3-D PhysiCell simulation of ductal carcinoma in situ - deterministic necrosis model
This is Video S3 in Ghaffarizadeh et al. (2018).
Paper: Ghaffarizadeh et al. (2018).
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 immediately become 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 4 hours and 24 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.
Legend:
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.
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