A Toolbox for Quantifying Memory in Dynamics Along Reaction Coordinates
Abstract
Memory effects in time-series of experimental observables are ubiquitous, have important cosequences for the interpretation of kinetic data, and may even affect the function of biomolecular nanomachines such as enzymes. Here we propose a set of complementary methods for quantifying conclusively the magnitude and duration of memory in a time series of a reaction coordinate. The toolbox is general, robust, easy to use, and does not rely on any underlying microscopic model. As a proof of concept we apply it to the analysis of memory in the dynamics of the end-to-end distance of the analytically solvable Rouse-polymer model, an experimental time-series of extensions of a single DNA hairpin measured by optical tweezers, and the fraction of native contacts in a small protein probed by atomistic Molecular Dynamics simulations.
Cite
@article{arxiv.2101.05237,
title = {A Toolbox for Quantifying Memory in Dynamics Along Reaction Coordinates},
author = {Alessio Lapolla and Aljaž Godec},
journal= {arXiv preprint arXiv:2101.05237},
year = {2021}
}
Comments
Revised version with additional examples; accepted for publication in Phys. Rev. Res