Contributed Examples

This example model demonstrates how to obtain consistent results in physical units together with the freedom to choose arbitrary lattice and time discretizations. Introduction Often, one starts to build a model with a particular lattice size and time scaling.

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.

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:

Spatial relaxation oscillator produces spatial dynamics and spiral waves Introduction We consider a full spatial variant of the Morpheus Model ID: M2012"model of a F-actin negative feedback to GTPase system.

ODEs for GTPase interacting with F-actin Introduction Here, we explore the time behavior of a well-mixed GTPase model with negative feedback from F-actin to the GTPase. Description We assume that GTPase ($G$) leads to actin assembly, and that F-actin, denoted by the variable ($F$), leads to GTPase inactivation:

Simulations of a diffusing field Introduction Here, we build up a simulation of diffusion over three successive files by: Starting with 1D and a short time scale in Diffusion1a_main.

Waves produced by an excitable FitzHugh–Nagumo PDE. Introduction We will here take a closer look at waves produced by an excitable FitzHugh–Nagumo PDE in a periodic 1D domain, in a periodic 2D domain.

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.

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.