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,

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Three parallel programming paradigms: Comparisons on an archetypal PDE computation

Three paradigms for distributed-memory parallel computation that free the application programmer from the details of message passing are compared for an archetypal structured scientific computation -- a nonlinear, structured-grid partial differential equation boundary value problem -- using the same algorithm on the same hardware. All of the paradigms -- parallel languages represented by the Portland Group's HPF, (semi-)automated serial-to-parallel source-to-source translation represented by CAP-Tools from the University of Greenwich, and parallel libraries represented by Argonne's PETSc -- are found to be easy to use for this problem class, and all are reasonably effective in exploiting concurrency after a short learning curve. The level of involvement required by the application programmer under any paradigm includes specification of the data partitioning, corresponding to a geometrically simple decomposition of the domain of the PDE. Programming in SPMD style for the PETSc library requires writing only the routines that discretize the PDE and its Jacobian, managing subdomain-to-processor mappings (affine global-to-local index mappings), and interfacing to library solver routines. Programming for HPF requires a complete sequential implementation of the same algorithm as a starting point, introduction of concurrency through subdomain blocking (a task similar to the index mapping), and modest experimentation with rewriting loops to elucidate to the compiler the latent concurrency. Programming with CAPTools involves feeding the same sequential implementation to the CAPTools interactive parallelization system, and guiding the source-to-source code transformation by responding to various queries about quantities knowable only at runtime. Results representative of "the state of the practice" for a scaled sequence of structured grid problems are given on three of the most important contemporary high-performance platforms: the IBM SP, the SGI Origin 2000, and the CRAYY T3E.

Numerical ‘health check’ for scientific codes: the CADNA approach

Scientific computation has unavoidable approximations built into its very fabric. One important source of error that is difficult to detect and control is round-off error propagation which originates from the use of finite precision arithmetic. We propose that there is a need to perform regular numerical `health checks' on scientific codes in order to detect the cancerous effect of round-off error propagation. This is particularly important in scientific codes that are built on legacy software. We advocate the use of the CADNA library as a suitable numerical screening tool. We present a case study to illustrate the practical use of CADNA in scientific codes that are of interest to the Computer Physics Communications readership. In doing so we hope to stimulate a greater awareness of round-off error propagation and present a practical means by which it can be analyzed and managed.

Solving tri-diagonal linear systems using field programmable gate arrays

In this paper, we present the outcomes of a project on the exploration of the use of Field Programmable Gate Arrays(FPGAs) as co-processors for scientific computation. We designed a custom circuit for the pipelined solving of multiple tri-diagonal linear systems. The design is well suited for applications that require many independent tri diagonal system solves, such as finite difference methods for solving PDEs or applications utilising cubic spline interpolation. The selected solver algorithm was the Tri Diagonal Matrix Algorithm (TDMA or Thomas Algorithm). Our solver supports user specified precision thought the use of a custom floating point VHDL library supporting addition, subtraction, multiplication and division. The variable precision TDMA solver was tested for correctness in simulation mode. The TDMA pipeline was tested successfully in hardware using a simplified solver model. The details of implementation, the limitations, and future work are also discussed.

Solving tri-diagonal linear systems using field programmable gate arrays

In this paper, we present the outcomes of a project on the exploration of the use of Field Programmable Gate Arrays (FPGAs) as co-processors for scientific computation. We designed a custom circuit for the pipelined solving of multiple tri-diagonal linear systems. The design is well suited for applications that require many independent tri-diagonal system solves, such as finite difference methods for solving PDEs or applications utilising cubic spline interpolation. The selected solver algorithm was the Tri-Diagonal Matrix Algorithm (TDMA or Thomas Algorithm). Our solver supports user specified precision thought the use of a custom floating point VHDL library supporting addition, subtraction, multiplication and division. The variable precision TDMA solver was tested for correctness in simulation mode. The TDMA pipeline was tested successfully in hardware using a simplified solver model. The details of implementation, the limitations, and future work are also discussed.

