A fast variational method for the construction of resolution adaptive C-2-smooth molecular surfaces

doi:10.1016/j.cma.2008.12.042

	A fast variational method for the construction of resolution adaptive C-2-smooth molecular surfaces
	Bajaj, Chandrajit L.1; Xu, Guoliang 2; Zhang, Qin
刊名	COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
	2009
卷号	198 期号:21-26 页码:1684-1690
关键词	Variational methods High-order level-set Molecular surface Geometric partial differential equation
ISSN号	0045-7825
DOI	10.1016/j.cma.2008.12.042
英文摘要	We present a variational approach to smooth molecular (proteins, nucleic acids) surface constructions, starting from atomic coordinates. as available from the protein and nucleic acid data banks. Molecular dynamics (MD) simulations traditionally used in understanding protein and nucleic acid folding processes, are based on molecular force fields, and require smooth models of these molecular surfaces. To accelerate MD simulations, a popular methodology is to employ coarse grained molecular models, which represent clusters of atoms with similar physical properties by psuedo-atoms, resulting in coarser resolution molecular surfaces. We consider generation of these mixed-resolution or adaptive molecular surfaces. Our approach starts from deriving a general form second order geometric partial differential equation in the level-set formulation, by minimizing a first order energy functional which additionally includes a regularization term to minimize the occurrence of chemically infeasible molecular surface pockets or tunnel-like artifacts. To achieve even higher computational efficiency, a fast cubic B-spline C-2 interpolation algorithm is also utilized. A narrow band, tri-cubic B-spline level-set method is then used to provide C-2 smooth and resolution adaptive molecular surfaces. (C) 2009 Published by Elsevier B.V.
资助项目	NSF[CNS-0540033] ; NIH[P20-RR020647] ; NIH[R01-CM074258] ; NIH[R01-CM07308] ; NIH[R01-EB004873] ; NIH[R01-GM074258] ; NIH[R01-GM07308] ; NSFC[60773165] ; National Key Basic Research Project of China[2004CB318000]
WOS研究方向	Engineering ; Mathematics ; Mechanics
语种	英语
出版者	ELSEVIER SCIENCE SA
WOS记录号	WOS:000265902900005
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/7175]
专题	中国科学院数学与系统科学研究院
通讯作者	Bajaj, Chandrajit L.
作者单位	1.Univ Texas Austin, CVC, Dept Comp Sci, Inst Computat Engn & Sci, Austin, TX 78712 USA 2.Chinese Acad Sci, LSEC, Inst Computat Math, Acad Math & Syst Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Bajaj, Chandrajit L.,Xu, Guoliang,Zhang, Qin. A fast variational method for the construction of resolution adaptive C-2-smooth molecular surfaces[J]. COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING,2009,198(21-26):1684-1690.
APA	Bajaj, Chandrajit L.,Xu, Guoliang,&Zhang, Qin.(2009).A fast variational method for the construction of resolution adaptive C-2-smooth molecular surfaces.COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING,198(21-26),1684-1690.
MLA	Bajaj, Chandrajit L.,et al."A fast variational method for the construction of resolution adaptive C-2-smooth molecular surfaces".COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING 198.21-26(2009):1684-1690.