José M. Alonso

Universitat Politècnica de València | UPV · Department of Computer Systems and Computation

This paper presents three different alternatives to evaluate the matrix hyperbolic cosine using Bernoulli matrix polynomials, comparing them from the point of view of accuracy and computational complexity. The first two alternatives are derived from two different Bernoulli series expansions of the matrix hyperbolic cosine, while the third one is ba...

Differential matrix models provide an elementary blueprint for the adequate and efficient treatment of many important applications in science and engineering. In the present work, we suggest a procedure, extending our previous research results, to represent the solutions of nonlinear matrix differential problems of fourth order given in the form Y(...

This paper presents a new series expansion based on Bernoulli matrix polynomials to approximate the matrix cosine function. An approximation based on this series is not a straightforward exercise since there exist different options to implement such a solution. We dive into these options and include a thorough comparative of performance and accurac...

There are, currently, very few implementations to compute the hyperbolic cosine of a matrix. This work tries to fill this gap. To this end, we first introduce both a new rational-polynomial Hermite matrix expansion and a formula for the forward relative error of Hermite approximation in exact arithmetic with a sharp bound for the forward error. Thi...

The action of the matrix exponential on a vector eAtv, A∈Cn×n, v∈Cn, appears in problems that arise in mathematics, physics, and engineering, such as the solution of systems of linear ordinary differential equations with constant coefficients. Nowadays, several state-of-the-art approximations are available for estimating this type of action. In thi...

Hyperbolic Matrix functions cosh (A) and sinh (A) emerge in various areas of science and technology, and its computation has attracted significant attention due to their usefulness in the solution of systems of second-order linear differential equations. In this work, we introduce Bernoulli matrix polynomial series expansions for hyperbolic matrix...

Matrix differential equations are at the heart of many science and engineering problems. In this paper, a procedure based on higher-order matrix splines is proposed to provide the approximated numerical solution of special nonlinear third-order matrix differential equations, having the form Y(3)(x)=f(x,Y(x)). Some numerical test problems are also i...

The most popular method for computing the matrix logarithm is a combination of the inverse scaling and squaring method in conjunction with a Padé approximation, sometimes accompanied by the Schur decomposition. In this work, we present a Taylor series algorithm, based on the free-transformation approach of the inverse scaling and squaring technique...

In this paper, we introduce two approaches to compute the matrix hyperbolic tangent. While one of them is based on its own definition and uses the matrix exponential, the other one is focused on the expansion of its Taylor series. For this second approximation, we analyse two different alternatives to evaluate the corresponding matrix polynomials....

We present in this paper a new method based on Bernoulli matrix polynomials to approximate the exponential of a matrix. The developed method has given rise to two new algorithms whose efficiency and precision are compared to the most efficient implementations that currently exist. For that, a state-of-the-art test matrix battery, that allows deeply...

The VTAM arguments file contains information about the parameters that will drive the optimization procedure. This file has a plain text format and must be provided altogether with the file that describes the optimization problem to be submitted to the VTAM web site. Please, check for updates of this document following the link provided in the firs...

The computation of matrix trigonometric functions has received remarkable attention in the last decades due to its usefulness in the solution of systems of second order linear differential equations. Recently, several state-of-the-art algorithms have been provided for computing these matrix functions, in particular for the matrix cosine function.

Matrix exponentials are widely used to efficiently tackle systems of linear differential equations. To be able to solve systems of fractional differential equations, the Caputo matrix exponential of the index α > 0 was introduced. It generalizes and adapts the conventional matrix exponential to systems of fractional differential equations with cons...

Bernoulli polynomials and Bernoulli numbers have been extensively used in several areas of mathematics (especially in number theory) because they appear in many mathematical formulas: as in the residual term of the Euler-Maclaurian quadrature rule, in the Taylor series expansion of the trigonometric functions tan (x), csc (x) and cot (x), in the Ta...

In this paper we show new algorithms for computing hyperbolic matrix sine and cosine approximations using Hermite matrix Series Expansions

This paper describes the developments to produce EC3 (Elastic Cloud Computing Cluster), a tool that creates self-managed cost-efficient virtual hybrid elastic clusters on top of Infrastructure as a Service (IaaS) Clouds. Using spot instances, together with checkpointing techniques, EC3 can significantly reduce the total cost of executions while int...

This paper describes the characteristics of a new high performance computing application (Architrave v.2011) designed for structural analysis of buildings or civil engineering structures. To check its performance against the well-known and widespread computer programme, SAP2000® v.15, a set of test has been designed for static and dynamic analysis....

This paper describes the migration of a scientific application, related to the structural analysis of buildings and civil engineering structures, to the Cloud. For that, two different approaches have been carried out: one of them based on the Generic Worker, a web-role implementation that manages the execution of the remote tasks in a Windows Azure...

