TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique

doi:10.1021/ct100376g

	TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique
	Chen, Minxin 1; Lu, Benzhuo2
	2011
发表期刊	JOURNAL OF CHEMICAL THEORY AND COMPUTATION
ISSN	1549-9618
卷号	7 期号:1 页码:203-212
摘要	Qualified, stable, and efficient molecular surface meshing appears to be necessitated by recent developments for realistic mathematical modeling and numerical simulation of biomolecules, especially in implicit solvent modeling (e.g., see a review in B. Z. Lu et al. Commun. Comput. Phys. 2008, 3, 973-1009). In this paper, we present a new method: tracing molecular surface for meshing (TMSmesh) the Gaussian surface of biomolecules. The method computes the surface points by solving a nonlinear equation directly, polygonizes by connecting surface points through a trace technique, and finally outputs a triangulated mesh. TMSmesh has a linear complexity with respect to the number of atoms and is shown to be capable of handling molecules consisting of more than one million atoms, which is usually difficult for the existing methods for surface generation used in molecular visualization and geometry analysis. Moreover, the meshes generated by TMSmesh are successfully tested in boundary element solutions of the Poisson-Boltzmann equation, which directly gives rise to a route to simulate electrostatic solvation of large-scale molecular systems. The binary version of TMSmesh and a set of representative PQR benchmark molecules are downloadable at our Web page http://lsec.cc.ac.cn/similar to lubz/Meshing.html.
DOI	10.1021/ct100376g
语种	英语
资助项目	China NSF[NSFC20872107] ; China NSF[NSFC10971218] ; Chinese Academy of Sciences ; State Key Laboratory of Scientific/Engineering Computing
WOS研究方向	Chemistry ; Physics
WOS类目	Chemistry, Physical ; Physics, Atomic, Molecular & Chemical
WOS记录号	WOS:000285990300022
出版者	AMER CHEMICAL SOC
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/11352
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, Inst Computat Math, State Key Lab Sci Engn Comp, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Chen, Minxin,Lu, Benzhuo. TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique[J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION,2011,7(1):203-212.
APA	Chen, Minxin,&Lu, Benzhuo.(2011).TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique.JOURNAL OF CHEMICAL THEORY AND COMPUTATION,7(1),203-212.
MLA	Chen, Minxin,et al."TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique".JOURNAL OF CHEMICAL THEORY AND COMPUTATION 7.1(2011):203-212.