The PiLLoW/Ciao library for INTERNET/WWW programming using computational logic systems

We discuss from a practical point of view a number of issues involved in writing Internet and WWW applications using LP/CLP systems. We describe PiLLoW, an Internet and WWW programming library for LP/CLP systems which we argüe significantly simplifies the process of writing such applications. PiLLoW provides facilities for generating HTML structured documents, producing HTML forms, writing form handlers, accessing and parsing WWW documents, and accessing code posted at HTTP addresses. We also describe the architecture of some application classes, using a high-level model of client-server interaction, active modules. Finally we describe an architecture for automatic LP/CLP code downloading for local execution, using generic browsers. The PiLLoW library has been developed in the context of the &-Prolog and CIAO systems, but it has been adapted to a number of popular LP/CLP systems, supporting most of its functionality.

An approach to profiling for run-time checking of computational properties and performance debugging in logic programs.

Although several profiling techniques for identifying performance bottlenecks in logic programs have been developed, they are generally not automatic and in most cases they do not provide enough information for identifying the root causes of such bottlenecks. This complicates using their results for guiding performance improvement. We present a profiling method and tool that provides such explanations. Our profiler associates cost centers to certain program elements and can measure different types of resource-related properties that affect performance, preserving the precedence of cost centers in the call graph. It includes an automatic method for detecting procedures that are performance bottlenecks. The profiling tool has been integrated in a previously developed run-time checking framework to allow verification of certain properties when they cannot be verified statically. The approach allows checking global computational properties which require complex instrumentation tracking information about previous execution states, such as, e.g., that the execution time accumulated by a given procedure is not greater than a given bound. We have built a prototype implementation, integrated it in the Ciao/CiaoPP system and successfully applied it to performance improvement, automatic optimization (e.g., resource-aware specialization of programs), run-time checking, and debugging of global computational properties (e.g., resource usage) in Prolog programs.

