{"title":"你试过关机再开机吗?增强抽样的随机重置","authors":"Ofir Blumer, Barak Hirshberg","doi":"10.1002/wcms.70038","DOIUrl":null,"url":null,"abstract":"<p>Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant obstacle in describing phenomena such as conformational transitions of biomolecules and polymorphism in molecular crystals. Recently, stochastic resetting, that is, randomly stopping and restarting the simulations, emerged as a powerful enhanced sampling approach, which is collective variable-free, highly parallelized, and easily implemented in existing molecular dynamics codes. Resetting expedites sampling rare events while enabling the inference of kinetic observables of the underlying process. It can be employed as a standalone tool or in combination with other enhanced sampling methods, such as Metadynamics, with each technique compensating for the drawbacks of the other. Here, we comprehensively describe resetting and its theoretical background, review recent developments in stochastic resetting for enhanced sampling, and provide instructive guidelines for practitioners.</p><p>This article is categorized under:\n\n </p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 4","pages":""},"PeriodicalIF":16.8000,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.70038","citationCount":"0","resultStr":"{\"title\":\"Have You Tried Turning It Off and On Again? Stochastic Resetting for Enhanced Sampling\",\"authors\":\"Ofir Blumer, Barak Hirshberg\",\"doi\":\"10.1002/wcms.70038\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant obstacle in describing phenomena such as conformational transitions of biomolecules and polymorphism in molecular crystals. Recently, stochastic resetting, that is, randomly stopping and restarting the simulations, emerged as a powerful enhanced sampling approach, which is collective variable-free, highly parallelized, and easily implemented in existing molecular dynamics codes. Resetting expedites sampling rare events while enabling the inference of kinetic observables of the underlying process. It can be employed as a standalone tool or in combination with other enhanced sampling methods, such as Metadynamics, with each technique compensating for the drawbacks of the other. Here, we comprehensively describe resetting and its theoretical background, review recent developments in stochastic resetting for enhanced sampling, and provide instructive guidelines for practitioners.</p><p>This article is categorized under:\\n\\n </p>\",\"PeriodicalId\":236,\"journal\":{\"name\":\"Wiley Interdisciplinary Reviews: Computational Molecular Science\",\"volume\":\"15 4\",\"pages\":\"\"},\"PeriodicalIF\":16.8000,\"publicationDate\":\"2025-07-16\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.70038\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Wiley Interdisciplinary Reviews: Computational Molecular Science\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1002/wcms.70038\",\"RegionNum\":2,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"CHEMISTRY, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Wiley Interdisciplinary Reviews: Computational Molecular Science","FirstCategoryId":"92","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/wcms.70038","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
Have You Tried Turning It Off and On Again? Stochastic Resetting for Enhanced Sampling
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant obstacle in describing phenomena such as conformational transitions of biomolecules and polymorphism in molecular crystals. Recently, stochastic resetting, that is, randomly stopping and restarting the simulations, emerged as a powerful enhanced sampling approach, which is collective variable-free, highly parallelized, and easily implemented in existing molecular dynamics codes. Resetting expedites sampling rare events while enabling the inference of kinetic observables of the underlying process. It can be employed as a standalone tool or in combination with other enhanced sampling methods, such as Metadynamics, with each technique compensating for the drawbacks of the other. Here, we comprehensively describe resetting and its theoretical background, review recent developments in stochastic resetting for enhanced sampling, and provide instructive guidelines for practitioners.
期刊介绍:
Computational molecular sciences harness the power of rigorous chemical and physical theories, employing computer-based modeling, specialized hardware, software development, algorithm design, and database management to explore and illuminate every facet of molecular sciences. These interdisciplinary approaches form a bridge between chemistry, biology, and materials sciences, establishing connections with adjacent application-driven fields in both chemistry and biology. WIREs Computational Molecular Science stands as a platform to comprehensively review and spotlight research from these dynamic and interconnected fields.