PyAFV

PyAFV is a Python implementation of the active-finite-Voronoi (AFV) model in 2D.

The AFV framework was introduced and developed in, for example, Refs. [1, 2, 3].

Check out the Getting started, Examples, and API reference section for further information, including how to install the project, usage examples, and the complete API reference.

Note

This project is under active development, see GitHub for the latest updates.

Contents

• Home
• 1. Getting started
  • 1.1. Installation
    • 1.1.1. Install using pip
    • 1.1.2. Install from source
  • 1.2. A simple example
• 2. Examples
  • 2.1. Relaxation to mechanical equilibrium
  • 2.2. Active-Finite-Voronoi (AFV) dynamics
  • 2.3. Connectivity between cells
  • 2.4. Custom plotting
  • 2.5. Periodic boundary conditions
  • 2.6. Varying cell target areas from cell to cell
• 3. API reference
  • 3.1. pyafv
  • 3.2. pyafv.PhysicalParams
    • 3.2.1. pyafv.PhysicalParams.get_steady_state
    • 3.2.2. pyafv.PhysicalParams.with_optimal_radius
    • 3.2.3. pyafv.PhysicalParams.with_delta
  • 3.3. pyafv.FiniteVoronoiSimulator
    • 3.3.1. pyafv.FiniteVoronoiSimulator.preferred_areas
    • 3.3.2. pyafv.FiniteVoronoiSimulator.build
    • 3.3.3. pyafv.FiniteVoronoiSimulator.plot_2d
    • 3.3.4. pyafv.FiniteVoronoiSimulator.update_params
    • 3.3.5. pyafv.FiniteVoronoiSimulator.update_positions
    • 3.3.6. pyafv.FiniteVoronoiSimulator.update_preferred_areas
    • 3.3.7. pyafv.FiniteVoronoiSimulator._build_voronoi_with_extensions
    • 3.3.8. pyafv.FiniteVoronoiSimulator._per_cell_geometry
  • 3.4. pyafv.target_delta

Warning

This is an early release of the software. Features and APIs may change in future versions.

References

[1]

J. Huang, H. Levine, and D. Bi. Bridging the gap between collective motility and epithelial–mesenchymal transitions through the active finite voronoi model. Soft Matter, 19(48):9389–9398, 2023. doi:10.1039/D3SM00327B.

[2]

E. Teomy, D. A. Kessler, and H. Levine. Confluent and nonconfluent phases in a model of cell tissue. Phys. Rev. E, 98:042418, Oct 2018. doi:10.1103/PhysRevE.98.042418.

[3]

W. Wang and B. A. Camley. Divergence of detachment forces in the finite-voronoi model, manuscript in preparation. manuscript in preparation, 2026.