Numerical Error Prediction and its applications in CFD using tau-estimation

Nowadays, Computational Fluid Dynamics (CFD) solvers are widely used within the industry to model fluid flow phenomenons. Several fluid flow model equations have been employed in the last decades to simulate and predict forces acting, for example, on different aircraft configurations. Computational time and accuracy are strongly dependent on the fluid flow model equation and the spatial dimension of the problem considered. While simple models based on perfect flows, like panel methods or potential flow models can be very fast to solve, they usually suffer from a poor accuracy in order to simulate real flows (transonic, viscous). On the other hand, more complex models such as the full Navier- Stokes equations provide high fidelity predictions but at a much higher computational cost. Thus, a good compromise between accuracy and computational time has to be fixed for engineering applications. A discretisation technique widely used within the industry is the so-called Finite Volume approach on unstructured meshes. This technique spatially discretises the flow motion equations onto a set of elements which form a mesh, a discrete representation of the continuous domain. Using this approach, for a given flow model equation, the accuracy and computational time mainly depend on the distribution of nodes forming the mesh. Therefore, a good compromise between accuracy and computational time might be obtained by carefully defining the mesh. However, defining an optimal mesh for complex flows and geometries requires a very high level expertize in fluid mechanics and numerical analysis, and in most cases a simple guess of regions of the computational domain which might affect the most the accuracy is impossible. Thus, it is desirable to have an automatized remeshing tool, which is more flexible with unstructured meshes than its structured counterpart. However, adaptive methods currently in use still have an opened question: how to efficiently drive the adaptation ? Pioneering sensors based on flow features generally suffer from a lack of reliability, so in the last decade more effort has been made in developing numerical error-based sensors, like for instance the adjoint-based adaptation sensors. While very efficient at adapting meshes for a given functional output, the latter method is very expensive as it requires to solve a dual set of equations and computes the sensor on an embedded mesh. Therefore, it would be desirable to develop a more affordable numerical error estimation method. The current work aims at estimating the truncation error, which arises when discretising a partial differential equation. These are the higher order terms neglected in the construction of the numerical scheme. The truncation error provides very useful information as it is strongly related to the flow model equation and its discretisation. On one hand, it is a very reliable measure of the quality of the mesh, therefore very useful in order to drive a mesh adaptation procedure. On the other hand, it is strongly linked to the flow model equation, so that a careful estimation actually gives information on how well a given equation is solved, which may be useful in the context of _ -extrapolation or zonal modelling. The following work is organized as follows: Chap. 1 contains a short review of mesh adaptation techniques as well as numerical error prediction. In the first section, Sec. 1.1, the basic refinement strategies are reviewed and the main contribution to structured and unstructured mesh adaptation are presented. Sec. 1.2 introduces the definitions of errors encountered when solving Computational Fluid Dynamics problems and reviews the most common approaches to predict them. Chap. 2 is devoted to the mathematical formulation of truncation error estimation in the context of finite volume methodology, as well as a complete verification procedure. Several features are studied, such as the influence of grid non-uniformities, non-linearity, boundary conditions and non-converged numerical solutions. This verification part has been submitted and accepted for publication in the Journal of Computational Physics. Chap. 3 presents a mesh adaptation algorithm based on truncation error estimates and compares the results to a feature-based and an adjoint-based sensor (in collaboration with Jorge Ponsín, INTA). Two- and three-dimensional cases relevant for validation in the aeronautical industry are considered. This part has been submitted and accepted in the AIAA Journal. An extension to Reynolds Averaged Navier- Stokes equations is also included, where _ -estimation-based mesh adaptation and _ -extrapolation are applied to viscous wing profiles. The latter has been submitted in the Proceedings of the Institution of Mechanical Engineers, Part G: Journal of Aerospace Engineering. Keywords: mesh adaptation, numerical error prediction, finite volume Hoy en día, la Dinámica de Fluidos Computacional (CFD) es ampliamente utilizada dentro de la industria para obtener información sobre fenómenos fluidos. La Dinámica de Fluidos Computacional considera distintas modelizaciones de las ecuaciones fluidas (Potencial, Euler, Navier-Stokes, etc) para simular y predecir las fuerzas que actúan, por ejemplo, sobre una configuración de aeronave. El tiempo de cálculo y la precisión en la solución