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

doi:10.1137/16MI1099704

CORC > 数学与系统科学研究院 > 中国科学院数学与系统科学研究院 > 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, Tiantian 1,2; Chen, Minxin 3; Lu, Benzhuo2
刊名	SIAM JOURNAL ON SCIENTIFIC COMPUTING
	2018
卷号	40 期号:2 页码:B507-B527
关键词	surface mesh generation Gaussian surface triangulation adaptive partition trilinear polynomial
ISSN号	1064-8275
DOI	10.1137/16MI1099704
英文摘要	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.
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
语种	英语
出版者	SIAM PUBLICATIONS
WOS记录号	WOS:000431100400033
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/30218]
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.