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bioRxiv · 10.1101/695866

Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation

Gomes, B.·de Cesare, I.·Guarino, A.·di Bernardo, M.·Renson, L.·Marucci, L.
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Abstract

AO_SCPLOWBSTRACTC_SCPLOWMathematical modelling is routinely used in Systems Biology to understand the mechanisms causing nonlinear phenomena in gene expression, such as switch-like behaviours and temporal oscillations. The reliability of model predictions and bifurcation analysis depend on modelling assumptions and specific choices of model parameters; however, the identification of models is highly challenging due to the complexity of biochemical interactions and noise in experimental data. This paper numerically investigates the use of control-based continuation (CBC) for tracking dynamical features of biochemical systems and, in particular, the bistable dynamics of a gene regulating pluripotency in embryonic stem cells. CBC is a method that exploits feedback control and path following algorithms to explore the dynamic features of a nonlinear physical system directly during experimental tests. CBC applications have so far been limited to non-living (i.e. electro-mechanical) systems. Our numerical simulations show that, in principle, CBC could also be applied to biological experiments to characterise the switch-like dynamics of genes that are important for cell decision making.

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Gomes, B., de Cesare, I., Guarino, A., di Bernardo, M., Renson, L., Marucci, L.. 2019-07-08. Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation. https://doi.org/10.1101/695866

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