Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation
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Publication:346360
DOI10.1016/J.JCP.2013.01.029zbMATH Open1349.78083arXiv1301.5914OpenAlexW2075229464MaRDI QIDQ346360FDOQ346360
Authors: Weihua Geng 
Publication date: 5 December 2016
Published in: Journal of Computational Physics (Search for Journal in Brave)
Abstract: In this paper, we present a parallel higher-order 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 linear solver such as GMRES. The molecular surfaces are first discretized with flat triangles and then converted to curved triangles with the assistance of normal information at vertices. To maintain the desired accuracy, four-point Gauss-Radau quadratures are used on regular triangles and sixteen-point Gauss-Legendre quadratures together with regularization transformations are applied on singular triangles. To speed up our method, we take advantage of the embarrassingly parallel feature of boundary integral formulation, and parallelize the schemes with the message passing interface (MPI) implementation. Numerical tests show significantly improved accuracy and convergence of the proposed higher-order boundary integral Poisson-Boltzmann (HOBI-PB) solver compared with boundary integral PB solver using often-seen centroid collocation on flat triangles. The higher-order accuracy results achieved by present method are important to sensitive solvation analysis of biomolecules, particularly when accurate electrostatic surface potentials are critical in the molecular simulation. In addition, the higher-order boundary integral schemes presented here and their associated parallelization potentially can be applied to solving boundary integral equations in a general sense.
Full work available at URL: https://arxiv.org/abs/1301.5914
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Boltzmann equations (35Q20) Electromagnetic effects in solid mechanics (74F15) Boundary element methods applied to problems in optics and electromagnetic theory (78M15)
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Cited In (10)
- On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver
- An implicit boundary integral method for computing electric potential of macromolecules in solvent
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- A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver
- A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations
- A high-order fast boundary element method with near-boundary stability for field emission from nanoscale structures
- Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy
- Optimized parallelization of boundary integral Poisson-Boltzmann solvers
- Fully implicit ADI schemes for solving the nonlinear Poisson-Boltzmann equation
- An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics
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