This paper describes the characteristics of a new high performance computing application (Architrave v.2011) designed for structural analysis of buildings or civil engineering structures. To check its performance against the well-known and widespread computer programme, SAP2000® v.15, a set of test has been designed for static and dynamic analysis....

This paper describes the development of a high throughput and reliable Cloud Service to perform on-demand structural analysis over the Windows Azure-based Cloud infrastructure provided by the EC VENUS-C project. All the simulations in the Cloud are governed by Architrave®, an advanced software environment for the design, 3D linear static and dynami...

The advent of service-oriented architectures in Grid environments has fostered the development of applications in distributed deployments. The Globus Toolkit 4 (GT4) and its implementation of stateful Web services, via the WS-Resource Framework (WSRF), is a suitable platform to develop these Grid services. This way, its increased usage in many scie...

During acute myocardial ischemia, reentrant episodes may lead to ventricular fibrillation (VF), giving rise to potentially mortal arrhythmias. VF has been traditionally related to dispersion of refractoriness and more recently to the source-sink relationship. Our goal is to theoretically investigate the relative role of dispersion of refractoriness...

The design of proteins with targeted properties is a computationally intensive task with large memory requirements. We have developed a novel approach that combines a dimensional reduction of the problem with a High Performance Computing platform to efficiently design large proteins. This tool overcomes the memory limits of the process, allowing th...

This paper describes a Grid Computing application for the 3D dynamic analysis of large dimension buildings. A previously developed software composed of parallel implementations of eight direct integration methods has been integrated on this application, in order to perform structural simulations on a Grid deployment. The GMarte software abstraction...

This paper describes a Grid service developed over the Globus Toolkit 4, which provides multi-user resource brokering on computational Grids. Both the architecture and implementation details are covered, emphasising the usage of the WSRF specifications and GSI-based security to create a generic, secure and interoperable metascheduler. In addition,...

Traditionally, VF has been directly related to dispersion of refractoriness. However, further theoretical studies relating refractoriness and reentry generation would be helpful to understand their implication. Recently, the safety factor for conduction (SF) has been proposed as a useful parameter to analyze propagation of action potential (AP) and...

Atrial fibrillation (AF) is the most common atrial tachyarrhythmia. Recently, pulmonary vein ectopic focus has been demonstrated that it can trigger reentry in the presence of a vulnerable substrate and lead to AF. We examined the effects of ectopic focus frequency on the generation of AF. In this study, the effects of remodelling on ionic currents...

This paper presents a High Performance Computing-based application for 3D structural analysis of buildings. Since the solution of a large linear system of sparse equations supposes the most time-consuming phase, several public domain parallel numerical libraries, with state-of-the-art capabilities, have been tested. The parallel application develop...

Sudden cardiac death is mainly provoked by arrhythmogenic processes. During myocardial ischemia many malignant arrhythmias, such as reentry, take place and can degenerate into ventricular fibrillation. It is thus of great interest to unravel the intricate mechanisms underlying the initiation and maintenance of a reentry. In this computational study...

Diesel engines are fuel efficient which benefits the reduction of CO₂ released to the atmosphere compared with gasoline engines, but still result in negative environmental impact related to their emissions. As new degrees of freedom are created, due to advances in technology, the complicated processes of emission formation are difficult...

Grid computing technologies are mature enough to be successfully applied to computationally intensive scientific applications. However, the current process of applying grid computing to them is still hard and difficult for the least experienced users. In this paper we describe the adaptations made to the GMarte metascheduling framework in order to...

El estudio de las causas de la generación y mantenimiento de los episodios arr'itmicos siempre ha suscitado un gran interés. Recientemente, el factor de seguridad (SF) se ha propuesto como un parámetro muy útil para el análisis de la propagación y bloqueo del impulso eléctrico card'iaco. En este trabajo se ha estudiado la vulnerabilidad a la reentr...

Grid Computing technologies enable the aggregation and usage of geographically distributed computational resources to establish a collaborative framework to solve challenging scientific and engineering problems. Being a recent technology, Grids have become a priority research line in the major funding agencies. Also, universities are including Grid...

The development of parallel applications requires adequate tools to help the programmer to create applications that can efficiently execute on a wide range of computing platforms. This paper describes a joint effort to build a programming framework that can transparently execute parallel applications on multiprocessor systems, clusters and computat...

This paper describes Grid4Build, a high performance Grid approach that enables to perform 3D linear analysis and visualisation of building structures. The system involves three independent components: a GUI Client, a Structural Analysis Grid Service and an HPC-based structural simulator. The GUI Client is in charge to assist the user in the pre-pro...

