BioMet®Tools: from modeling and simulation to product design and development

BioMet®Tools is a set of software applications developed for the biometrical characterization of voice in different fields as voice quality evaluation in laryngology, speech therapy and rehabilitation, education of the singing voice, forensic voice analysis in court, emotional detection in voice, secure access to facilities and services, etc. Initially it was conceived as plain research code to estimate the glottal source from voice and obtain the biomechanical parameters of the vocal folds from the spectral density of the estimate. This code grew to what is now the Glottex®Engine package (G®E). Further demands from users in medical and forensic fields instantiated the development of different Graphic User Interfaces (GUI’s) to encapsulate user interaction with the G®E. This required the personalized design of different GUI’s handling the same G®E. In this way development costs and time could be saved. The development model is described in detail leading to commercial production and distribution. Study cases from its application to the field of laryngology and speech therapy are given and discussed.

Molecular dynamics modeling and simulation of void growth in two dimensions

The mechanisms of growth of a circular void by plastic deformation were studied by means of molecular dynamics in two dimensions (2D). While previous molecular dynamics (MD) simulations in three dimensions (3D) have been limited to small voids (up to ≈10 nm in radius), this strategy allows us to study the behavior of voids of up to 100 nm in radius. MD simulations showed that plastic deformation was triggered by the nucleation of dislocations at the atomic steps of the void surface in the whole range of void sizes studied. The yield stress, defined as stress necessary to nucleate stable dislocations, decreased with temperature, but the void growth rate was not very sensitive to this parameter. Simulations under uniaxial tension, uniaxial deformation and biaxial deformation showed that the void growth rate increased very rapidly with multiaxiality but it did not depend on the initial void radius. These results were compared with previous 3D MD and 2D dislocation dynamics simulations to establish a map of mechanisms and size effects for plastic void growth in crystalline solids.

Agent-based modeling and simulation for the design of the future european Air Traffic Management system: the experience of CASSIOPEIA

The SESAR (Single European Sky ATM Research) program is an ambitious re-search and development initiative to design the future European air traffic man-agement (ATM) system. The study of the behavior of ATM systems using agent-based modeling and simulation tools can help the development of new methods to improve their performance. This paper presents an overview of existing agent-based approaches in air transportation (paying special attention to the challenges that exist for the design of future ATM systems) and, subsequently, describes a new agent-based approach that we proposed in the CASSIOPEIA project, which was developed according to the goals of the SESAR program. In our approach, we use agent models for different ATM stakeholders, and, in contrast to previous work, our solution models new collaborative decision processes for flow traffic management, it uses an intermediate level of abstraction (useful for simulations at larger scales), and was designed to be a practical tool (open and reusable) for the development of different ATM studies. It was successfully applied in three stud-ies related to the design of future ATM systems in Europe.

Modeling and Simulation of Upper Brachial Plexus Injury

This article presents the first musculoskeletal model and simulation of upper plexus brachial injury. From this model is possible to analyse forces and movement ranges in order to develop a robotic exoskeleton to improve rehabilitation. The software that currently exists for musculoskeletal modeling is varied and most have advanced features for proper analysis and study of motion simulations. Whilst more powerful computer packages are usually expensive, there are other free and open source packages available which offer different tools to perform animations and simulations and which obtain forces and moments of inertia. Among them, Musculoskeletal Modeling Software was selected to construct a model of the upper limb, which has 7 degrees of freedom and 10 muscles. These muscles are important for two of the movements simulated in this article that are part of the post-surgery rehabilitation protocol. We performed different movement animations which are made using the inertial measurement unit to capture real data from movements made by a human being. We also performed the simulation of forces produced in elbow flexion-extension and arm abduction-adduction of a healthy subject and one with upper brachial plexus injury in a postoperative state to compare the force that is capable of being produced in both cases.

