Volume 13, Issue 1
Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver

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

Commun. Comput. Phys., 13 (2013), pp. 107-128.

Published online: 2013-01

Preview Full PDF 606 2807
Export citation
  • Abstract

This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann (AFMPB) solver. We introduce and discuss the following components in order: the Poisson-Boltzmann model, boundary integral equation reformulation, surface mesh generation, the node-patch discretization approach, Krylov iterative methods, the new version of fast multipole methods (FMMs), and a dynamic prioritization technique for scheduling parallel operations. For each component, we also remark on feasible approaches for further improvements in efficiency, accuracy and applicability of the AFMPB solver to large-scale long-time molecular dynamics simulations. The potential of the solver is demonstrated with preliminary numerical results.

  • Keywords

  • AMS Subject Headings

  • Copyright

COPYRIGHT: © Global Science Press

  • Email address
  • BibTex
  • RIS
  • TXT
@Article{CiCP-13-107, author = {}, title = {Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver}, journal = {Communications in Computational Physics}, year = {2013}, volume = {13}, number = {1}, pages = {107--128}, abstract = {

This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann (AFMPB) solver. We introduce and discuss the following components in order: the Poisson-Boltzmann model, boundary integral equation reformulation, surface mesh generation, the node-patch discretization approach, Krylov iterative methods, the new version of fast multipole methods (FMMs), and a dynamic prioritization technique for scheduling parallel operations. For each component, we also remark on feasible approaches for further improvements in efficiency, accuracy and applicability of the AFMPB solver to large-scale long-time molecular dynamics simulations. The potential of the solver is demonstrated with preliminary numerical results.

}, issn = {1991-7120}, doi = {https://doi.org/10.4208/cicp.210711.111111s}, url = {http://global-sci.org/intro/article_detail/cicp/7214.html} }
TY - JOUR T1 - Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver JO - Communications in Computational Physics VL - 1 SP - 107 EP - 128 PY - 2013 DA - 2013/01 SN - 13 DO - http://doi.org/10.4208/cicp.210711.111111s UR - https://global-sci.org/intro/article_detail/cicp/7214.html KW - AB -

This paper summarizes the mathematical and numerical theories and computational elements of the adaptive fast multipole Poisson-Boltzmann (AFMPB) solver. We introduce and discuss the following components in order: the Poisson-Boltzmann model, boundary integral equation reformulation, surface mesh generation, the node-patch discretization approach, Krylov iterative methods, the new version of fast multipole methods (FMMs), and a dynamic prioritization technique for scheduling parallel operations. For each component, we also remark on feasible approaches for further improvements in efficiency, accuracy and applicability of the AFMPB solver to large-scale long-time molecular dynamics simulations. The potential of the solver is demonstrated with preliminary numerical results.

Bo Zhang, Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, Nikos P. Pitsianis, Xiaobai Sun & J. Andrew McCammon. (2020). Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver. Communications in Computational Physics. 13 (1). 107-128. doi:10.4208/cicp.210711.111111s
Copy to clipboard
The citation has been copied to your clipboard