ARGoS: a modular, multi-engine simulator for heterogeneous swarm robotics

We present ARGoS, a novel open source multi-robot simulator. The main design focus of ARGoS is the real-time simulation of large heterogeneous swarms of robots. Existing robot simulators obtain scalability by imposing limitations on their extensibility and on the accuracy of the robot models. By contrast, in ARGoS we pursue a deeply modular approach that allows the user both to easily add custom features and to allocate computational resources where needed by the experiment. A unique feature of ARGoS is the possibility to use multiple physics engines of different types and to assign them to different parts of the environment. Robots can migrate from one engine to another transparently. This feature enables entirely novel classes of optimizations to improve scalability and paves the way for a new approach to parallelism in robotics simulation. Results show that ARGoS can simulate about 10,000 simple wheeled robots 40% faster than real-time.

Education and Training of Future Nuclear Engineers Through the use of an Interactive Plant Simulator

The successful experience of the Jose Cabrera Nuclear Power Plant Interactive Graphical Simulator implementation in the Nuclear Engineering Department in the Universidad Polite´cnica de Madrid, for the Education and Training of nuclear engineers is shown in this paper. The paper starts with the objectives and the description of the Simulator Aula, and the methodology of work following the recommendations of the IAEA for the use of nuclear reactor simulators for education. The practices and material prepared for the students, as well as the operational and accident situations simulated are provided.

Managing Industrial Simulator Visual Databases Using Geographic Information Systems

Geographic Information Systems are developed to handle enormous volumes of data and are equipped with numerous functionalities intended to capture, store, edit, organise, process and analyse or represent the geographically referenced information. On the other hand, industrial simulators for driver training are real-time applications that require a virtual environment, either geospecific, geogeneric or a combination of the two, over which the simulation programs will be run. In the final instance, this environment constitutes a geographic location with its specific characteristics of geometry, appearance, functionality, topography, etc. The set of elements that enables the virtual simulation environment to be created and in which the simulator user can move, is usually called the Visual Database (VDB). The main idea behind the work being developed approaches a topic that is of major interest in the field of industrial training simulators, which is the problem of analysing, structuring and describing the virtual environments to be used in large driving simulators. This paper sets out a methodology that uses the capabilities and benefits of Geographic Information Systems for organising, optimising and managing the visual Database of the simulator and for generally enhancing the quality and performance of the simulator.

Computational Schemes for Optimizing Domains of Attraction in Dynamical Systems

In this paper, several computational schemes are presented for the optimal tuning of the global behavior of nonlinear dynamical sys- tems. Specifically, the maximization of the size of domains of attraction associated with invariants in parametrized dynamical sys- tems is addressed. Cell Mapping (CM) tech- niques are used to estimate the size of the domains, and such size is then maximized via different optimization tools. First, a ge- netic algorithm is tested whose performance shows to be good for determining global maxima at the expense of high computa- tional cost. Secondly, an iterative scheme based on a Stochastic Approximation proce- dure (the Kiefer-Wolfowitz algorithm) is eval- uated showing acceptable performance at low cost. Finally, several schemes combining neu- ral network based estimations and optimiza- tion procedures are addressed with promising results. The performance of the methods is illus- trated with two applications: first on the well-known van der Pol equation with stan- dard parametrization, and second the tuning of a controller for saturated systems.

A visual object counter based on a multimodal data association for embedded systems with limited computational power

A low complex but highly-efficient object counter algorithm is presented that can be embedded in hardware with a low computational power. This is achieved by a novel soft-data association strategy that can handle multimodal distributions.

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 cali 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.

Estimating the computational cost of logic programs

Information about the computational cost of programs is potentially useful for a variety of purposes, including selecting among different algorithms, guiding program transformations, in granularity control and mapping decisions in parallelizing compilers, and query optimization in deductive databases. Cost analysis of logic programs is complicated by nondeterminism: on the one hand, procedures can return múltiple Solutions, making it necessary to estímate the number of solutions in order to give nontrivial upper bound cost estimates; on the other hand, the possibility of failure has to be taken into account while estimating lower bounds. Here we discuss techniques to address these problems to some extent.

The role of computational logic as a hinge paradigm among deduction, problem solving, programming, and parallelism

This paper presents some brief considerations on the role of Computational Logic in the construction of Artificial Intelligence systems and in programming in general. It does not address how the many problems in AI can be solved but, rather more modestly, tries to point out some advantages of Computational Logic as a tool for the AI scientist in his quest. It addresses the interaction between declarative and procedural views of programs (deduction and action), the impact of the intrinsic limitations of logic, the relationship with other apparently competing computational paradigms, and finally discusses implementation-related issues, such as the efficiency of current implementations and their capability for efficiently exploiting existing and future sequential and parallel hardware. The purpose of the discussion is in no way to present Computational Logic as the unique overall vehicle for the development of intelligent systems (in the firm belief that such a panacea is yet to be found) but rather to stress its strengths in providing reasonable solutions to several aspects of the task.

WWW Programming using computational logic systems (and the PiLLoW/Ciao library)

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 Pd_l_oW, a public-domain Internet and WWW programming library for LP/CLP systems which we argüe significantly simplifies the process of writing such applications. Pd_l_oW 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. We then propose an architecture for automatic LP/CLP code downloading for local execution, using generic browsers. Finally, we also provide an overview of related work on the topic. 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.

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.

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.

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.

Aircraft trajectory simulator using a three degrees of freedom aircraft point mass model

Aircraft Operators Companies (AOCs) are always willing to keep the cost of a flight as low as possible. These costs could be modelled using a function of the fuel consumption, time of flight and fixed cost (over flight cost, maintenance, etc.). These are strongly dependant on the atmospheric conditions, the presence of winds and the aircraft performance. For this reason, much research effort is being put in the development of numerical and graphical techniques for defining the optimal trajectory. This paper presents a different approach to accommodate AOCs preferences, adding value to their activities, through the development of a tool, called aircraft trajectory simulator. This tool is able to simulate the actual flight of an aircraft with the constraints imposed. The simulator is based on a point mass model of the aircraft. The aim of this paper is to evaluate 3DoF aircraft model errors with BADA data through real data from Flight Data Recorder FDR. Therefore, to validate the proposed simulation tool a comparative analysis of the state variables vector is made between an actual flight and the same flight using the simulator. Finally, an example of a cruise phase is presented, where a conventional levelled flight is compared with a continuous climb flight. The comparison results show the potential benefits of following user-preferred routes for commercial flights.

Simplified computational method for non-linear seismic analysis of bridges

After the experience gained during the past years it seems clear that nonlinear analysis of bridges are very important to compute ductility demands and to localize potential hinges. This is specially true for irregular bridges in which it is not clear weather or not it is possible to use a linear computation followed by a correction using a behaviour factor. To simplify the numerical effort several approximate methods have been proposed. Among them, the so-called Dynamic Plastic Hinge Method in which an evolutionary shape function is used to reduce the structure to a single degree of freedom system seems to mantein a good balance between accuracy and simplicity. This paper presents results obtained in a parametric study conducted under the auspicies of PREC-8 european research program.