depende en gran medida de los modelos utilizados, así como de la dimensión espacial del problema considerado. Mientras que modelos simples basados en flujos perfectos, como modelos de flujos potenciales, se pueden resolver rápidamente, por lo general aducen de una baja precisión a la hora de simular flujos reales (viscosos, transónicos, etc). Por otro lado, modelos más complejos tales como el conjunto de ecuaciones de Navier-Stokes proporcionan predicciones de alta fidelidad, a expensas de un coste computacional mucho más elevado. Por lo tanto, en términos de aplicaciones de ingeniería se debe fijar un buen compromiso entre precisión y tiempo de cálculo. Una técnica de discretización ampliamente utilizada en la industria es el método de los Volúmenes Finitos en mallas no estructuradas. Esta técnica discretiza espacialmente las ecuaciones del movimiento del flujo sobre un conjunto de elementos que forman una malla, una representación discreta del dominio continuo. Utilizando este enfoque, para una ecuación de flujo dado, la precisión y el tiempo computacional dependen principalmente de la distribución de los nodos que forman la malla. Por consiguiente, un buen compromiso entre precisión y tiempo de cálculo se podría obtener definiendo cuidadosamente la malla, concentrando sus elementos en aquellas zonas donde sea estrictamente necesario. Sin embargo, la definición de una malla óptima para corrientes y geometrías complejas requiere un nivel muy alto de experiencia en la mecánica de fluidos y el análisis numérico, así como un conocimiento previo de la solución. Aspecto que en la mayoría de los casos no está disponible. Por tanto, es deseable tener una herramienta que permita adaptar los elementos de malla de forma automática, acorde a la solución fluida (remallado). Esta herramienta es generalmente más flexible en mallas no estructuradas que con su homóloga estructurada. No obstante, los métodos de adaptación actualmente en uso todavía dejan una pregunta abierta: cómo conducir de manera eficiente la adaptación. Sensores pioneros basados en las características del flujo en general, adolecen de una falta de fiabilidad, por lo que en la última década se han realizado grandes esfuerzos en el desarrollo numérico de sensores basados en el error, como por ejemplo los sensores basados en el adjunto. A pesar de ser muy eficientes en la adaptación de mallas para un determinado funcional, este último método resulta muy costoso, pues requiere resolver un doble conjunto de ecuaciones: la solución y su adjunta. Por tanto, es deseable desarrollar un método numérico de estimación de error más asequible. El presente trabajo tiene como objetivo estimar el error local de truncación, que aparece cuando se discretiza una ecuación en derivadas parciales. Estos son los términos de orden superior olvidados en la construcción del esquema numérico. El error de truncación proporciona una información muy útil sobre la solución: es una medida muy fiable de la calidad de la malla, obteniendo información que permite llevar a cabo un procedimiento de adaptación de malla. Está fuertemente relacionado al modelo matemático fluido, de modo que una estimación precisa garantiza la idoneidad de dicho modelo en un campo fluido, lo que puede ser útil en el contexto de modelado zonal. Por último, permite mejorar la precisión de la solución resolviendo un nuevo sistema donde el error local actúa como término fuente (_ -extrapolación). El presenta trabajo se organiza de la siguiente manera: Cap. 1 contiene una breve reseña de las técnicas de adaptación de malla, así como de los métodos de predicción de los errores numéricos. En la primera sección, Sec. 1.1, se examinan las estrategias básicas de refinamiento y se presenta la principal contribución a la adaptación de malla estructurada y no estructurada. Sec 1.2 introduce las definiciones de los errores encontrados en la resolución de problemas de Dinámica Computacional de Fluidos y se examinan los enfoques más comunes para predecirlos. Cap. 2 está dedicado a la formulación matemática de la estimación del error de truncación en el contexto de la metodología de Volúmenes Finitos, así como a un procedimiento de verificación completo. Se estudian varias características que influyen en su estimación: la influencia de la falta de uniformidad de la malla, el efecto de las no linealidades del modelo matemático, diferentes condiciones de contorno y soluciones numéricas no convergidas. Esta parte de verificación ha sido presentada y aceptada para su publicación en el Journal of Computational Physics. Cap. 3 presenta un algoritmo de adaptación de malla basado en la estimación del error de truncación y compara los resultados con sensores de featured-based y adjointbased (en colaboración con Jorge Ponsín del INTA). Se consideran casos en dos y tres dimensiones, relevantes para la validación en la industria aeronáutica. Este trabajo ha sido presentado y aceptado en el AIAA Journal. También se incluye una extensión de estos métodos a las ecuaciones RANS (Reynolds Average Navier- Stokes), en donde adaptación de malla basada en _ y _ -extrapolación son aplicados a perfiles con viscosidad de alas. Este último trabajo se ha presentado en los Actas de la Institución de Ingenieros Mecánicos, Parte G: Journal of Aerospace Engineering. Palabras clave: adaptación de malla, predicción del error numérico, volúmenes finitos

