithm (TGSA), d'un mètode que proporcionés aquells alineaments que coincideixen amb la intuïció química. El resultat és un programa informàtic, codificat en Fortran 90, el qual alinea les molècules per parelles considerant tan sols nombres i distàncies atòmiques. La total absència de paràmetres teòrics permet desenvolupar un mètode de sobreposició molecular general, que proporcioni una sobreposició intuïtiva, i també de forma rellevant, de manera ràpida i amb poca intervenció de l'usuari. L'ús màxim del TGSA s'ha dedicat a calcular semblances per al seu ús posterior en QSAR, les quals majoritàriament no corresponen al valor que s'obtindria d'emprar la regla de la màxima semblança, sobretot si hi ha àtoms pesats en joc. Finalment, en l'últim tema, dedicat a la Semblança Quàntica en el marc del QSAR, es tracten tres aspectes diferents: - Ús de matrius de semblança. Aquí intervé l'anomenada matriu de semblança, calculada a partir de les semblances per parelles d'entre un conjunt de molècules. Aquesta matriu és emprada posteriorment, degudament tractada, com a font de descriptors moleculars per a estudis QSAR. Dins d'aquest àmbit s'han fet diversos estudis de correlació d'interès farmacològic, toxicològic, així com de diverses propietats físiques. - Aplicació de l'energia d'interacció electró-electró, assimilat com a una forma d'autosemblança. Aquesta modesta contribució consisteix breument en prendre el valor d'aquesta magnitud, i per analogia amb la notació de l'autosemblança molecular quàntica, assimilar-la com a cas particular de d'aquesta mesura. Aquesta energia d'interacció s'obté fàcilment a partir de programari mecanoquàntic, i esdevé ideal per a fer un primer estudi preliminar de correlació, on s'utilitza aquesta magnitud com a únic descriptor. - Càlcul d'autosemblances, on la densitat ha estat modificada per a augmentar el paper d'un substituent. Treballs previs amb densitats de fragments, tot i donar molt bons resultats, manquen de cert rigor conceptual en aïllar un fragment, suposadament responsable de l'activitat molecular, de la totalitat de l'estructura molecular, tot i que les densitats associades a aquest fragment ja difereixen degut a pertànyer a esquelets amb diferents substitucions. Un procediment per a omplir aquest buit que deixa la simple separació del fragment, considerant així la totalitat de la molècula (calcular-ne l'autosemblança), però evitant al mateix temps valors d'autosemblança no desitjats provocats per àtoms pesats, és l'ús de densitats de Forats de fermi, els quals es troben definits al voltant del fragment d'interès. Aquest procediment modifica la densitat de manera que es troba majoritàriament concentrada a la regió d'interès, però alhora permet obtenir una funció densitat, la qual es comporta matemàticament igual que la densitat electrònica regular, podent-se així incorporar dins del marc de la semblança molecular. Les autosemblances calculades amb aquesta metodologia han portat a bones correlacions amb àcids aromàtics substituïts, podent així donar una explicació al seu comportament. Des d'un altre punt de vista, també s'han fet contribucions conceptuals. S'ha implementat una nova mesura de semblança, la d'energia cinètica, la qual consisteix en prendre la recentment desenvolupada funció densitat d'energia cinètica, la qual al comportar-se matemàticament igual a les densitats electròniques regulars, s'ha incorporat en el marc de la semblança. A partir d'aquesta mesura s'han obtingut models QSAR satisfactoris per diferents conjunts moleculars. Dins de l'aspecte del tractament de les matrius de semblança s'ha implementat l'anomenada transformació estocàstica com a alternativa a l'ús de l'índex Carbó. Aquesta transformació de la matriu de semblança permet obtenir una nova matriu no simètrica, la qual pot ser posteriorment tractada per a construir models QSAR.

