PolyHoop: Soft particle and tissue dynamics with topological transitions
arXiv:2307.15006 · doi:10.1016/j.cpc.2024.109128
Abstract
We present PolyHoop, a lightweight standalone C++ implementation of a mechanical model to simulate the dynamics of soft particles and cellular tissues in two dimensions. With only few geometrical and physical parameters, PolyHoop is capable of simulating a wide range of particulate soft matter systems: from biological cells and tissues to vesicles, bubbles, foams, emulsions, and other amorphous materials. The soft particles or cells are represented by continuously remodeling, non-convex, high-resolution polygons that can undergo growth, division, fusion, aggregation, and separation. With PolyHoop, a tissue or foam consisting of a million cells with high spatial resolution can be simulated on conventional laptop computers.
arXiv comment14 pages, 4 figures, 3 tables
References in corpus (11)
- A density-independent glass transition in biological tissues
- Jamming of Deformable Polygons
- Study on Multicellular Systems Using a Phase Field Model
- LBIBCell: A Cell-Based Simulation Environment for Morphogenetic Problems
- Morphological Phases of Crumpled Wire
- Bubbly vertex dynamics: a dynamical and geometrical model for epithelial tissues with curved cell shapes
- The role of deformability in determining the structural and mechanical properties of bubbles and emulsions
- The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions
- LBfoam: An open-source software package for the simulation of foaming using the Lattice Boltzmann Method
- Finite Element Simulation of Dense Wire Packings
- Jamming and force distribution in growing epithelial tissue