• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验

轨迹数据的经验分类:机器学习在分子动力学中应用的契机。

Empirical Classification of Trajectory Data: An Opportunity for the Use of Machine Learning in Molecular Dynamics.

作者信息

Carpenter Barry K, Ezra Gregory S, Farantos Stavros C, Kramer Zeb C, Wiggins Stephen

机构信息

School of Chemistry , Cardiff University , Cardiff CF10 3AT , United Kingdom.

Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853-1301 , United States.

出版信息

J Phys Chem B. 2018 Apr 5;122(13):3230-3241. doi: 10.1021/acs.jpcb.7b08707. Epub 2017 Oct 12.

DOI:10.1021/acs.jpcb.7b08707
PMID:28968092
Abstract

Classical Hamiltonian trajectories are initiated at random points in phase space on a fixed energy shell of a model two degrees of freedom potential, consisting of two interacting minima in an otherwise flat energy plane of infinite extent. Below the energy of the plane, the dynamics are demonstrably chaotic. However, most of the work in this paper involves trajectories at a fixed energy that is 1% above that of the plane, in which regime the dynamics exhibit behavior characteristic of chaotic scattering. The trajectories are analyzed without reference to the potential, as if they had been generated in a typical direct molecular dynamics simulation. The questions addressed are whether one can recover useful information about the structures controlling the dynamics in phase space from the trajectory data alone, and whether, despite the at least partially chaotic nature of the dynamics, one can make statistically meaningful predictions of trajectory outcomes from initial conditions. It is found that key unstable periodic orbits, which can be identified on the analytical potential, appear by simple classification of the trajectories, and that the specific roles of these periodic orbits in controlling the dynamics are also readily discerned from the trajectory data alone. Two different approaches to predicting trajectory outcomes from initial conditions are evaluated, and it is shown that the more successful of them has ∼90% success. The results are compared with those from a simple neural network, which has higher predictive success (97%) but requires the information obtained from the "by-hand" analysis to achieve that level. Finally, the dynamics, which occur partly on the very flat region of the potential, show characteristics of the much-studied phenomenon called "roaming." On this potential, it is found that roaming trajectories are effectively "failed" periodic orbits and that angular momentum can be identified as a key controlling factor, despite the fact that it is not a strictly conserved quantity. It is also noteworthy that roaming on this potential occurs in the absence of a "roaming saddle," which has previously been hypothesized to be a necessary feature for roaming to occur.

摘要

经典哈密顿轨迹在一个具有两个自由度的模型势的固定能量壳层的相空间中的随机点处起始,该模型势由在无限延伸的平坦能量平面中的两个相互作用的极小值组成。在平面能量以下,动力学明显是混沌的。然而,本文的大部分工作涉及在比平面能量高1%的固定能量处的轨迹,在该能量区域,动力学表现出混沌散射的特征行为。对轨迹进行分析时不考虑势,就好像它们是在典型的直接分子动力学模拟中生成的一样。所解决的问题是,仅从轨迹数据中能否恢复关于控制相空间动力学的结构的有用信息,以及尽管动力学至少部分具有混沌性质,能否从初始条件对轨迹结果进行具有统计意义的预测。结果发现,可以通过对轨迹进行简单分类来识别在解析势上可确定的关键不稳定周期轨道,并且仅从轨迹数据中也能轻易辨别出这些周期轨道在控制动力学中的具体作用。评估了两种从初始条件预测轨迹结果的不同方法,结果表明其中更成功的方法成功率约为90%。将结果与一个简单神经网络的结果进行了比较,该神经网络具有更高的预测成功率(97%),但需要从“手工”分析中获得的信息才能达到该水平。最后,部分发生在势的非常平坦区域的动力学表现出被广泛研究的“漫游”现象的特征。在这个势上,发现漫游轨迹实际上是“失败”的周期轨道,并且角动量可被识别为一个关键控制因素,尽管它不是一个严格守恒的量。同样值得注意的是,在这个势上的漫游发生时不存在“漫游鞍点”,而之前曾假设漫游鞍点是漫游发生的必要特征。

