Mathematical and Numerical Aspects of the Adaptive Fast Multipole Poisson-Boltzmann Solver  

作　　者：Bo Zhang Benzhuo Lu Xiaolin Cheng Jingfang Huang Nikos P.Pitsianis Xiaobai Sun JAndrew McCammon 

机构地区：[1]Department of Computer Science,Duke University,NC 27708,USA [2]Institute of Computational Mathematics and Scientific/Engineering Computing,Academy of Mathematics and Systems Science,Chinese Academy of Sciences,Beijing 100910,China [3]Center for Molecular Biophysics,Oak Ridge National Laboratory,TN 37831,USA [4]Department of Mathematics,University of North Carolina,Chapel Hill,NC 27599,USA [5]Department of Electrical and Computer Engineering,Aristotle University,Thessaloniki,54124,Greece [6]Department of Chemistry&Biochemistry,Center for Theoretical Biological Physics,Department of Pharmacology,Howard Hughes Medical Institute,University of California,San Diego,CA 92093,USA

出　　处：《Communications in Computational Physics》2013年第1期107-128,共22页计算物理通讯（英文）

基　　金：supported by NSF,DOE,HHMI,and NIH(B.Z./X.S./N.P.:NSF 0905164,B.Z./J.H.:NSF 0811130 and NSF 0905473,J.A.M.:NSF MCB1020765 and NIH GM31749);the NSF Center of Theoretical Biological Physics(CTBP);partially funded by the Chinese Academy of Sciences,the State Key Laboratory of Scientific/Engineering Computing,and the China NSF(NSFC1097218).

摘　　要：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 nodepatch 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 largescale long-time molecular dynamics simulations.The potential of the solver is demonstrated with preliminary numerical results.

关 键 词：Biomolecular system ELECTROSTATICS Poisson-Boltzmann equation fast multipole methods mesh generation directed acyclic graph dynamic prioritization PARALLELIZATION 

分 类 号：O17[理学—数学]