2D

Introduction Collective motion of human breast cancer cells of the cell line MDA-MB-231 was studied by Lee et al. for individual crawling cells, cell doublets, cell quadruplets and for confluent populations on a two-dimensional substrate.

Introduction Brook et al. studied the effect of distinct immune phenotypes on cellular-scale viral propagation in three mammalian kidney cell lines with different interferon pathways (IFN). Differences in the IFN response upon pathogen invasion allowed to experimentally observe, model and numerically simulate viral dynamics in cells with

Spatial distribution of GTPase activity Introduction The actin cytoskeleton is regulated by a set of proteins called Small GTPases. The spatial distribution of GTPase activity changes on a timescale of seconds in rapidly moving cells like white blood cells (neutrophils).

Creating patterns using the Schnakenberg reaction-diffusion system Introduction We use the Schnakenberg system to generate patterns using a pair of reaction-diffusion (RD) equations, build up from 1D to 2D and explore parameter dependence.

Pattern formation is robust to noise. Introduction Morpheus can also simulate ODE and PDE models with noise. One example (in the GUI menu Examples → ODE → LateralSignaling.xml) with coupled noisy ODE systems is explained in M0004.

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.

Cells' consumption of cytokine concentration Introduction This example serves to demonstrate the implementation of cells consuming a substrate field, e.g. cytokine. Please also see the built-in docu at MorpheuML/Global/Field and Global/System/DiffEqn.

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.

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.

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.