title: Transient dynamics and their control in time-delay autonomous Boolean ring networks.
abstract: Biochemical systems with switch-like interactions, such as gene regulatory networks, are well modeled by autonomous Boolean networks. Specifically, the topology and logic of gene interactions can be described by systems of continuous piecewise-linear differential equations, enabling analytical predictions of the dynamics of specific networks. However, most models do not account for time delays along links associated with spatial transport, mRNA transcription, and translation. To address this issue, we have developed an experimental test bed to realize a time-delay autonomous Boolean network with three inhibitory nodes, known as a repressilator, and use it to study the dynamics that arise as time delays along the links vary. We observe various nearly periodic oscillatory transient patterns with extremely long lifetime, which emerge in small network motifs due to the delay, and which are distinct from the eventual asymptotically stable periodic attractors. For repeated experiments with a given network, we find that stochastic processes give rise to a broad distribution of transient times with an exponential tail. In some cases, the transients are so long that it is doubtful the attractors will ever be approached in a biological system that has a finite lifetime. To counteract the long transients, we show experimentally that small, occasional perturbations applied to the time delays can force the trajectories to rapidly approach the attractors.
authors.affiliation: Department of Physics, Duke University, Durham, North Carolina 27708, USA.|Institut für Theoretische Physik, Technische Universität Berlin, 10623 Berlin, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Lohmann
authors.affiliation: Department of Physics, Duke University, Durham, North Carolina 27708, USA.
authors.forename: Otti
authors.initials: O
authors.lastname: D'Huys
authors.affiliation: Department of Physics, Duke University, Durham, North Carolina 27708, USA.
authors.forename: Nicholas D
authors.initials: ND
authors.lastname: Haynes
authors.affiliation: Institut für Theoretische Physik, Technische Universität Berlin, 10623 Berlin, Germany.
authors.forename: Eckehard
authors.initials: E
authors.lastname: Schöll
authors.affiliation: Department of Physics, Duke University, Durham, North Carolina 27708, USA.|Department of Physics, The Ohio State University, Columbus, Ohio 43210, USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Gauthier