相似文献

1
Empirical Classification of Trajectory Data: An Opportunity for the Use of Machine Learning in Molecular Dynamics.轨迹数据的经验分类:机器学习在分子动力学中应用的契机。
J Phys Chem B. 2018 Apr 5;122(13):3230-3241. doi: 10.1021/acs.jpcb.7b08707. Epub 2017 Oct 12.
2
Roaming dynamics in ion-molecule reactions: phase space reaction pathways and geometrical interpretation.离子-分子反应中的漫游动力学:相空间反应路径及几何解释
J Chem Phys. 2014 Apr 7;140(13):134112. doi: 10.1063/1.4870060.
3
Roaming: A Phase Space Perspective.漫游:相空间视角
Annu Rev Phys Chem. 2017 May 5;68:499-524. doi: 10.1146/annurev-physchem-052516-050613. Epub 2017 Mar 31.
4
The phase space geometry underlying roaming reaction dynamics.漫游反应动力学背后的相空间几何结构。
J Math Chem. 2018;56(8):2341-2378. doi: 10.1007/s10910-018-0895-4. Epub 2018 Mar 8.
5
Toward Understanding the Roaming Mechanism in H + MgH → Mg + HH Reaction.迈向理解H + MgH → Mg + HH反应中的漫游机制
J Phys Chem A. 2016 Jul 14;120(27):5145-54. doi: 10.1021/acs.jpca.6b00682. Epub 2016 Mar 11.
6
Dynamics of three noncorotating vortices in Bose-Einstein condensates.玻色-爱因斯坦凝聚体中三个非共转涡旋的动力学
Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Apr;89(4):042905. doi: 10.1103/PhysRevE.89.042905. Epub 2014 Apr 7.
7
Energy transfer mechanisms in a dipole chain: From energy equipartition to the formation of breathers.偶极链中的能量转移机制:从能量均分到声子形成。
Phys Rev E. 2018 Aug;98(2-1):022202. doi: 10.1103/PhysRevE.98.022202.
8
Crossing the dividing surface of transition state theory. IV. Dynamical regularity and dimensionality reduction as key features of reactive trajectories.穿越过渡态理论的分界面。四、反应轨迹的动力学规律和降维作为关键特征。
J Chem Phys. 2017 Apr 7;146(13):134310. doi: 10.1063/1.4979567.
9
Phase space analysis of the dynamics on a potential energy surface with an entrance channel and two potential wells.
Phys Rev E. 2020 Jul;102(1-1):012215. doi: 10.1103/PhysRevE.102.012215.
10
On chaotic dynamics in "pseudobilliard" Hamiltonian systems with two degrees of freedom.关于具有两个自由度的“伪台球”哈密顿系统中的混沌动力学
Chaos. 1997 Dec;7(4):710-730. doi: 10.1063/1.166269.

引用本文的文献

1
Hamiltonian Computational Chemistry: Geometrical Structures in Chemical Dynamics and Kinetics.哈密顿计算化学:化学动力学与反应动力学中的几何结构
Entropy (Basel). 2024 Apr 30;26(5):399. doi: 10.3390/e26050399.
2
Application of Computational Biology and Artificial Intelligence Technologies in Cancer Precision Drug Discovery.计算生物学和人工智能技术在癌症精准药物发现中的应用。
Biomed Res Int. 2019 Nov 11;2019:8427042. doi: 10.1155/2019/8427042. eCollection 2019.
3
Post-transition state bifurcations induce dynamical detours in Pummerer-like reactions.
转变后状态的分支在类Pummerer反应中引发动力学迂回。
Chem Sci. 2018 Oct 4;9(48):8937-8945. doi: 10.1039/c8sc02653j. eCollection 2018 Dec 28.
4
The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics.张量分子-0.1模型化学:一种融入长程物理的神经网络。
Chem Sci. 2018 Jan 18;9(8):2261-2269. doi: 10.1039/c7sc04934j. eCollection 2018 Feb 28.