Simulation Tool and Case Study for Planning Wireless Sensor Network

In this paper, a simulation tool for assisting the deployment of wireless sensor network is introduced and simulation results are verified under a specific indoor environment. The simulation tool supports two modes: deterministic mode and stochastic mode. The deterministic mode is environment dependent in which the information of environment should be provided beforehand. Ray tracing method and deterministic propagation model are employed in order to increase the accuracy of the estimated coverage, connectivity and routing; the stochastic mode is useful for large scale random deployment without previous knowledge on geographic information. Dynamic Source Routing protocol (DSR) and Ad hoc On-Demand Distance Vector Routing protocol (AODV) are implemented in order to calculate the topology of WSN. Hence this tool gives direct view on the performance of WSN and assists users in finding the potential problems of wireless sensor network before real deployment. At the end, a case study is realized in Centro de Electronica Industrial (CEI), the simulation results on coverage, connectivity and routing are verified by the measurement.

Aplicación de la metodología ISA al análisis de la secuencia de pérdida del sistema de agua de refrigeración de componentes en una central nuclear con reactor de agua a presión

La metodología Integrated Safety Analysis (ISA), desarrollada en el área de Modelación y Simulación (MOSI) del Consejo de Seguridad Nuclear (CSN), es un método de Análisis Integrado de Seguridad que está siendo evaluado y analizado mediante diversas aplicaciones impulsadas por el CSN; el análisis integrado de seguridad, combina las técnicas evolucionadas de los análisis de seguridad al uso: deterministas y probabilistas. Se considera adecuado para sustentar la Regulación Informada por el Riesgo (RIR), actual enfoque dado a la seguridad nuclear y que está siendo desarrollado y aplicado en todo el mundo. En este contexto se enmarcan, los proyectos Safety Margin Action Plan (SMAP) y Safety Margin Assessment Application (SM2A), impulsados por el Comité para la Seguridad de las Instalaciones Nucleares (CSNI) de la Agencia de la Energía Nuclear (NEA) de la Organización para la Cooperación y el Desarrollo Económicos (OCDE) en el desarrollo del enfoque adecuado para el uso de las metodologías integradas en la evaluación del cambio en los márgenes de seguridad debidos a cambios en las condiciones de las centrales nucleares. El comité constituye un foro para el intercambio de información técnica y de colaboración entre las organizaciones miembro, que aportan sus propias ideas en investigación, desarrollo e ingeniería. La propuesta del CSN es la aplicación de la metodología ISA, especialmente adecuada para el análisis según el enfoque desarrollado en el proyecto SMAP que pretende obtener los valores best-estimate con incertidumbre de las variables de seguridad que son comparadas con los límites de seguridad, para obtener la frecuencia con la que éstos límites son superados. La ventaja que ofrece la ISA es que permite el análisis selectivo y discreto de los rangos de los parámetros inciertos que tienen mayor influencia en la superación de los límites de seguridad, o frecuencia de excedencia del límite, permitiendo así evaluar los cambios producidos por variaciones en el diseño u operación de la central que serían imperceptibles o complicados de cuantificar con otro tipo de metodologías. La ISA se engloba dentro de las metodologías de APS dinámico discreto que utilizan la generación de árboles de sucesos dinámicos (DET) y se basa en la Theory of Stimulated Dynamics (TSD), teoría de fiabilidad dinámica