PDE

  • Scaled Diffusion

    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.

  • Actin Waves

    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.

  • Diffusion

    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.

  • FitzHugh–Nagumo Waves

    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.

  • Wave-Pinning

    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).

  • Schnakenberg System

    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.

  • Field-Cell Interaction

    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.

  • Diffusion in Liver Lobule

    Diffusion in Liver Lobule Introduction This model considers diffusion of a marker with concentration $c(x,y,t)$ across a liver lobule. The lobule is patterned into a central zone around the central vein (center of simulation domain) and portal zones around (here six) portal triads that here act as sinks ($c = 0$).

  • Noisy Turing

    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.

Last updated on Fri, 05 Jan 2024