Preprint Open Access

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


JSON-LD (schema.org) Export

{
  "description": "<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>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Engineering Mathematics Department, University of Bristol, Bristol BS8 1UB,\u00a0UK", 
      "@type": "Person", 
      "name": "Gomes,\u00a0Brandon"
    }, 
    {
      "affiliation": "Department of Electrical Engineering and Information Technology, University of Naples, Naples 80125 Naples,\u00a0Italy", 
      "@type": "Person", 
      "name": "de Cesare,\u00a0Irene"
    }, 
    {
      "affiliation": "Department of Electrical Engineering and Information Technology, University of Naples, Naples 80125 Naples,\u00a0Italy", 
      "@type": "Person", 
      "name": "Guarino,\u00a0Agostino"
    }, 
    {
      "affiliation": "Engineering Mathematics Department, University of Bristol, Bristol BS8 1UB,\u00a0UK - Department of Electrical Engineering and Information Technology, University of Naples, Naples 80125 Naples,\u00a0Italy -\u00a0Bristol Centre for Synthetic Biology, University of Bristol, Life Sciences Building Tyndall Avenue, Bristol, BS8 1TQ,\u00a0UK", 
      "@type": "Person", 
      "name": "di Bernardo,\u00a0Mario"
    }, 
    {
      "affiliation": "Engineering Mathematics Department, University of Bristol, Bristol BS8 1UB,\u00a0UK", 
      "@type": "Person", 
      "name": "Renson,\u00a0Ludovic"
    }, 
    {
      "affiliation": "Engineering Mathematics Department, University of Bristol, Bristol BS8 1UB,\u00a0UK -\u00a0Bristol Centre for Synthetic Biology, University of Bristol, Life Sciences Building Tyndall Avenue, Bristol, BS8 1TQ,\u00a0UK", 
      "@type": "Person", 
      "name": "Marucci,\u00a0Lucia"
    }
  ], 
  "headline": "Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation", 
  "image": "https://zenodo.org/static/img/logos/zenodo-gradient-round.svg", 
  "datePublished": "2019-11-18", 
  "url": "https://zenodo.org/record/4837515", 
  "@context": "https://schema.org/", 
  "identifier": "https://doi.org/10.1101/695866", 
  "@id": "https://doi.org/10.1101/695866", 
  "@type": "ScholarlyArticle", 
  "name": "Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation"
}
2
4
views
downloads
Views 2
Downloads 4
Data volume 1.1 MB
Unique views 2
Unique downloads 4

Share

Cite as