利用机器学习的纳米粒子全局优化分而治之法

IF 5.6 2区 化学 Q1 CHEMISTRY, MEDICINAL Journal of Chemical Information and Modeling Pub Date : 2024-11-15 DOI:10.1021/acs.jcim.4c01516
Nicholas B Smith, Anna L Garden
{"title":"利用机器学习的纳米粒子全局优化分而治之法","authors":"Nicholas B Smith, Anna L Garden","doi":"10.1021/acs.jcim.4c01516","DOIUrl":null,"url":null,"abstract":"<p><p>Global optimization of the structure of atomic nanoparticles is often hampered by the presence of many funnels on the potential energy surface. While broad funnels are readily encountered and easily exploited by the search, narrow funnels are more difficult to locate and explore, presenting a problem if the global minimum is situated in such a funnel. Here, a divide-and-conquer approach is applied to overcome the issue posed by the multifunnel effect using a machine learning approach, without using <i>a priori</i> knowledge of the potential energy surface. This approach begins with a truncated exploration to gather coarse-grained knowledge of the potential energy surface. This is then used to train a machine learning Gaussian mixture model to divide up the potential energy surface into separate regions, with each region then being explored in more detail (or conquered) separately. This scheme was tested on a variety of multifunnel systems and yielded significant improvements to the times taken to locate the global minima of Lennard-Jones (LJ) nanoparticles, LJ<sub>75</sub> and LJ<sub>104</sub>, as well as two metallic systems, Au<sub>55</sub> and Pd<sub>88</sub>. However, difficulties were encountered for LJ<sub>98</sub>, providing insight into how the scheme could be further improved.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":null,"pages":null},"PeriodicalIF":5.6000,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"A Divide-and-Conquer Approach to Nanoparticle Global Optimisation Using Machine Learning.\",\"authors\":\"Nicholas B Smith, Anna L Garden\",\"doi\":\"10.1021/acs.jcim.4c01516\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Global optimization of the structure of atomic nanoparticles is often hampered by the presence of many funnels on the potential energy surface. While broad funnels are readily encountered and easily exploited by the search, narrow funnels are more difficult to locate and explore, presenting a problem if the global minimum is situated in such a funnel. Here, a divide-and-conquer approach is applied to overcome the issue posed by the multifunnel effect using a machine learning approach, without using <i>a priori</i> knowledge of the potential energy surface. This approach begins with a truncated exploration to gather coarse-grained knowledge of the potential energy surface. This is then used to train a machine learning Gaussian mixture model to divide up the potential energy surface into separate regions, with each region then being explored in more detail (or conquered) separately. This scheme was tested on a variety of multifunnel systems and yielded significant improvements to the times taken to locate the global minima of Lennard-Jones (LJ) nanoparticles, LJ<sub>75</sub> and LJ<sub>104</sub>, as well as two metallic systems, Au<sub>55</sub> and Pd<sub>88</sub>. However, difficulties were encountered for LJ<sub>98</sub>, providing insight into how the scheme could be further improved.</p>\",\"PeriodicalId\":44,\"journal\":{\"name\":\"Journal of Chemical Information and Modeling \",\"volume\":null,\"pages\":null},\"PeriodicalIF\":5.6000,\"publicationDate\":\"2024-11-15\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Chemical Information and Modeling \",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://doi.org/10.1021/acs.jcim.4c01516\",\"RegionNum\":2,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"CHEMISTRY, MEDICINAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Information and Modeling ","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.jcim.4c01516","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MEDICINAL","Score":null,"Total":0}
引用次数: 0

摘要

原子纳米粒子结构的全局优化通常会受到势能面上许多漏斗的阻碍。宽漏斗很容易遇到并被搜索利用,而窄漏斗则更难定位和探索,如果全局最小值位于这样的漏斗中,就会出现问题。在此,我们采用一种分而治之的方法,在不使用势能面先验知识的情况下,利用机器学习方法克服多漏斗效应带来的问题。这种方法从截断探索开始,收集势能面的粗粒度知识。然后利用这些知识训练机器学习高斯混合模型,将势能面划分为不同的区域,然后分别对每个区域进行更详细的探索(或征服)。该方案在多种多通道系统上进行了测试,并显著缩短了定位伦纳德-琼斯(LJ)纳米粒子 LJ75 和 LJ104 以及两个金属系统 Au55 和 Pd88 的全局最小值所需的时间。然而,在 LJ98 方面遇到了困难,这为如何进一步改进该方案提供了启示。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
A Divide-and-Conquer Approach to Nanoparticle Global Optimisation Using Machine Learning.

Global optimization of the structure of atomic nanoparticles is often hampered by the presence of many funnels on the potential energy surface. While broad funnels are readily encountered and easily exploited by the search, narrow funnels are more difficult to locate and explore, presenting a problem if the global minimum is situated in such a funnel. Here, a divide-and-conquer approach is applied to overcome the issue posed by the multifunnel effect using a machine learning approach, without using a priori knowledge of the potential energy surface. This approach begins with a truncated exploration to gather coarse-grained knowledge of the potential energy surface. This is then used to train a machine learning Gaussian mixture model to divide up the potential energy surface into separate regions, with each region then being explored in more detail (or conquered) separately. This scheme was tested on a variety of multifunnel systems and yielded significant improvements to the times taken to locate the global minima of Lennard-Jones (LJ) nanoparticles, LJ75 and LJ104, as well as two metallic systems, Au55 and Pd88. However, difficulties were encountered for LJ98, providing insight into how the scheme could be further improved.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
CiteScore
9.80
自引率
10.70%
发文量
529
审稿时长
1.4 months
期刊介绍: The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery. Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field. As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.
期刊最新文献
Structural basis for inositol pyrophosphate gating of the phosphate channel XPR1. Time to take stock. A Divide-and-Conquer Approach to Nanoparticle Global Optimisation Using Machine Learning. Combining a Chemical Language Model and the Structure-Activity Relationship Matrix Formalism for Generative Design of Potent Compounds with Core Structure and Substituent Modifications. Putting wellbeing at the core of diabetes care
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1