Computational methods to create and analyze a digital gene expression atlas of embryo development from microscopy images

Abstract The creation of atlases, or digital models where information from different subjects can be combined, is a field of increasing interest in biomedical imaging. When a single image does not contain enough information to appropriately describe the organism under study, it is then necessary to acquire images of several individuals, each of them containing complementary data with respect to the rest of the components in the cohort. This approach allows creating digital prototypes, ranging from anatomical atlases of human patients and organs, obtained for instance from Magnetic Resonance Imaging, to gene expression cartographies of embryo development, typically achieved from Light Microscopy. Within such context, in this PhD Thesis we propose, develop and validate new dedicated image processing methodologies that, based on image registration techniques, bring information from multiple individuals into alignment within a single digital atlas model. We also elaborate a dedicated software visualization platform to explore the resulting wealth of multi-dimensional data and novel analysis algo-rithms to automatically mine the generated resource in search of bio¬logical insights. In particular, this work focuses on gene expression data from developing zebrafish embryos imaged at the cellular resolution level with Two-Photon Laser Scanning Microscopy. Disposing of quantitative measurements relating multiple gene expressions to cell position and their evolution in time is a fundamental prerequisite to understand embryogenesis multi-scale processes. However, the number of gene expressions that can be simultaneously stained in one acquisition is limited due to optical and labeling constraints. These limitations motivate the implementation of atlasing strategies that can recreate a virtual gene expression multiplex. The developed computational tools have been tested in two different scenarios. The first one is the early zebrafish embryogenesis where the resulting atlas constitutes a link between the phenotype and the genotype at the cellular level. The second one is the late zebrafish brain where the resulting atlas allows studies relating gene expression to brain regionalization and neurogenesis. The proposed computational frameworks have been adapted to the requirements of both scenarios, such as the integration of partial views of the embryo into a whole embryo model with cellular resolution or the registration of anatom¬ical traits with deformable transformation models non-dependent on any specific labeling. The software implementation of the atlas generation tool (Match-IT) and the visualization platform (Atlas-IT) together with the gene expression atlas resources developed in this Thesis are to be made freely available to the scientific community. Lastly, a novel proof-of-concept experiment integrates for the first time 3D gene expression atlas resources with cell lineages extracted from live embryos, opening up the door to correlate genetic and cellular spatio-temporal dynamics. La creación de atlas, o modelos digitales, donde la información de distintos sujetos puede ser combinada, es un campo de creciente interés en imagen biomédica. Cuando una sola imagen no contiene suficientes datos como para describir apropiadamente el organismo objeto de estudio, se hace necesario adquirir imágenes de varios individuos, cada una de las cuales contiene información complementaria respecto al resto de componentes del grupo. De este modo, es posible crear prototipos digitales, que pueden ir desde atlas anatómicos de órganos y pacientes humanos, adquiridos por ejemplo mediante Resonancia Magnética, hasta cartografías de la expresión genética del desarrollo de embrionario, típicamente adquiridas mediante Microscopía Optica. Dentro de este contexto, en esta Tesis Doctoral se introducen, desarrollan y validan nuevos métodos de procesado de imagen que, basándose en técnicas de registro de imagen, son capaces de alinear imágenes y datos provenientes de múltiples individuos en un solo atlas digital. Además, se ha elaborado una plataforma de visualization específicamente diseñada para explorar la gran cantidad de datos, caracterizados por su multi-dimensionalidad, que resulta de estos métodos. Asimismo, se han propuesto novedosos algoritmos de análisis y minería de datos que permiten inspeccionar automáticamente los atlas generados en busca de conclusiones biológicas significativas. En particular, este trabajo se centra en datos de expresión genética del desarrollo embrionario del pez cebra, adquiridos mediante Microscopía dos fotones con resolución celular. Disponer de medidas cuantitativas que relacionen estas expresiones genéticas con las posiciones celulares y su evolución en el tiempo es un prerrequisito fundamental para comprender los procesos multi-escala característicos de la morfogénesis. Sin embargo, el número de expresiones genéticos que pueden ser simultáneamente etiquetados en una sola adquisición es reducido debido a limitaciones tanto ópticas como del etiquetado. Estas limitaciones requieren la implementación de estrategias de creación de atlas que puedan recrear un multiplexado virtual de expresiones genéticas. Las herramientas computacionales desarrolladas han sido validadas en dos escenarios distintos. El primer escenario es el desarrollo embrionario temprano del pez cebra, donde el atlas resultante permite constituir un vínculo, a nivel celular, entre el fenotipo y el genotipo de este organismo modelo. El segundo escenario corresponde a estadios tardíos del desarrollo del cerebro del pez cebra, donde el atlas resultante permite relacionar expresiones genéticas con la regionalización del cerebro y la formación de neuronas. La plataforma computacional desarrollada ha sido adaptada a los requisitos y retos planteados en ambos escenarios, como la integración, a resolución celular, de vistas parciales dentro de un modelo consistente en un embrión completo, o el alineamiento entre estructuras de referencia anatómica equivalentes, logrado mediante el uso de modelos de transformación deformables que no requieren ningún marcador específico. Está previsto poner a disposición de la comunidad científica tanto la herramienta de generación de atlas (Match-IT), como su plataforma de visualización (Atlas-IT), así como las bases de datos de expresión genética creadas a partir de estas herramientas. Por último, dentro de la presente Tesis Doctoral, se ha incluido una prueba conceptual innovadora que permite integrar los mencionados atlas de expresión genética tridimensionales dentro del linaje celular extraído de una adquisición in vivo de un embrión. Esta prueba conceptual abre la puerta a la posibilidad de correlar, por primera vez, las dinámicas espacio-temporales de genes y células.

