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A robust approach to estimating rates from time-correlation functions

Please always quote using this URN:urn:nbn:de:0296-matheon-10532
  • While seemingly straightforward in principle, the reliable estimation of rate constants is seldom easy in practice. Numerous issues, such as the complication of poor reaction coordinates, cause obvious approaches to yield unreliable estimates. When a reliable order parameter is available, the reactive flux theory of Chandler allows the rate constant to be extracted from the plateau region of an appropriate reactive flux correlation function. However, when applied to real data from single- molecule experiments or molecular dynamics simulations, the reactive flux correlation function requires the numerical differentiation of a noisy empirical correlation function, which can result in an unacceptably poor estimate of the rate and pathological dependence on the sampling interval. We present a modified version of this theory which does not require numerical derivatives, allowing rate constants to be robustly estimated from the time-correlation function directly. We illustrate the approach using single-molecule passive force spectroscopy measurements of an RNA hairpin.

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Metadaten
Author:John D. Chodera, Philip Elms, William C. Swope, Jan-Hendrik Prinz, Susan Marqusee, Carlos Bustamante, Frank Noe, Vijay S. Pande
URN:urn:nbn:de:0296-matheon-10532
Referee:Christof Schütte
Document Type:Preprint, Research Center Matheon
Language:English
Date of first Publication:2012/02/02
Release Date:2012/02/02
Institute:Research Center Matheon
Freie Universität Berlin
MSC-Classification:82-XX STATISTICAL MECHANICS, STRUCTURE OF MATTER / 82-08 Computational methods
Preprint Number:914
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