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

Gomes, Brandon; de Cesare, Irene; Guarino, Agostino; di Bernardo, Mario; Renson, Ludovic; Marucci, Lucia


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  <dc:creator>Gomes, Brandon</dc:creator>
  <dc:creator>de Cesare, Irene</dc:creator>
  <dc:creator>Guarino, Agostino</dc:creator>
  <dc:creator>di Bernardo, Mario</dc:creator>
  <dc:creator>Renson, Ludovic</dc:creator>
  <dc:creator>Marucci, Lucia</dc:creator>
  <dc:date>2019-11-18</dc:date>
  <dc:description>Abstract

Mathematical 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.</dc:description>
  <dc:identifier>https://zenodo.org/record/4837515</dc:identifier>
  <dc:identifier>10.1101/695866</dc:identifier>
  <dc:identifier>oai:zenodo.org:4837515</dc:identifier>
  <dc:relation>info:eu-repo/grantAgreement/EC/H2020/766840/</dc:relation>
  <dc:relation>url:https://zenodo.org/communities/cosy-bio</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  <dc:source>biorxiv</dc:source>
  <dc:title>Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation</dc:title>
  <dc:type>info:eu-repo/semantics/preprint</dc:type>
  <dc:type>publication-preprint</dc:type>
</oai_dc:dc>
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