Probabilistic reasoning with an enzyme-driven DNA device

We present a biomolecular probabilistic model driven by the action of a DNA toolbox made of a set of DNA templates and enzymes that is able to perform Bayesian inference. The model will take single-stranded DNA as input data, representing the presence or absence of a specific molecular signal (the evidence). The program logic uses different DNA templates and their relative concentration ratios to encode the prior probability of a disease and the conditional probability of a signal given the disease. When the input and program molecules interact, an enzyme-driven cascade of reactions (DNA polymerase extension, nicking and degradation) is triggered, producing a different pair of single-stranded DNA species. Once the system reaches equilibrium, the ratio between the output species will represent the application of Bayes? law: the conditional probability of the disease given the signal. In other words, a qualitative diagnosis plus a quantitative degree of belief in that diagno- sis. Thanks to the inherent amplification capability of this DNA toolbox, the resulting system will be able to to scale up (with longer cascades and thus more input signals) a Bayesian biosensor that we designed previously.

Multiple proportion case-basing driven CBRE and its application in the evaluation of possible failure of firms

Case-based reasoning (CBR) is a unique tool for the evaluation of possible failure of firms (EOPFOF) for its eases of interpretation and implementation. Ensemble computing, a variation of group decision in society, provides a potential means of improving predictive performance of CBR-based EOPFOF. This research aims to integrate bagging and proportion case-basing with CBR to generate a method of proportion bagging CBR for EOPFOF. Diverse multiple case bases are first produced by multiple case-basing, in which a volume parameter is introduced to control the size of each case base. Then, the classic case retrieval algorithm is implemented to generate diverse member CBR predictors. Majority voting, the most frequently used mechanism in ensemble computing, is finally used to aggregate outputs of member CBR predictors in order to produce final prediction of the CBR ensemble. In an empirical experiment, we statistically validated the results of the CBR ensemble from multiple case bases by comparing them with those of multivariate discriminant analysis, logistic regression, classic CBR, the best member CBR predictor and bagging CBR ensemble. The results from Chinese EOPFOF prior to 3 years indicate that the new CBR ensemble, which significantly improved CBRs predictive ability, outperformed all the comparative methods.

A model-driven approach to teaching concurrency

We present an undergraduate course on concurrent programming where formal models are used in different stages of the learning process. The main practical difference with other approaches lies in the fact that the ability to develop correct concurrent software relies on a systematic transformation of formal models of inter-process interaction (so called shared resources), rather than on the specific constructs of some programming language. Using a resource-centric rather than a language-centric approach has some benefits for both teachers and students. Besides the obvious advantage of being independent of the programming language, the models help in the early validation of concurrent software design, provide students and teachers with a lingua franca that greatly simplifies communication at the classroom and during supervision, and help in the automatic generation of tests for the practical assignments. This method has been in use, with slight variations, for some 15 years, surviving changes in the programming language and course length. In this article, we describe the components and structure of the current incarnation of the course?which uses Java as target language?and some tools used to support our method. We provide a detailed description of the different outcomes that the model-driven approach delivers (validation of the initial design, automatic generation of tests, and mechanical generation of code) from a teaching perspective. A critical discussion on the perceived advantages and risks of our approach follows, including some proposals on how these risks can be minimized. We include a statistical analysis to show that our method has a positive impact in the student ability to understand concurrency and to generate correct code.

High power beam dump project for the accelerator prototype LIPAc: Cooling design and analysis

