EFFICIENT AND QUALIFIED MESH GENERATION FOR GAUSSIAN MOLECULAR SURFACE USING ADAPTIVE PARTITION AND PIECEWISE POLYNOMIAL APPROXIMATION

doi:10.1137/16MI1099704

	EFFICIENT AND QUALIFIED MESH GENERATION FOR GAUSSIAN MOLECULAR SURFACE USING ADAPTIVE PARTITION AND PIECEWISE POLYNOMIAL APPROXIMATION
	Liu, Tiantian 1,2; Chen, Minxin 3; Lu, Benzhuo2
	2018
发表期刊	SIAM JOURNAL ON SCIENTIFIC COMPUTING
ISSN	1064-8275
卷号	40 期号:2 页码:B507-B527
摘要	Recent 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.
关键词	surface mesh generation Gaussian surface triangulation adaptive partition trilinear polynomial
DOI	10.1137/16MI1099704
语种	英语
资助项目	Science 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研究方向	Mathematics
WOS类目	Mathematics, Applied
WOS记录号	WOS:000431100400033
出版者	SIAM PUBLICATIONS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/30219
专题	计算数学与科学工程计算研究所
通讯作者	Chen, Minxin
作者单位	1.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
推荐引用方式 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.