Self-organisation of a dynamic meshwork structure in the mesoderm during the development of a chick embryo and its characterisation using persistent homology

Morphogenesis is a fundamental process of development. Appropriate morphogenesis of tissues is achieved by coordinated motion of individual cells. To elucidate the mechanism behind this self-organisation of cells, one needs to develop a theoretical model based on experimental observations. In our recent study, our experimental colleague found that the mesoderm cells in early chick embryo organise into a meshwork structure, which changes dynamically. To understand the mechanism behind this dynamic meshwork structure formation, we developed an agent-based mechanical model of cells that interact through a short-range attractive interaction. To compare the simulation results with the experiment, we utilized persistent homology, a method of topological data analysis that allows to systematically characterise irregular structures. In this seminar, we will talk about the mechanical mechanism behind the mesoderm structure formation during the development of the early chick embryo, and how the persistent homology analysis is applied to our biological system.