CompuCell3D

Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Ho-ge-weg model and the CompuCell3D modeling environment. The CompuCell3D modeling environment provides a convenient platform for biofilm simulations using the Glazier-Graner-Hogeweg (GGH) model, a cell-oriented framework designed to simulate growth and pattern formation due to biological cells’ behaviors. We show how to develop such a simulation, based on the hybrid (continuum-discrete) model of Picioreanu, van Loosdrecht, and Heijnen (PLH), simulate the growth of a single-species bacterial biofilm, and study the roles of cell-cell and cell-field interactions in determining biofilm morphology. In our simulations, which generalize the PLH model by treating cells as spatially extended, deformable bodies, differential adhesion between cells, and their competition for a substrate (nutrient), suffice to produce a fingering instability that generates the finger shapes of biofilms. Our results agree with most features of the PLH model, although our inclu- sion of cell adhesion, which is difficult to implement using other modeling approaches, results in slightly different patterns. Our simulations thus pro- vide the groundwork for simulations of medically and industrially important multispecies biofilms.


References in zbMATH (referenced in 23 articles , 1 standard article )

Showing results 1 to 20 of 23.
Sorted by year (citations)

1 2 next

  1. Leschiera, Emma; Lorenzi, Tommaso; Shen, Shensi; Almeida, Luis; Audebert, Chloe: A mathematical model to study the impact of intra-tumour heterogeneity on anti-tumour CD(8^+) T cell immune response (2022)
  2. Tikka, Pauli; Mercker, Moritz; Skovorodkin, Ilya; Saarela, Ulla; Vainio, Seppo; Ronkainen, Veli-Pekka; Sluka, James P.; Glazier, James A.; Marciniak-Czochra, Anna; Schaefer, Franz: Computational modelling of nephron progenitor cell movement and aggregation during kidney organogenesis (2022)
  3. Hamis, Sara; Yates, James; Chaplain, Mark A. J.; Powathil, Gibin G.: Targeting cellular DNA damage responses in cancer: an in vitro-calibrated agent-based model simulating monolayer and spheroid treatment responses to ATR-inhibiting drugs (2021)
  4. Pramanik, D.; Jolly, M. K.; Bhat, R.: Matrix adhesion and remodeling diversifies modes of cancer invasion across spatial scales (2021)
  5. Cooper et al.: Chaste: Cancer, Heart and Soft Tissue Environment (2020) not zbMATH
  6. Macfarlane, Fiona R.; Chaplain, Mark A. J.; Lorenzi, Tommaso: A hybrid discrete-continuum approach to model Turing pattern formation (2020)
  7. Chowkwale, M.; Mahler, G. J.; Huang, P.; Murray, B. T.: A multiscale \textitinsilico model of endothelial to mesenchymal transformation in a tumor microenvironment (2019)
  8. Jiang, J.; Garikipati, K.; Rudraraju, S.: A diffuse interface framework for modeling the evolution of multi-cell aggregates as a soft packing problem driven by the growth and division of cells (2019)
  9. Sheraton, M. V.; Melnikov, V. R.; Sloot, P. M. A.: Prediction and quantification of bacterial biofilm detachment using Glazier-Graner-Hogeweg method based model simulations (2019)
  10. Chen, Zhan; Zou, Yuting: A multiscale model for heterogeneous tumor spheroid in vitro (2018)
  11. Hamis, Sara; Nithiarasu, Perumal; Powathil, Gibin G.: What does not kill a tumour may make it stronger: \textitinsilico insights into chemotherapeutic drug resistance (2018)
  12. Allena, R.; Scianna, M.; Preziosi, L.: A cellular Potts model of single cell migration in presence of durotaxis (2016)
  13. Knútsdóttir, Hildur; Pálsson, Eirikur; Edelstein-Keshet, Leah: Mathematical model of macrophage-facilitated breast cancer cells invasion (2014)
  14. Li, Jonathan F.; Lowengrub, John: The effects of cell compressibility, motility and contact inhibition on the growth of tumor cell clusters using the cellular Potts model (2014)
  15. Vanegas-Acosta, J. C.; Garzón-Alvarado, D. A.: Biological modelling and computational implementation using the finite elements method (2014)
  16. Zhang, Yong-Tao; Alber, Mark S.; Newman, Stuart A.: Mathematical modeling of vertebrate limb development (2013)
  17. Scianna, Marco: A multiscale hybrid model for pro-angiogenic calcium signals in a vascular endothelial cell (2012)
  18. Backes, Tracy M.; Latterman, Russell; Small, Stephen A.; Mattis, Steven; Pauley, Gwyn; Reilly, Emily; Lubkin, Sharon R.: Convergent extension by intercalation without mediolaterally fixed cell motion (2009)
  19. Galle, J.; Hoffmann, M.; Aust, G.: From single cells to tissue architecture -- a bottom-up approach to modelling the spatio-temporal organisation of complex multi-cellular systems (2009)
  20. Popławski, Nikodem J.; Agero, Ubirajara; Gens, J. Scott; Swat, Maciej; Glazier, James A.; Anderson, Alexander R. A.: Front instabilities and invasiveness of simulated avascular tumors (2009)

1 2 next


Further publications can be found at: https://compucell3d.org/Publications