An Informatics Technical Note on Interaction of DNA - Graphene Chemical Sensor System as Reaction-Diffusion Wave-Based Computing System in Ionised Gaseous environments and their Applications Using Theoretical Studies and Scientific Computation Overview

The physics of plasmas encompasses basic problems from the universe and has assured us of promises in diverse applications to be implemented in a wider range of scientific and engineering domains, linked to most of the evolved and evolving fundamental problems. Substantial part of this domain could be described by R–D mechanisms involving two or more species (reaction–diffusion mechanisms). These could further account for the simultaneous non-linear effects of heating, diffusion and other related losses. We mention here that in laboratory scale experiments, a suitable combination of these processes is of vital importance and very much decisive to investigate and compute the net behaviour of plasmas under consideration. Plasmas are being used in the revolution of information processing, so we considered in this technical note a simple framework to discuss and pave the way for better formalisms and Informatics, dealing with diverse domains of science and technologies. The challenging and fascinating aspects of plasma physics is that it requires a great deal of insight in formulating the relevant design problems, which in turn require ingenuity and flexibility in choosing a particular set of mathematical (and/or experimental) tools to implement them.

Punched card methods in scientific computation,

Mode of access: Internet.

Modelagem matemática e simulação numérica do resfriamento rápido de morango com ar forçado

This work approaches the forced air cooling of strawberry by numerical simulation. The mathematical model that was used describes the process of heat transfer, based on the Fourier's law, in spherical coordinates and simplified to describe the one-dimensional process. For the resolution of the equation expressed for the mathematical model, an algorithm was developed based on the explicit scheme of the numerical method of the finite differences and implemented in the scientific computation program MATLAB 6.1. The validation of the mathematical model was made by the comparison between theoretical and experimental data, where strawberries had been cooled with forced air. The results showed to be possible the determination of the convective heat transfer coefficient by fitting the numerical and experimental data. The methodology of the numerical simulations was showed like a promising tool in the support of the decision to use or to develop equipment in the area of cooling process with forced air of spherical fruits.

Periodic Reordering

For many networks in nature, science and technology, it is possible to order the nodes so that most links are short-range, connecting near-neighbours, and relatively few long-range links, or shortcuts, are present. Given a network as a set of observed links (interactions), the task of finding an ordering of the nodes that reveals such a range-dependent structure is closely related to some sparse matrix reordering problems arising in scientific computation. The spectral, or Fiedler vector, approach for sparse matrix reordering has successfully been applied to biological data sets, revealing useful structures and subpatterns. In this work we argue that a periodic analogue of the standard reordering task is also highly relevant. Here, rather than encouraging nonzeros only to lie close to the diagonal of a suitably ordered adjacency matrix, we also allow them to inhabit the off-diagonal corners. Indeed, for the classic small-world model of Watts & Strogatz (1998, Collective dynamics of ‘small-world’ networks. Nature, 393, 440–442) this type of periodic structure is inherent. We therefore devise and test a new spectral algorithm for periodic reordering. By generalizing the range-dependent random graph class of Grindrod (2002, Range-dependent random graphs and their application to modeling large small-world proteome datasets. Phys. Rev. E, 66, 066702-1–066702-7) to the periodic case, we can also construct a computable likelihood ratio that suggests whether a given network is inherently linear or periodic. Tests on synthetic data show that the new algorithm can detect periodic structure, even in the presence of noise. Further experiments on real biological data sets then show that some networks are better regarded as periodic than linear. Hence, we find both qualitative (reordered networks plots) and quantitative (likelihood ratios) evidence of periodicity in biological networks.

