Mathematical modeling of microbial community dynamics: a methodological review

HS Song, WR Cannon, AS Beliaev, A Konopka - Processes, 2014 - mdpi.com
Microorganisms in nature form diverse communities that dynamically change in structure
and function in response to environmental variations. As a complex adaptive system …

Continuum and discrete approach in modeling biofilm development and structure: a review

MR Mattei, L Frunzo, B D'acunto, Y Pechaud… - Journal of mathematical …, 2018 - Springer
The scientific community has recognized that almost 99% of the microbial life on earth is
represented by biofilms. Considering the impacts of their sessile lifestyle on both natural and …

A mechanistic Individual-based Model of microbial communities

PG Jayathilake, P Gupta, B Li, C Madsen, O Oyebamiji… - PloS one, 2017 - journals.plos.org
Accurate predictive modelling of the growth of microbial communities requires the credible
representation of the interactions of biological, chemical and mechanical processes …

Architecture of soil microaggregates: Advanced methodologies to explore properties and functions

W Amelung, N Tang, N Siebers… - Journal of Plant …, 2024 - Wiley Online Library
The functions of soils are intimately linked to their three‐dimensional pore space and the
associated biogeochemical interfaces, mirrored in the complex structure that developed …

Extracellular polymeric substance production and aggregated bacteria colonization influence the competition of microbes in biofilms

PG Jayathilake, S Jana, S Rushton, D Swailes… - Frontiers in …, 2017 - frontiersin.org
The production of extracellular polymeric substance (EPS) is important for the survival of
biofilms. However, EPS production is costly for bacteria and the bacterial strains that …

Lattice Boltzmann-based approaches for pore-scale reactive transport

H Yoon, Q Kang, AJ Valocchi - Reviews in Mineralogy …, 2015 - pubs.geoscienceworld.org
Important geoscience and environmental applications such as geologic carbon storage,
environmental remediation, and unconventional oil and gas recovery are best understood in …

The physics of biofilms—an introduction

MG Mazza - Journal of Physics D: Applied Physics, 2016 - iopscience.iop.org
Biofilms are complex, self-organized consortia of microorganisms that produce a functional,
protective matrix of biomolecules. Physically, the structure of a biofilm can be described as …

Coupling scales in process‐based soil organic carbon modeling including dynamic aggregation

S Zech, A Prechtel, N Ray - Journal of Plant Nutrition and Soil …, 2024 - Wiley Online Library
Background Carbon storage and turnover in soils depend on the interplay of soil
architecture, microbial activities, and soil organic matter (SOM) dynamics. For a fundamental …

A mixed-culture biofilm model with cross-diffusion

KA Rahman, R Sudarsan, HJ Eberl - Bulletin of mathematical biology, 2015 - Springer
We propose a deterministic continuum model for mixed-culture biofilms. A crucial aspect is
that movement of one species is affected by the presence of the other. This leads to a …

How water connectivity and substrate supply shape the turnover of organic matter–Insights from simulations at the scale of microaggregates

S Zech, T Ritschel, N Ray, KU Totsche, A Prechtel - Geoderma, 2022 - Elsevier
Microaggregates are hot spots of microbial activity at a scale that frequently poses a severe
experimental challenge or defies a direct observation. Mathematical models that combine …