An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics

doi:10.1021/ct900083k

	An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics
	Lu, Benzhuo1 ; Cheng, Xiaolin 2; Huang, Jingfang 3; McCammon, J. Andrew 4
	2009-06-01
发表期刊	JOURNAL OF CHEMICAL THEORY AND COMPUTATION
ISSN	1549-9618
卷号	5 期号:6 页码:1692-1699
摘要	The numerical solution of the Poisson-Boltzmann (PB) equation is a useful but a computationally demanding tool for studying electrostatic solvation effects in chemical and biomolecular systems. Recently, we have described a boundary integral equation-based PB solver accelerated by a new version of the fast multipole method (FMM). The overall algorithm shows an order N complexity in both the computational cost and memory usage. Here, we present an updated version of the solver by using an adaptive FMM for accelerating the convolution type matrix-vector multiplications. The adaptive algorithm, when compared to our previous nonadaptive one, not only significantly improves the performance of the overall memory usage but also remarkably speeds the calculation because of an improved load balancing between the local- and far-field calculations. We have also implemented a node-patch discretization scheme that leads to a reduction of unknowns by a factor of 2 relative to the constant element method without sacrificing accuracy. As a result of these improvements, the new solver makes the PB calculation truly feasible for large-scale biomolecular systems such as a 30S ribosome molecule even on a typical 2008 desktop computer.
DOI	10.1021/ct900083k
语种	英语
资助项目	HHMI ; NIH ; NSF[NSF0811130] ; NSF[NSF0411920] ; NSF[MCB0506593] ; NSF Center of Theoretical Biological Physics (CTBP) ; Chinese Academy of Sciences, China ; Computer Science and Mathematics Division at Oak Ridge National Laboratory
WOS研究方向	Chemistry ; Physics
WOS类目	Chemistry, Physical ; Physics, Atomic, Molecular & Chemical
WOS记录号	WOS:000266865000024
出版者	AMER CHEMICAL SOC
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/9015
专题	计算数学与科学工程计算研究所
通讯作者	Lu, Benzhuo
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Inst Computat Math & Sci Engn Comp, Beijing 100190, Peoples R China 2.Oak Ridge Natl Lab, Ctr Biophys Mol, Oak Ridge, TN 37831 USA 3.Univ N Carolina, Dept Math, Chapel Hill, NC 27599 USA 4.Univ Calif San Diego, Dept Chem & Biochem, Ctr Theoret Biol Phys, Howard Hughes Med Inst,Dept Pharmacol, San Diego, CA 92093 USA
推荐引用方式 GB/T 7714	Lu, Benzhuo,Cheng, Xiaolin,Huang, Jingfang,et al. An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics[J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION,2009,5(6):1692-1699.
APA	Lu, Benzhuo,Cheng, Xiaolin,Huang, Jingfang,&McCammon, J. Andrew.(2009).An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics.JOURNAL OF CHEMICAL THEORY AND COMPUTATION,5(6),1692-1699.
MLA	Lu, Benzhuo,et al."An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics".JOURNAL OF CHEMICAL THEORY AND COMPUTATION 5.6(2009):1692-1699.