KMS Of Academy of mathematics and systems sciences, CAS
| Automated Parallel and Body-Fitted Mesh Generation in Finite Element Simulation of Macromolecular Systems | |
Xie, Yan1; Liu, Tiantian1; Tu, Bin2; Lu, Benzhuo1 ; Zhang, Linbo1
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| 2016-03-01 | |
| Source Publication | COMMUNICATIONS IN COMPUTATIONAL PHYSICS
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| ISSN | 1815-2406 |
| Volume | 19Issue:3Pages:582-602 |
| Abstract | Mesh generation is a bottleneck for finite element simulations of biomolecules. A robust and efficient approach, based on the immersed boundary method proposed in [8], has been developed and implemented to generate large-scale mesh body-fitted to molecular shape for general parallel finite element simulations. The molecular Gaussian surface is adopted to represent the molecular surface, and is finally approximated by piecewise planes via the tool phgSurfaceCut in PHG [43], which is improved and can reliably handle complicated molecular surfaces, through mesh refinement steps. A coarse background mesh is imported first and then is distributed into each process using a mesh partitioning algorithm such as space filling curve [5] or METIS [22]. A bisection method is used for the mesh refinements according to the molecular PDB or PQR file which describes the biomolecular region. After mesh refinements, the mesh is optionally repartitioned and redistributed for load balancing. For finite element simulations, the modification of region mark and boundary types is done in parallel. Our parallel mesh generation method has been successfully applied to a sphere cavity model, a DNA fragment, a gramicidin A channel and a huge Dengue virus system. The results of numerical experiments show good parallel efficiency. Computations of electrostatic potential and solvation energy also validate the method. Moreover, the meshing process and adaptive finite element computation can be integrated as one PHG project to avoid the mesh importing and exporting costs, and improve the convenience of application as well. |
| Keyword | Parallel mesh generation body-fitted PHG biomolecules finite element simulation |
| DOI | 10.4208/cicp.161114.021015a |
| Language | 英语 |
| Funding Project | National 973 Project of China[2011CB309703] ; National 863 Project of China[2012AA01A309] ; China NSF[91430215] ; China NSF[91530323] ; China NSF[11321061] ; China NSF[91230106] ; China NSF[91530102] ; China NSF[21573274] ; State Key Laboratory of Scientific/Engineering Computing ; National Center for Mathematics and Interdisciplinary Sciences of Chinese Academy of Sciences ; State Key Laboratory of Scientific/Engineering Computing, National Center for Mathematics and Interdisciplinary Sciences, the Chinese Academy of Sciences |
| WOS Research Area | Physics |
| WOS Subject | Physics, Mathematical |
| WOS ID | WOS:000372156900002 |
| Publisher | GLOBAL SCIENCE PRESS |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/22297 |
| Collection | 计算数学与科学工程计算研究所 |
| Corresponding Author | Lu, Benzhuo; Zhang, Linbo |
| Affiliation | 1.Chinese Acad Sci, Acad Math & Syst Sci, Inst Computat Math & Sci Engn Comp, State Key Lab Sci & Engn Comp, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Natl Ctr Nanosci & Technol, Beijing 100190, Peoples R China |
| Recommended Citation GB/T 7714 | Xie, Yan,Liu, Tiantian,Tu, Bin,et al. Automated Parallel and Body-Fitted Mesh Generation in Finite Element Simulation of Macromolecular Systems[J]. COMMUNICATIONS IN COMPUTATIONAL PHYSICS,2016,19(3):582-602. |
| APA | Xie, Yan,Liu, Tiantian,Tu, Bin,Lu, Benzhuo,&Zhang, Linbo.(2016).Automated Parallel and Body-Fitted Mesh Generation in Finite Element Simulation of Macromolecular Systems.COMMUNICATIONS IN COMPUTATIONAL PHYSICS,19(3),582-602. |
| MLA | Xie, Yan,et al."Automated Parallel and Body-Fitted Mesh Generation in Finite Element Simulation of Macromolecular Systems".COMMUNICATIONS IN COMPUTATIONAL PHYSICS 19.3(2016):582-602. |
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