Built-In Examples

Introduction A 2D activator-inhibitor model (Gierer and Meinhardt, 1972), solved in a irregular domain that is loaded from an image file. Spot pattern in Gierer-Meinhardt model with irregular domain.

Introduction This model shows the pattern formation abilities of Turing’s linear activator-inhibitor model (Miyazawa et al., 2010). It shows how to vary parameters as a function of space. Spots and stripes appear under various conditions in linear Turing model.

Introduction This example uses the Barkley model of excitable media, similar to the Fitzhugh-Nagumo model to show how to model and visualize reaction-diffusion models in 3D. Scroll wave appears in Barkley model of excitable media in 3D.

Introduction This model shows the original cellular Potts model (a.k.a. Glazier-Graner model) of cell sorting based on the Steinberg’s differential adhesion hypothesis. Yellow cells engulf the red cells as a result of differential adhesion.

Introduction This model shows a simulation of a growing cell population, using the cellular Potts model. Growing cell population. Description The model specifies CellType which has a VolumeConstraint and a Proliferation plugin.

Introduction This example shows self-organized collective motion of cells as a result of persistence (‘cellular inertia’). A similar model has recently been used by Czirók et al. (2013). Persistence of individual cells causes self-organized collective motion.

Introduction This model shows a CPM simulation of a growing cell population in 3D. Cell population grown from single initial cell. Description The model specifies CellType which has a VolumeConstraint and a Proliferation plugin.

Introduction This example models a single cell that moves according to a Lévy walk: a random walk with occassional occurrence of long straight walks. Modeling cell movements as a Lévy walk.

Introduction This illustrative example shows the emergence of clonal populations from stem cells in an intestinal crypt. Stem cells in the bottom of the crypt divide asymmetrically and produce a population of transit amplifying (TA) cells.

Introduction This example models a cellular Potts model for autocrine chemotaxis by coupling a CPM to a diffusive chemoattractant. Cell cluster due to chemotaxis towards self-produced chemoattractant. Description It exemplifies the combination of a CPM with a PDE through the chemotaxis towards a diffusive chemoattractant produced by cells.