LBIBCell: A Cell-Based Simulation Environment for Morphogenetic Problems

TL;DR

LBIBCell is an open-source, flexible simulation environment that models morphogenetic tissue dynamics by integrating cell mechanics, signalling, and fluid interactions at cellular resolution.

Contribution

It introduces a novel, tightly coupled simulation framework combining cell mechanics, signalling, and fluid dynamics for morphogenetic studies.

Findings

Successfully simulates signalling-dependent tissue dynamics

Extends the IBCell model with fluid-structure interaction

Provides a flexible platform for custom biological extensions

Abstract

The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events, such as cell division, cell-cell interactions, and spatially restricted signalling events. A tightly coupled cell-based mechano-regulatory simulation tool is therefore required. We developed an open-source software framework for morphogenetic problems. The environment offers core functionalities for the tissue and signalling models. In addition, the software offers great flexibility to add custom extensions and biologically motivated processes. Cells are represented as highly resolved, massless elastic polygons; the viscous properties of the tissue are modelled by a Newtonian fluid. The Immersed Boundary method is used to model the interaction between the viscous and elastic properties of the cells, thus extending on the IBCell model. The fluid and signalling processes are solved using the Lattice Boltzmann method. As application examples we simulate signalling-dependent tissue dynamics.