Computational tools for the study of allergens

Allergy is a major cause of morbidity worldwide. The number of characterized allergens and related information is increasing rapidly creating demands for advanced information storage, retrieval and analysis. Bioinformatics provides useful tools for analysing allergens and these are complementary to traditional laboratory techniques for the study of allergens. Specific applications include structural analysis of allergens, identification of B- and T-cell epitopes, assessment of allergenicity and cross-reactivity, and genome analysis. In this paper, the most important bioinformatic tools and methods with relevance to the study of allergy have been reviewed.

Development of computational tools for the integrated analysis of DNA microarray data with applications in cancer research

The MAP-i Doctoral Program of the Universities of Minho, Aveiro and Porto

Algorithms and computational tools for metabolic flux analysis

PhD thesis in Biomedical Engineering

Computational tools for comparing asymmetric GARCH models via Bayes factors

In this paper we use Markov chain Monte Carlo (MCMC) methods in order to estimate and compare GARCH models from a Bayesian perspective. We allow for possibly heavy tailed and asymmetric distributions in the error term. We use a general method proposed in the literature to introduce skewness into a continuous unimodal and symmetric distribution. For each model we compute an approximation to the marginal likelihood, based on the MCMC output. From these approximations we compute Bayes factors and posterior model probabilities. (C) 2012 IMACS. Published by Elsevier B.V. All rights reserved.

Development of one-dimensional and two-dimensional computational tools that simulate steady internal condensing flows in terrestrial and zero-gravity environments

This dissertation presents an effective quasi one-dimensional (1-D) computational simulation tool and a full two-dimensional (2-D) computational simulation methodology for steady annular/stratified internal condensing flows of pure vapor. These simulation tools are used to investigate internal condensing flows in both gravity as well as shear driven environments. Through accurate numerical simulations of the full two dimensional governing equations, results for laminar/laminar condensing flows inside mm-scale ducts are presented. The methodology has been developed using MATLAB/COMSOL platform and is currently capable of simulating film-wise condensation for steady (and unsteady flows). Moreover, a novel 1-D solution technique, capable of simulating condensing flows inside rectangular and circular ducts with different thermal boundary conditions is also presented. The results obtained from the 2-D scientific tool and 1-D engineering tool, are validated and synthesized with experimental results for gravity dominated flows inside vertical tube and inclined channel; and, also, for shear/pressure driven flows inside horizontal channels. Furthermore, these simulation tools are employed to demonstrate key differences of physics between gravity dominated and shear/pressure driven flows. A transition map that distinguishes shear driven, gravity driven, and “mixed” driven flow zones within the non-dimensional parameter space that govern these duct flows is presented along with the film thickness and heat transfer correlations that are valid in these zones. It has also been shown that internal condensing flows in a micro-meter scale duct experiences shear driven flow, even in different gravitational environments. The full 2-D steady computational tool has been employed to investigate the length of annularity. The result for a shear driven flow in a horizontal channel shows that in absence of any noise or pressure fluctuation at the inlet, the onset of non-annularity is partly due to insufficient shear at the liquid-vapor interface. This result is being further corroborated/investigated by R. R. Naik with the help of the unsteady simulation tool. The condensing flow results and flow physics understanding developed through these simulation tools will be instrumental in reliable design of modern micro-scale and spacebased thermal systems.

Computational tools to investigate genetic cardiac channelopathies

The aim of this perspective article is to share with the community of ion channel scientists our thoughts and expectations regarding the increasing role that computational tools will play in the future of our field. The opinions and comments detailed here are the result of a 3-day long international exploratory workshop that took place in October 2013 and that was supported by the Swiss National Science Foundation.

Computational Tools for Stereo and Light Field Photography

This thesis covers a broad part of the field of computational photography, including video stabilization and image warping techniques, introductions to light field photography and the conversion of monocular images and videos into stereoscopic 3D content. We present a user assisted technique for stereoscopic 3D conversion from 2D images. Our approach exploits the geometric structure of perspective images including vanishing points. We allow a user to indicate lines, planes, and vanishing points in the input image, and directly employ these as guides of an image warp that produces a stereo image pair. Our method is most suitable for scenes with large scale structures such as buildings and is able to skip the step of constructing a depth map. Further, we propose a method to acquire 3D light fields using a hand-held camera, and describe several computational photography applications facilitated by our approach. As the input we take an image sequence from a camera translating along an approximately linear path with limited camera rotations. Users can acquire such data easily in a few seconds by moving a hand-held camera. We convert the input into a regularly sampled 3D light field by resampling and aligning them in the spatio-temporal domain. We also present a novel technique for high-quality disparity estimation from light fields. Finally, we show applications including digital refocusing and synthetic aperture blur, foreground removal, selective colorization, and others.