Numerical integration of coupled stochastic oscillators driven by Random Forces

Trabalho apresentado no International Conference on Scientific Computation And Differential Equations 2015

Estudos de algumas ferramentas de coleta e visualização de dados e desempenho de aplicações paralelas no ambiente MPI

The last years have presented an increase in the acceptance and adoption of the parallel processing, as much for scientific computation of high performance as for applications of general intention. This acceptance has been favored mainly for the development of environments with massive parallel processing (MPP - Massively Parallel Processing) and of the distributed computation. A common point between distributed systems and MPPs architectures is the notion of message exchange, that allows the communication between processes. An environment of message exchange consists basically of a communication library that, acting as an extension of the programming languages that allow to the elaboration of applications parallel, such as C, C++ and Fortran. In the development of applications parallel, a basic aspect is on to the analysis of performance of the same ones. Several can be the metric ones used in this analysis: time of execution, efficiency in the use of the processing elements, scalability of the application with respect to the increase in the number of processors or to the increase of the instance of the treat problem. The establishment of models or mechanisms that allow this analysis can be a task sufficiently complicated considering parameters and involved degrees of freedom in the implementation of the parallel application. An joined alternative has been the use of collection tools and visualization of performance data, that allow the user to identify to points of strangulation and sources of inefficiency in an application. For an efficient visualization one becomes necessary to identify and to collect given relative to the execution of the application, stage this called instrumentation. In this work it is presented, initially, a study of the main techniques used in the collection of the performance data, and after that a detailed analysis of the main available tools is made that can be used in architectures parallel of the type to cluster Beowulf with Linux on X86 platform being used libraries of communication based in applications MPI - Message Passing Interface, such as LAM and MPICH. This analysis is validated on applications parallel bars that deal with the problems of the training of neural nets of the type perceptrons using retro-propagation. The gotten conclusions show to the potentiality and easinesses of the analyzed tools.

Sub-Optimal Orbital Maneuvers for Artificial Satellites

The determination of a specific orbit and the procedure to calculate orbital maneuvers of artificial satellites are problems of extreme importance in the study of orbital mechanics. Therefore, the transferring problem of a spaceship from one orbit to another, and the attention due to this subject has in increased during the last years. Many applications can be found in several space activities, for example, to put a satellite in a geostationary orbit, to change the position of a spaceship, to maintain a specific satellite's orbit, in the design of an interplanetary mission, and others. The Brazilian Satellite SCD-1 (Data Collecting Satellite) will be used as example in this paper. It is the first satellite developed entirely in Brazil, and it remains in operation to this date. SCD-1 was designed, developed, built, and tested by Brazilian scientists, engineers, and technicians working at INPE (National Institute for Space Research, and in Brazilian Industries. During the lifetime, it might be necessary do some complementary maneuvers, being this one either an orbital transferring, or just to make periodical corrections. The purpose of transferring problem is to change the position, velocity and the satellite's mass to a new pre determined state. This transfer can be totally linked (in the case of "Rendezvous") or partially free (free time, free final velocity, etc). In the global case, the direction, the orientation and the magnitude of the thrust to be applied must be chosen, respecting the equipment's limit. In order to make this transferring, either sub-optimal or optimal maneuvers may be used. In the present study, only the sub-optimal will be shown. Hence, this method will simplify the direction of thrust application, to allow a fast calculation that may be used in real time, with a very fast processing. The thrust application direction to be applied will be assumed small and constant, and the purpose of this paper is to find the time interval that the thrust is applied. This paper is basically divided into three parts: during the first one the sub-optimal maneuver is explained and detailed, the second presents the Satellite SCD-1, and finally the last part shows the results using the sub-optimal maneuver applied to the Brazilian Satellite.

