CSpace  > 计算数学与科学工程计算研究所
EFFICIENT AND QUALIFIED MESH GENERATION FOR GAUSSIAN MOLECULAR SURFACE USING ADAPTIVE PARTITION AND PIECEWISE POLYNOMIAL APPROXIMATION
Liu, Tiantian1,2; Chen, Minxin3; Lu, Benzhuo2
2018
Source PublicationSIAM JOURNAL ON SCIENTIFIC COMPUTING
ISSN1064-8275
Volume40Issue:2Pages:B507-B527
AbstractRecent developments for mathematical modeling and numerical simulation of biomolecular systems raise new demands for qualified, stable, and efficient surface meshing, especially in implicit-solvent modeling [B. Z. Lu et al., Commun. Comput. Phys., 3 (2008), pp. 973-1009]. In our former work, we have developed an algorithm for manifold triangular meshing for large Gaussian molecular surfaces, TMSmesh [M. Chen and B. Lu, T. Chem. Theory Comput., 7 (2011), pp. 203-212; M. Chen, B. Tu, and B. Lu, T. Molecular Graphics Model., 38 (2012), pp. 411-418]. In this paper, we present new algorithms to greatly improve the meshing efficiency and qualities, and implement them into a new program version, TMSmesh 2.0. In TMSmesh 2.0, in the first step, a new adaptive partition and estimation algorithm is proposed to locate the cubes in which the surface is approximated by a piecewise trilinear surface with controllable precision. Then, the piecewise trilinear surface is divided into single valued pieces by tracing along the fold curves, which ensures that the generated surface meshes are manifolds. Numerical test results show that TMSmesh 2.0 is capable of handling arbitrary sizes of molecules and achieves ten to hundreds of times speedup over the previous algorithm. In all of our extensively tested molecules, the resulting surface meshes are all manifolds and can be used in boundary element method (BEM) and finite element method (FEM) simulation.
Keywordsurface mesh generation Gaussian surface triangulation adaptive partition trilinear polynomial
DOI10.1137/16MI1099704
Language英语
Funding ProjectScience Challenge Project[SCP TZ2016003-1] ; National Key Research and Development Program China[2016YFB0201304] ; China NSF[NSFC 91530102] ; China NSF[NSFC 21573274] ; China NSF[NSFC 11301368] ; China NSF[NSFC 11404300] ; NSF of Jiangsu Province[BK20130278]
WOS Research AreaMathematics
WOS SubjectMathematics, Applied
WOS IDWOS:000431100400033
PublisherSIAM PUBLICATIONS
Citation statistics
Cited Times:2[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/30219
Collection计算数学与科学工程计算研究所
Affiliation1.Soochow Univ, Dept Math, Suzhou 215006, Peoples R China
2.Chinese Acad Sci, Acad Math & Syst Sci, State Key Lab Sci & Engn Comp, Beijing 100190, Peoples R China
3.Soochow Univ, Dept Math, Suzhou 215006, Peoples R China
Recommended Citation
GB/T 7714
Liu, Tiantian,Chen, Minxin,Lu, Benzhuo. EFFICIENT AND QUALIFIED MESH GENERATION FOR GAUSSIAN MOLECULAR SURFACE USING ADAPTIVE PARTITION AND PIECEWISE POLYNOMIAL APPROXIMATION[J]. SIAM JOURNAL ON SCIENTIFIC COMPUTING,2018,40(2):B507-B527.
APA Liu, Tiantian,Chen, Minxin,&Lu, Benzhuo.(2018).EFFICIENT AND QUALIFIED MESH GENERATION FOR GAUSSIAN MOLECULAR SURFACE USING ADAPTIVE PARTITION AND PIECEWISE POLYNOMIAL APPROXIMATION.SIAM JOURNAL ON SCIENTIFIC COMPUTING,40(2),B507-B527.
MLA Liu, Tiantian,et al."EFFICIENT AND QUALIFIED MESH GENERATION FOR GAUSSIAN MOLECULAR SURFACE USING ADAPTIVE PARTITION AND PIECEWISE POLYNOMIAL APPROXIMATION".SIAM JOURNAL ON SCIENTIFIC COMPUTING 40.2(2018):B507-B527.
Files in This Item:
There are no files associated with this item.
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[Liu, Tiantian]'s Articles
[Chen, Minxin]'s Articles
[Lu, Benzhuo]'s Articles
Baidu academic
Similar articles in Baidu academic
[Liu, Tiantian]'s Articles
[Chen, Minxin]'s Articles
[Lu, Benzhuo]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[Liu, Tiantian]'s Articles
[Chen, Minxin]'s Articles
[Lu, Benzhuo]'s Articles
Terms of Use
No data!
Social Bookmark/Share
All comments (0)
No comment.
 

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.