InPartSBiome
This package contains InPartS models used in publications of the Emergent Dynamics in Living Systems group at MPI-DS.
Model definitions can be found in the src directory, interactive examples are in examples.
List of models
The models listed below are based on a simple framework for modelling growing and dividing agents with steric interactions, as described in L. Hupe & Y. G. Pollack et al., arXiv:2409.01959 (2024). There are two different classes of models, represesented in code by abstract supertypes:
- for
Dumbbellmodels, the cell shape is modelled as a dumbbell of two spherical nodes that grow by moving apart until fully separate. - for
Spherocylindermodels, the cell shape is modelled as a cylinder with hemispherical caps
InPartSBiome comes with a basic model for both of these classes, as well as some more specialized models which add additional features.
| Particle type | Supertype | Model description | Main authors |
|---|---|---|---|
DiskCell |
Dumbbell |
Simple growing, nonmotile dumbbell model | Lukas Hupe |
DiskCell3D |
Dumbbell |
DiskCell model extended to work in three dimensions |
Lukas Hupe |
SpheroidDiskCell |
Dumbbell |
Modified version of DiskCell3D with randomized initial direction, cell-cell tractive forces and random direction reversal |
Torben Sunkel |
RodCell |
Spherocylinder |
Simple growing, nonmotile spherocylinder model | Lukas Hupe |
MetabolicTetCell |
Spherocylinder |
Modified version of RodCell with metabolism, tetracycline resistance regulation 1 and interdependencies 2. |
Philip Bittihn, Thomas Boukéké-Lesplulier |
Publications
This is a list of publications and preprints using code included in this package:
- M. Stevanovic et al., Front. Microbiol. 13, (2022)
- J. Isensee et al., J. R. Soc. Interface. 19, 20220512 (2022)
- T. Sunkel, L. Hupe, and P. Bittihn, arXiv:2403.11002 (2024)
- L. Hupe & Y. G. Pollack et al., arXiv:2409.01959 (2024)