Borau, C. orcid.org/0000-0002-3784-1140, Chisholm, R. orcid.org/0000-0003-3379-9042, Richmond, P. orcid.org/0000-0002-4657-5518 et al. (1 more author) (2024) An agent-based model for cell microenvironment simulation using FLAMEGPU2. Computers in Biology and Medicine, 179. 108831. ISSN 0010-4825
Abstract
This work presents an advanced agent-based model developed within the FLAMEGPU2 framework, aimed at simulating the intricate dynamics of cell microenvironments. Our primary objective is to showcase FLAMEGPU2's potential in modelling critical features such as cell-cell and cell-ECM interactions, species diffusion, vascularisation, cell migration, and/or cell cycling. By doing so, we provide a versatile template that serves as a foundational platform for researchers to model specific biological mechanisms or processes. We highlight the utility of our approach as a microscale component within multiscale frameworks. Through four example applications, we demonstrate the model's versatility in capturing phenomena such as strain-stiffening behaviour of hydrogels, cell migration patterns within hydrogels, spheroid formation and fibre reorientation, and the simulation of diffusion processes within a vascularised and deformable domain. This work aims to bridge the gap between computational efficiency and biological fidelity, offering a scalable and flexible platform to advance our understanding of tissue biology and engineering.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2024 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
Keywords: | Agent-based model; Cell microenvironment; Extracellular matrix; FLAMEGPU2; GPU; Models, Biological; Humans; Cellular Microenvironment; Computer Simulation; Cell Movement; Hydrogels |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Engineering (Sheffield) > Department of Computer Science (Sheffield) |
Funding Information: | Funder Grant number EUROPEAN COMMISSION - HORIZON 2020 826494 |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 29 Oct 2024 08:32 |
Last Modified: | 29 Oct 2024 08:32 |
Status: | Published |
Publisher: | Elsevier BV |
Refereed: | Yes |
Identification Number: | 10.1016/j.compbiomed.2024.108831 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:218965 |