Simulating Organogenesis in COMSOL Multiphysics®: Image-Based Modeling

D. Iber[1,3], Z. Karimaddini[1,3], E. Unal[1,2], D. Menshykau[1,3]
[1]D-BSSE, ETH Zurich, Basel, Switzerland
[2]DBM University of Basel, Basel, Switzerland
[3]Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
Published in 2014

Mathematical Modeling has a long history in developmental biology. Advances in experimental techniques and computational algorithms now permit the development of increasingly more realistic models of organogenesis. In particular, 3D geometries of developing organs have recently become available. In this paper, we show how to use image-based data for simulations of organogenesis in the COMSOL Multiphysics® software. As an example, we use limb bud development, a classical model system in mouse developmental biology. We discuss how embryonic geometries with several subdomains can be read into COMSOL using the LiveLink™ for MATLAB® add-on, and how these can be used to simulate models on growing embryonic domains. The ALE method is used to solve signaling models even on strongly deforming domains.