El problema del rozamiento en el análisis de estructuras de fábrica mediante modelos de sólidos rígidos

La evaluación de la seguridad de estructuras antiguas de fábrica es un problema abierto.El material es heterogéneo y anisótropo, el estado previo de tensiones difícil de conocer y las condiciones de contorno inciertas. A comienzos de los años 50 se demostró que el análisis límite era aplicable a este tipo de estructuras, considerándose desde entonces como una herramienta adecuada. En los casos en los que no se produce deslizamiento la aplicación de los teoremas del análisis límite estándar constituye una herramienta formidable por su simplicidad y robustez. No es necesario conocer el estado real de tensiones. Basta con encontrar cualquier solución de equilibrio, y que satisfaga las condiciones de límite del material, en la seguridad de que su carga será igual o inferior a la carga real de inicio de colapso. Además esta carga de inicio de colapso es única (teorema de la unicidad) y se puede obtener como el óptimo de uno cualquiera entre un par de programas matemáticos convexos duales. Sin embargo, cuando puedan existir mecanismos de inicio de colapso que impliquen deslizamientos, cualquier solución debe satisfacer tanto las restricciones estáticas como las cinemáticas, así como un tipo especial de restricciones disyuntivas que ligan las anteriores y que pueden plantearse como de complementariedad. En este último caso no está asegurada la existencia de una solución única, por lo que es necesaria la búsqueda de otros métodos para tratar la incertidumbre asociada a su multiplicidad. En los últimos años, la investigación se ha centrado en la búsqueda de un mínimo absoluto por debajo del cual el colapso sea imposible. Este método es fácil de plantear desde el punto de vista matemático, pero intratable computacionalmente, debido a las restricciones de complementariedad 0 y z 0 que no son ni convexas ni suaves. El problema de decisión resultante es de complejidad computacional No determinista Polinomial (NP)- completo y el problema de optimización global NP-difícil. A pesar de ello, obtener una solución (sin garantía de exito) es un problema asequible. La presente tesis propone resolver el problema mediante Programación Lineal Secuencial, aprovechando las especiales características de las restricciones de complementariedad, que escritas en forma bilineal son del tipo y z = 0; y 0; z 0 , y aprovechando que el error de complementariedad (en forma bilineal) es una función de penalización exacta. Pero cuando se trata de encontrar la peor solución, el problema de optimización global equivalente es intratable (NP-difícil). Además, en tanto no se demuestre la existencia de un principio de máximo o mínimo, existe la duda de que el esfuerzo empleado en aproximar este mínimo esté justificado. En el capítulo 5, se propone hallar la distribución de frecuencias del factor de carga, para todas las soluciones de inicio de colapso posibles, sobre un sencillo ejemplo. Para ello, se realiza un muestreo de soluciones mediante el método de Monte Carlo, utilizando como contraste un método exacto de computación de politopos. El objetivo final es plantear hasta que punto está justificada la busqueda del mínimo absoluto y proponer un método alternativo de evaluación de la seguridad basado en probabilidades. Las distribuciones de frecuencias, de los factores de carga correspondientes a las soluciones de inicio de colapso obtenidas para el caso estudiado, muestran que tanto el valor máximo como el mínimo de los factores de carga son muy infrecuentes, y tanto más, cuanto más perfecto y contínuo es el contacto. Los resultados obtenidos confirman el interés de desarrollar nuevos métodos probabilistas. En el capítulo 6, se propone un método de este tipo basado en la obtención de múltiples soluciones, desde puntos de partida aleatorios y calificando los resultados mediante la Estadística de Orden. El propósito es determinar la probabilidad de inicio de colapso para cada solución.El método se aplica (de acuerdo a la reducción de expectativas propuesta por la Optimización Ordinal) para obtener una solución que se encuentre en un porcentaje determinado de las peores. Finalmente, en el capítulo 7, se proponen métodos híbridos, incorporando metaheurísticas, para los casos en que la búsqueda del mínimo global esté justificada. Abstract Safety assessment of the historic masonry structures is an open problem. The material is heterogeneous and anisotropic, the previous state of stress is hard to know and the boundary conditions are uncertain. In the early 50's it was proven that limit analysis was applicable to this kind of structures, being considered a suitable tool since then. In cases where no slip occurs, the application of the standard limit analysis theorems constitutes an excellent tool due to its simplicity and robustness. It is enough find any equilibrium solution which satisfy the limit constraints of the material. As we are certain that this load will be equal to or less than the actual load of the onset of collapse, it is not necessary to know the actual stresses state. Furthermore this load for the onset of collapse is unique (uniqueness theorem), and it can be obtained as the optimal from any of two mathematical convex duals programs However, if the mechanisms of the onset of collapse involve sliding, any solution must satisfy both static and kinematic constraints, and also a special kind of disjunctive constraints linking the previous ones, which can be formulated as complementarity constraints. In the latter case, it is not guaranted the existence of a single solution, so it is necessary to look for other ways to treat the uncertainty associated with its multiplicity. In recent years, research has been focused on finding an absolute minimum below which collapse is impossible. This method is easy to set from a mathematical point of view, but computationally intractable. This is due to the complementarity constraints 0 y z 0 , which are neither convex nor smooth. The computational complexity of the resulting decision problem is "Not-deterministic Polynomialcomplete" (NP-complete), and the corresponding global optimization problem is NP-hard. However, obtaining a solution (success is not guaranteed) is an affordable problem. This thesis proposes solve that problem through Successive Linear Programming: taking advantage of the special characteristics of complementarity constraints, which written in bilinear form are y z = 0; y 0; z 0 ; and taking advantage of the fact that the complementarity error (bilinear form) is an exact penalty function. But when it comes to finding the worst solution, the (equivalent) global optimization problem is intractable (NP-hard). Furthermore, until a minimum or maximum principle is not demonstrated, it is questionable that the effort expended in approximating this minimum is justified. XIV In chapter 5, it is proposed find the frequency distribution of the load factor, for all possible solutions of the onset of collapse, on a simple example. For this purpose, a Monte Carlo sampling of solutions is performed using a contrast method "exact computation of polytopes". The ultimate goal is to determine to which extent the search of the global minimum is justified, and to propose an alternative approach to safety assessment based on probabilities. The frequency distributions for the case study show that both the maximum and the minimum load factors are very infrequent, especially when the contact gets more perfect and more continuous. The results indicates the interest of developing new probabilistic methods. In Chapter 6, is proposed a method based on multiple solutions obtained from random starting points, and qualifying the results through Order Statistics. The purpose is to determine the probability for each solution of the onset of collapse. The method is applied (according to expectations reduction given by the Ordinal Optimization) to obtain a solution that is in a certain percentage of the worst. Finally, in Chapter 7, hybrid methods incorporating metaheuristics are proposed for cases in which the search for the global minimum is justified.

Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes

Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein-ligand interactions. We present here a computational study of protein-ligand complexes formed between five nsLTPs and seven lipids bound in two different ways in every receptor protein. After optimizing geometries inmolecular dynamics calculations, we computed Poisson- Boltzmann electrostatic potentials, solvation energies, properties of the protein-ligand interfaces, and estimates of binding free energies of the resulting complexes. Our results provide the first quantitative information on the ligand abilities of nsLTPs, shed new light into protein-lipid interactions, and reveal new features which supplement commonly held assumptions on their lack of binding specificity.

Preprocessing and analyzing genetic data with complex networks: An application to Obstructive Nephropathy

Many diseases have a genetic origin, and a great effort is being made to detect the genes that are responsible for their insurgence. One of the most promising techniques is the analysis of genetic information through the use of complex networks theory. Yet, a practical problem of this approach is its computational cost, which scales as the square of the number of features included in the initial dataset. In this paper, we propose the use of an iterative feature selection strategy to identify reduced subsets of relevant features, and show an application to the analysis of congenital Obstructive Nephropathy. Results demonstrate that, besides achieving a drastic reduction of the computational cost, the topologies of the obtained networks still hold all the relevant information, and are thus able to fully characterize the severity of the disease.