Java-XSC : módulo complexo e complexo intervalar

This work aims to develop modules that will increase the computational power of the Java-XSC library, and XSC an acronym for "Language Extensions for Scientific Computation . This library is actually an extension of the Java programming language that has standard functions and routines elementary mathematics useful interval. in this study two modules were added to the library, namely, the modulus of complex numbers and complex numbers of module interval which together with the modules original numerical applications that are designed to allow, for example in the engineering field, can be used in devices running Java programs

Modelagem matemática e simulação numérica do resfriamento rápido de morango com ar forçado

Este trabalho abordou o resfriamento rápido com ar forçado de morango via simulação numérica. Para tanto, foi empregado o modelo matemático que descreve o processo de transferência de calor, com base na lei de Fourier, escrito em coordenadas esféricas e simplificado para descrever o processo unidimensional. A resolução da equação expressa pelo modelo matemático deu-se por meio da implementação de um algoritmo, fundamentado no esquema explícito do método numérico das diferenças finitas, executado no ambiente de computação científica MATLAB 6.1. A validação do modelo matemático foi realizada a partir da comparação de dados teóricos com dados obtidos num experimento, no qual morangos foram resfriados com ar forçado. Os resultados mostraram que esse tipo de investigação para a determinação do coeficiente de transferência de calor por convecção é promissora como ferramenta no suporte à decisão do uso ou desenvolvimento de equipamentos na área de resfriamento rápido de frutos esféricos com ar forçado.

Matrix-vector multiplication and triangular linear solver using GPGPU for symmetric positive definite matrices derived from elliptic equations

The modern GPUs are well suited for intensive computational tasks and massive parallel computation. Sparse matrix multiplication and linear triangular solver are the most important and heavily used kernels in scientific computation, and several challenges in developing a high performance kernel with the two modules is investigated. The main interest it to solve linear systems derived from the elliptic equations with triangular elements. The resulting linear system has a symmetric positive definite matrix. The sparse matrix is stored in the compressed sparse row (CSR) format. It is proposed a CUDA algorithm to execute the matrix vector multiplication using directly the CSR format. A dependence tree algorithm is used to determine which variables the linear triangular solver can determine in parallel. To increase the number of the parallel threads, a coloring graph algorithm is implemented to reorder the mesh numbering in a pre-processing phase. The proposed method is compared with parallel and serial available libraries. The results show that the proposed method improves the computation cost of the matrix vector multiplication. The pre-processing associated with the triangular solver needs to be executed just once in the proposed method. The conjugate gradient method was implemented and showed similar convergence rate for all the compared methods. The proposed method showed significant smaller execution time.

Bioconductor: Open software development for computational biology and bioinformatics

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software paradigms and operational strategies that have allowed a small number of researchers to provide a wide variety of innovative, extensible, software solutions in a relatively short time. The use of an object oriented programming paradigm, the adoption and development of a software package system, designing by contract, distributed development and collaboration with other projects are elements of this project's success. Individually, each of these concepts are useful and important but when combined they have provided a strong basis for rapid development and deployment of innovative and flexible research software for scientific computation. A primary objective of this initiative is achievement of total remote reproducibility of novel algorithmic research results.

The Boundary Element Method in elastodynamics

As is well known B.E.M. is obtained as a mixture of the integral representation formula of classical elasticity and the discretization philosophy of the finite element method (F.E.M.). The paper presents the application of B.E.M. to elastodynamic problems. Both the transient and steady state solutions are presented as well as some techniques to simplify problems with a free-stress boundary.

Automated wordlength optimization framework for multi-source statistical interval-based analysis of nonlinear systems with control-flow structures