En el campo de la fusión nuclear y desarrollándose en paralelo a ITER (International Thermonuclear Experimental Reactor), el proyecto IFMIF (International Fusion Material Irradiation Facility) se enmarca dentro de las actividades complementarias encaminadas a solucionar las barreras tecnológicas que aún plantea la fusión. En concreto IFMIF es una instalación de irradiación cuya misión es caracterizar materiales resistentes a condiciones extremas como las esperadas en los futuros reactores de fusión como DEMO (DEMOnstration power plant). Consiste de dos aceleradores de deuterones que proporcionan un haz de 125 mA y 40 MeV cada uno, que al colisionar con un blanco de litio producen un flujo neutrónico intenso (1017 neutrones/s) con un espectro similar al de los neutrones de fusión [1], [2]. Dicho flujo neutrónico es empleado para irradiar los diferentes materiales candidatos a ser empleados en reactores de fusión, y las muestras son posteriormente examinadas en la llamada instalación de post-irradiación. Como primer paso en tan ambicioso proyecto, una fase de validación y diseño llamada IFMIFEVEDA (Engineering Validation and Engineering Design Activities) se encuentra actualmente en desarrollo. Una de las actividades contempladas en esta fase es la construcción y operación de una acelarador prototipo llamado LIPAc (Linear IFMIF Prototype Accelerator). Se trata de un acelerador de deuterones de alta intensidad idéntico a la parte de baja energía de los aceleradores de IFMIF. Los componentes del LIPAc, que será instalado en Japón, son suministrados por diferentes países europeos. El acelerador proporcionará un haz continuo de deuterones de 9 MeV con una potencia de 1.125 MW que tras ser caracterizado con diversos instrumentos deberá pararse de forma segura. Para ello se requiere un sistema denominado bloque de parada (Beam Dump en inglés) que absorba la energía del haz y la transfiera a un sumidero de calor. España tiene el compromiso de suministrar este componente y CIEMAT (Centro de Investigaciones Energéticas Medioambientales y Tecnológicas) es responsable de dicha tarea. La pieza central del bloque de parada, donde se para el haz de iones, es un cono de cobre con un ángulo de 3.5o, 2.5 m de longitud y 5 mm de espesor. Dicha pieza está refrigerada por agua que fluye en su superficie externa por el canal que se forma entre el cono de cobre y otra pieza concéntrica con éste. Este es el marco en que se desarrolla la presente tesis, cuyo objeto es el diseño del sistema de refrigeración del bloque de parada del LIPAc. El diseño se ha realizado utilizando un modelo simplificado unidimensional. Se han obtenido los parámetros del agua (presión, caudal, pérdida de carga) y la geometría requerida en el canal de refrigeración (anchura, rugosidad) para garantizar la correcta refrigeración del bloque de parada. Se ha comprobado que el diseño permite variaciones del haz respecto a la situación nominal siendo el flujo crítico calorífico al menos 2 veces superior al nominal. Se han realizado asimismo simulaciones fluidodinámicas 3D con ANSYS-CFX en aquellas zonas del canal de refrigeración que lo requieren. El bloque de parada se activará como consecuencia de la interacción del haz de partículas lo que impide cualquier cambio o reparación una vez comenzada la operación del acelerador. Por ello el diseño ha de ser muy robusto y todas las hipótesis utilizadas en la realización de éste deben ser cuidadosamente comprobadas. Gran parte del esfuerzo de la tesis se centra en la estimación del coeficiente de transferencia de calor que es determinante en los resultados obtenidos, y que se emplea además como condición de contorno en los cálculos mecánicos. Para ello por un lado se han buscado correlaciones cuyo rango de aplicabilidad sea adecuado para las condiciones del bloque de parada (canal anular, diferencias de temperatura agua-pared de decenas de grados). En un segundo paso se han comparado los coeficientes de película obtenidos a partir de la correlación seleccionada (Petukhov-Gnielinski) con los que se deducen de simulaciones fluidodinámicas, obteniendo resultados satisfactorios. Por último se ha realizado una validación experimental utilizando un prototipo y un circuito hidráulico que proporciona un flujo de agua con los parámetros requeridos en el bloque de parada. Tras varios intentos y mejoras en el experimento se han obtenido los coeficientes de película para distintos caudales y potencias de calentamiento. Teniendo en cuenta la incertidumbre de las medidas, los valores experimentales concuerdan razonablemente bien (en el rango de 15%) con los deducidos de las correlaciones. Por motivos radiológicos es necesario controlar la calidad del agua de refrigeración y minimizar la corrosión del cobre. Tras un estudio bibliográfico se identificaron los parámetros del agua más adecuados (conductividad, pH y concentración de oxígeno disuelto). Como parte de la tesis se ha realizado asimismo un estudio de la corrosión del circuito de refrigeración del bloque de parada con el doble fin de determinar si puede poner en riesgo la integridad del componente, y de obtener una estimación de la velocidad de corrosión para dimensionar el sistema de purificación del agua. Se ha utilizado el código TRACT (TRansport and ACTivation code) adaptándalo al caso del bloque de parada, para lo cual se trabajó con el responsable (Panos Karditsas) del código en Culham (UKAEA). Los resultados confirman que la corrosión del cobre en las condiciones seleccionadas no supone un problema. La Tesis se encuentra estructurada de la siguiente manera: En el primer capítulo se realiza una introducción de los proyectos IFMIF y LIPAc dentro de los cuales se enmarca esta Tesis. Además se describe el bloque de parada, siendo el diseño del sistema de rerigeración de éste el principal objetivo de la Tesis. En el segundo y tercer capítulo se realiza un resumen de la base teórica así como de las diferentes herramientas empleadas en el diseño del sistema de refrigeración. El capítulo cuarto presenta los resultados del relativos al sistema de refrigeración. Tanto los obtenidos del estudio unidimensional, como los obtenidos de las