IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v362y2006i2p382-402.html
   My bibliography  Save this article

A simulation model of biofilms with autonomous cells: I. Analysis of a two-dimensional version

Author

Listed:
  • Tatek, Yergou B.
  • Slater, Gary W.

Abstract

We introduce a single-cell based simulation model of biofilm growth. Each microbial cell is modelled as an autonomous agent whose behavior is controlled by thermodynamic parameters, mechanical properties, physiological rules and environmental conditions. In the two-dimensional version presented here, a cell is represented by a closed chain of self-avoiding beads linked together using the bond fluctuation algorithm. The cell is thus controlled both by the rigidity of its membrane and a pressure difference. The model is complemented by key features such as the explicit presence of nutrient diffusion and flow, the processes of cell-division and cell-death, and the attractive interactions between the cell and the surface on which the colony grows. Tuning the parameters of the model can lead to the growth and maturation of various types of biofilms. In this first article, we describe the main properties of a two-dimensional version of the model, and we discuss the extension to three dimensions.

Suggested Citation

  • Tatek, Yergou B. & Slater, Gary W., 2006. "A simulation model of biofilms with autonomous cells: I. Analysis of a two-dimensional version," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 362(2), pages 382-402.
    • Handle: RePEc:eee:phsmap:v:362:y:2006:i:2:p:382-402
    DOI: 10.1016/j.physa.2005.08.011
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437105008393
    Download Restriction: Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000
    File URL: https://libkey.io/10.1016/j.physa.2005.08.011?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Matsushita, M & Wakita, J & Itoh, H & Watanabe, K & Arai, T & Matsuyama, T & Sakaguchi, H & Mimura, M, 1999. "Formation of colony patterns by a bacterial cell population," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 274(1), pages 190-199.
    2. Matsushita, Mitsugu & Fujikawa, Hiroshi, 1990. "Diffusion-limited growth in bacterial colony formation," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 168(1), pages 498-506.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Blessing O Emerenini & Burkhard A Hense & Christina Kuttler & Hermann J Eberl, 2015. "A Mathematical Model of Quorum Sensing Induced Biofilm Detachment," PLOS ONE, Public Library of Science, vol. 10(7), pages 1-25, July.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Mansour, M.B.A., 2007. "Traveling wave solutions of a reaction–diffusion model for bacterial growth," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 383(2), pages 466-472.
    2. Csahók, Zoltán & Czirók, András, 1997. "Hydrodynamics of bacterial motion," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 243(3), pages 304-318.
    3. Ben-Jacob, Eshel, 1998. "Bacterial wisdom, Gödel's theorem and creative genomic webs," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 248(1), pages 57-76.
    4. Lin Chen & Javad Noorbakhsh & Rhys M Adams & Joseph Samaniego-Evans & Germaine Agollah & Dmitry Nevozhay & Jennie Kuzdzal-Fick & Pankaj Mehta & Gábor Balázsi, 2014. "Two-Dimensionality of Yeast Colony Expansion Accompanied by Pattern Formation," PLOS Computational Biology, Public Library of Science, vol. 10(12), pages 1-14, December.
    5. Golding, Ido & Kozlovsky, Yonathan & Cohen, Inon & Ben-Jacob, Eshel, 1998. "Studies of bacterial branching growth using reaction–diffusion models for colonial development," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 260(3), pages 510-554.
    6. Muzzio, Nicolás E. & Horowitz, Claudio M. & Azzaroni, Omar & Moya, Sergio E. & Pasquale, Miguel A., 2021. "Tilted mammalian cell colony propagation dynamics on patterned substrates," Chaos, Solitons & Fractals, Elsevier, vol. 146(C).
    7. Ruzicka, Marek C. & Fridrich, Mirek & Burkhard, Martin, 1995. "A bacterial colony is not self-similar," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 216(4), pages 382-385.
    8. Ben-Jacob, Eshel & Tenenbaum, Adam & Shochet, Ofer & Avidan, Orna, 1994. "Holotransformations of bacterial colonies and genome cybernetics," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 202(1), pages 1-47.
    9. Ben-Jacob, Eshel & Cohen, Inon & Czirók, András & Vicsek, Tamás & Gutnick, David L., 1997. "Chemomodulation of cellular movement, collective formation of vortices by swarming bacteria, and colonial development," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 238(1), pages 181-197.
    10. Salcedo-Sanz, S. & Cuadra, L., 2019. "Hybrid L-systems–Diffusion Limited Aggregation schemes," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 514(C), pages 592-605.
    11. Ben-Jacob, Eshel & Cohen, Inon & Golding, Ido & Gutnick, David L. & Tcherpakov, Marianna & Helbing, Dirk & Ron, Ilan G., 2000. "Bacterial cooperative organization under antibiotic stress," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 282(1), pages 247-282.
    12. Frey, Erwin, 2010. "Evolutionary game theory: Theoretical concepts and applications to microbial communities," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(20), pages 4265-4298.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:phsmap:v:362:y:2006:i:2:p:382-402. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.