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Deterministic characterization of phase noise in biomolecular oscillators.

Koeppl, H. and Hafner, M. and Ganguly, A. and Mehrotra, A. (2011):
Deterministic characterization of phase noise in biomolecular oscillators.
In: Physical biology, p. 55008, 8, (5), [Online-Edition: http://iopscience.iop.org/1478-3975/8/5/055008/fulltext/],
[Article]

Abstract

On top of the many external perturbations, cellular oscillators also face intrinsic perturbations due the randomness of chemical kinetics. Biomolecular oscillators, distinct in their parameter sets or distinct in their architecture, show different resilience with respect to such intrinsic perturbations. Assessing this resilience can be done by ensemble stochastic simulations. These are computationally costly and do not permit further insights into the mechanistic cause of the observed resilience. For reaction systems operating at a steady state, the linear noise approximation (LNA) can be used to determine the effect of molecular noise. Here we show that methods based on LNA fail for oscillatory systems and we propose an alternative ansatz. It yields an asymptotic expression for the phase diffusion coefficient of stochastic oscillators. Moreover, it allows us to single out the noise contribution of every reaction in an oscillatory system. We test the approach on the one-loop model of the Drosophila circadian clock. Our results are consistent with those obtained through stochastic simulations with a gain in computational efficiency of about three orders of magnitude.

Item Type: Article
Erschienen: 2011
Creators: Koeppl, H. and Hafner, M. and Ganguly, A. and Mehrotra, A.
Title: Deterministic characterization of phase noise in biomolecular oscillators.
Language: English
Abstract:

On top of the many external perturbations, cellular oscillators also face intrinsic perturbations due the randomness of chemical kinetics. Biomolecular oscillators, distinct in their parameter sets or distinct in their architecture, show different resilience with respect to such intrinsic perturbations. Assessing this resilience can be done by ensemble stochastic simulations. These are computationally costly and do not permit further insights into the mechanistic cause of the observed resilience. For reaction systems operating at a steady state, the linear noise approximation (LNA) can be used to determine the effect of molecular noise. Here we show that methods based on LNA fail for oscillatory systems and we propose an alternative ansatz. It yields an asymptotic expression for the phase diffusion coefficient of stochastic oscillators. Moreover, it allows us to single out the noise contribution of every reaction in an oscillatory system. We test the approach on the one-loop model of the Drosophila circadian clock. Our results are consistent with those obtained through stochastic simulations with a gain in computational efficiency of about three orders of magnitude.

Journal or Publication Title: Physical biology
Volume: 8
Number: 5
Uncontrolled Keywords: Animals,Biological,Circadian Rhythm,Circadian Rhythm: physiology,Drosophila,Drosophila: physiology,Models,Stochastic Processes
Divisions: 18 Department of Electrical Engineering and Information Technology
18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications > Bioinspired Communication Systems
18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications
Date Deposited: 04 Apr 2014 12:43
Official URL: http://iopscience.iop.org/1478-3975/8/5/055008/fulltext/
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