KMS Of Academy of mathematics and systems sciences, CAS
| An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics | |
Lu, Benzhuo1 ; Cheng, Xiaolin2; Huang, Jingfang3; McCammon, J. Andrew4
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| 2009-06-01 | |
| Source Publication | JOURNAL OF CHEMICAL THEORY AND COMPUTATION
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| ISSN | 1549-9618 |
| Volume | 5Issue:6Pages:1692-1699 |
| Abstract | 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 |
| Language | 英语 |
| Funding Project | 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 Research Area | Chemistry ; Physics |
| WOS Subject | Chemistry, Physical ; Physics, Atomic, Molecular & Chemical |
| WOS ID | WOS:000266865000024 |
| Publisher | AMER CHEMICAL SOC |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/9015 |
| Collection | 计算数学与科学工程计算研究所 |
| Corresponding Author | Lu, Benzhuo |
| Affiliation | 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 |
| Recommended Citation 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. |
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