simplificada que permite la cuantificación del riesgo de cada una de las secuencias. Con la ISA se modelan y simulan todas las interacciones relevantes en una central: diseño, condiciones de operación, mantenimiento, actuaciones de los operadores, eventos estocásticos, etc. Por ello requiere la integración de códigos de: simulación termohidráulica y procedimientos de operación; delineación de árboles de sucesos; cuantificación de árboles de fallos y sucesos; tratamiento de incertidumbres e integración del riesgo. La tesis contiene la aplicación de la metodología ISA al análisis integrado del suceso iniciador de la pérdida del sistema de refrigeración de componentes (CCWS) que genera secuencias de pérdida de refrigerante del reactor a través de los sellos de las bombas principales del circuito de refrigerante del reactor (SLOCA). Se utiliza para probar el cambio en los márgenes, con respecto al límite de la máxima temperatura de pico de vaina (1477 K), que sería posible en virtud de un potencial aumento de potencia del 10 % en el reactor de agua a presión de la C.N. Zion. El trabajo realizado para la consecución de la tesis, fruto de la colaboración de la Escuela Técnica Superior de Ingenieros de Minas y Energía y la empresa de soluciones tecnológicas Ekergy Software S.L. (NFQ Solutions) con el área MOSI del CSN, ha sido la base para la contribución del CSN en el ejercicio SM2A. Este ejercicio ha sido utilizado como evaluación del desarrollo de algunas de las ideas, sugerencias, y los algoritmos detrás de la metodología ISA. Como resultado se ha obtenido un ligero aumento de la frecuencia de excedencia del daño (DEF) provocado por el aumento de potencia. Este resultado demuestra la viabilidad de la metodología ISA para obtener medidas de las variaciones en los márgenes de seguridad que han sido provocadas por modificaciones en la planta. También se ha mostrado que es especialmente adecuada en escenarios donde los eventos estocásticos o las actuaciones de recuperación o mitigación de los operadores pueden tener un papel relevante en el riesgo. Los resultados obtenidos no tienen validez más allá de la de mostrar la viabilidad de la metodología ISA. La central nuclear en la que se aplica el estudio está clausurada y la información relativa a sus análisis de seguridad es deficiente, por lo que han sido necesarias asunciones sin comprobación o aproximaciones basadas en estudios genéricos o de otras plantas. Se han establecido tres fases en el proceso de análisis: primero, obtención del árbol de sucesos dinámico de referencia; segundo, análisis de incertidumbres y obtención de los dominios de daño; y tercero, cuantificación del riesgo. Se han mostrado diversas aplicaciones de la metodología y ventajas que presenta frente al APS clásico. También se ha contribuido al desarrollo del prototipo de herramienta para la aplicación de la metodología ISA (SCAIS). ABSTRACT The Integrated Safety Analysis methodology (ISA), developed by the Consejo de Seguridad Nuclear (CSN), is being assessed in various applications encouraged by CSN. An Integrated Safety Analysis merges the evolved techniques of the usually applied safety analysis methodologies; deterministic and probabilistic. It is considered as a suitable tool for assessing risk in a Risk Informed Regulation framework, the approach under development that is being adopted on Nuclear Safety around the world. In this policy framework, the projects Safety Margin Action Plan (SMAP) and Safety Margin Assessment Application (SM2A), set up by the Committee on the Safety of Nuclear Installations (CSNI) of the Nuclear Energy Agency within the Organization for Economic Co-operation and Development (OECD), were aimed to obtain a