Alfonso Gijón , Miguel Molina-Solana , Juan Gómez-Romero
{"title":"加速水团阴离子蒙特卡罗模拟的图神经网络势能面","authors":"Alfonso Gijón , Miguel Molina-Solana , Juan Gómez-Romero","doi":"10.1016/j.jocs.2024.102383","DOIUrl":null,"url":null,"abstract":"<div><p>Regression of potential energy functions stands as one of the most prevalent applications of machine learning in the realm of materials simulation, offering the prospect of accelerating simulations by several orders of magnitude. Recently, graph-based architectures have emerged as particularly adept for modeling molecular systems. However, the development of robust and transferable potentials, leading to stable simulations for different sizes and physical conditions, remains an ongoing area of investigation. In this study, we compare the performance of several graph neural networks for predicting the energy of water cluster anions, a system of fundamental interest in Chemistry and Biology. Following the identification of the graph attention network as the optimal aggregation procedure for this task, we obtained an efficient and accurate energy model. This model is then employed to conduct Monte Carlo simulations of clusters across different sizes, demonstrating stable behavior. Notably, the predicted surface-to-interior state transition point and the bulk energy of the system are consistent with findings from other investigations, at a computational cost three-orders of magnitude lower.</p></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"81 ","pages":"Article 102383"},"PeriodicalIF":3.1000,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Graph-neural-network potential energy surface to speed up Monte Carlo simulations of water cluster anions\",\"authors\":\"Alfonso Gijón , Miguel Molina-Solana , Juan Gómez-Romero\",\"doi\":\"10.1016/j.jocs.2024.102383\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Regression of potential energy functions stands as one of the most prevalent applications of machine learning in the realm of materials simulation, offering the prospect of accelerating simulations by several orders of magnitude. Recently, graph-based architectures have emerged as particularly adept for modeling molecular systems. However, the development of robust and transferable potentials, leading to stable simulations for different sizes and physical conditions, remains an ongoing area of investigation. In this study, we compare the performance of several graph neural networks for predicting the energy of water cluster anions, a system of fundamental interest in Chemistry and Biology. Following the identification of the graph attention network as the optimal aggregation procedure for this task, we obtained an efficient and accurate energy model. This model is then employed to conduct Monte Carlo simulations of clusters across different sizes, demonstrating stable behavior. Notably, the predicted surface-to-interior state transition point and the bulk energy of the system are consistent with findings from other investigations, at a computational cost three-orders of magnitude lower.</p></div>\",\"PeriodicalId\":48907,\"journal\":{\"name\":\"Journal of Computational Science\",\"volume\":\"81 \",\"pages\":\"Article 102383\"},\"PeriodicalIF\":3.1000,\"publicationDate\":\"2024-07-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Computational Science\",\"FirstCategoryId\":\"94\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1877750324001765\",\"RegionNum\":3,\"RegionCategory\":\"计算机科学\",\"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 Science","FirstCategoryId":"94","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1877750324001765","RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS","Score":null,"Total":0}
Graph-neural-network potential energy surface to speed up Monte Carlo simulations of water cluster anions
Regression of potential energy functions stands as one of the most prevalent applications of machine learning in the realm of materials simulation, offering the prospect of accelerating simulations by several orders of magnitude. Recently, graph-based architectures have emerged as particularly adept for modeling molecular systems. However, the development of robust and transferable potentials, leading to stable simulations for different sizes and physical conditions, remains an ongoing area of investigation. In this study, we compare the performance of several graph neural networks for predicting the energy of water cluster anions, a system of fundamental interest in Chemistry and Biology. Following the identification of the graph attention network as the optimal aggregation procedure for this task, we obtained an efficient and accurate energy model. This model is then employed to conduct Monte Carlo simulations of clusters across different sizes, demonstrating stable behavior. Notably, the predicted surface-to-interior state transition point and the bulk energy of the system are consistent with findings from other investigations, at a computational cost three-orders of magnitude lower.
期刊介绍:
Computational Science is a rapidly growing multi- and interdisciplinary field that uses advanced computing and data analysis to understand and solve complex problems. It has reached a level of predictive capability that now firmly complements the traditional pillars of experimentation and theory.
The recent advances in experimental techniques such as detectors, on-line sensor networks and high-resolution imaging techniques, have opened up new windows into physical and biological processes at many levels of detail. The resulting data explosion allows for detailed data driven modeling and simulation.
This new discipline in science combines computational thinking, modern computational methods, devices and collateral technologies to address problems far beyond the scope of traditional numerical methods.
Computational science typically unifies three distinct elements:
• Modeling, Algorithms and Simulations (e.g. numerical and non-numerical, discrete and continuous);
• Software developed to solve science (e.g., biological, physical, and social), engineering, medicine, and humanities problems;
• Computer and information science that develops and optimizes the advanced system hardware, software, networking, and data management components (e.g. problem solving environments).