IF 6.2 Q1 CHEMISTRY, MULTIDISCIPLINARY Digital discovery Pub Date : 2025-01-08 DOI:10.1039/d4dd00374h
Max Pinheiro, Matheus de Oliveira Bispo, Rafael S Mattos, Mariana Telles do Casal, Bidhan Chandra Garain, Josene M Toldo, Saikat Mukherjee, Mario Barbatti
{"title":"ULaMDyn: enhancing excited-state dynamics analysis through streamlined unsupervised learning.","authors":"Max Pinheiro, Matheus de Oliveira Bispo, Rafael S Mattos, Mariana Telles do Casal, Bidhan Chandra Garain, Josene M Toldo, Saikat Mukherjee, Mario Barbatti","doi":"10.1039/d4dd00374h","DOIUrl":null,"url":null,"abstract":"<p><p>The analysis of nonadiabatic molecular dynamics (NAMD) data presents significant challenges due to its high dimensionality and complexity. To address these issues, we introduce ULaMDyn, a Python-based, open-source package designed to automate the unsupervised analysis of large datasets generated by NAMD simulations. ULaMDyn integrates seamlessly with the Newton-X platform and employs advanced dimensionality reduction and clustering techniques to uncover hidden patterns in molecular trajectories, enabling a more intuitive understanding of excited-state processes. Using the photochemical dynamics of fulvene as a test case, we demonstrate how ULaMDyn efficiently identifies critical molecular geometries and critical nonadiabatic transitions. The package offers a streamlined, scalable solution for interpreting large NAMD datasets. It is poised to facilitate advances in the study of excited-state dynamics across a wide range of molecular systems.</p>","PeriodicalId":72816,"journal":{"name":"Digital discovery","volume":" ","pages":""},"PeriodicalIF":6.2000,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774233/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Digital discovery","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1039/d4dd00374h","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0

摘要

由于非绝热分子动力学(NAMD)数据的高维性和复杂性,对其进行分析面临着巨大挑战。为了解决这些问题,我们推出了 ULaMDyn,这是一款基于 Python 的开源软件包,旨在自动对 NAMD 模拟生成的大型数据集进行无监督分析。ULaMDyn 与 Newton-X 平台无缝集成,采用先进的降维和聚类技术来揭示分子轨迹中隐藏的模式,从而更直观地了解激发态过程。我们以富勒烯的光化学动力学为测试案例,展示了 ULaMDyn 如何高效地识别临界分子几何形状和临界非绝热转变。该软件包为解释大型 NAMD 数据集提供了简化、可扩展的解决方案。它将推动对各种分子系统激发态动力学的研究取得进展。
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
ULaMDyn: enhancing excited-state dynamics analysis through streamlined unsupervised learning.

The analysis of nonadiabatic molecular dynamics (NAMD) data presents significant challenges due to its high dimensionality and complexity. To address these issues, we introduce ULaMDyn, a Python-based, open-source package designed to automate the unsupervised analysis of large datasets generated by NAMD simulations. ULaMDyn integrates seamlessly with the Newton-X platform and employs advanced dimensionality reduction and clustering techniques to uncover hidden patterns in molecular trajectories, enabling a more intuitive understanding of excited-state processes. Using the photochemical dynamics of fulvene as a test case, we demonstrate how ULaMDyn efficiently identifies critical molecular geometries and critical nonadiabatic transitions. The package offers a streamlined, scalable solution for interpreting large NAMD datasets. It is poised to facilitate advances in the study of excited-state dynamics across a wide range of molecular systems.

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
2.80
自引率
0.00%
发文量
0
期刊最新文献
Biophysics-guided uncertainty-aware deep learning uncovers high-affinity plastic-binding peptides. Back cover Predicting hydrogen atom transfer energy barriers using Gaussian process regression. Active learning driven prioritisation of compounds from on-demand libraries targeting the SARS-CoV-2 main protease. ULaMDyn: enhancing excited-state dynamics analysis through streamlined unsupervised learning.
×
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