12787
Marcos Novalbos, Jaime Gonzalez, Miguel A. Otaduy, Roberto Martinez Benito, Alberto Sanchez
Molecular dynamics simulations allow us to study the behavior of complex biomolecular systems by modeling the pairwise interaction forces between all atoms. Molecular systems are subject to slowly decaying electrostatic potentials, which turn molecular dynamics into an n-body problem. In this paper, we present a parallel and scalable solution to compute long-range molecular forces, based […]
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Jianbin Fang, Ana Lucia Varbanescu, Baldomero Imbernon, Jose M. Cecilia, Horacio Perez-Sanchez
Currently, medical research for the discovery of new drugs is increasingly using Virtual Screening (VS) methods. In these methods, the calculation of the non-bonded interactions, such as electrostatic or van der Waals, plays an important role, representing up to 80% of the total execution time. These are computationally intensive operations, and massively parallel in nature, […]
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Shyam Mohan K T, Jayaraj P B
Methods for Molecular Dynamics(MD) simulations are investigated. MD simulation is the widely used computer simulation approach to study the properties of molecular system. Force calculation in MD is computationally intensive. Parallel programming techniques can be applied to improve those calculations. The major aim of this paper is to speed up the MD simulation calculations by/using […]
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Jose Colmenares, Antonella Galizia, Jesus Ortiz, Andrea Clematis, Walter Rocchia
The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational Structural Biology to estimate the electrostatic energetic component of the assembly of molecular biological systems. In the last decades the amount of structural data concerning proteins and other […]
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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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