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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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{
  "DOI": "10.1101/695866", 
  "container_title": "biorxiv", 
  "author": [
    {
      "family": "Gomes,\u00a0Brandon"
    }, 
    {
      "family": "de Cesare,\u00a0Irene"
    }, 
    {
      "family": "Guarino,\u00a0Agostino"
    }, 
    {
      "family": "di Bernardo,\u00a0Mario"
    }, 
    {
      "family": "Renson,\u00a0Ludovic"
    }, 
    {
      "family": "Marucci,\u00a0Lucia"
    }
  ], 
  "issued": {
    "date-parts": [
      [
        2019, 
        11, 
        18
      ]
    ]
  }, 
  "abstract": "<p><strong>Abstract</strong></p>\n\n<p>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.</p>\n\n<p>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.</p>\n\n<p>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.</p>", 
  "title": "Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation", 
  "type": "article", 
  "id": "4837515"
}
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