Computational approaches for simulating luminogenesis

Kana Fuji (1) , Sakurako Tanida , Masaki Sano , Makiko Nonomura , Daniel Riveline (2) , Hisao Honda , Tetsuya Hiraiwa (3)

1 UTokyo - The University of Tokyo
2 IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire
3 MBI - Mechanobiology Institute [Singapore]

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.

Mots clés: Luminogenesis; Theoretical modeling; Computational simulations; Luminogenesis

Domaines: Biophysique [physics.bio-ph]

Kana Fuji, Sakurako Tanida, Masaki Sano, Makiko Nonomura, Daniel Riveline, et al.. Computational approaches for simulating luminogenesis. Seminars in Cell and Developmental Biology, 2022, 131, pp.173-185. ⟨10.1016/j.semcdb.2022.05.021⟩. ⟨hal-03835943⟩