PolyHoop: Soft particle and tissue dynamics with topological transitions

TL;DR

PolyHoop is a lightweight C++ tool that efficiently simulates the complex dynamics of soft particles and tissues in two dimensions, accommodating various biological and physical systems with high resolution.

Contribution

It introduces a versatile, high-resolution polygon-based model capable of simulating large-scale soft matter systems with minimal computational resources.

Findings

Simulates tissues with up to a million cells on a laptop

Handles growth, division, fusion, and separation of particles

Applicable to biological tissues, foams, and emulsions

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.