Cellular Potts Model

Hybrid continuum-chemical and agent-based cell model Introduction The idea that the diffusion of extracellular signaling molecules sets up non-local cellular communications can also be used to simulate non-local forces using chemoattraction and repulsion.

Simulations of four types of cells with different shapes to demonstrate how the combined target volume, surface area, and medium contact interaction determine the shape of the cell Introduction By setting the volume, surface, and length constraints, a CPM simulation can produce a variety of cell shapes.

Changing the adhesion parameters CPM/Interaction/Contact value during simulation runtime Introduction This example model demonstrates the use of variable adhesion values in the CPM/Interaction/Contact/HomophilicAdhesion plugin. Please also see the built-in docu at MorpheuML/CPM/Interaction/Contact/HomophilicAdhesion.

This model also requires the separate file Population_M.csv with the list of lattice nodes where cells shall be initialized. Introduction Initializing the spatial configuration of cells is a key step of every simulation and Morpheus offers all the flexibility for this:

Diffusion model with cells endowed with chemotactic ability Introduction Previously developed diffusion models can be used to model chemotaxis by adding cells endowed with chemotactic ability. Here, chemotaxis of a group of cells towards a chemical diffusing into the domain with a high level at the right boundary is demonstrated, as well as in a second model, Keller-Segel cells being the sources of their own attractant.

A simplified version of the Morpheus cell sorting example Introduction A simplified version of the Morpheus built-in example of M0021"cell sorting showing the effect of cell-cell and cell-medium contact energies on the tissue configuration.

An agent-based model where each cell’s position and velocity is tracked Introduction We expand our exploration of local and non-local models to the class of agent-based models. Description Instead of tracking continuous distributions of cell density, neural activity, or other properties that vary continuously across space, we adopt a different kind of modeling approach by tracking the trajectories and behavior of individual cells.

Hepatocyte–sinusoid alignment (HSA) supports the coordination of hepatocytes during liver regeneration after damage by carbon tetrachloride. Introduction The regenerative capacity of the mammalian liver did already inspire the fate of Prometheus in Greek Myth but it still poses many questions today that call for spatio-temporal multicellular modeling.

Just over 30 years ago, the cellular Potts model (CPM) was introduced to explain experimental observations of spontaneous cell sorting …

Membrane pattern allows anisotropic release of substance into a chemical synapse Introduction Special cell types, like neurons or immune cells, communicate through a chemical synapse. This includes the anisotropic secretion of a substance into the gap between two cells.