El uso de aritmética de punto fijo es una opción de diseño muy extendida en sistemas con fuertes restricciones de área, consumo o rendimiento. Para producir implementaciones donde los costes se minimicen sin impactar negativamente en la precisión de los resultados debemos llevar a cabo una asignación cuidadosa de anchuras de palabra. Encontrar la combinación óptima de anchuras de palabra en coma fija para un sistema dado es un problema combinatorio NP-hard al que los diseñadores dedican entre el 25 y el 50 % del ciclo de diseño. Las plataformas hardware reconfigurables, como son las FPGAs, también se benefician de las ventajas que ofrece la aritmética de coma fija, ya que éstas compensan las frecuencias de reloj más bajas y el uso más ineficiente del hardware que hacen estas plataformas respecto a los ASICs. A medida que las FPGAs se popularizan para su uso en computación científica los diseños aumentan de tamaño y complejidad hasta llegar al punto en que no pueden ser manejados eficientemente por las técnicas actuales de modelado de señal y ruido de cuantificación y de optimización de anchura de palabra. En esta Tesis Doctoral exploramos distintos aspectos del problema de la cuantificación y presentamos nuevas metodologías para cada uno de ellos: Las técnicas basadas en extensiones de intervalos han permitido obtener modelos de propagación de señal y ruido de cuantificación muy precisos en sistemas con operaciones no lineales. Nosotros llevamos esta aproximación un paso más allá introduciendo elementos de Multi-Element Generalized Polynomial Chaos (ME-gPC) y combinándolos con una técnica moderna basada en Modified Affine Arithmetic (MAA) estadístico para así modelar sistemas que contienen estructuras de control de flujo. Nuestra metodología genera los distintos caminos de ejecución automáticamente, determina las regiones del dominio de entrada que ejercitarán cada uno de ellos y extrae los momentos estadísticos del sistema a partir de dichas soluciones parciales. Utilizamos esta técnica para estimar tanto el rango dinámico como el ruido de redondeo en sistemas con las ya mencionadas estructuras de control de flujo y mostramos la precisión de nuestra aproximación, que en determinados casos de uso con operadores no lineales llega a tener tan solo una desviación del 0.04% con respecto a los valores de referencia obtenidos mediante simulación. Un inconveniente conocido de las técnicas basadas en extensiones de intervalos es la explosión combinacional de términos a medida que el tamaño de los sistemas a estudiar crece, lo cual conlleva problemas de escalabilidad. Para afrontar este problema presen tamos una técnica de inyección de ruidos agrupados que hace grupos con las señales del sistema, introduce las fuentes de ruido para cada uno de los grupos por separado y finalmente combina los resultados de cada uno de ellos. De esta forma, el número de fuentes de ruido queda controlado en cada momento y, debido a ello, la explosión combinatoria se minimiza. También presentamos un algoritmo de particionado multi-vía destinado a minimizar la desviación de los resultados a causa de la pérdida de correlación entre términos de ruido con el objetivo de mantener los resultados tan precisos como sea posible. La presente Tesis Doctoral también aborda el desarrollo de metodologías de optimización de anchura de palabra basadas en simulaciones de Monte-Cario que se ejecuten en tiempos razonables. Para ello presentamos dos nuevas técnicas que exploran la reducción del tiempo de ejecución desde distintos ángulos: En primer lugar, el método interpolativo aplica un interpolador sencillo pero preciso para estimar la sensibilidad de cada señal, y que es usado después durante la etapa de optimización. En segundo lugar, el método incremental gira en torno al hecho de que, aunque es estrictamente necesario mantener un intervalo de confianza dado para los resultados finales de nuestra búsqueda, podemos emplear niveles de confianza más relajados, lo cual deriva en un menor número de pruebas por simulación, en las etapas iniciales de la búsqueda, cuando todavía estamos lejos de las soluciones optimizadas. Mediante estas dos aproximaciones demostramos que podemos acelerar el tiempo de ejecución de los algoritmos clásicos de búsqueda voraz en factores de hasta x240 para problemas de tamaño pequeño/mediano. Finalmente, este libro presenta HOPLITE, una infraestructura de cuantificación automatizada, flexible y modular que incluye la implementación de las técnicas anteriores y se proporciona de forma pública. Su objetivo es ofrecer a desabolladores e investigadores un entorno común para prototipar y verificar nuevas metodologías de cuantificación de forma sencilla. Describimos el flujo de trabajo, justificamos las decisiones de diseño tomadas, explicamos su API pública y hacemos una demostración paso a paso de su funcionamiento. Además mostramos, a través de un ejemplo sencillo, la forma en que conectar nuevas extensiones a la herramienta con las interfaces ya existentes para poder así expandir y mejorar las capacidades