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

Authored by Robert J Clegg, Jan-Ulrich Kreft

Date Published: 2017

DOI: 10.1016/j.jtbi.2017.04.016

Sponsors: No sponsors listed

Platforms: Java

Model Documentation: Other Narrative Mathematical description

Model Code URLs: https://ars.els-cdn.com/content/image/1-s2.0-S0022519317301807-mmc2.zip

Abstract

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. (C) 2017 Elsevier Ltd. All rights reserved.

Tags

Agent-based model Individual-based model systems Model heuristics growth Spatial structure Automaton approach Biofilm structure Biofilm Spheres