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Lookup NU author(s): Dr Oluwole Oyebamiji, Professor Darren Wilkinson, Dr Bowen LiORCiD, Dr Paolo Zuliani, Professor Thomas CurtisORCiD
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
© 2018 Individual-based (IB) modelling has been widely used for studying the emergence of complex interactions of bacterial biofilms and their environment. We describe the emulation and calibration of an expensive dynamic simulator of an IB model of microbial communities. We used a combination of multivariate dynamic linear models (DLM) and a Gaussian process to estimate the model parameters of our dynamic emulators. The emulators incorporate a smoothly varying and nonstationary trend that is modelled as a deterministic function of explanatory variables while the Gaussian process (GP) is allowed to capture the remaining intrinsic local variations. We applied this emulation strategy for parameter calibration of a newly developed model for simulation of microbial communities against the iDynoMiCS model. The percentage of variance explained for the four outputs biomass concentration, the total number of particles, biofilm average height and surface roughness range between 84—92% and 97–99% for univariate and multivariate emulators respectively. The simulation-based sensitivity analysis identified carbon substrate, oxygen concentration and maximum specific growth rate for heterotrophic bacteria as the most critical variables for predictions. The calibration results also indicated a general reduction of uncertainty levels in most of the parameters. The study has helped us identify the tradeoff in using different types of models for microbial simulation. The approach illustrated here provides a tractable and computationally efficient technique for calibrating the parameters of an expensive computer model.
Author(s): Oyebamiji OK, Wilkinson DJ, Li B, Jayathilake PG, Zuliani P, Curtis TP
Publication type: Article
Publication status: Published
Journal: Journal of Computational Science
Year: 2019
Volume: 30
Pages: 194-208
Print publication date: 01/01/2019
Online publication date: 19/12/2018
Acceptance date: 12/12/2018
Date deposited: 10/01/2019
ISSN (print): 1877-7503
Publisher: Elsevier B.V.
URL: https://doi.org/10.1016/j.jocs.2018.12.007
DOI: 10.1016/j.jocs.2018.12.007
Data Access Statement: https://doi.org/10.17634/123172-4
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