de HOPLITE. ABSTRACT Using fixed-point arithmetic is one of the most common design choices for systems where area, power or throughput are heavily constrained. In order to produce implementations where the cost is minimized without negatively impacting the accuracy of the results, a careful assignment of word-lengths is required. The problem of finding the optimal combination of fixed-point word-lengths for a given system is a combinatorial NP-hard problem to which developers devote between 25 and 50% of the design-cycle time. Reconfigurable hardware platforms such as FPGAs also benefit of the advantages of fixed-point arithmetic, as it compensates for the slower clock frequencies and less efficient area utilization of the hardware platform with respect to ASICs. As FPGAs become commonly used for scientific computation, designs constantly grow larger and more complex, up to the point where they cannot be handled efficiently by current signal and quantization noise modelling and word-length optimization methodologies. In this Ph.D. Thesis we explore different aspects of the quantization problem and we present new methodologies for each of them: The techniques based on extensions of intervals have allowed to obtain accurate models of the signal and quantization noise propagation in systems with non-linear operations. We take this approach a step further by introducing elements of MultiElement Generalized Polynomial Chaos (ME-gPC) and combining them with an stateof- the-art Statistical Modified Affine Arithmetic (MAA) based methodology in order to model systems that contain control-flow structures. Our methodology produces the different execution paths automatically, determines the regions of the input domain that will exercise them, and extracts the system statistical moments from the partial results. We use this technique to estimate both the dynamic range and the round-off noise in systems with the aforementioned control-flow structures. We show the good accuracy of our approach, which in some case studies with non-linear operators shows a 0.04 % deviation respect to the simulation-based reference values. A known drawback of the techniques based on extensions of intervals is the combinatorial explosion of terms as the size of the targeted systems grows, which leads to scalability problems. To address this issue we present a clustered noise injection technique that groups the signals in the system, introduces the noise terms in each group independently and then combines the results at the end. In this way, the number of noise sources in the system at a given time is controlled and, because of this, the combinato rial explosion is minimized. We also present a multi-way partitioning algorithm aimed at minimizing the deviation of the results due to the loss of correlation between noise terms, in order to keep the results as accurate as possible. This Ph.D. Thesis also covers the development of methodologies for word-length optimization based on Monte-Carlo simulations in reasonable times. We do so by presenting two novel techniques that explore the reduction of the execution times approaching the problem in two different ways: First, the interpolative method applies a simple but precise interpolator to estimate the sensitivity of each signal, which is later used to guide the optimization effort. Second, the incremental method revolves on the fact that, although we strictly need to guarantee a certain confidence level in the simulations for the final results of the optimization process, we can do it with more relaxed levels, which in turn implies using a considerably smaller amount of samples, in the initial stages of the process, when we are still far from the optimized solution. Through these two approaches we demonstrate that the execution time of classical greedy techniques can be accelerated by factors of up to ×240 for small/medium sized problems. Finally, this book introduces HOPLITE, an automated, flexible and modular framework for quantization that includes the implementation of the previous techniques and is provided for public access. The aim is to offer a common ground for developers and researches for prototyping and verifying new techniques for system modelling and word-length optimization easily. We describe its work flow, justifying the taken design decisions, explain its public API and we do a step-by-step demonstration of its execution. We also show, through an example, the way new extensions to the flow should be connected to the existing interfaces in order to expand and improve the capabilities of HOPLITE.

Simultaneous material and structural optimization by multiscale topology optimization

Acknowledgments The authors acknowledge the support from Engineering and Physical Sciences Research Council, grant number EP/M002322/1. The authors would also like to thank Numerical Analysis Group at the Rutherford Appleton Laboratory for their FORTRAN HSL packages (HSL, a collection of Fortran codes for large-scale scientific computation. See http://www.hsl.rl.ac.uk/).