methodology and its application for the integration of risk and safety margins in the assessment of the changes to the overall safety as a result of changes in the nuclear plant condition. The committee provides a forum for the exchange of technical information and cooperation among member organizations which contribute their respective approaches in research, development and engineering. The ISA methodology, proposed by CSN, specially fits with the SMAP approach that aims at obtaining Best Estimate Plus Uncertainty values of the safety variables to be compared with the safety limits. This makes it possible to obtain the exceedance frequencies of the safety limit. The ISA has the advantage over other methods of allowing the specific and discrete evaluation of the most influential uncertain parameters in the limit exceedance frequency. In this way the changes due to design or operation variation, imperceptibles or complicated to by quantified by other methods, are correctly evaluated. The ISA methodology is one of the discrete methodologies of the Dynamic PSA framework that uses the generation of dynamic event trees (DET). It is based on the Theory of Stimulated Dynamics (TSD), a simplified version of the theory of Probabilistic Dynamics that allows the risk quantification. The ISA models and simulates all the important interactions in a Nuclear Power Plant; design, operating conditions, maintenance, human actuations, stochastic events, etc. In order to that, it requires the integration of codes to obtain: Thermohydraulic and human actuations; Even trees delineation; Fault Trees and Event Trees quantification; Uncertainty analysis and risk assessment. This written dissertation narrates the application of the ISA methodology to the initiating event of the Loss of the Component Cooling System (CCWS) generating sequences of loss of reactor coolant through the seals of the reactor coolant pump (SLOCA). It is used to test the change in margins with respect to the maximum clad temperature limit (1477 K) that would be possible under a potential 10 % power up-rate effected in the pressurized water reactor of Zion NPP. The work done to achieve the thesis, fruit of the collaborative agreement of the School of Mining and Energy Engineering and the company of technological solutions Ekergy Software S.L. (NFQ Solutions) with de specialized modeling and simulation branch of the CSN, has been the basis for the contribution of the CSN in the exercise SM2A. This exercise has been used as an assessment of the development of some of the ideas, suggestions, and algorithms behind the ISA methodology. It has been obtained a slight increase in the Damage Exceedance Frequency (DEF) caused by the power up-rate. This result shows that ISA methodology allows quantifying the safety margin change when design modifications are performed in a NPP and is specially suitable for scenarios where stochastic events or human responses have an important role to prevent or mitigate the accidental consequences and the total risk. The results do not have any validity out of showing the viability of the methodology ISA. Zion NPP was retired and information of its safety analysis is scarce, so assumptions without verification or approximations based on generic studies have been required. Three phases are established in the analysis process: first, obtaining the reference dynamic event tree; second, uncertainty analysis and obtaining the damage domains; third, risk quantification. There have been shown various applications of the methodology and advantages over the classical PSA. It has also contributed to the development of the prototype tool for the implementation of the ISA methodology (SCAIS).

