Transient dynamics around unstable periodic orbits in the generalized repressilator model

DOI10.1063/1.3574387zbMATH Open1317.37108arXiv1012.3938OpenAlexW3102206939WikidataQ84486782 ScholiaQ84486782MaRDI QIDQ5264509FDOQ5264509

Authors: Natalja Strelkowa, Mauricio Barahona 

Publication date: 27 July 2015

Published in: Chaos: An Interdisciplinary Journal of Nonlinear Science (Search for Journal in Brave)

Abstract: We study the spatio-temporal dynamics of the generalized repressilator, a system of coupled repressing genes arranged in a directed ring topology, and give analytical conditions for the emergence of a cascade of unstable periodic orbits (UPOs) that lead to reachable long-lived oscillating transients. Such transients dominate the finite time horizon dynamics that is relevant in confined, noisy environments such as bacterial cells (see our previous work [Strelkowa and Barahona, 2010]) and are therefore of interest for bioengineering and synthetic biology. We show that the family of unstable orbits possesses spatial symmetries and can also be understood in terms of traveling wave solutions of kink-like topological defects. The long-lived oscillatory transients correspond to the propagation of quasistable two-kink configurations that unravel over a long time. We also assess the similarities between the generalized repressilator model and other unidirectionally coupled electronic systems, such as magnetic flux gates, which have been implemented experimentally.

Full work available at URL: https://arxiv.org/abs/1012.3938

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Mathematics Subject Classification ID

Qualitative investigation and simulation of ordinary differential equation models (34C60) Dynamical systems in biology (37N25) Bifurcation theory for ordinary differential equations (34C23) Cell biology (92C37)

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Cited In (12)

• ``Quorum sensing generated multistability and chaos in a synthetic genetic oscillator
• Chaos in gene regulatory networks: effects of time delays and interaction structure
• Quasiperiodicity and chaos through Hopf-Hopf bifurcation in minimal ring neural oscillators due to a single shortcut
• Coexistence of Hamiltonian-like and dissipative dynamics in rings of coupled phase oscillators with skew-symmetric coupling
• Cyclic feedback systems with quorum sensing coupling
• Hopf bifurcation in the full repressilator equations
• Modeling synthetic gene oscillators
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• Dynamic stabilization in the PU1-GATA1 circuit using a model with time-dependent kinetic change
• The regulation of gene expression in eukaryotes: bistability and oscillations in repressilator models
• Effects of asymmetric coupling and self-coupling on metastable dynamical transient rotating waves in a ring of sigmoidal neurons
• Grazing bifurcations, homoclinic orbits and chaos in a ring network of linear neuron-like elements with a single nonmonotonic piecewise constant output function

Uses Software

• Eigtool

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