Adhesion

Examples Menu To explore the potential and modeling features, it is the best to learn by example. Morpheus comes with a range of fully functional example models showcasing a number of model formalism and modeling features.

Converting the model from the previous chapter into a 2D model is trivial in Morpheus. In the Space section, you only need to change the Size of the Lattice to e.

Introduction The mass-conserving secretion and uptake of (signaling) molecules by cells can in Morpheus be achieved with Mappers and scaling fluxes by cell.volume. The intracellular amount of signal may trigger a change in a state variable that could downstream change cell behaviors.

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:

Neighborhood choices in CPM should not be done single-handed. In terms of isotropy some neighborhoods constitute sweet spots and should thus be preferred.

Transferring CPM models between simulators may require parameter conversion of the cell surface mechanics, due to different neighborhood choices of the simulators.

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.

Example demonstrating how adhesion energies affect cell shape and the cell-cell contact region Introduction We simulate two CPM cells of the same type to demonstrate how adhesion energies affect cell shape and the cell-cell contact region.

This multiscale mechanistic liver lobule model is composed of various interacting cell types, such as hepatocytes, residential Kupffer cells and macrophages. It captures hepatocellular acetaminophen (APAP) metabolism, DNA damage response activation, necrotic cell death, macrophage recruitment and the regulation of hepatocellular senescence and proliferation, with qualitatively different outcomes as a function of the initial APAP concentration in blood plasma.

Introduction Comparison of spatio-temporal model output to experimental measurements or between model variants all require the application of summary statistics. For multicellular models, statistical properties of the cell configuration at given times or across time are of interest and Morpheus provides some Analysis/Trackers for that: CellTracker, DisplacementTracker, ClusteringTracker and ContactLogger.