Stoyan Markov, Peicho Petkov, Damyan Grancharov, Georgi Georgiev
We investigated the possible way for treatment of electrostatic interactions by solving numerically Poisson’s equation using Conjugate Gradient method and Stabilized BiConjugate Gradient method. The aim of the research was to test the execution time of prototype programs running on BLueGene/P and CPU/GPU system. The results show that the tested methods are applicable for electrostatics […]
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Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba
The continuum theory applied to bimolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and […]
Dimitar Pashov
The aim of this dCSE project was to improve the TBE code which is based on the tight binding model with self consistent multipole charge transfer. Given an appropriate parameterisation, the code is general and can be used to simulate a wide variety of systems and phenomena such as bond breaking, charge and magnetic polarisation. […]
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Timothy S. Lyes, K. A. Hawick
Visualising and simulating charged plasma systems present additional challenges to conventional particle methods. Plasmas exhibit multi scale phenomena that often prevent the use of standard localisation approximations. Plasmas as particle systems that emit light are important in many interesting components of games, computer animated movies such as weapons fire, explosions, astronomical effects. They also have […]
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Shuaiwen Song, Chunyi Su, Barry Rountree, Kirk W. Cameron
Emergent heterogeneous systems must be optimized for both power and performance at exascale. Massive parallelism combined with complex memory hierarchies form a barrier to efficient application and architecture design. These challenges are exacerbated with GPUs as parallelism increases orders of magnitude and power consumption can easily double. Models have been proposed to isolate power and […]
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Christopher Cooper, Lorena A. Barba
The PyGBe code solves the linearized Poisson-Boltzmann equation using a boundary-integral formulation. We use a boundary element method with a collocation approach, and solve it via a Krylov-subspace method. To do this efficiently, the matrix-vector multiplications in the Krylov iterations are accelerated with a treecode, achieving O(N log N) complexity. The code presents a Python […]
Weihua Geng, Ferosh Jacob
In this paper, we present a GPU-accelerated direct-sum boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov subspace based linear algebraic solver such as the GMRES. The molecular surfaces are discretized with flat triangles and centroid collocation. […]
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Michael Commer, Filipe R. N. C. Maia, Gregory A. Newman
Many geoscientific applications involve boundary value problems arising in simulating electrostatic and electromagnetic fields for geophysical prospecting and subsurface imaging of electrical resistivity. Modeling complex geological media with three-dimensional finite difference grids gives rise to large sparse linear systems of equations. For such systems, we have implemented three common iterative Krylov solution methods on graphics […]
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Thomas Muller, Jorg Frauendiener
We study the motion of charged particles constrained to arbitrary two-dimensional curved surfaces but interacting in three-dimensional space via the Coulomb potential. To speed-up the interaction calculations, we use the parallel compute capability of the Compute Unified Device Architecture (CUDA) of todays graphics boards. The particles and the curved surfaces are shown using the Open […]
Mayank Daga, Wu-chun Feng
BACKGROUND: Calculating the electrostatic surface potential (ESP) of a biomolecule is critical towards understanding biomolecular function. Because of its quadratic computational complexity (as a function of the number of atoms in a molecule), there have been continual efforts to reduce its complexity either by improving the algorithm or the underlying hardware on which the calculations […]
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W. Michael Brown, Axel Kohlmeyer, Steven J. Plimpton, Arnold N. Tharrington
The use of accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high-performance computers, machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), are now becoming more […]
Raul Ernesto Torres Carvajal
This document proposes an alternative method for the comparison of molecular electrostatic potential (MEP), based on parallel computing algorithms on graphics cards using NVIDIA CUDA platform and kernel methods for pattern recognition. The proposed solution optimizes the construction process of a particular representation of MEP, presents options for improving this representation, and offers 11 kernel […]
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