TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique
文献类型：期刊论文
| 作者 | Chen, Minxin1; Lu, Benzhuo2
|
| 刊名 | JOURNAL OF CHEMICAL THEORY AND COMPUTATION
 |
| 出版日期 | 2011 |
| 卷号 | 7期号:1页码:203-212 |
| ISSN号 | 1549-9618 |
| DOI | 10.1021/ct100376g |
| 英文摘要 | 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. |
| 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 |
| 语种 | 英语 |
| WOS记录号 | WOS:000285990300022 |
| 出版者 | AMER CHEMICAL SOC |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/11351]  |
| 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. |
入库方式： OAI收割
来源：数学与系统科学研究院
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