3-D PhysiCell simulation of a hanging drop spheroid - deterministic necrosis model
Ahmadreza Ghaffarizadeh
Randy Heiland
Samuel Friedman
Shannon Mumenthaler
Paul Macklin
10.6084/m9.figshare.5716600.v1
https://figshare.com/articles/media/3-D_PhysiCell_simulation_of_a_hanging_drop_spheroid_-_deterministic_necrosis_model/5716600
<p>This is Video S1 in Ghaffarizadeh
et al. (2018). A higher-resolution (1080p) video can be streamed
at <a href="https://www.youtube.com/watch?v=WMhYW9D4SqM">https://www.youtube.com/watch?v=WMhYW9D4SqM</a>
</p>
<p><b>Paper:</b> <a href="https://doi.org/10.1371/journal.pcbi.1005991">https://doi.org/10.1371/journal.pcbi.1005991</a><br></p>
<p>3-D agent-based simulation of a hanging drop spheroid
experiment. 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 82 hours and 23 minutes to run (including
data saves once per simulated hour). It took 66 hours and 56 minutes to
simulate 17 days to the first ~1 million cells. Simulations without file I/O
are significantly faster.</p>
<p>The tumor maintains its expected
spherical symmetry until the end of the simulation, when the tumor nears the
computational boundary and experiences higher oxygenation that drive
non-spherical growth.</p>
<p><b>Legend:</b></p>
<p><u>Dark circles</u>: cell
nuclei</p>
<p><u>Green cells</u>: Proliferating Ki67+ cells, prior to mitosis</p>
<p><u>Magenta cells</u>: Proliferating Ki67+ cells, after mitosis</p>
<p><u>Red cells</u>: Apoptotic cells (cleaved Caspase-3 positive)</p>
<p><u>Pale blue cells</u>: Quiescent Ki67- cells</p>
<p><u>Brown cells</u>: Necrotic cells</p>
<p>This work is based on PhysiCell, an
open source 3-D modeling package for multicellular biology at <a href="http://physicell.mathcancer.org/">http://PhysiCell.MathCancer.org</a>.</p>
<p><b>Method: </b>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.</p>
<p><b>Software source: </b>PhysiCell is available as open
source at <a href="http://physicell.mathcancer.org/">http://PhysiCell.MathCancer.org</a>, <a href="http://physicell.sf.net/">http://PhysiCell.sf.net</a>, and <a href="https://github.com/mathcancer/physicell/releases">https://github.com/mathcancer/physicell/releases</a>.</p>
2017-12-20 05:20:43
hanging drop spheroid
PhysiCell
open source
biomathematics
computational oncology
necrosis
cancer
tumor
simulation
agent-based models
Computational Biology
Open Software
Bioinformatics Software
Cancer
Simulation and Modelling