Agent-based modelling for cement hydration

The Agent-Based Modelling and simulation (ABM) is a rather new approach for studying complex systems withinteracting autonomous agents that has lately undergone great growth in various fields such as biology, physics, social science, economics and business. Efforts to model and simulate the highly complex cement hydration process have been made over the past 40 years, with the aim of predicting the performance of concrete and designing innovative and enhanced cementitious materials. The ABM presented here - based on previous work - focuses on the early stages of cement hydration by modelling the physical-chemical processes at the particle level. The model considers the cement hydration process as a time and 3D space system, involving multiple diffusing and reacting species of spherical particles. Chemical reactions are simulated by adaptively selecting discrete stochastic simulation for the appropriate reaction, whenever that is necessary. Interactions between particles are also considered. The model has been inspired by reported cellular automata?s approach which provides detailed predictions of cement microstructure at the expense of significant computational difficulty. The ABM approach herein seeks to bring about an optimal balance between accuracy and computational efficiency.

An integral model for natural regeneration of Pinus pinea L. in the Northern Plateau (Spain) = Modelo integral de regeneración natural para Pinus pinea L. en la Meseta Norte (España)

Natural regeneration is an ecological key-process that makes plant persistence possible and, consequently, it constitutes an essential element of sustainable forest management. In this respect, natural regeneration in even-aged stands of Pinus pinea L. located in the Spanish Northern Plateau has not always been successfully achieved despite over a century of pine nut-based management. As a result, natural regeneration has recently become a major concern for forest managers when we are living a moment of rationalization of investment in silviculture. The present dissertation is addressed to provide answers to forest managers on this topic through the development of an integral regeneration multistage model for P. pinea stands in the region. From this model, recommendations for natural regeneration-based silviculture can be derived under present and future climate scenarios. Also, the model structure makes it possible to detect the likely bottlenecks affecting the process. The integral model consists of five submodels corresponding to each of the subprocesses linking the stages involved in natural regeneration (seed production, seed dispersal, seed germination, seed predation and seedling survival). The outputs of the submodels represent the transitional probabilities between these stages as a function of climatic and stand variables, which in turn are representative of the ecological factors driving regeneration. At subprocess level, the findings of this dissertation should be interpreted as follows. The scheduling of the shelterwood system currently conducted over low density stands leads to situations of dispersal limitation since the initial stages of the regeneration period. Concerning predation, predator activity appears to be only limited by the occurrence of severe summer droughts and masting events, the summer resulting in a favourable period for seed survival. Out of this time interval, predators were found to almost totally deplete seed crops. Given that P. pinea dissemination occurs in summer (i.e. the safe period against predation), the likelihood of a seed to not be destroyed is conditional to germination occurrence prior to the intensification of predator activity. However, the optimal conditions for germination seldom take place, restraining emergence to few days during the fall. Thus, the window to reach the seedling stage is narrow. In addition, the seedling survival submodel predicts extremely high seedling mortality rates and therefore only some individuals from large cohorts will be able to persist. These facts, along with the strong climate-mediated masting habit exhibited by P. pinea, reveal that viii the overall probability of establishment is low. Given this background, current management –low final stand densities resulting from intense thinning and strict felling schedules– conditions the occurrence of enough favourable events to achieve natural regeneration during the current rotation time. Stochastic simulation and optimisation computed through the integral model confirm this circumstance, suggesting that more flexible and progressive regeneration fellings should be conducted. From an ecological standpoint, these results inform a reproductive strategy leading to uneven-aged stand structures, in full accordance with the medium shade-tolerant behaviour of the species. As a final remark, stochastic simulations performed under a climate-change scenario show that regeneration in the species will not be strongly hampered in the future. This resilient behaviour highlights the fundamental ecological role played by P. pinea in demanding areas where other tree species fail to persist.

An optimized QoS scheme for IMS-NEMO in heterogeneous networks

The network mobility (NEMO) is proposed to support the mobility management when users move as a whole. In IP Multimedia Subsystem (IMS), the individual Quality of Service (QoS) control for NEMO results in excessive signaling cost. On the other hand, current QoS schemes have two drawbacks: unawareness of the heterogeneous wireless environment and inefficient utilization of the reserved bandwidth. To solve these problems, we present a novel heterogeneous bandwidth sharing (HBS) scheme for QoS provision under IMS-based NEMO (IMS-NEMO). The HBS scheme selects the most suitable access network for each session and enables the new coming non-real-time sessions to share bandwidth with the Variable Bit Rate (VBR) coded media flows. The modeling and simulation results demonstrate that the HBS can satisfy users' QoS requirement and obtain a more efficient use of the scarce wireless bandwidth.

Network-based biomarkers in Alzheimer's disease: review and future directions

By 2050 it is estimated that the number of worldwide Alzheimer?s disease (AD) patients will quadruple from the current number of 36 million people. To date, no single test, prior to postmortem examination, can confirm that a person suffers from AD. Therefore, there is a strong need for accurate and sensitive tools for the early diagnoses of AD. The complex etiology and multiple pathogenesis of AD call for a system-level understanding of the currently available biomarkers and the study of new biomarkers via network-based modeling of heterogeneous data types. In this review, we summarize recent research on the study of AD as a connectivity syndrome. We argue that a network-based approach in biomarker discovery will provide key insights to fully understand the network degeneration hypothesis (disease starts in specific network areas and progressively spreads to connected areas of the initial loci-networks) with a potential impact for early diagnosis and disease-modifying treatments. We introduce a new framework for the quantitative study of biomarkers that can help shorten the transition between academic research and clinical diagnosis in AD.