An approach to automatic learning assessment based on the computational theory of perceptions

E-learning systems output a huge quantity of data on a learning process. However, it takes a lot of specialist human resources to manually process these data and generate an assessment report. Additionally, for formative assessment, the report should state the attainment level of the learning goals defined by the instructor. This paper describes the use of the granular linguistic model of a phenomenon (GLMP) to model the assessment of the learning process and implement the automated generation of an assessment report. GLMP is based on fuzzy logic and the computational theory of perceptions. This technique is useful for implementing complex assessment criteria using inference systems based on linguistic rules. Apart from the grade, the model also generates a detailed natural language progress report on the achieved proficiency level, based exclusively on the objective data gathered from correct and incorrect responses. This is illustrated by applying the model to the assessment of Dijkstra’s algorithm learning using a visual simulation-based graph algorithm learning environment, called GRAPHs

Computational Fluid Dynamics Expert System using Artificial Neural Networks

The design of a modern aircraft is based on three pillars: theoretical results, experimental test and computational simulations. As a results of this, Computational Fluid Dynamic (CFD) solvers are widely used in the aeronautical field. These solvers require the correct selection of many parameters in order to obtain successful results. Besides, the computational time spent in the simulation depends on the proper choice of these parameters. In this paper we create an expert system capable of making an accurate prediction of the number of iterations and time required for the convergence of a computational fluid dynamic (CFD) solver. Artificial neural network (ANN) has been used to design the expert system. It is shown that the developed expert system is capable of making an accurate prediction the number of iterations and time required for the convergence of a CFD solver.

Accessing advanced computational resources in Africa through Cloud Computing

Low resources in many African locations do not allow many African scientists and physicians to access the latest advances in technology. This deficiency hinders the daily life of African professionals that often cannot afford, for instance, the cost of internet fees or software licenses. The AFRICA BUILD project, funded by the European Commission and formed by four European and four African institutions, intends to provide advanced computational tools to African institutions in order to solve current technological limitations. In the context of AFRICA BUILD we have carried out, a series of experiments to test the feasibility of using Cloud Computing technologies in two different locations in Africa: Egypt and Burundi. The project aims to create a virtual platform to provide access to a wide range of biomedical informatics and learning resources to professionals and researchers in Africa.

Computational Methods for Identification of Vibrating Structures

System identification deals with the problem of building mathematical models of dynamical systems based on observed data from the system" [1]. In the context of civil engineering, the system refers to a large scale structure such as a building, bridge, or an offshore structure, and identification mostly involves the determination of modal parameters (the natural frequencies, damping ratios, and mode shapes). This paper presents some modal identification results obtained using a state-of-the-art time domain system identification method (data-driven stochastic subspace algorithms [2]) applied to the output-only data measured in a steel arch bridge. First, a three dimensional finite element model was developed for the numerical analysis of the structure using ANSYS. Modal analysis was carried out and modal parameters were extracted in the frequency range of interest, 0-10 Hz. The results obtained from the finite element modal analysis were used to determine the location of the sensors. After that, ambient vibration tests were conducted during April 23-24, 2009. The response of the structure was measured using eight accelerometers. Two stations of three sensors were formed (triaxial stations). These sensors were held stationary for reference during the test. The two remaining sensors were placed at the different measurement points along the bridge deck, in which only vertical and transversal measurements were conducted (biaxial stations). Point estimate and interval estimate have been carried out in the state space model using these ambient vibration measurements. In the case of parametric models (like state space), the dynamic behaviour of a system is described using mathematical models. Then, mathematical relationships can be established between modal parameters and estimated point parameters (thus, it is common to use experimental modal analysis as a synonym for system identification). Stable modal parameters are found using a stabilization diagram. Furthermore, this paper proposes a method for assessing the precision of estimates of the parameters of state-space models (confidence interval). This approach employs the nonparametric bootstrap procedure [3] and is applied to subspace parameter estimation algorithm. Using bootstrap results, a plot similar to a stabilization diagram is developed. These graphics differentiate system modes from spurious noise modes for a given order system. Additionally, using the modal assurance criterion, the experimental modes obtained have been compared with those evaluated from a finite element analysis. A quite good agreement between numerical and experimental results is observed.

Comparison of turbulence models for the computational fluid dynamics simulation of wind turbine wakes in the atmospheric boundary layer

An elliptic computational fluid dynamics wake model based on the actuator disk concept is used to simulate a wind turbine, approximated by a disk upon which a distribution of forces, defined as axial momentum sources, is applied on an incoming non-uniform shear flow. The rotor is supposed to be uniformly loaded with the exerted forces estimated as a function of the incident wind speed, thrust coefficient and rotor diameter. The model is assessed in terms of wind speed deficit and added turbulence intensity for different turbulence models and is validated from experimental measurements of the Sexbierum wind turbine experiment.

