23 research outputs found

    Large-scale parallelised boundary element method electrostatics for biomolecular simulation

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    Large-scale biomolecular simulations require a model of particle interactions capable of incorporating the behaviour of large numbers of particles over relatively long timescales. If water is modelled as a continuous medium then the most important intermolecular forces between biomolecules can be modelled as long-range electrostatics governed by the Poisson- Boltzmann Equation (PBE). We present a linearised PBE solver called the "Boundary Element Electrostatics Program"(BEEP). BEEP is based on the Boundary Element Method (BEM), in combination with a recently developed O(N) Fast Multipole Method (FMM) algorithm which approximates the far-�field integrals within the BEM, yielding a method which scales linearly with the number of particles. BEEP improves on existing methods by parallelising the underlying algorithms for use on modern cluster architectures, as well as taking advantage of recent progress in the �field of GPGPU (General Purpose GPU) Programming, to exploit the highly parallel nature of graphics cards. We found the stability and numerical accuracy of the BEM/FMM method to be highly dependent on the choice of surface representation and integration method. For real proteins we demonstrate the critical level of surface detail required to produce converged electrostatic solvation energies, and introduce a curved surface representation based on Point-Normal G1-continuous triangles which we �find generally improves numerical stability compared to a simpler surface constructed from planar triangles. Despite our improvements upon existing BEM methods, we �find that it is not possible to directly integrate BEM surface solutions to obtain intermolecular electrostatic forces. It is, however, practicable to use the total electrostatic solvation energy calculated by BEEP to drive a Monte-Carlo simulation

    Bioinformatics

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    This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here

    Large Scale Computing and Storage Requirements for Biological and Environmental Research

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    Acta Cybernetica : Volume 20. Number 1.

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    Generalized averaged Gaussian quadrature and applications

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    A simple numerical method for constructing the optimal generalized averaged Gaussian quadrature formulas will be presented. These formulas exist in many cases in which real positive GaussKronrod formulas do not exist, and can be used as an adequate alternative in order to estimate the error of a Gaussian rule. We also investigate the conditions under which the optimal averaged Gaussian quadrature formulas and their truncated variants are internal

    MS FT-2-2 7 Orthogonal polynomials and quadrature: Theory, computation, and applications

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    Quadrature rules find many applications in science and engineering. Their analysis is a classical area of applied mathematics and continues to attract considerable attention. This seminar brings together speakers with expertise in a large variety of quadrature rules. It is the aim of the seminar to provide an overview of recent developments in the analysis of quadrature rules. The computation of error estimates and novel applications also are described

    Computer Science & Technology Series : XIX Argentine Congress of Computer Science. Selected papers

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    CACIC’13 was the nineteenth Congress in the CACIC series. It was organized by the Department of Computer Systems at the CAECE University in Mar del Plata. The Congress included 13 Workshops with 165 accepted papers, 5 Conferences, 3 invited tutorials, different meetings related with Computer Science Education (Professors, PhD students, Curricula) and an International School with 5 courses. CACIC 2013 was organized following the traditional Congress format, with 13 Workshops covering a diversity of dimensions of Computer Science Research. Each topic was supervised by a committee of 3-5 chairs of different Universities. The call for papers attracted a total of 247 submissions. An average of 2.5 review reports were collected for each paper, for a grand total of 676 review reports that involved about 210 different reviewers. A total of 165 full papers, involving 489 authors and 80 Universities, were accepted and 25 of them were selected for this book.Red de Universidades con Carreras en Informática (RedUNCI

    Proceedings of the 2018 Canadian Society for Mechanical Engineering (CSME) International Congress

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    Published proceedings of the 2018 Canadian Society for Mechanical Engineering (CSME) International Congress, hosted by York University, 27-30 May 2018

    Understanding Quantum Technologies 2022

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    Understanding Quantum Technologies 2022 is a creative-commons ebook that provides a unique 360 degrees overview of quantum technologies from science and technology to geopolitical and societal issues. It covers quantum physics history, quantum physics 101, gate-based quantum computing, quantum computing engineering (including quantum error corrections and quantum computing energetics), quantum computing hardware (all qubit types, including quantum annealing and quantum simulation paradigms, history, science, research, implementation and vendors), quantum enabling technologies (cryogenics, control electronics, photonics, components fabs, raw materials), quantum computing algorithms, software development tools and use cases, unconventional computing (potential alternatives to quantum and classical computing), quantum telecommunications and cryptography, quantum sensing, quantum technologies around the world, quantum technologies societal impact and even quantum fake sciences. The main audience are computer science engineers, developers and IT specialists as well as quantum scientists and students who want to acquire a global view of how quantum technologies work, and particularly quantum computing. This version is an extensive update to the 2021 edition published in October 2021.Comment: 1132 pages, 920 figures, Letter forma
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