Computational approaches for simulating luminogenesis

Lumens, liquid-filled cavities surrounded by polarized tissue cells, are elementary units involved in the morphogenesis of organs. Theoretical modeling and computations, which can integrate various factors involved in biophysics of morphogenesis of cell assembly and lumens, may play significant roles to elucidate the mechanisms in formation of such complex tissue with lumens. However, up to present, it has not been documented well what computational approaches or frameworks can be applied for this purpose and how we can choose the appropriate approach for each problem. In this review, we report some typical lumen morphologies and basic mechanisms for the development of lumens, focusing on three keywords - mechanics, hydraulics and geometry - while outlining pros and cons of the current main computational strategies. We also describe brief guidance of readouts, i.e., what we should measure in experiments to make the comparison with the model's assumptions and predictions.

Automated summary

This review discusses the elementary units of liquid-filled cavities called lumens. Theoretical modeling and computations are important tools to understand the biophysics of cell assembly and lumen formation. However, the appropriate computational approaches for this purpose have not been well-documented. The review provides an overview of typical lumen morphologies and development mechanisms, while discussing the pros and cons of current computational strategies and providing guidance on experimental measurements for comparison with model assumptions and predictions.