A comparative study of Monte Carlo-coupled depletion codes applied to a Sodium Fast Reactor design loaded with minor actinides

inor actinides (MAs) transmutation is a main design objective of advanced nuclear systems such as generation IV Sodium Fast Reactors (SFRs). In advanced fuel cycles, MA contents in final high level waste packages are main contributors to short term heat production as well as to long-term radiotoxicity. Therefore, MA transmutation would have an impact on repository designs and would reduce the environment burden of nuclear energy. In order to predict such consequences Monte Carlo (MC) transport codes are used in reactor design tasks and they are important complements and references for routinely used deterministic computational tools. In this paper two promising Monte Carlo transport-coupled depletion codes, EVOLCODE and SERPENT, are used to examine the impact of MA burning strategies in a SFR core, 3600 MWth. The core concept proposal for MA loading in two configurations is the result of an optimization effort upon a preliminary reference design to reduce the reactivity insertion as a consequence of sodium voiding, one of the main concerns of this technology. The objective of this paper is double. Firstly, efficiencies of the two core configurations for MA transmutation are addressed and evaluated in terms of actinides mass changes and reactivity coefficients. Results are compared with those without MA loading. Secondly, a comparison of the two codes is provided. The discrepancies in the results are quantified and discussed.

Core physics and safety analysis of Generation-IV Sodium Fast Reactors using existing and newly developed computational tools