The Court of Justice of the European Union as a fundamental rights tribunal: challenges for the effective delivery of fundamental rights in the area of freedom, security and justice. CEPS Paper in Liberty and Security in Europe No. 49, 29 August 2012

This paper reflects on the challenges facing the effective implementation of the new EU fundamental rights architecture that emerged from the Lisbon Treaty. Particular attention is paid to the role of the Court of Justice of the European Union (CJEU) and its ability to function as a ‘fundamental rights tribunal’. The paper first analyses the praxis of the European Court of Human Rights in Strasbourg and its long-standing experience in overseeing the practical implementation of the European Convention for the Protection of Human Rights and Fundamental Freedoms. Against this analysis, it then examines the readiness of the CJEU to live up to its consolidated and strengthened mandate on fundamental rights as one of the prime guarantors of the effective implementation of the EU Charter of Fundamental Rights. We specifically review the role of ‘third-party interventions’ by non-governmental organisations, international and regional human rights actors as well as ‘interim relief measures’ when ensuring effective judicial protection of vulnerable individuals in cases of alleged violations of fundamental human rights. To flesh out our arguments, we rely on examples within the scope of the relatively new and complex domain of EU legislation, the Area of Freedom, Security and Justice (AFSJ), and its immigration, external border and asylum policies. In view of the fundamental rights-sensitive nature of these domains, which often encounter shifts of accountability and responsibility in their practical application, and the Lisbon Treaty’s expansion of the jurisdiction of the CJEU to interpret and review EU AFSJ legislation, this area can be seen as an excellent test case for the analyses at hand. The final section puts forth a set of policy suggestions that can assist the CJEU in the process of adjusting itself to the new fundamental rights context in a post-Lisbon Treaty setting.

Virtual reality as a visualisation tool: benefits and constraints

The benefits and applications of virtual reality (VR) in the construction industry have been investigated for almost a decade. However, the practical implementation of VR in the construction industry has yet to reach maturity owing to technical constraints. The need for effective information management presents challenges: both transfer of building data to, and organisation of building information within, the virtual environment require consideration. This paper reviews the applications and benefits of VR in the built environment field and reports on a collaboration between Loughborough University and South Bank University to overcome constraints on the use of the overall VR model for whole lifecycle visualisation. The work at each research centre is concerned with an aspect of information management within VR applications for the built environment, and both data transfer and internal data organisation have been investigated. In this paper, similarities and differences between computer-aided design (CAD) and VR packages are first discussed. Three different approaches to the creation of VR models during the design stage are identified and described, with a view to providing sharing understanding across the interdiscipliary groups involved. The suitable organisation of building information within the virtual environment is then further investigated. This work focused on the visualisation of the degradation of a building, through its lifespan, with the view to provide a visual aid for developing an effective and economic project maintenance programme. Finally consideration is given to the potential of emerging standards to facilitate an integrated use of VR. The convergence towards similar data structures in VR and other construction packages may enable visualisation to be better utilised in the overall lifecycle model.

Decentralized PID self-tuning control of industrial robots

A three degrees of freedom industrial robot is controlled by applying PID self-tuning (PID/ST) controllers. This control is considered as a corrective term to a nominal value, centrally computed from an inaccurate and/ or simplified dynamic model. An identification scheme on an assumed linear plant describing the deviation from the desired trajectory is employed in order to tune the controller coefficients and thus accomplish a behaviour prescribed through a desired pole placement. A salient feature of our approach is the decentralized nature of the controllers producing the corrective term for each joint. This opens the way to practical implementation, as recent computing requirement calculations for similar set-ups have shown in the literature. Numerical results are presented.

Facing the future: energy performance certificates and commercial property

Purpose – The paper aims to present the findings of a “situation review” of the Energy Performance of Buildings Directive (EPBD), focusing on energy performance certificates (EPCs) to highlight areas of specific importance for the UK property investment community. The paper is based on research commissioned by the Investment Property Forum (IPF) and funded through the IPF Research Programme (2006-2009). Design/methodology/approach – Interviews were undertaken with experts from the fields of property investment and building engineering. The interviews were undertaken with to identify: the current knowledge of EPCs in the property investment sector; key issues with practical implementation of the legislation; and perceptions of the potential impacts of legislation, particularly in relation to value stakeholder and behaviour. Findings – The paper finds that, although the regulations have been published, there is still a need for clarification in the marketplace with regard to some of the detail of regulations and the certification process. The following areas are of most concern to property investors: costs of surveys; potential difficulties with the process; and a shortage of assessors. With respect to these impacts it is becoming clear that investors who have not yet started considering the EPBD and its requirements within their strategy are likely to face difficulties in the short term. The most significant value-related impacts of EPBD are expected to be value differentiation of properties and “price chipping” against the rental or capital value of the property, where an occupier or potential purchaser will use the recommendations contained within an EPC to force a reduction in value. The latter is expected to emerge in the short term, whereas the former is expected to be realised over the medium to long term. Both these impacts have potentially significant implications for property investment holdings and also future investment behaviour.

