Reducing discrepancies between 3D and 2D simulations due to cell packing density

Robert Clegg, Jan-Ulrich Kreft

Research output: Contribution to journalLetterpeer-review

2 Citations (Scopus)
206 Downloads (Pure)


Modelling all three spatial dimensions is often much more computationally expensive than modelling a two-dimensional simplification of the same system. Researchers comparing these approaches in individual-based models of microbial biofilms report quantitative, but not qualitative, differences between 2D and 3D simulations. We show that a large part of the discrepancy is due to the different space packing densities of circles versus spheres, and demonstrate methods to compensate for this: the internal density of individuals or the distances between them can be scaled. This result is likely to be useful in similar models, such as smoothed particle hydrodynamics.
Original languageEnglish
Pages (from-to)26-30
Number of pages5
JournalJournal of Theoretical Biology
Early online date17 Apr 2017
Publication statusPublished - 21 Jun 2017


  • Individual-based model
  • Agent-based model
  • Spatial structure
  • Biofilm
  • Heuristics


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