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

doi:10.1016/j.cma.2008.12.042

CSpace

	A fast variational method for the construction of resolution adaptive C-2-smooth molecular surfaces
	Bajaj, Chandrajit L.1; Xu, Guoliang 2; Zhang, Qin
	2009
发表期刊	COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
ISSN	0045-7825
卷号	198 期号:21-26 页码:1684-1690
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.
关键词	Variational methods High-order level-set Molecular surface Geometric partial differential equation
DOI	10.1016/j.cma.2008.12.042
语种	英语
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
WOS类目	Engineering, Multidisciplinary ; Mathematics, Interdisciplinary Applications ; Mechanics
WOS记录号	WOS:000265902900005
出版者	ELSEVIER SCIENCE SA
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/7176
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.