CPM

  • Init Population

    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:

  • Mixed Cell Types

    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.

  • Non-local Chemical Signals

    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.

  • Agent-based Model

    An agent-based model where each cell’s position and velocity is tracked Introduction We expand our exploration of local and non-local models to the class of agent-based models. Description Instead of tracking continuous distributions of cell density, neural activity, or other properties that vary continuously across space, we adopt a different kind of modeling approach by tracking the trajectories and behavior of individual cells.

  • Cell Sorting (Simplified)

    A simplified version of the Morpheus cell sorting example Introduction A simplified version of the Morpheus built-in example of M0021"cell sorting showing the effect of cell-cell and cell-medium contact energies on the tissue configuration.

  • Chemotaxis

    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.

  • One CPM Cell

    Time sequence showing the changing shape of a CPM cell Introduction Not all cell shapes are circular. In this example, a single cell undergoes a whole series of deformations resulting in the development of irregular cell shapes.

  • One Random Walker

    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.

  • Parameter Plane

    Two-parameter plane showing all possible regimes of behavior for a single CPM cell Introduction The idea is based on figure 3 in the referenced paper. Description But here, we use two dimensionless parameters:

  • Two CPM Cells Adhesion

    Example demonstrating how adhesion energies affect cell shape and the cell-cell contact region Introduction We simulate two CPM cells of the same type to demonstrate how adhesion energies affect cell shape and the cell-cell contact region.

  • Mix and Sort

    Changing the adhesion parameters CPM/Interaction/Contact value during simulation runtime Introduction This example model demonstrates the use of variable adhesion values in the CPM/Interaction/Contact/HomophilicAdhesion plugin. Please also see the built-in docu at MorpheuML/CPM/Interaction/Contact/HomophilicAdhesion.

  • Correlated Random Walkers

    Particles moving left and right (as well as up) to mimic actin filament barbed ends Introduction Particles are moving left and right (as well as up) to mimic actin filament barbed ends as motivated by the referenced paper.

  • Circle Dance

    Demonstration of dynamically regulated cell-cell adhesion as a function of changing cell properties Model Get this model via: Morpheus-Link or  Download: CircleDance.xml XML Preview <MorpheusModel version="4"> <Description> <Title>Example-CircleDance</Title> <Details>Demonstration of dynamically regulated cell-cell adhesion as a function of changing cell properties.

  • Sister Reunion

    Track MotherId (cell.id of mother) and compare it between neighboring cells Introduction This example model demonstrates the tracking of the cell.id of any cell’s mother and to compare these MotherIds between neighboring cells upon contact to trigger special behaviors if sister cells meet in a SisterReunion.

  • Logical Operators

    Use logical operators and, or and xor in Condition for ChangeCellType. Introduction This example model demonstrates the use of logical operators. Please also see the built-in docu at GUI/Documentation/MathematicalExpressions.

Last updated on Thu, 09 Nov 2023