2D

Introduction A 2D activator-inhibitor model (Gierer and Meinhardt, 1972), solved in a irregular domain that is loaded from an image file. Spot pattern in Gierer-Meinhardt model with irregular domain.

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.

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.

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).

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.

Unbiased and biased random walkers Introduction We can simulate the swimming motion of a cell, such as a bacterium, by interspersing short periods of directed motion with random turns or random scrambling of the cell’s velocity.

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.

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.