Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook. Issue 4 (9th March 2021)

• Record Type: Journal Article
• Authors: Bolhuis, Peter G.; Swenson, David W. H.
• Is Part Of: Advanced theory and simulations. Volume 4:Issue 4(2021)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2021-03-09
• Subjects: importance sampling -- molecular dynamics -- path ensembles -- rare events; Science -- Simulation methods -- Periodicals; Science -- Methodology -- Periodicals; Engineering -- Simulation methods -- Periodicals; Engineering -- Methodology -- Periodicals; 507.21
• DOI: 10.1002/adts.202000237
• Languages: English
• ISSNs: 2513-0390

Abstract

Abstract: The development of enhanced sampling methods to investigate rare but important events has always been a focal point in the molecular simulation field. Such methods often rely on prior knowledge of the reaction coordinate. However, the search for this reaction coordinate is at the heart of the rare event problem. Transition path sampling (TPS) circumvents this problem by generating an ensemble of dynamical trajectories undergoing the activated event. The reaction coordinate is extracted from the resulting path ensemble using variants of machine learning, making it an output of the method instead of an input. Over the last 20 years, since its inception, many extensions of TPS have been developed. Perhaps surprisingly, large‐scale TPS simulations on complex molecular systems have become possible only recently. Other important developments include the transition interface sampling (TIS) methodology to compute rate constants, the application to multiple states, and adaptive path sampling. The development of OpenPathSampling and PyRETIS has enabled easy and flexible use and implementation of these and other novel path sampling algorithms. In this progress report, a brief overview of recent developments, novel algorithms, and software is given. In addition, several application areas are discussed, and a future outlook for the next decade is given. Abstract : Essentially a Markov Chain Monte Carlo algorithm in trajectory space, transition path sampling can explore molecular dynamics of complex rare event processes. This review discusses several recent path sampling algorithms that are developed by exploiting the analogy between sampling in trajectory space and in configuration space. This powerful analogy will likely continue to yield novel methods in the next decade.