simulaciones fluidodinámicas 3D mediante el empleo del código ANSYS-CFX. En el quinto capítulo se presentan los resultados referentes al análisis de corrosión del circuito de refrigeración del bloque de parada. El capítulo seis se centra en la descripción del montaje experimental para la obtención de los valores de pérdida de carga y coeficiente de transferencia del calor. Asimismo se presentan los resultados obtenidos en dichos experimentos. Finalmente encontramos un capítulo de apéndices en el que se describen una serie de experimentos llevados a cabo como pasos intermedios en la obtención del resultado experimental del coeficiente de película. También se presenta el código informático empleado para el análisis unidimensional del sistema de refrigeración del bloque de parada llamado CHICA (Cooling and Heating Interaction and Corrosion Analysis). ABSTRACT In the nuclear fusion field running in parallel to ITER (International Thermonuclear Experimental Reactor) as one of the complementary activities headed towards solving the technological barriers, IFMIF (International Fusion Material Irradiation Facility) project aims to provide an irradiation facility to qualify advanced materials resistant to extreme conditions like the ones expected in future fusion reactors like DEMO (DEMOnstration Power Plant). IFMIF consists of two constant wave deuteron accelerators delivering a 125 mA and 40 MeV beam each that will collide on a lithium target producing an intense neutron fluence (1017 neutrons/s) with a similar spectra to that of fusion neutrons [1], [2]. This neutron flux is employed to irradiate the different material candidates to be employed in the future fusion reactors, and the samples examined after irradiation at the so called post-irradiative facilities. As a first step in such an ambitious project, an engineering validation and engineering design activity phase called IFMIF-EVEDA (Engineering Validation and Engineering Design Activities) is presently going on. One of the activities consists on the construction and operation of an accelerator prototype named LIPAc (Linear IFMIF Prototype Accelerator). It is a high intensity deuteron accelerator identical to the low energy part of the IFMIF accelerators. The LIPAc components, which will be installed in Japan, are delivered by different european countries. The accelerator supplies a 9 MeV constant wave beam of deuterons with a power of 1.125 MW, which after being characterized by different instruments has to be stopped safely. For such task a beam dump to absorb the beam energy and take it to a heat sink is needed. Spain has the compromise of delivering such device and CIEMAT (Centro de Investigaciones Energéticas Medioambientales y Tecnológicas) is responsible for such task. The central piece of the beam dump, where the ion beam is stopped, is a copper cone with an angle of 3.5o, 2.5 m long and 5 mm width. This part is cooled by water flowing on its external surface through the channel formed between the copper cone and a concentric piece with the latter. The thesis is developed in this realm, and its objective is designing the LIPAc beam dump cooling system. The design has been performed employing a simplified one dimensional model. The water parameters (pressure, flow, pressure loss) and the required annular channel geometry (width, rugoisty) have been obtained guaranteeing the correct cooling of the beam dump. It has been checked that the cooling design allows variations of the the beam with respect to the nominal position, being the CHF (Critical Heat Flux) at least twice times higher than the nominal deposited heat flux. 3D fluid dynamic simulations employing ANSYS-CFX code in the beam dump cooling channel sections which require a more thorough study have also been performed. The beam dump will activateasaconsequenceofthe deuteron beam interaction, making impossible any change or maintenance task once the accelerator operation has started. Hence the design has to be very robust and all the hypotheses employed in the design mustbecarefully checked. Most of the work in the thesis is concentrated in estimating the heat transfer coefficient which is decisive in the obtained results, and is also employed as boundary condition in the mechanical analysis. For such task, correlations which applicability range is the adequate for the beam dump conditions (annular channel, water-surface temperature differences of tens of degrees) have been compiled. In a second step the heat transfer coefficients obtained from the selected correlation (Petukhov- Gnielinski) have been compared with the ones deduced from the 3D fluid dynamic simulations, obtaining satisfactory results. Finally an experimental validation has been performed employing a prototype and a hydraulic circuit that supplies a flow with the requested parameters in the beam dump. After several tries and improvements in the experiment, the heat transfer coefficients for different flows and heating powers have been obtained. Considering the uncertainty in the measurements the experimental values agree reasonably well (in the order of 15%) with the ones obtained from the correlations. Due to radiological reasons the quality of the cooling water must be controlled, hence minimizing the copper corrosion. After performing a bibligraphic study the most adequate water parameters were identified (conductivity, pH and dissolved oxygen concentration). As part of this thesis a corrosion study of the beam dump cooling circuit has been performed with the double aim of determining if corrosion can pose a risk for the copper beam dump , and obtaining an estimation of the corrosion velocitytodimension the water purification system. TRACT code(TRansport and ACTivation) has been employed for such study adapting the code for the beam dump case. For such study a collaboration with the code responsible (Panos Karditsas) at Culham (UKAEA) was established. The work developed in this thesis has supposed the publication of three articles in JCR journals (”Journal of Nuclear Materials” y ”Fusion Engineering and Design”), as well as presentations in more than four conferences and relevant meetings.

