High-resolution mapping of bifurcations in nonlinear biochemical circuits.

Nature chemistry

PubMedID: 27442281

Genot AJ, Baccouche A, Sieskind R, Aubert-Kato N, Bredeche N, Bartolo JF, Taly V, Fujii T, Rondelez Y. High-resolution mapping of bifurcations in nonlinear biochemical circuits. Nat Chem. 2016;8(8):760-7.
Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate. Here, using droplet-based microfluidics, we map with high resolution and dimensionality the bifurcation diagrams of two synthetic, out-of-equilibrium and nonlinear programs: a bistable DNA switch and a predator-prey DNA oscillator. The diagrams delineate where function is optimal, dynamics bifurcates and models fail. Inverse problem solving on these large-scale data sets indicates interference from enzymatic coupling. Additionally, data mining exposes the presence of rare, stochastically bursting oscillators near deterministic bifurcations.