El futuro de la energía nuclear de fisión dependerá, entre otros factores, de la capacidad que las nuevas tecnologías demuestren para solventar los principales retos a largo plazo que se plantean. Los principales retos se pueden resumir en los siguientes aspectos: la capacidad de proporcionar una solución final, segura y fiable a los residuos radiactivos; así como dar solución a la limitación de recursos naturales necesarios para alimentar los reactores nucleares; y por último, una mejora robusta en la seguridad de las centrales que en definitiva evite cualquier daño potencial tanto en la población como en el medio ambiente como consecuencia de cualquier escenario imaginable o más allá de lo imaginable. Siguiendo estas motivaciones, la Generación IV de reactores nucleares surge con el compromiso de proporcionar electricidad de forma sostenible, segura, económica y evitando la proliferación de material fisible. Entre los sistemas conceptuales que se consideran para la Gen IV, los reactores rápidos destacan por su capacidad potencial de transmutar actínidos a la vez que permiten una utilización óptima de los recursos naturales. Entre los refrigerantes que se plantean, el sodio parece una de las soluciones más prometedoras. Como consecuencia, esta tesis surgió dentro del marco del proyecto europeo CP-ESFR con el principal objetivo de evaluar la física de núcleo y seguridad de los reactores rápidos refrigerados por sodio, al tiempo que se desarrollaron herramientas apropiadas para dichos análisis. Efectivamente, en una primera parte de la tesis, se abarca el estudio de la física del núcleo de un reactor rápido representativo, incluyendo el análisis detallado de la capacidad de transmutar actínidos minoritarios. Como resultado de dichos análisis, se publicó un artículo en la revista Annals of Nuclear Energy [96]. Por otra parte, a través de un análisis de un hipotético escenario nuclear español, se evalúo la disponibilidad de recursos naturales necesarios en el caso particular de España para alimentar una flota específica de reactores rápidos, siguiendo varios escenarios de demanda, y teniendo en cuenta la capacidad de reproducción de plutonio que tienen estos sistemas. Como resultado de este trabajo también surgió una publicación en otra revista científica de prestigio internacional como es Energy Conversion and Management [97]. Con objeto de realizar esos y otros análisis, se desarrollaron diversos modelos del núcleo del ESFR siguiendo varias configuraciones, y para diferentes códigos. Por otro lado, con objeto de poder realizar análisis de seguridad de reactores rápidos, son necesarias herramientas multidimensionales de alta fidelidad específicas para reactores rápidos. Dichas herramientas deben integrar fenómenos relacionados con la neutrónica y con la termo-hidráulica, entre otros, mediante una aproximación multi-física. Siguiendo este objetivo, se evalúo el código de difusión neutrónica ANDES para su aplicación a reactores rápidos. ANDES es un código de resolución nodal que se encuentra implementado dentro del sistema COBAYA3 y está basado en el método ACMFD. Por lo tanto, el método ACMFD fue sometido a una revisión en profundidad para evaluar su aptitud para la aplicación a reactores rápidos. Durante ese proceso, se identificaron determinadas limitaciones que se discutirán a lo largo de este trabajo, junto con los desarrollos que se han elaborado e implementado para la resolución de dichas dificultades. Por otra parte, se desarrolló satisfactoriamente el acomplamiento del código neutrónico ANDES con un código termo-hidráulico de subcanales llamado SUBCHANFLOW, desarrollado recientemente en el KIT. Como conclusión de esta parte, todos los desarrollos implementados son evaluados y verificados. En paralelo con esos desarrollos, se calcularon para el núcleo del ESFR las secciones eficaces en multigrupos homogeneizadas a nivel nodal, así como otros parámetros neutrónicos, mediante los códigos ERANOS, primero, y SERPENT, después. Dichos parámetros se utilizaron más adelante para realizar cálculos estacionarios con ANDES. Además, como consecuencia de la contribución de la UPM al paquete de seguridad del proyecto CP-ESFR, se calcularon mediante el código SERPENT los parámetros de cinética puntual que se necesitan introducir en los típicos códigos termo-hidráulicos de planta, para estudios de seguridad. En concreto, dichos parámetros sirvieron para el análisis del impacto que tienen los actínidos minoritarios en el comportamiento de transitorios. Concluyendo, la tesis presenta una aproximación sistemática y multidisciplinar aplicada al análisis de seguridad y comportamiento neutrónico de los reactores rápidos de sodio de la Gen-IV, usando herramientas de cálculo existentes y recién desarrolladas ad' hoc para tal aplicación. Se ha empleado una cantidad importante de tiempo en identificar limitaciones de los métodos nodales analíticos en su aplicación en multigrupos a reactores rápidos, y se proponen interesantes soluciones para abordarlas. ABSTRACT The future of nuclear reactors will depend, among other aspects, on the capability to solve the long-term challenges linked to this technology. These are the capability to provide a definite, safe and reliable solution to the nuclear wastes; the limitation of natural resources, needed to fuel the reactors; and last but not least, the improved safety, which would avoid any potential damage on the public and or environment as a consequence of any imaginable and beyond imaginable circumstance. Following these motivations, the IV Generation of nuclear reactors arises, with the aim to provide sustainable, safe, economic and proliferationresistant electricity. Among the systems considered for the Gen IV, fast reactors have a representative role thanks to their potential capacity to transmute actinides together with the optimal usage of natural resources, being the sodium fast reactors the most promising concept. As a consequence, this thesis was born in the framework of the CP-ESFR project with the generic aim of evaluating the core physics and safety of sodium fast reactors, as well as the development of the approppriated tools to perform such analyses. Indeed, in a first part of this thesis work, the main core physics of the representative sodium fast reactor are assessed, including a detailed analysis of the capability to transmute minor actinides. A part of the results obtained have been published in Annals of Nuclear Energy [96]. Moreover, by means of the analysis of a hypothetical Spanish nuclear scenario, the availability of natural resources required to deploy an specific fleet of fast reactor is assessed, taking into account the breeding properties of such systems. This work also led to a publication in Energy Conversion and Management [97]. In order to perform those and other analyses, several models of the ESFR core were created for different codes. On the other hand, in order to perform safety studies of sodium fast reactors, high fidelity multidimensional analysis tools for sodium fast reactors are required. Such tools should integrate neutronic and thermal-hydraulic phenomena in a multi-physics approach. Following this motivation, the neutron diffusion code ANDES is assessed for sodium fast reactor applications. ANDES is the nodal solver implemented inside the multigroup pin-by-pin diffusion COBAYA3 code, and is based on the analytical method ACMFD. Thus, the ACMFD was verified for SFR applications and while doing so, some limitations were encountered, which are discussed through this work. In order to solve those, some new developments are proposed and implemented in ANDES. Moreover, the code was satisfactorily coupled with the thermal-hydraulic code SUBCHANFLOW, recently developed at KIT. Finally, the different implementations are verified. In addition to those developments, the node homogenized multigroup cross sections and other neutron parameters were obtained for the ESFR core using ERANOS and SERPENT codes, and employed afterwards by ANDES to perform steady state calculations. Moreover, as a result of the UPM contribution to the safety package of the CP-ESFR project, the point kinetic parameters required by the typical plant thermal-hydraulic codes were computed for the ESFR core using SERPENT, which final aim was the assessment of the impact of minor actinides in transient behaviour. All in all, the thesis provides a systematic and multi-purpose approach applied to the assessment of safety and performance parameters of Generation-IV SFR, using existing and newly developed analytical tools. An important amount of time was employed in identifying the limitations that the analytical nodal diffusion methods present when applied to fast reactors following a multigroup approach, and interesting solutions are proposed in order to overcome them.

Computational model for local damage assesment of structures

In the last years many studies have been developed to analyze the seismic behavior throug the damage concept. In fact, the evaluation of the structural damage is important in order to quantify the safety of new and existing structures and, also, to establish a framework for seismic retrofitting decision making of structures. Most proposed models are based on a post-earthquake evaluation in such a way they uncouple the computation of the structural response from that of damage. However, there are other models which include explicity the existing coupling between the degradation and the structural mechanical beaviour. Those models are closer to the physical reality and its formulation is based on the principles of Continuum Damage Mechanics. In the present work, a coupled model is formulated using a simplified application of the Continuum Damage Mechanics to the analysis of frames and allows its representation in standard finite element programs. This work is part of the activities developed by the Structural Mechanics Department (UPM) within ICONS (European Research Project on Innovative Seismic Design Concepts for New and Existing Structures).