A novel energy-driven computing paradigm for e-health scenarios

A first-rate e-Health system saves lives, provides better patient care, allows complex but useful epidemiologic analysis and saves money. However, there may also be concerns about the costs and complexities associated with e-health implementation, and the need to solve issues about the energy footprint of the high-demanding computing facilities. This paper proposes a novel and evolved computing paradigm that: (i) provides the required computing and sensing resources; (ii) allows the population-wide diffusion; (iii) exploits the storage, communication and computing services provided by the Cloud; (iv) tackles the energy-optimization issue as a first-class requirement, taking it into account during the whole development cycle. The novel computing concept and the multi-layer top-down energy-optimization methodology obtain promising results in a realistic scenario for cardiovascular tracking and analysis, making the Home Assisted Living a reality.

Fast ignition driven by quasi-monoenergetic ions: Optimal ion type and reduction of ignition energies with an ion beam array

Fast ignition of inertial fusion targets driven by quasi-monoenergetic ion beams is investigated by means of numerical simulations. Light and intermediate ions such as lithium, carbon, aluminum and vanadium have been considered. Simulations show that the minimum ignition energies of an ideal configuration of compressed Deuterium-Tritium are almost independent on the ion atomic number. However, they are obtained for increasing ion energies, which scale, approximately, as Z2, where Z is the ion atomic number. Assuming that the ion beam can be focused into 10 ?m spots, a new irradiation scheme is proposed to reduce the ignition energies. The combination of intermediate Z ions, such as 5.5 GeV vanadium, and the new irradiation scheme allows a reduction of the number of ions required for ignition by, roughly, three orders of magnitude when compared with the standard proton fast ignition scheme.

An ontology-driven communication architecture for spontaneous interoperability in Home Automation systems

Current solutions to the interoperability problem in Home Automation systems are based on a priori agreements where protocols are standardized and later integrated through specific gateways. In this regards, spontaneous interoperability, or the ability to integrate new devices into the system with minimum planning in advance, is still considered a major challenge that requires new models of connectivity. In this paper we present an ontology-driven communication architecture whose main contribution is that it facilitates spontaneous interoperability at system model level by means of semantic integration. The architecture has been validated through a prototype and the main challenges for achieving complete spontaneous interoperability are also evaluated.

Designer-driven 3D buildings generated using variable neighborhood search

This paper presents a mechanism to generate virtual buildings considering designer constraints and guidelines. This mechanism is implemented as a pipeline of different Variable Neighborhood Search (VNS) optimization processes in which several subproblems are tackled (1) rooms locations, (2) connectivity graph, and (3) element placement. The core VNS algorithm includes some variants to improve its performance, such as, for example constraint handling and biased operator selection. The optimization process uses a toolkit of construction primitives implemented as "smart objects" providing basic elements such as rooms, doors, staircases and other connectors. The paper also shows experimental results of the application of different designer constraints to a wide range of buildings from small houses to a large castle with several underground levels.

Ontology-driven legal support-system in air transport passenger domain

This paper aims to present a preliminary version of asupport-system in the air transport passenger domain. This system relies upon an underlying on-tological structure representing a normative framework to facilitatethe provision of contextualized relevant legal information.This information includes the pas-senger's rights and itenhances self-litigation and the decision-making process of passengers.Our contribution is based in the attempt of rendering a user-centric-legal informationgroundedon case-scenarios of the most pronounced incidents related to the consumer complaints in the EU.A number ofadvantages with re-spect to the current state-of-the-art services are discussed and a case study illu-strates a possible technological application.

PRISMA: Model-driven development of aspect-oriented software architectures

This summary presents a methodology for supporting the development of AOSAs following the MDD paradigm. This new methodology is called PRISMA and allows the code generation from models which specify functional and non-functional requirements.

