Analysis of the Geometrical Evolution in On-the-Fly Surface-Hopping Nonadiabatic Dynamics with Machine Learning Dimensionality Reduction Approaches: Classical Multidimensional Scaling and Isometric Feature Mapping
文献类型：期刊论文
| 作者 | Li, Xusong1,2,3,4; Xie, Yu1 ; Hu, Deping1,3; Lan, Zhenggang1,2,3
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| 刊名 | JOURNAL OF CHEMICAL THEORY AND COMPUTATION
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| 出版日期 | 2017-10-01 |
| 卷号 | 13期号:10页码:4611-4623 |
| DOI | 10.1021/acs.jctc.7b00394 |
| 文献子类 | Article |
| 英文摘要 | On-the-fly trajectory-based nonadiabatic dynamics simulation has become an important approach to study ultrafast photochemical and photophysical processes in recent years. Because a large number of trajectories are generated from the dynamics simulation of polyatomic molecular systems with many degrees of freedom, the analysis of simulation results often suffers from the large amount of high-dimensional data. It is very challenging but meaningful to find dominating active coordinates from very complicated molecular motions. Dimensionality reduction techniques provide ideal tools to realize this purpose. We apply two dimensionality reduction approaches (classical multidimensional scaling and isometric feature mapping) to analyze the results of the on-the-fly surface-hopping nonadiabatic dynamics simulation. Two representative model systems, CH2NH2+ and the phytochromobilin chromophore model, are chosen to examine the performance of these dimensionality reduction approaches. The results show that these approaches are very promising, because they can extract the major molecular motion from complicated time-dependent molecular evolution without preknown knowledge. |
| WOS关键词 | FREE-ENERGY LANDSCAPES ; RELATE 2 SETS ; MOLECULAR-DYNAMICS ; SEMIEMPIRICAL METHODS ; CONICAL INTERSECTIONS ; QUANTUM DYNAMICS ; DIFFUSION MAPS ; SKETCH-MAP ; IMPLEMENTATION ; REPRESENTATION |
| WOS研究方向 | Chemistry ; Physics |
| 语种 | 英语 |
| WOS记录号 | WOS:000412965700002 |
| 资助机构 | NSFC(21673266 ; Natural Science Foundation of Shandong Province(JQ201504) ; 21503248) |
| 源URL | [http://ir.qibebt.ac.cn/handle/337004/9564]  |
| 专题 | 青岛生物能源与过程研究所_先进材料理论与模拟团队 |
| 作者单位 | 1.Chinese Acad Sci, CAS Key Lab Biobased Mat, Qingdao Inst Bioenergy & Bioproc Technol, Qingdao 266101, Peoples R China 2.Univ Chinese Acad Sci, Sinodanish Ctr Educ & Res, Sinodanish Coll, Beijing 100049, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Tech Univ Denmark, Dept Chem, Kemitorvet 207, DK-2800 Lyngby, Denmark |
| 推荐引用方式 GB/T 7714 | Li, Xusong,Xie, Yu,Hu, Deping,et al. Analysis of the Geometrical Evolution in On-the-Fly Surface-Hopping Nonadiabatic Dynamics with Machine Learning Dimensionality Reduction Approaches: Classical Multidimensional Scaling and Isometric Feature Mapping[J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION,2017,13(10):4611-4623. |
| APA | Li, Xusong,Xie, Yu,Hu, Deping,&Lan, Zhenggang.(2017).Analysis of the Geometrical Evolution in On-the-Fly Surface-Hopping Nonadiabatic Dynamics with Machine Learning Dimensionality Reduction Approaches: Classical Multidimensional Scaling and Isometric Feature Mapping.JOURNAL OF CHEMICAL THEORY AND COMPUTATION,13(10),4611-4623. |
| MLA | Li, Xusong,et al."Analysis of the Geometrical Evolution in On-the-Fly Surface-Hopping Nonadiabatic Dynamics with Machine Learning Dimensionality Reduction Approaches: Classical Multidimensional Scaling and Isometric Feature Mapping".JOURNAL OF CHEMICAL THEORY AND COMPUTATION 13.10(2017):4611-4623. |
入库方式： OAI收割
来源：青岛生物能源与过程研究所
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