Content area

Abstract

Bacterial colonies can form a wide variety of shapes and structures based on ambient and internal conditions. To help understand the mechanisms that determine the structure of and the diversity within these colonies, various numerical modeling techniques have been applied. The most commonly used ones are continuum models, agent-based models, and lattice models. Continuum models are usually computationally fast, but disregard information at the level of the individual, which can be crucial to understanding diversity in a colony. Agent-based models resolve local details to a greater level, but are computationally costly. Lattice-based approaches strike a balance between these two limiting cases. However, this is known to come at the price of introducing undesirable artifacts into the structure of the colonies. For instance, square lattices tend to produce square colonies even where an isotropic shape is expected. Here, we aim to overcome these limitations and we therefore study lattice-induced orientational symmetry in a class of hybrid numerical methods that combine aspects of lattice-based and continuum descriptions. We characterize these artifacts and show that they can be circumvented through the use of a disordered lattice which derives from an unstructured fluid. The main advantage of this approach is that the lattice itself does not imbue the colony with a preferential directionality. We demonstrate that our implementation enables the study of colony growth involving millions of individuals within hours of computation time on an ordinary desktop computer, while retaining many of the desirable features of agent-based models. Furthermore, our method can be readily adapted for a wide range of applications, opening up new avenues for studying the formation of colonies with diverse shapes and complex internal interactions.

Details

1009240
Title
Fluid-derived lattices for unbiased modeling of bacterial colony growth
Publication title
PLoS One; San Francisco
Volume
20
Issue
8
First page
e0330491
Number of pages
25
Publication year
2025
Publication date
Aug 2025
Section
Research Article
Publisher
Public Library of Science
Place of publication
San Francisco
Country of publication
United States
e-ISSN
19326203
Source type
Scholarly Journal
Language of publication
English
Document type
Journal Article
Publication history
 
 
Milestone dates
2025-02-18 (Received); 2025-08-03 (Accepted); 2025-08-28 (Published)
ProQuest document ID
3244812427
Document URL
https://www.proquest.com/scholarly-journals/fluid-derived-lattices-unbiased-modeling/docview/3244812427/se-2?accountid=208611
Copyright
© 2025 Verhoef et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
Last updated
2025-08-29
Database
ProQuest One Academic