A comparative review of dimension reduction methods in approximate Bayesian computation

Approximate Bayesian computation (ABC) methods make use of comparisons between simulated and observed summary statistics to overcome the problem of computationally intractable likelihood functions. As the practical implementation of ABC requires computations based on vectors of summary statistics, rather than full data sets, a central question is how to derive low-dimensional summary statistics from the observed data with minimal loss of information. In this article we provide a comprehensive review and comparison of the performance of the principal methods of dimension reduction proposed in the ABC literature. The methods are split into three nonmutually exclusive classes consisting of best subset selection methods, projection techniques and regularization. In addition, we introduce two new methods of dimension reduction. The first is a best subset selection method based on Akaike and Bayesian information criteria, and the second uses ridge regression as a regularization procedure. We illustrate the performance of these dimension reduction techniques through the analysis of three challenging models and data sets.

Is the Helmholtz equation really sign-indefinite?

The usual variational (or weak) formulations of the Helmholtz equation are sign-indefinite in the sense that the bilinear forms cannot be bounded below by a positive multiple of the appropriate norm squared. This is often for a good reason, since in bounded domains under certain boundary conditions the solution of the Helmholtz equation is not unique at wavenumbers that correspond to eigenvalues of the Laplacian, and thus the variational problem cannot be sign-definite. However, even in cases where the solution is unique for all wavenumbers, the standard variational formulations of the Helmholtz equation are still indefinite when the wavenumber is large. This indefiniteness has implications for both the analysis and the practical implementation of finite element methods. In this paper we introduce new sign-definite (also called coercive or elliptic) formulations of the Helmholtz equation posed in either the interior of a star-shaped domain with impedance boundary conditions, or the exterior of a star-shaped domain with Dirichlet boundary conditions. Like the standard variational formulations, these new formulations arise just by multiplying the Helmholtz equation by particular test functions and integrating by parts.

Cross-sector surveys assessing perceptions of key stakeholders towards barriers, concerns and facilitators to the appropriate use of adaptive designs in confirmatory trials

Background Appropriately conducted adaptive designs (ADs) offer many potential advantages over conventional trials. They make better use of accruing data, potentially saving time, trial participants, and limited resources compared to conventional, fixed sample size designs. However, one can argue that ADs are not implemented as often as they should be, particularly in publicly funded confirmatory trials. This study explored barriers, concerns, and potential facilitators to the appropriate use of ADs in confirmatory trials among key stakeholders. Methods We conducted three cross-sectional, online parallel surveys between November 2014 and January 2015. The surveys were based upon findings drawn from in-depth interviews of key research stakeholders, predominantly in the UK, and targeted Clinical Trials Units (CTUs), public funders, and private sector organisations. Response rates were as follows: 30(55 %) UK CTUs, 17(68 %) private sector, and 86(41 %) public funders. A Rating Scale Model was used to rank barriers and concerns in order of perceived importance for prioritisation. Results Top-ranked barriers included the lack of bridge funding accessible to UK CTUs to support the design of ADs, limited practical implementation knowledge, preference for traditional mainstream designs, difficulties in marketing ADs to key stakeholders, time constraints to support ADs relative to competing priorities, lack of applied training, and insufficient access to case studies of undertaken ADs to facilitate practical learning and successful implementation. Associated practical complexities and inadequate data management infrastructure to support ADs were reported as more pronounced in the private sector. For funders of public research, the inadequate description of the rationale, scope, and decision-making criteria to guide the planned AD in grant proposals by researchers were all viewed as major obstacles. Conclusions There are still persistent and important perceptions of individual and organisational obstacles hampering the use of ADs in confirmatory trials research. Stakeholder perceptions about barriers are largely consistent across sectors, with a few exceptions that reflect differences in organisations’ funding structures, experiences and characterisation of study interventions. Most barriers appear connected to a lack of practical implementation knowledge and applied training, and limited access to case studies to facilitate practical learning. Keywords: Adaptive designs; flexible designs; barriers; surveys; confirmatory trials; Phase 3; clinical trials; early stopping; interim analyses