Analysis of Chromatic Aberration Effects in Triple-Junction Solar Cells Using Advanced Distributed Models

The consideration of real operating conditions for the design and optimization of a multijunction solar cell receiver-concentrator assembly is indispensable. Such a requirement involves the need for suitable modeling and simulation tools in order to complement the experimental work and circumvent its well-known burdens and restrictions. Three-dimensional distributed models have been demonstrated in the past to be a powerful choice for the analysis of distributed phenomena in single- and dual-junction solar cells, as well as for the design of strategies to minimize the solar cell losses when operating under high concentrations. In this paper, we present the application of these models for the analysis of triple-junction solar cells under real operating conditions. The impact of different chromatic aberration profiles on the short-circuit current of triple-junction solar cells is analyzed in detail using the developed distributed model. Current spreading conditions the impact of a given chromatic aberration profile on the solar cell I-V curve. The focus is put on determining the role of current spreading in the connection between photocurrent profile, subcell voltage and current, and semiconductor layers sheet resistance.

Nanoinformatics: developing new computing applications for nanomedicine

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others.

Nanoinformatics: a new area of research in nanomedicine

Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities. Some of these challenges are strongly related to informatics issues, dealing, for instance, with the management and integration of heterogeneous information, defining nomenclatures, taxonomies and classifications for various types of nanomaterials, and research on new modeling and simulation techniques for nanoparticles. Nanoinformatics has recently emerged in the USA and Europe to address these issues. In this paper, we present a review of nanoinformatics, describing its origins, the problems it addresses, areas of interest, and examples of current research initiatives and informatics resources. We suggest that nanoinformatics could accelerate research and development in nanomedicine, as has occurred in the past in other fields. For instance, biomedical informatics served as a fundamental catalyst for the Human Genome Project, and other genomic and ?omics projects, as well as the translational efforts that link resulting molecular-level research to clinical problems and findings.

An energy efficient adaptive HELLO algorithm for mobile ad hoc networks

HELLO protocol or neighborhood discovery is essential in wireless ad hoc networks. It makes the rules for nodes to claim their existence/aliveness. In the presence of node mobility, no fix optimal HELLO frequency and optimal transmission range exist to maintain accurate neighborhood tables while reducing the energy consumption and bandwidth occupation. Thus a Turnover based Frequency and transmission Power Adaptation algorithm (TFPA) is presented in this paper. The method enables nodes in mobile networks to dynamically adjust both their HELLO frequency and transmission range depending on the relative speed. In TFPA, each node monitors its neighborhood table to count new neighbors and calculate the turnover ratio. The relationship between relative speed and turnover ratio is formulated and optimal transmission range is derived according to battery consumption model to minimize the overall transmission energy. By taking advantage of the theoretical analysis, the HELLO frequency is adapted dynamically in conjunction with the transmission range to maintain accurate neighborhood table and to allow important energy savings. The algorithm is simulated and compared to other state-of-the-art algorithms. The experimental results demonstrate that the TFPA algorithm obtains high neighborhood accuracy with low HELLO frequency (at least 11% average reduction) and with the lowest energy consumption. Besides, the TFPA algorithm does not require any additional GPS-like device to estimate the relative speed for each node, hence the hardware cost is reduced.

Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research

Nanotechnology represents an area of particular promise and significant opportunity across multiple scientific disciplines. Ongoing nanotechnology research ranges from the characterization of nanoparticles and nanomaterials to the analysis and processing of experimental data seeking correlations between nanoparticles and their functionalities and side effects. Due to their special properties, nanoparticles are suitable for cellular-level diagnostics and therapy, offering numerous applications in medicine, e.g. development of biomedical devices, tissue repair, drug delivery systems and biosensors. In nanomedicine, recent studies are producing large amounts of structural and property data, highlighting the role for computational approaches in information management. While in vitro and in vivo assays are expensive, the cost of computing is falling. Furthermore, improvements in the accuracy of computational methods (e.g. data mining, knowledge discovery, modeling and simulation) have enabled effective tools to automate the extraction, management and storage of these vast data volumes. Since this information is widely distributed, one major issue is how to locate and access data where it resides (which also poses data-sharing limitations). The novel discipline of nanoinformatics addresses the information challenges related to nanotechnology research. In this paper, we summarize the needs and challenges in the field and present an overview of extant initiatives and efforts.