3-D PhysiCell simulation of a hanging drop spheroid - stochastic necrosis model

This is Video S2 in Ghaffarizadeh et al. (2018). A higher-resolution (1080p) video can be streamed at https://www.youtube.com/watch?v=xrOqqJ_Exd4

Paper: https://doi.org/10.1371/journal.pcbi.1005991

3-D agent-based simulation of a hanging drop spheroid experiment. In this simulation, cells have a pO2-dependent probability of becoming necrotic wherever pO2 < 5 mmHg. This simulation was completed on a single HPC compute node (dual Xeon 6-core CPUs at 3.4 GHz), requiring 73 hours and 25 minutes to run (including data saves once per simulated hour). It took 60 hours and 56 minutes to simulate 17 days to the first ~800k cells. Simulations without file I/O are significantly faster.


Dark circles: cell nuclei

Green cells: Proliferating Ki67+ cells, prior to mitosis

Magenta cells: Proliferating Ki67+ cells, after mitosis

Red cells: Apoptotic cells (cleaved Caspase-3 positive)

Pale blue cells: Quiescent Ki67- cells

Brown cells: Necrotic cells

This work is based on PhysiCell, an open source 3-D modeling package for multicellular biology at http://PhysiCell.MathCancer.org.

Method: Demonstration of PhysiCell, an agent-based, lattice-free model. Cell velocities determined by balance of adhesive, repulsive, and motile forces. Each cell has a phenotypic state governed by stochastic processes derived from nonhomogeneous Poisson processes.

Software source: PhysiCell is available as open source at http://PhysiCell.MathCancer.org, http://PhysiCell.sf.net, and https://github.com/mathcancer/physicell/releases.