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

doi:10.1021/acs.jctc.7b00394

	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
	Li, Xusong 1,2,3,4; Xie, Yu1 ; Hu, Deping 1,3; Lan, Zhenggang 1,2,3
	2017-10-01
发表期刊	JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷号	13 期号:10 页码:4611-4623
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.
文章类型	Article
WOS标题词	Science & Technology ; Physical Sciences
DOI	10.1021/acs.jctc.7b00394
关键词[WOS]	FREE-ENERGY LANDSCAPES ; RELATE 2 SETS ; MOLECULAR-DYNAMICS ; SEMIEMPIRICAL METHODS ; CONICAL INTERSECTIONS ; QUANTUM DYNAMICS ; DIFFUSION MAPS ; SKETCH-MAP ; IMPLEMENTATION ; REPRESENTATION
收录类别	SCI
语种	英语
WOS研究方向	Chemistry ; Physics
项目资助者	NSFC(21673266 ; Natural Science Foundation of Shandong Province(JQ201504) ; 21503248)
WOS类目	Chemistry, Physical ; Physics, Atomic, Molecular & Chemical
WOS记录号	WOS:000412965700002
引用统计
文献类型	期刊论文
条目标识符	http://ir.qibebt.ac.cn/handle/337004/9564
专题	先进材料理论与模拟团队（过去）
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.