The second of the two case studies in the POWADIMA research project, the Valencia water-distribution network, serves a population of approximately 1.2 million and is supplied by surface water via two treatment plants which have significantly different production costs. The only storage available is located at the treatment plants, each of which has...

Grid computing technologies are now being largely deployed with the widespread adoption of the Globus Toolkit as the industrial standard Grid middleware. However, its inherent steep learning curve discourages the use of these technologies for non-experts. Therefore, to increase the use of Grid computing, it is important to have high-level tools tha...

The safety factor (SF) is an indicator of the safeness of electrical conduction in the myocardium. In the present work, the estimation of the SF based on the formulation proposed by Shaw and Rudy (1997) has been extended to 2D (SF-2D) and evaluated. Furthermore, the effect of the increment of extracellular potassium concentration ([K+]o) on the SF-...

In this paper we describe the implementation of a service oriented environment that enables to couple a parallel application, which performs the 3D linear dynamic structural analysis of high-rise buildings, to a Grid Computing infrastructure. The Grid service, developed under Globus Toolkit 4, exposes the dynamic simulation as a service to the stru...

El factor de seguridad en la conducción (SF) es un indicador de la seguridad en la propagación del impulso eléctrico card'iaco. En este trabajo, la definición del SF propuesta por Shaw y Rudy se ha extendido a 2D (SF-2D) y se ha evaluado. También se ha estudiado la influencia de la concentración de potasio extracelular ([K+]0) en el SF-2D de un fre...

This paper exposes the implementation of a service oriented platform that performs an on demand 3D static and dynamic structural analysis of high-rise buildings using a Grid Computing infrastructure. The Grid Service has been developed over Globus Toolkit 4, offering to the structural scientific community an on-line multi-user service. The requirem...

The usage of Grid Computing technologies in the field of structural dynamics enables to exploit the available distributed computing resources in order to tackle a realistic 3D dynamic analysis of high rise buildings, in a reasonable period of time. Notwithstanding, the development of a service-oriented architecture for structural dynamics presents...

The realistic 3D analysis of large dimension structures, due to its computational and memory requirements, demands a parallel platform to solve the problem in a reasonable period of time. Therefore, as structural engineers rarely own this special hardware, a service-oriented system that publishes a Structural Analysis Grid Service has been develope...

In this paper, an MPI-based parallel application for the 3D modal analysis of large dimension buildings has been implemented. The application considers all the nodes of the structure without movement constraints, and it assumes six degrees of freedom for each node. Several state-of-the-art parallel numerical libraries, such as ARPACK and SLEPc, hav...

It is well known that short-long (S-L) sequences frequently precede the onset of malignant ventricular arrhythmias. Experimental studies have shown that a single long coupled extra-beat (L) after a previous basic cycle length resulted in a critical increase of the dispersion of repolarization pattern that promoted reentrant excitation. However, in...

Building and calibrating models of water distribution systems is a tedious task that may take a long time. Former models were built combining information collected from CAD for cartography, from data-loggers for field measurements, and from billing for consumptions. Calibration was carried out manually or assisted by data processors, which was time...

With the recent advent of Grid Computing technologies, resource-starved applications can greatly benefit from the power that the Grid aims to deliver. In this paper, we focus on the application of Grid Computing to a biomedical computationally intensive application that simulates the electrical activity on cardiac tissues. A user level tool, called...

With the advent of grid technologies, much interest has arisen in the application of these computational techniques to multiple fields. However, grid computing technologies have a steep learning curve that tends to discourage scientists from the usage of grid facilities applied to their research, preventing a widespread adoption of grid computing....

Este art'iculo presenta una aplicación basada en Tecnolog'ias Grid para el análisis dinámico lineal 3D de edificios de gran dimensión. Esta aplicación ha sido desarrollada sobre GMarte, una capa de abstracción software que simplifica el proceso de ejecutar remotamente un conjunto de tareas en una infraestructura Grid basada en Globus. Además, dicha...

This paper describes a Grid Computing application for the 3D dynamic analysis of large dimension buildings. A previously developed software composed of parallel implementations of eight direct integration methods has been integrated on this application, in order to perform structural simulations on a Grid deployment. The GMarte software abstraction...

Este libro va destinado a todos aquellos estudiantes de primeros cursos de ingeniería en sus diferentes vertientes, incluyendo la ingeniería en informática, que reciben formación básica en programación de computadores en lenguaje C. No obstante, debido al nivel del libro, perfectamente podría ser utilizado también en academias, en cursos de bachill...

Challenging problems such as single or multi-objective optimizations often require running thousands of simulations in order to achieve the task. In this context, the use of properly trained Artificial Neural Networks (ANN), as a substitute for the hydraulic simulator, can drastically reduce the computing time required by the new algorithms. In thi...