Avaliação dos algoritmos de Picard-Krylov e Newton-Krylov na solução da equação de Richards

A engenharia geotécnica é uma das grandes áreas da engenharia civil que estuda a interação entre as construções realizadas pelo homem ou de fenômenos naturais com o ambiente geológico, que na grande maioria das vezes trata-se de solos parcialmente saturados. Neste sentido, o desempenho de obras como estabilização, contenção de barragens, muros de contenção, fundações e estradas estão condicionados a uma correta predição do fluxo de água no interior dos solos. Porém, como a área das regiões a serem estudas com relação à predição do fluxo de água são comumente da ordem de quilômetros quadrados, as soluções dos modelos matemáticos exigem malhas computacionais de grandes proporções, ocasionando sérias limitações associadas aos requisitos de memória computacional e tempo de processamento. A fim de contornar estas limitações, métodos numéricos eficientes devem ser empregados na solução do problema em análise. Portanto, métodos iterativos para solução de sistemas não lineares e lineares esparsos de grande porte devem ser utilizados neste tipo de aplicação. Em suma, visto a relevância do tema, esta pesquisa aproximou uma solução para a equação diferencial parcial de Richards pelo método dos volumes finitos em duas dimensões, empregando o método de Picard e Newton com maior eficiência computacional. Para tanto, foram utilizadas técnicas iterativas de resolução de sistemas lineares baseados no espaço de Krylov com matrizes pré-condicionadoras com a biblioteca numérica Portable, Extensible Toolkit for Scientific Computation (PETSc). Os resultados indicam que quando se resolve a equação de Richards considerando-se o método de PICARD-KRYLOV, não importando o modelo de avaliação do solo, a melhor combinação para resolução dos sistemas lineares é o método dos gradientes biconjugados estabilizado mais o pré-condicionador SOR. Por outro lado, quando se utiliza as equações de van Genuchten deve ser optar pela combinação do método dos gradientes conjugados em conjunto com pré-condicionador SOR. Quando se adota o método de NEWTON-KRYLOV, o método gradientes biconjugados estabilizado é o mais eficiente na resolução do sistema linear do passo de Newton, com relação ao pré-condicionador deve-se dar preferência ao bloco Jacobi. Por fim, há evidências que apontam que o método PICARD-KRYLOV pode ser mais vantajoso que o método de NEWTON-KRYLOV, quando empregados na resolução da equação diferencial parcial de Richards.

自动微分程序设计及在PETSc中的集成与应用

大规模科学计算已经广泛应用在气象、海洋、化学、生物医药、电子工程等领域。科学计算软件的开发是科学计算的关键环节。开发一个具有良好可靠性的计算工具，并与大型计算工具箱集成而完成大规模、复杂实际问题的计算，具有重要意义。 PETSc（Portable, Extensible Toolkit for Scientific Computation）是国际流行的科学计算工具箱，它可用于偏微分方程的求解及相关的高性能计算问题。本文分析了PETSc的主要功能、结构与特色，并剖析了其核心组件，包括向量、矩阵、线性方程组求解器KSP、非线性求解器SNES等。 自动微分是计算函数导数的重要方法，它可以应用在最优化问题的实际计算中。在PETSc中提供了ADIC、ADIFOR等自动微分软件包的接口。本文分析了自动微分计算函数一阶导数的切线性模式与伴随模式的基本原理，介绍了现有的自动微分软件的情况，特别是ADIC的开发及其与PETSc的接口。 DTC（Differentiation Transforming System in C）是针对C语言自动微分工具，用于生成切线性模式。DTC生成的切线性代码可用于计算雅可比矩阵-向量乘积等。本文详细介绍了DTC系统的设计及关键技术，包括编译技术、输入/输出（IO）相关分析等。针对PETSc的复杂数据结构，开发了DTC与PETSc的接口，将两者集成，并应用在求解二维全球正压大气浅水波方程中。最后给出了DTC系统的相关测试结果。

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.