The transition between stochastic and deterministic behavior in an excitable gene circuit

We explore the connection between a stochastic simulation model and an ordinary differential equations (ODEs) model of the dynamics of an excitable gene circuit that exhibits noise-induced oscillations. Near a bifurcation point in the ODE model, the stochastic simulation model yields behavior dramatically different from that predicted by the ODE model. We analyze how that behavior depends on the gene copy number and find very slow convergence to the large number limit near the bifurcation point. The implications for understanding the dynamics of gene circuits and other birth-death dynamical systems with small numbers of constituents are discussed.Comment: PLoS ONE: Research Article, published 11 Apr 201

Complex and unexpected dynamics in simple genetic regulatory networks

Peer reviewedPublisher PD

Noise regulation by quorum sensing in low mRNA copy number systems

<p>Abstract</p> <p>Background</p> <p>Cells must face the ubiquitous presence of noise at the level of signaling molecules. The latter constitutes a major challenge for the regulation of cellular functions including communication processes. In the context of prokaryotic communication, the so-called quorum sensing (QS) mechanism relies on small diffusive molecules that are produced and detected by cells. This poses the intriguing question of how bacteria cope with the fluctuations for setting up a reliable information exchange.</p> <p>Results</p> <p>We present a stochastic model of gene expression that accounts for the main biochemical processes that describe the QS mechanism close to its activation threshold. Within that framework we study, both numerically and analytically, the role that diffusion plays in the regulation of the dynamics and the fluctuations of signaling molecules. In addition, we unveil the contribution of different sources of noise, intrinsic and transcriptional, in the QS mechanism.</p> <p>Conclusions</p> <p>The interplay between noisy sources and the communication process produces a repertoire of dynamics that depends on the diffusion rate. Importantly, the total noise shows a non-monotonic behavior as a function of the diffusion rate. QS systems seems to avoid values of the diffusion that maximize the total noise. These results point towards the direction that bacteria have adapted their communication mechanisms in order to improve the signal-to-noise ratio.</p

Unraveling gene regulatory networks from time-resolved gene expression data -- a measures comparison study

Peer reviewedPublisher PD

Stability of amplitude chimeras in oscillator networks

This work was supported by DFG in the framework of SFB 91

Detuning-dependent dominance of oscillation death in globally coupled synthetic genetic oscillators

We study dynamical regimes of globally coupled genetic relaxation oscillators in the presence of small detuning. Using bifurcation analysis, we find that under strong coupling via the slow variable, the detuning can eliminate standard oscillatory solutions in a large region of the parameter space, providing the dominance of oscillation death. This result is substantially different from previous results on oscillation quenching, where for homogeneous populations, the coexistence of oscillation death and limit cycle oscillations is always present. We propose further that this effect of detuning-dependent dominance could be a powerful regulator of genetic network's dynamics