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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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  <identifier identifierType="URL">https://zenodo.org/record/4837515</identifier>
  <creators>
    <creator>
      <creatorName>Gomes, Brandon</creatorName>
      <givenName>Brandon</givenName>
      <familyName>Gomes</familyName>
      <affiliation>Engineering Mathematics Department, University of Bristol, Bristol BS8 1UB, UK</affiliation>
    </creator>
    <creator>
      <creatorName>de Cesare, Irene</creatorName>
      <givenName>Irene</givenName>
      <familyName>de Cesare</familyName>
      <affiliation>Department of Electrical Engineering and Information Technology, University of Naples, Naples 80125 Naples, Italy</affiliation>
    </creator>
    <creator>
      <creatorName>Guarino, Agostino</creatorName>
      <givenName>Agostino</givenName>
      <familyName>Guarino</familyName>
      <affiliation>Department of Electrical Engineering and Information Technology, University of Naples, Naples 80125 Naples, Italy</affiliation>
    </creator>
    <creator>
      <creatorName>di Bernardo, Mario</creatorName>
      <givenName>Mario</givenName>
      <familyName>di Bernardo</familyName>
      <affiliation>Engineering Mathematics Department, University of Bristol, Bristol BS8 1UB, UK - Department of Electrical Engineering and Information Technology, University of Naples, Naples 80125 Naples, Italy - Bristol Centre for Synthetic Biology, University of Bristol, Life Sciences Building Tyndall Avenue, Bristol, BS8 1TQ, UK</affiliation>
    </creator>
    <creator>
      <creatorName>Renson, Ludovic</creatorName>
      <givenName>Ludovic</givenName>
      <familyName>Renson</familyName>
      <affiliation>Engineering Mathematics Department, University of Bristol, Bristol BS8 1UB, UK</affiliation>
    </creator>
    <creator>
      <creatorName>Marucci, Lucia</creatorName>
      <givenName>Lucia</givenName>
      <familyName>Marucci</familyName>
      <affiliation>Engineering Mathematics Department, University of Bristol, Bristol BS8 1UB, UK - Bristol Centre for Synthetic Biology, University of Bristol, Life Sciences Building Tyndall Avenue, Bristol, BS8 1TQ, UK</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2019</publicationYear>
  <dates>
    <date dateType="Issued">2019-11-18</date>
  </dates>
  <resourceType resourceTypeGeneral="Text">Preprint</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4837515</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.1101/695866</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/cosy-bio</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;Abstract&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/766840/">766840</awardNumber>
      <awardTitle>Control Engineering of Biological Systems for Reliable Synthetic Biology Applications</awardTitle>
    </fundingReference>
  </fundingReferences>
</resource>
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