Biomolecular clocks produce sustained oscillations in mRNA/protein copy numbers that are subject to inherent copy-number fluctuations with important implications for proper cellular timekeeping. These random fluctuations embedded within periodic variations in copy numbers make the quantification of noise particularly challenging in stochastic gene oscillatory systems, unlike other non-oscillatory circuits. Motivated by diurnal cycles driving circadian clocks, we investigate the noise properties in the well-known Goodwin oscillator in the presence and absence of a periodic driving signal. We use two approaches to compute the noise as a function of time: (i) solving the moment dynamics derived from the linear noise approximation (LNA) assuming fluctuations are small relative to the mean and (ii) analyzing trajectories obtained from exact stochastic simulations of the Goodwin oscillator. Our results demonstrate that the LNA can predict the noise behavior quite accurately when the system shows damped oscillations or in the presence of external periodic forcing. However, the LNA could be misleading in the case of sustained oscillations without an external signal due to the propagation of large noise. Finally, we study the effect of random bursting of gene products on the clock stochastic dynamics. Our analysis reveals that the burst of mRNAs enhances the noise in the copy number regardless of the presence of external forcing, although the extent of fluctuations becomes less due to the forcing.
- Downloaded 104 times
- Download rankings, all-time:
- Site-wide: 129,567
- In systems biology: 2,797
- Year to date:
- Site-wide: 92,269
- Since beginning of last month:
- Site-wide: 58,248
Downloads over time
Distribution of downloads per paper, site-wide
- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!