On three genetic repressilator topologies
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Publication:6307172
arXiv1809.08840MaRDI QIDQ6307172FDOQ6307172
Authors: Maša Dukarić, Hassan Errami, Roman Jerala, Tina Lebar, Valery G. Romanovski, J. Tóth, Andreas Weber 
Publication date: 24 September 2018
Abstract: Novel mathematical models of three different repressilator topologies are introduced. As designable transcription factors have been shown to bind to DNA non-cooperatively, we have chosen models containing non-cooperative elements. The extended topologies involve three additional transcription regulatory elements---which can be easily implemented by synthetic biology---forming positive feedback loops. This increases the number of variables to six, and extends the complexity of the equations in the model. To perform our analysis we had to use combinations of modern symbolic algorithms of computer algebra systems Mathematica and Singular. The study shows that all the three models have simple dynamics what can also be called regular behaviour: they have a single asymptotically stable steady state with small amplitude oscillations in the 3D case and no oscillation in one of the 6D cases and damping oscillation in the second 6D case. Using the program QeHopf we were able to exclude the presence of Hopf bifurcation in the 3D system.
Topological structure of integral curves, singular points, limit cycles of ordinary differential equations (34C05) Chemical kinetics in thermodynamics and heat transfer (80A30)
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