{"title":"探索自由能源格局的策略:多样性中的统一和未来的挑战","authors":"Fabio Pietrucci","doi":"10.1016/j.revip.2017.05.001","DOIUrl":null,"url":null,"abstract":"<div><p>Computer simulations play an important role in the study of transformation processes of condensed matter, including phase transitions, chemical reactions, and conformational changes of biomolecules. In principle, atomic trajectories, such as those generated using the molecular dynamics approach, contain detailed structural, thermodynamic, and kinetic information about activated processes. In practice, due to free energy barriers, there is often a wide gap between the time scale of the transformation and the time scale accessible with simulations. This review offers a practical guide to the ingenious methods aimed to accelerate the exploration and reconstruction of free energy landscapes of complex systems. The focus is on basic unifying concepts, successful strategies, and pitfalls, illustrated with examples of application to scientific problems from different disciplines. The current challenges in the field consist mainly in the cumbersome identification of optimal reaction coordinates and in the extensive recourse to expert human supervision and fine tuning of the algorithms. The full achievement of wide-spectrum formulations and easy reproducibility of results would constitute the breakthrough necessary to enter the era of routine use of enhanced sampling simulations.</p></div>","PeriodicalId":37875,"journal":{"name":"Reviews in Physics","volume":"2 ","pages":"Pages 32-45"},"PeriodicalIF":0.0000,"publicationDate":"2017-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.revip.2017.05.001","citationCount":"110","resultStr":"{\"title\":\"Strategies for the exploration of free energy landscapes: Unity in diversity and challenges ahead\",\"authors\":\"Fabio Pietrucci\",\"doi\":\"10.1016/j.revip.2017.05.001\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Computer simulations play an important role in the study of transformation processes of condensed matter, including phase transitions, chemical reactions, and conformational changes of biomolecules. In principle, atomic trajectories, such as those generated using the molecular dynamics approach, contain detailed structural, thermodynamic, and kinetic information about activated processes. In practice, due to free energy barriers, there is often a wide gap between the time scale of the transformation and the time scale accessible with simulations. This review offers a practical guide to the ingenious methods aimed to accelerate the exploration and reconstruction of free energy landscapes of complex systems. The focus is on basic unifying concepts, successful strategies, and pitfalls, illustrated with examples of application to scientific problems from different disciplines. The current challenges in the field consist mainly in the cumbersome identification of optimal reaction coordinates and in the extensive recourse to expert human supervision and fine tuning of the algorithms. The full achievement of wide-spectrum formulations and easy reproducibility of results would constitute the breakthrough necessary to enter the era of routine use of enhanced sampling simulations.</p></div>\",\"PeriodicalId\":37875,\"journal\":{\"name\":\"Reviews in Physics\",\"volume\":\"2 \",\"pages\":\"Pages 32-45\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2017-11-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://sci-hub-pdf.com/10.1016/j.revip.2017.05.001\",\"citationCount\":\"110\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Reviews in Physics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2405428317300059\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"Physics and Astronomy\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Reviews in Physics","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2405428317300059","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"Physics and Astronomy","Score":null,"Total":0}
Strategies for the exploration of free energy landscapes: Unity in diversity and challenges ahead
Computer simulations play an important role in the study of transformation processes of condensed matter, including phase transitions, chemical reactions, and conformational changes of biomolecules. In principle, atomic trajectories, such as those generated using the molecular dynamics approach, contain detailed structural, thermodynamic, and kinetic information about activated processes. In practice, due to free energy barriers, there is often a wide gap between the time scale of the transformation and the time scale accessible with simulations. This review offers a practical guide to the ingenious methods aimed to accelerate the exploration and reconstruction of free energy landscapes of complex systems. The focus is on basic unifying concepts, successful strategies, and pitfalls, illustrated with examples of application to scientific problems from different disciplines. The current challenges in the field consist mainly in the cumbersome identification of optimal reaction coordinates and in the extensive recourse to expert human supervision and fine tuning of the algorithms. The full achievement of wide-spectrum formulations and easy reproducibility of results would constitute the breakthrough necessary to enter the era of routine use of enhanced sampling simulations.
期刊介绍:
Reviews in Physics is a gold open access Journal, publishing review papers on topics in all areas of (applied) physics. The journal provides a platform for researchers who wish to summarize a field of physics research and share this work as widely as possible. The published papers provide an overview of the main developments on a particular topic, with an emphasis on recent developments, and sketch an outlook on future developments. The journal focuses on short review papers (max 15 pages) and these are freely available after publication. All submitted manuscripts are fully peer-reviewed and after acceptance a publication fee is charged to cover all editorial, production, and archiving costs.