A Toolbox for Quantifying Memory in Dynamics Along Reaction Coordinates

Alessio Lapolla; Aljaž Godec

doi:10.1103/physrevresearch.3.l022018

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arXiv · 2101.05237

A Toolbox for Quantifying Memory in Dynamics Along Reaction Coordinates

Alessio Lapolla·Aljaž Godec

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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.

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BibTeX RIS

Alessio Lapolla, Aljaž Godec. 2021-01-13. A Toolbox for Quantifying Memory in Dynamics Along Reaction Coordinates. https://doi.org/10.1103/physrevresearch.3.l022018

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