A fast variational method for the construction of resolution adaptive C-2-smooth molecular surfaces
文献类型：期刊论文
| 作者 | Bajaj, Chandrajit L.1; Xu, Guoliang2; Zhang, Qin |
| 刊名 | COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
 |
| 出版日期 | 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 |
| WOS记录号 | WOS:000265902900005 |
| 出版者 | ELSEVIER SCIENCE SA |
| 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. |
入库方式： OAI收割
来源：数学与系统科学研究院
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