MorphoSim: An efficient and scalable phase-field framework for accurately simulating multicellular morphologies

TL;DR

MorphoSim is a new phase-field simulation framework that significantly improves efficiency and scalability, enabling detailed modeling of multicellular morphologies and complex cellular interactions.

Contribution

This work introduces MorphoSim, an optimized phase-field model with stabilized schemes and volume constraints, achieving 100x efficiency and supporting large-scale multicellular simulations.

Findings

MorphoSim can simulate over 100 interacting cells.

It accurately reproduces multicellular assembly and dissociation.

The framework is 100 times more efficient than previous models.

Abstract

The phase field model can accurately simulate the evolution of microstructures with complex morphologies, and it has been widely used for cell modeling in the last two decades. However, compared to other cellular models such as the coarse-grained model and the vertex model, its high computational cost caused by three-dimensional spatial discretization hampered its application and scalability, especially for multicellular organisms. Recently, we built a phase field model coupled with in vivo imaging data to accurately reconstruct the embryonic morphogenesis of Caenorhabditis elegans from 1- to 8-cell stages [Kuang et al, PLoS Comput. Biol., 2022]. In this work, we propose an improved phase field model by using the stabilized numerical scheme and modified volume constriction. Then we present a scalable phase-field framework, MorphoSim, which is 100 times more efficient than the previous one, and can simulate over 100 mechanically interacting cells. Finally, we demonstrate how MorphoSim can be successfully applied to reproduce the assembly, self-repairing, and dissociation of a synthetic artificial multicellular system - the synNotch system.