TY - JOUR
T1 - Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver
AU - Bo Zhang, Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, Nikos P. Pitsianis, Xiaobai Sun & J. Andrew McCammon
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 - <p style="text-align: justify;">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.</p>