Visualization of a student predictive model for 3D virtual environments driven to procedural training

This document presents theimplementation ofa Student Behavior Predictor Viewer(SBPV)for a student predictive model. The student predictive model is part of an intelligent tutoring system, and is built from logs of students’ behaviors in the “Virtual Laboratory of Agroforestry Biotechnology”implemented in a previous work.The SBPVis a tool for visualizing a 2D graphical representationof the extended automaton associated with any of the clusters ofthe student predictive model. Apart from visualizing the extended automaton, the SBPV supports the navigation across the automaton by means of desktop devices. More precisely, the SBPV allows user to move through the automaton, to zoom in/out the graphic or to locate a given state. In addition, the SBPV also allows user to modify the default layout of the automaton on the screen by changing the position of the states by means of the mouse. To developthe SBPV, a web applicationwas designedand implementedrelying on HTML5, JavaScript and C#.

Identification and correction of besouro's faults: impact on test‐driven development experiments

Context. This thesis is framed in experimental software engineering. More concretely, it addresses the problems arisen when assessing process conformance in test-driven development experiments conducted by UPM's Experimental Software Engineering group. Process conformance was studied using the Eclipse's plug-in tool Besouro. It has been observed that Besouro does not work correctly in some circumstances. It creates doubts about the correction of the existing experimental data which render it useless. Aim. The main objective of this work is the identification and correction of Besouro's faults. A secondary goal is fixing the datasets already obtained in past experiments to the maximum possible extent. This way, existing experimental results could be used with confidence. Method. (1) Testing Besouro using different sequences of events (creation methods, assertions etc..) to identify the underlying faults. (2) Fix the code and (3) fix the datasets using code specially created for this purpose. Results. (1) We confirmed the existence of several fault in Besouro's code that affected to Test-First and Test-Last episode identification. These faults caused the incorrect identification of 20% of episodes. (2) We were able to fix Besouro's code. (3) The correction of existing datasets was possible, subjected to some restrictions (such us the impossibility of tracing code size increase to programming time. Conclusion. The results of past experiments dependent upon Besouro's data could no be trustable. We have the suspicion that more faults remain in Besouro's code, whose identification requires further analysis.

A framework to identify primitives that represent usability within model-driven development methods

Nowadays, there are sound methods and tools which implement the Model-Driven Development approach (MDD) satisfactorily. However, MDD approaches focus on representing and generating code that represents functionality, behaviour and persistence, putting the interaction, and more specifically the usability, in a second place. If we aim to include usability features in a system developed with a MDD tool, we need to extend manually the generated code

Change-impact driven agile architecting

Trabajo Ya Publicado de Congreso CORE A

Pattern formation of parametrically driven surface waves induced by vibration

Esta tesis se centra en la generación de ondas superficiales subarmónicas en fluidos sometidos a vibración forzada en el régimen gravitatorio capilar con líquidos de baja viscosidad. Tres problemas diferentes han sido estudiados: un contenedor rectangular con vibración horizontal, la misma geometría pero con una combinación de vibración vertical y horizontal y un obstáculo completamente sumergido vibrado verticalmente en un contenedor grande. Se deriva una ecuación de amplitud desde primeros principios para describir las ondas subarmónicas con forzamiento parámetrico inducido por la vibración. La ecuación es bidimensional mientras que el problema original es tridimensional y admite un forzamiento espacial no uniforme. Usando esta ecuación los tres sistemas han sido analizados, centrándose en calcular la amplitud crítica, la orientación de los patrones y el carácter temporal de los patrones espaciotemporales, que pueden ser estrictamente subarmónicos o cuasiperiodicos con una frecuencia de modulación temporal. La dependencia con los parámetros adimensionales también se considera. La teoría será comparada con los experimentos disponibles en la literatura. Abstract This thesis focus on the generation of subharmonic surface waves on fluids subject to forced vibration in the gravity-capillary regime with liquids of small viscosity. Three different problems have been considered: a rectangular container under horizontal vibration; the same geometry but under a combination of horizontal and vertical vibration; and a fully submerged vertically vibrated obstacle in a large container. An amplitude equation is derived from first principles that fairly precisely describes the subharmonic surfaces waves parametrically driven by vibration. That equation is two dimensional while the underlying problem is three-dimensional and permits spatially nonuniform forcing. Using this equation, the three systems have been analyzed, focusing on the calculation of the threshold amplitude, the pattern orientation, and the temporal character of the spatio-temporal patterns, which can be either strictly subharmonic or quasi-periodic, showing an additional modulation frequency. Dependence on the non-dimensional parameters is also considered. The theory is compared with the experiments available in the literature.