CPM

Let’s go through an example. We’ll construct a model in which an intracellular cell cycle network (ODE) regulates the division of motile cells which (CPM) release a diffusive cytokine (PDE) which, in turn, controls the cell cycle (ODE).

At this point, you may be asking yourself: ‘All nice and well, but how can I control the relative time scales between the various models?’ And I’d respond:

In this course, we have constructed a small multiscale model in which an ODE model, a CPM model and a PDE model are mutually coupled to each other. The main aim was to show how one can couple such models with relative ease in Morpheus and how you can control such couplings.

Glazier-Graner Model of cell sorting Introduction This model shows the original cellular Potts model (a.k.a. Glazier-Graner model) of cell sorting based on the Steinberg’s differential adhesion hypothesis. Figure 1.

ODE model of the Xenopus oocyte cell cycle coupled to 2D shaped CPM cells that perform divide based on component concentrations Introduction This multiscale model example shows how to define a coupled system of continuous ODEs in discrete CPM cells, how to specify and change time scales between these model formalisms.

How does the architectural heterogeneity of the liver with its array of peri-central zones lead to the metabolic zonation across the liver lobule? Introduction Liver micro-architecture is set by an array of central veins interspersed with portal triads.

Simulating cell migration within an environment of structural obstacles Introduction This repository contains the Morpheus model configuration file for simulating cell migration within an environment of structural obstacles.

How does immune cell polarity respond to changing stimuli? Introduction Neutrophils are fast-moving immune cells that polarize and reorient in response to external signals. Using optogenetic control of PI3K, recent experiments revealed that when a localized light stimulus becomes global, cells reverse their polarity — a behaviour not predicted by classical models.

How does the single zygote transform into a 128-cell stage? Introduction This project aims to simulate the development of a human embryo from a single zygote cell to the 128-cell stage using a Cellular Potts Model (CPM).