3D hybrid cellular Potts model with a discrete deformable fiber network: modeling cell contraction and extracellular matrix remodeling
Abstract
The extracellular matrix (ECM) is a fibrous and dynamic network that plays a critical role in development, homeostasis, and disease. Cells both respond to and remodel the ECM, engaging in a mechanical reciprocity that shapes tissues. To study these interactions, computational models have been developed that simulate either ECM mechanics or cell behavior. The Cellular Potts Model (CPM) is a flexible cell-based framework that has been extended to many biological processes, including coupling to a discrete deformable fiber network. So far, however, this extension has only been applied in two dimensions, even though a three-dimensional setting is biologically more relevant. Here, we present a 3D hybrid framework that couples the CPM with a discrete and deformable representation of the ECM. This model enables explicit simulation of cell-induced ECM remodeling, including fiber reorientation and matrix densification. By incorporating contractile forces through static adhesion points, the model captures how ECM elasticity and fiber stiffness influences cell shape. The simulations show that ECM stiffness, controlled by fiber crosslinking, resists contraction and reaches equilibrium, while crosslink density modulates fiber alignment and local matrix accumulation. This framework provides a versatile platform for studying cell-ECM mechanics and supports future studies of multicellular behavior in realistic 3D environments.
Related
- Paclitaxel induces NM2‐dependent cellular contraction through GEF‐H1 dissociation from microtubules and RhoA/ROCK activation in cancer cells
- House Dust Mite Induces Distinct Cellular and Extracellular Vesicle-Associated miRNA Signatures in BEAS-2B Cells: Targeted Analysis of IL-4 Responses
- Surface curvature promotes coordinated extracellular matrix remodeling and mechanotransductive signaling during osteoblast adaptation
- Extracellular matrix mechanics and collagen architecture remodeling in tissue regeneration: a microstructural analysis
- Genetic Anchoring of Stromal Cellular Programs Relevant to Ligamentum Flavum Remodeling in Lumbar Spinal Stenosis
BibTeX
@misc{keijzer2026hybrid,
title = {{3D hybrid cellular Potts model with a discrete deformable fiber network: modeling cell contraction and extracellular matrix remodeling}},
author = {Koen A. E. Keijzer and Roeland M. H. Merks},
howpublished = {arXiv},
year = {2026},
month = sep,
doi = {10.48550/arxiv.2609.02375},
eprint = {2609.02375},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2609.02375},
}
RIS
TY - UNPB
TI - 3D hybrid cellular Potts model with a discrete deformable fiber network: modeling cell contraction and extracellular matrix remodeling
AU - Koen A. E. Keijzer
AU - Roeland M. H. Merks
PY - 2026
DA - 2026/09/02
PB - arXiv
DO - 10.48550/arxiv.2609.02375
UR - https://arxiv.org/abs/2609.02375
AB - The extracellular matrix (ECM) is a fibrous and dynamic network that plays a critical role in development, homeostasis, and disease. Cells both respond to and remodel the ECM, engaging in a mechanical reciprocity that shapes tissues. To study these interactions, computational models have been developed that simulate either ECM mechanics or cell behavior. The Cellular Potts Model (CPM) is a flexible cell-based framework that has been extended to many biological processes, including coupling to a discrete deformable fiber network. So far, however, this extension has only been applied in two dimensions, even though a three-dimensional setting is biologically more relevant. Here, we present a 3D hybrid framework that couples the CPM with a discrete and deformable representation of the ECM. This model enables explicit simulation of cell-induced ECM remodeling, including fiber reorientation and matrix densification. By incorporating contractile forces through static adhesion points, the model captures how ECM elasticity and fiber stiffness influences cell shape. The simulations show that ECM stiffness, controlled by fiber crosslinking, resists contraction and reaches equilibrium, while crosslink density modulates fiber alignment and local matrix accumulation. This framework provides a versatile platform for studying cell-ECM mechanics and supports future studies of multicellular behavior in realistic 3D environments.
ER -