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3-D Agent-based demo simulation of a necrotic tumor spheroid (80k agents)

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Published on Nov 19, 2012

An early demo of our new 3-D agent-based cell model, growing from 10 to 80,000 agents in about 25 days (24-threaded simulation required about 5 hours). Rendered in 3-D using POVRAY (with a cutaway view when the tumor gets big enough).

Demo simulation incorporated:

1) Full oxygen transport in 1 mm x 1 mm x 1 mm volume (1,000,000 mesh points)

2) oxygen-dependent phenotype

3) Full physics-based cell-cell mechanical interactions

4) Full physics-based regulation of cell fluid and solid volume, separately in the cytoplasm and nucleus.

5) Necrotic cells swell (oncosis), lyse, shrink, and undergo pyknosis and karyorrhexis (nuclear degradation). Calcification implemented but switched off in this test.

6) Apoptotic cells shrink at biologically-reasonable rates

7) Cycling synthesize solids throughout the cycle and transport water through the membrane accordingly. (See 4.)

In this test, we see a very complex necrotic core structure emerge due to the mechanics. Also note the gradient of cycling cells (green) with respect to distance from the outer tumor boundary.

A refined version of this demo framework is currently in preparation for publication.

More recently, we have simulated over 500,000 cells on a high-end workstation, and include mechanical interactions with stroma, oxygen release by blood vessels, and mechanotransduction (alteration of cell phenotype by environmental mechanics).

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