3-D PhysiCell simulation of ductal carcinoma in situ - stochastic necrosis model

This is Video S4 in Ghaffarizadeh et al. (2018). A higher-resolution (1080p) video can be streamed at https://www.youtube.com/watch?v=-lRot-dfwJk

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

3-D agent-based simulation of ductal carcinoma in situ (DCIS), a type of breast cancer that is constrained to growth in the breast duct lumen by a basement membrane. 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 3 hours and 39 minutes to run (including data saves once per simulated hour). Simulations without file I/O are significantly faster. Shown here: A simulation of 30 days' growth in a 1 mm length of duct.

Shown here: A simulation of 30 days' growth in a 1 mm length of duct.


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.