With the advent of Grid technologies, the study of the electrical activity of the heart, by means of concurrent parametric simulations of the action potential propagation on cardiac tissues, can be greatly benefited. Studies of the electrical behaviour, such as late ischemia require the execution of multiple computational and memory intensive param...

Different experimental studies have shown that ventricular cells present several differences between epicardium, endocardium and M-cells. M-cells have longer APDs and higher sensitivity to agents with class III actions and they could contribute to APD heterogeneity in the ventriculum. However, in-vivo studies have observed that the strong cellular...

The Electrical Restitution Curve (ERC) may play an important role in the generation and maintenance of Ventricular fibrillation (VF). As VF usually appears in ischemic hearts, we have studied the changes exerted by acute ischemia in ERCs using computer simulations. Our results show that the main effects of ischemia on the ERC are that (a) it shifts...

In this article a parallel application for the 3D structural analysis of buildings is presented. Taking into account that solving the system of linear equations is the most time-consuming phase, several parallel public domain numerical libraries, that reflect the start-of-the-art, have been tested. A timing result comparison when analyzing two medi...

Simulation of action potential propagation on cardiac tissues represents both a computational and memory intensive task. The use of detailed ionic cellular models, combined with its application into three-dimensional geometries turn simulation into a problem only affordable, in reasonable time, with High Performance Computing techniques. This paper...

In this paper, a general approach is presented to exploit hydraulic models in the daily operation of water supply networks, by integrating them with SCADA and GIS systems. The process of building a model of the network by means of a GIS extension is briefly discussed first. Then its exploitation in a SCADA system is presented by means of an applica...

Los Sistema de Información Geográfica (SIG) están llamados a ser en el futuro los sistemas de gestión de toda la información relacionada con la explotación de las redes de suministro de agua potable. La unión de la información alfanumérica con la información geográfica en un SIG permite llevar a cabo un sinfín de aplicaciones que van desde las tare...

El estudio de la actividad eléctrica del corazón por medio de la simulación de la propagación del potencial de acción representa una tarea computacionalmente costosa, con elevados requerimientos de memoria. Este art'iculo presenta la combinación de dos estrategias computacionales con el objetivo de acelerar las simulaciones cardiacas. Por un lado,...

The Globus Toolkit is considered the de-facto standard for Grid Computing. However, its steep learning curve can discourage its widespread adoption. In order to overcome this disadvantage an Object-Oriented software has been developed, providing an intuitive interface which completely hides the direct interaction with Globus, what offers significan...

La Curva de Restitución Eléctrica (ERC) es de gran importancia en las distintas arritmogénesis. En este trabajo, hemos estudiado, mediante simulaciones, su comportamiento en isquemia aguda, ya que la fibrilación ventricular (FV) aparece normalmente en corazones isquémicos. Los resultados obtenidos, como otros estudios experimentales, sugieren que l...

La simulación de la propagación del potencial de acción en tejidos cardiacos representa una tarea computacionalmente intensa, con elevados requerimientos de memoria. El uso de detallados modelos celulares iónicos, combinado con su aplicación en geometr'ias tridimensionales, convierten a dicha simulación en un problema únicamente abordable, en tiemp...

The aim of this work was to analyze the vulnerability to reentry in a two-dimensional sheet of regionally-ischemic and anisotropic myocardial tissue at different stages of acute myocardial ischemia. We used computer modelling in order to elucidate the main factors responsible for initiation and maintenance of reentry. Simulations were carried out u...

This chapter discusses the computer simulation of action potential propagation on cardiac tissues. The chapter discusses a complete parallel computing implementation for the electrical activity simulation in a two-dimensional monodomain cardiac tissue, using a cost-effective beowulf cluster. High performance computing techniques have reduced the si...

La simulación de la propagación del potencial de acción en un tejido cardiaco es un proceso con unos elevados tiempos de computación y unos enormes requerimientos de memoria. La creciente necesidad de simular tejidos de mayores dimensiones durante más tiempo, junto con el uso de modelos celulares realistas, está demandando el uso de recursos comput...

The simulation of action potential propagation on cardiac tissues is a very intensive process, both in terms of memory and computational load. Complex ionic models such as the Luo-Rudy Phase 2, along with the ever-increasing need to simulate larger tissues during longer time, require the use of high performance parallelization strategies. This pape...

In this paper a parallel computing based software demonstrator for the simulation and leakage minimization of water networks is presented. This demonstrator, based on the EPANET package, tackles three different types of problems making use of parallel computing. First, the solution of the hydraulic problem is treated by means of the gradient method...