Mathematical and numerical aspects of the adaptive fast multipole Poisson-Boltzmann solver

DOI10.4208/CICP.210711.111111SMaRDI QIDQ4588741zbMATH OpenOpenAlexWikidataFDO

Authors Bo Zhang, Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, Nikos P. Pitsianis, Xiaobai Sun, J. Andrew McCammon

Publication date 27 October 2017

Published in Communications in Computational Physics (Search for Journal in Brave)

Full work available at URL https://semanticscholar.org/paper/2a57e52ddfc1d8f350f80ce9c82f6b5200a63097

Mathematics Subject Classification ID

Software, source code, etc. for problems pertaining to optics and electromagnetic theory (78-04) Multipole methods applied to problems in optics and electromagnetic theory (78M16)

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• Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation
• Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery
• Linear-scaling selected inversion based on hierarchical interpolative factorization for self Green's function for modified Poisson-Boltzmann equation in two dimensions
• On preconditioning the treecode-accelerated boundary integral (TABI) Poisson-Boltzmann solver
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• An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics
• Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy
• A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
• A weighted adaptive least-squares finite element method for the Poisson-Boltzmann equation
• An Adaptive, Finite Difference Solver for the Nonlinear Poisson-Boltzmann Equation with Applications to Biomolecular Computations
• Accurate p\(K_a\) computation using matched interface and boundary (MIB) method based Poisson-Boltzmann solver
• DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture
• AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems
• Cyclically parallelized treecode for fast computations of electrostatic interactions on molecular surfaces
• Adaptive numerical method for Poisson-Boltzmann equation and its application
• A new boundary condition for the nonlinear Poisson-Boltzmann equation in electrostatic analysis of proteins

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