From SMART to agent systems development

n order for agent-oriented software engineering to prove effective it must use principled notions of agents and enabling specification and reasoning, while still considering routes to practical implementation. This paper deals with the issue of individual agent specification and construction, departing from the conceptual basis provided by the smart agent framework. smart offers a descriptive specification of an agent architecture but omits consideration of issues relating to construction and control. In response, we introduce two new views to complement smart: a behavioural specification and a structural specification which, together, determine the components that make up an agent, and how they operate. In this way, we move from abstract agent system specification to practical implementation. These three aspects are combined to create an agent construction model, actsmart, which is then used to define the AgentSpeak(L) architecture in order to illustrate the application of actsmart.

Estimação de regressões aditivas via backfitting e integração marginal: performance em pequenas amostras

Nesta dissertação realizou-se um experimento de Monte Carlo para re- velar algumas características das distribuições em amostras finitas dos estimadores Backfitting (B) e de Integração Marginal(MI) para uma regressão aditiva bivariada. Está-se particularmente interessado em fornecer alguma evidência de como os diferentes métodos de seleção da janela hn, tais co- mo os métodos plug-in, impactam as propriedades em pequenas amostras dos estimadores. Está-se interessado, também, em fornecer evidência do comportamento de diferentes estimadores de hn relativamente a seqüência ótima de hn que minimiza uma função perda escolhida. O impacto de ignorar a dependência entre os regressores na estimação da janela é tam- bém investigado. Esta é uma prática comum e deve ter impacto sobre o desempenho dos estimadores. Além disso, não há nenhuma rotina atual- mente disponível nos pacotes estatísticos/econométricos para a estimação de regressões aditivas via os métodos de Backfitting e Integração Marginal. É um dos objetivos a criação de rotinas em Gauss para a implementação prática destes estimadores. Por fim, diferentemente do que ocorre atual- mente, quando a utilização dos estimadores-B e MI é feita de maneira completamente ad-hoc, há o objetivo de fornecer a usuários informação que permita uma escolha mais objetiva de qual estimador usar quando se está trabalhando com uma amostra finita.

Proposta de sistemática para a avaliação e controle de custos em propriedades rurais : o caso de uma empresa de criação de gado

Esta dissertação discute a gestão de Custos em propriedades rurais, tendo como objetivo principal a proposição de uma sistemática para avaliação e controle de custos em propriedades rurais, bem como mensurar os custos unitários dos produtos resultantes dos processos de produção referentes à pecuária. Para formulação desta sistemática, revisou-se a literatura sobre as mudanças ocorridas no decorrer dos últimos anos no setor primário da economia brasileira bem como, os sistemas de gestão em propriedades rurais. Uma revisão literária sobre os princípios de custeio (total, parcial e variável) e métodos de custeio (custo padrão, centro de custos e custeio baseado em atividades) também foi efetuada. A sistemática proposta foi estruturada em seis etapas: (1) análise dos contextos interno e externo da propriedade rural; (2) identificação da base conceitual; (3) estruturação do sistema de custos; (4) escolha do sistema de custos a utilizar; (5) aplicação prática do sistema de custos e análise da Evolução dos custos; (6) avaliação do resultado e identificação das oportunidades de melhoria. Com a aplicação prática do modelo em uma propriedade rural da região oeste do estado do Rio Grande do Sul foi possível concluir que a sistemática alcançou os objetivos já citados, e que a aplicação do método ABC seria um complemento refinado ao sistema de custos da empresa.

