Simulating Organogenesis in COMSOL: Parameter Optimization for PDE-based models

Abstract

Morphogenesis is a tightly regulated process that has been studied for decades. We are developing data-based and image-basd mechanistic models for a range of developmental processes with a view to integrate the available knowledge and to better understand the underlying regulatory logic. In our previous papers on simulating organogenesis with COMSOL (German et al COMSOL Conf Procedings 2011; Menshykau and Iber, COMSOL Conf Proceedings 2012) we discussed methods to efficiently solve such models on static and growing domains. A further challenge in modeling morphogenesis is the parameterization of such models. Here we discuss COMSOL-based methods for parameter optimization. These routines can be used to determine parameter sets, for which the simulations reproduce experimental data and constraints. Such data is often image based, but may also come from classical biochemical or genetic experiments.