Milestoning: An Efficient Approach for Atomically Detailed Simulations of Kinetics in Biophysics

Recent advances in theory and algorithms for atomically detailed simulations open the way to the study of the kinetics of a wide range of molecular processes in biophysics. The theories propose a shift from the traditionally very long molecular dynamic trajectories, which are exact but may not be ef...

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Bibliographic Details
Published in:Annual review of biophysics 2020-05, Vol.49 (1), p.69-85
Main Author: Elber, Ron
Format: Article
Language:English
Subjects:
Algorithms
Biophysical Phenomena
channels
enhanced sampling
Kinetics
membranes
Models, Biological
molecular dynamics
rate calculations
reaction coordinate
Thermodynamics
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Summary:Recent advances in theory and algorithms for atomically detailed simulations open the way to the study of the kinetics of a wide range of molecular processes in biophysics. The theories propose a shift from the traditionally very long molecular dynamic trajectories, which are exact but may not be efficient in the study of kinetics, to the use of a large number of short trajectories. The short trajectories exploit a mapping to a mesh in coarse space and allow for efficient calculations of kinetics and thermodynamics. In this review, I focus on one theory: Milestoning is a theory and an algorithm that offers a hierarchical calculation of properties of interest, such as the free energy profile and the mean first passage time. Approximations to the true long-time dynamics can be computed efficiently and assessed at different steps of the investigation. The theory is discussed and illustrated using two biophysical examples: ion permeation through a phospholipid membrane and protein translocation through a channel.
ISSN:1936-122X
1936-1238
DOI:10.1146/annurev-biophys-121219-081528