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.

A contribution to appendage drag extrapolation using computational tools

In this paper, the foundations of the beta method, widely used in todays ship appendage extrapolations, are explored. The present work pretends to validate the Beta Method using experimental and computational tools. The ship used is a rounded bow tugboat with two significant appendages, namely, a midship protective structure for the propulsion system and a stern keel. The experimental and computational data was obtained through Towing Tank trials and a RANSE CFD code, respectively.

Assessing computational tools for the discovery of transcription factor binding sites

The prediction of regulatory elements is a problem where computational methods offer great hope. Over the past few years, numerous tools have become available for this task. The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools.

Affordable prefabricated modular houses using cement and polymer based materials and advanced design tools

By taking advantage of the appropriate use of cement and polymer based materials and advanced computational tools, a pre-fabricated affordable house was built in a modular system. Modular system refers to the complete structure that is built-up by assembling pre-fabricated sandwich panels composed of steel fibre reinforced self-compacting concrete (SFRSCC) outer layers that are connected by innovative glass fibre reinforced polymer (GFRP) connectors, resulting in a panel with adequate structural, acoustic, and thermal insulation properties. The modular house was prepared for a typical family of six members, but its living area can be easily increased by assembling other pre-fabricated elements. The speed of construction and the cost of the constructive elements make these houses competitive when compared to traditional solutions. In this paper the relevant research subjacent to this project (LEGOUSE) is briefly described, as well as the construction process of the built real scale prototype.

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

BACKGROUND: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing. RESULTS: We present the Systems Biology Markup Language (SBML) Qualitative Models Package ("qual"), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the collective effort to define the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyse qualitative models. CONCLUSIONS: SBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks.

A integração do tutorial interativo TryLogic via IMS Learning Tools Interoperability: construindo uma infraestrutura para o ensino de Lógica através de estratégias de demonstração e refutação

Logic courses represent a pedagogical challenge and the recorded number of cases of failures and of discontinuity in them is often high. Amont other difficulties, students face a cognitive overload to understand logical concepts in a relevant way. On that track, computational tools for learning are resources that help both in alleviating the cognitive overload scenarios and in allowing for the practical experimenting with theoretical concepts. The present study proposes an interactive tutorial, namely the TryLogic, aimed at teaching to solve logical conjectures either by proofs or refutations. The tool was developed from the architecture of the tool TryOcaml, through support of the communication of the web interface ProofWeb in accessing the proof assistant Coq. The goals of TryLogic are: (1) presenting a set of lessons for applying heuristic strategies in solving problems set in Propositional Logic; (2) stepwise organizing the exposition of concepts related to Natural Deduction and to Propositional Semantics in sequential steps; (3) providing interactive tasks to the students. The present study also aims at: presenting our implementation of a formal system for refutation; describing the integration of our infrastructure with the Virtual Learning Environment Moodle through the IMS Learning Tools Interoperability specification; presenting the Conjecture Generator that works for the tasks involving proving and refuting; and, finally to evaluate the learning experience of Logic students through the application of the conjecture solving task associated to the use of the TryLogic

Methodology analysis of a computational tool used in electronic circuit design

This paper considers the importance of using a top-down methodology and suitable CAD tools in the development of electronic circuits. The paper presents an evaluation of the methodology used in a computational tool created to support the synthesis of digital to analog converter models by translating between different tools used in a wide variety of applications. This tool is named MS 2SV and works directly with the following two commercial tools: MATLAB/Simulink and SystemVision. Model translation of an electronic circuit is achieved by translating a mixed-signal block diagram developed in Simulink into a lower level of abstraction in VHDL-AMS and the simulation project support structure in SystemVision. The method validation was performed by analyzing the power spectral of the signal obtained by the discrete Fourier transform of a digital to analog converter simulation model. © 2011 IEEE.