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 Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/ae52280c-4db5-401c-a239-90458d06a3e7/Gomes%20et%20al%202018%20biorxiv.pdf"
      }, 
      "checksum": "md5:8a1e085dfcbb6b1835e29ff1b6fb0e59", 
      "bucket": "ae52280c-4db5-401c-a239-90458d06a3e7", 
      "key": "Gomes et al 2018 biorxiv.pdf", 
      "type": "pdf", 
      "size": 265585
    }
  ], 
  "owners": [
    44090
  ], 
  "doi": "10.1101/695866", 
  "stats": {
    "version_unique_downloads": 3.0, 
    "unique_views": 2.0, 
    "views": 2.0, 
    "version_views": 2.0, 
    "unique_downloads": 3.0, 
    "version_unique_views": 2.0, 
    "volume": 796755.0, 
    "version_downloads": 3.0, 
    "downloads": 3.0, 
    "version_volume": 796755.0
  }, 
  "links": {
    "doi": "https://doi.org/10.1101/695866", 
    "latest_html": "https://zenodo.org/record/4837515", 
    "bucket": "https://zenodo.org/api/files/ae52280c-4db5-401c-a239-90458d06a3e7", 
    "badge": "https://zenodo.org/badge/doi/10.1101/695866.svg", 
    "html": "https://zenodo.org/record/4837515", 
    "latest": "https://zenodo.org/api/records/4837515"
  }, 
  "created": "2021-05-28T19:14:33.985238+00:00", 
  "updated": "2021-05-30T02:20:47.097858+00:00", 
  "conceptrecid": "4837514", 
  "revision": 3, 
  "id": 4837515, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.1101/695866", 
    "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": {
      "id": "CC-BY-4.0"
    }, 
    "title": "Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation", 
    "journal": {
      "title": "biorxiv"
    }, 
    "relations": {
      "version": [
        {
          "count": 1, 
          "index": 0, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "4837514"
          }, 
          "is_last": true, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "4837515"
          }
        }
      ]
    }, 
    "grants": [
      {
        "code": "766840", 
        "links": {
          "self": "https://zenodo.org/api/grants/10.13039/501100000780::766840"
        }, 
        "title": "Control Engineering of Biological Systems for Reliable Synthetic Biology Applications", 
        "acronym": "COSY-BIO", 
        "program": "H2020", 
        "funder": {
          "doi": "10.13039/501100000780", 
          "acronyms": [], 
          "name": "European Commission", 
          "links": {
            "self": "https://zenodo.org/api/funders/10.13039/501100000780"
          }
        }
      }
    ], 
    "communities": [
      {
        "id": "cosy-bio"
      }
    ], 
    "publication_date": "2019-11-18", 
    "creators": [
      {
        "affiliation": "Engineering Mathematics Department, University of Bristol, Bristol BS8 1UB,\u00a0UK", 
        "name": "Gomes,\u00a0Brandon"
      }, 
      {
        "affiliation": "Department of Electrical Engineering and Information Technology, University of Naples, Naples 80125 Naples,\u00a0Italy", 
        "name": "de Cesare,\u00a0Irene"
      }, 
      {
        "affiliation": "Department of Electrical Engineering and Information Technology, University of Naples, Naples 80125 Naples,\u00a0Italy", 
        "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", 
        "name": "di Bernardo,\u00a0Mario"
      }, 
      {
        "affiliation": "Engineering Mathematics Department, University of Bristol, Bristol BS8 1UB,\u00a0UK", 
        "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", 
        "name": "Marucci,\u00a0Lucia"
      }
    ], 
    "access_right": "open", 
    "resource_type": {
      "subtype": "preprint", 
      "type": "publication", 
      "title": "Preprint"
    }
  }
}
2
3
views
downloads
Views 2
Downloads 3
Data volume 796.8 kB
Unique views 2
Unique downloads 3

Share

Cite as