A BDI-based approach for the assessment of driver's decision-making in commuter scenarios

The rapid growth of urban areas has a significant impact on traffic and transportation systems. New management policies and planning strategies are clearly necessary to cope with the more than ever limited capacity of existing road networks. The concept of Intelligent Transportation System (ITS) arises in this scenario; rather than attempting to increase road capacity by means of physical modifications to the infrastructure, the premise of ITS relies on the use of advanced communication and computer technologies to handle today’s traffic and transportation facilities. Influencing users’ behaviour patterns is a challenge that has stimulated much research in the ITS field, where human factors start gaining great importance to modelling, simulating, and assessing such an innovative approach. This work is aimed at using Multi-agent Systems (MAS) to represent the traffic and transportation systems in the light of the new performance measures brought about by ITS technologies. Agent features have good potentialities to represent those components of a system that are geographically and functionally distributed, such as most components in traffic and transportation. A BDI (beliefs, desires, and intentions) architecture is presented as an alternative to traditional models used to represent the driver behaviour within microscopic simulation allowing for an explicit representation of users’ mental states. Basic concepts of ITS and MAS are presented, as well as some application examples related to the subject. This has motivated the extension of an existing microscopic simulation framework to incorporate MAS features to enhance the representation of drivers. This way demand is generated from a population of agents as the result of their decisions on route and departure time, on a daily basis. The extended simulation model that now supports the interaction of BDI driver agents was effectively implemented, and different experiments were performed to test this approach in commuter scenarios. MAS provides a process-driven approach that fosters the easy construction of modular, robust, and scalable models, characteristics that lack in former result-driven approaches. Its abstraction premises allow for a closer association between the model and its practical implementation. Uncertainty and variability are addressed in a straightforward manner, as an easier representation of humanlike behaviours within the driver structure is provided by cognitive architectures, such as the BDI approach used in this work. This way MAS extends microscopic simulation of traffic to better address the complexity inherent in ITS technologies.

Characterization of the temperature, load and damage effects using piezoelectric transducer patches based on fuzzy clustering

Structural Health Monitoring (SHM) denotes a system with the ability to detect and interpret adverse changes in a structure. One of the critical challenges for practical implementation of SHM system is the ability to detect damage under changing environmental conditions. This paper aims to characterize the temperature, load and damage effects in the sensor measurements obtained with piezoelectric transducer (PZT) patches. Data sets are collected on thin aluminum specimens under different environmental conditions and artificially induced damage states. The fuzzy clustering algorithm is used to organize the sensor measurements into a set of clusters, which can attribute the variation in sensor data due to temperature, load or any induced damage.

Mutual coupling modeling in transmission lines directly in the phase domain

This paper describes a computational model based on lumped elements for the mutual coupling between phases in three-phase transmission lines without the explicit use of modal transformation matrices. The self and mutual parameters and the coupling between phases are modeled using modal transformation techniques. The modal representation is developed from the intrinsic consideration of the modal transformation matrix and the resulting system of time-domain differential equations is described as state equations. Thus, a detailed profile of the currents and the voltages through the line can be easily calculated using numerical or analytical integration methods. However, the original contribution of the article is the proposal of a time-domain model without the successive phase/mode transformations and a practical implementation based on conventional electrical circuits, without the use of electromagnetic theory to model the coupling between phases. © 2011 IEEE.

Equivalent representation of mutual coupling in transmission lines by discrete element

This paper describes a computational model based on lumped elements for the mutual coupling between phases in transmission lines without the explicit use of modal transformation matrices. The self and mutual parameters and the coupling between phases are modeled using modal transformation techniques. The modal representation is developed from the intrinsic consideration of the modal transformation matrix and the resulting system of time-domain differential equations is described as state equations. Thus, a detailed profile ofthe currents and the voltages through the line can be easily calculated using numerical or analytical integration methods. However, the original contribution of the article is the proposal of a time-domain model without the successive phase/mode transformations and a practical implementation based on conventional electrical circuits, without the use of electromagnetic theory to model the coupling between phases. © 2003-2012 IEEE.