Shuyuan Zhang , Ting Ye , Baocai Jing , Huiqi Yin , Dingyi Pan
{"title":"非马尔可夫智能耗散粒子动力学集成与机器学习增强粗粒度模拟","authors":"Shuyuan Zhang , Ting Ye , Baocai Jing , Huiqi Yin , Dingyi Pan","doi":"10.1016/j.jcp.2025.114356","DOIUrl":null,"url":null,"abstract":"<div><div>We propose a machine learning-based coarse-grained method that integrates molecular dynamics (MD) with dissipative particle dynamics (DPD) to address the limitations of the Markovian approximation in systems where particle motion and fluctuating forces exhibit overlapping time scales. Our approach, termed non-Markovian intelligent dissipative particle dynamics (NM-IDPD), utilizes MD data to train a neural network capable of predicting both conservative and dissipative forces within the DPD framework, effectively accounting for non-Markovian effects. We have also incorporated a pressure constraint mechanism into the neural network to accurately capture the system pressure, which is a challenging issue for most traditional coarse-grained methods. Through applications to star polymers, methane, and water systems, NM-IDPD has demonstrated good performance in replicating both the static and dynamic properties of simulated systems across various time scales. This advancement offers a promising avenue for material dynamics simulation, enhancing the accuracy and efficiency of computational modeling in complex systems.</div></div>","PeriodicalId":352,"journal":{"name":"Journal of Computational Physics","volume":"542 ","pages":"Article 114356"},"PeriodicalIF":3.8000,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Non-Markovian intelligent dissipative particle dynamics integrated with machine learning for enhancing coarse-grained simulations\",\"authors\":\"Shuyuan Zhang , Ting Ye , Baocai Jing , Huiqi Yin , Dingyi Pan\",\"doi\":\"10.1016/j.jcp.2025.114356\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>We propose a machine learning-based coarse-grained method that integrates molecular dynamics (MD) with dissipative particle dynamics (DPD) to address the limitations of the Markovian approximation in systems where particle motion and fluctuating forces exhibit overlapping time scales. Our approach, termed non-Markovian intelligent dissipative particle dynamics (NM-IDPD), utilizes MD data to train a neural network capable of predicting both conservative and dissipative forces within the DPD framework, effectively accounting for non-Markovian effects. We have also incorporated a pressure constraint mechanism into the neural network to accurately capture the system pressure, which is a challenging issue for most traditional coarse-grained methods. Through applications to star polymers, methane, and water systems, NM-IDPD has demonstrated good performance in replicating both the static and dynamic properties of simulated systems across various time scales. This advancement offers a promising avenue for material dynamics simulation, enhancing the accuracy and efficiency of computational modeling in complex systems.</div></div>\",\"PeriodicalId\":352,\"journal\":{\"name\":\"Journal of Computational Physics\",\"volume\":\"542 \",\"pages\":\"Article 114356\"},\"PeriodicalIF\":3.8000,\"publicationDate\":\"2025-09-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Computational Physics\",\"FirstCategoryId\":\"101\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0021999125006382\",\"RegionNum\":2,\"RegionCategory\":\"物理与天体物理\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Computational Physics","FirstCategoryId":"101","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0021999125006382","RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS","Score":null,"Total":0}
Non-Markovian intelligent dissipative particle dynamics integrated with machine learning for enhancing coarse-grained simulations
We propose a machine learning-based coarse-grained method that integrates molecular dynamics (MD) with dissipative particle dynamics (DPD) to address the limitations of the Markovian approximation in systems where particle motion and fluctuating forces exhibit overlapping time scales. Our approach, termed non-Markovian intelligent dissipative particle dynamics (NM-IDPD), utilizes MD data to train a neural network capable of predicting both conservative and dissipative forces within the DPD framework, effectively accounting for non-Markovian effects. We have also incorporated a pressure constraint mechanism into the neural network to accurately capture the system pressure, which is a challenging issue for most traditional coarse-grained methods. Through applications to star polymers, methane, and water systems, NM-IDPD has demonstrated good performance in replicating both the static and dynamic properties of simulated systems across various time scales. This advancement offers a promising avenue for material dynamics simulation, enhancing the accuracy and efficiency of computational modeling in complex systems.
期刊介绍:
Journal of Computational Physics thoroughly treats the computational aspects of physical problems, presenting techniques for the numerical solution of mathematical equations arising in all areas of physics. The journal seeks to emphasize methods that cross disciplinary boundaries.
The Journal of Computational Physics also publishes short notes of 4 pages or less (including figures, tables, and references but excluding title pages). Letters to the Editor commenting on articles already published in this Journal will also be considered. Neither notes nor letters should have an abstract.