1 research outputs found
LBIBCell: A Cell-Based Simulation Environment for Morphogenetic Problems
The simulation of morphogenetic problems requires the simultaneous and
coupled simulation of signalling and tissue dynamics. A cellular resolution of
the tissue domain is important to adequately describe the impact of cell-based
events, such as cell division, cell-cell interactions, and spatially restricted
signalling events. A tightly coupled cell-based mechano-regulatory simulation
tool is therefore required.
We developed an open-source software framework for morphogenetic problems.
The environment offers core functionalities for the tissue and signalling
models. In addition, the software offers great flexibility to add custom
extensions and biologically motivated processes. Cells are represented as
highly resolved, massless elastic polygons; the viscous properties of the
tissue are modelled by a Newtonian fluid. The Immersed Boundary method is used
to model the interaction between the viscous and elastic properties of the
cells, thus extending on the IBCell model. The fluid and signalling processes
are solved using the Lattice Boltzmann method. As application examples we
simulate signalling-dependent tissue dynamics.Comment: 15 pages, 23 pages with supplementary, 6 figures; Bioinformatics 201