Chalmers Conferences, 9th European Conference on Mathematical and Theoretical Biology

A Cell-Based Simulation Environment for Morphogenetic Problems
Simon Tanaka

Last modified: 2014-03-28


We developed a cell-based simulation framework to study morphogenetic problems. The tissue model is based on the visco-elastic cell model approach [1-2], which models interactions between the viscous interstitial fluid and cytoplasm, and the elastic structures such as cell membrane, cell-cell junctions and cytoskeleton using the immersed boundary method. The tissue model is coupled to a system of advection-diffusion-reaction partial differential equations to model signaling, and thus is predestinated to study cell-based mechanisms based on the interaction of tissue dynamics and signaling, as appearing in many morphogenetic problems.
We studied the dynamics of a Turing-type reaction-diffusion signaling system, which locally controls the proliferation rate, and demonstrate that, in comparison to the continuous formulation conterpart, surprising effects (such as dividing cell clusters) emerge.
The software will be published under the GPL license.
[1] Dillon, R., Owen, M., & Painter, K. (2000). A single-cell-based model of multicellular growth using the immersed boundary method. Contemporary Mathematics, 1–15.[2] K. A. Rejniak. An immersed boundary framework for modelling the growth of individual cells: an applicationto the early tumour development. Journal of theoretical biology, 247(1):186–204, July 2007.


cell-based simulation; morphogenesis