23 research outputs found
Large-scale parallelised boundary element method electrostatics for biomolecular simulation
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
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
Generalized averaged Gaussian quadrature and applications
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
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
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
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
Understanding Quantum Technologies 2022 is a creative-commons ebook that
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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