CompuCell3d cell sorting in a hexagonal lattice

Showcases hexagonal lattice use in CompuCell3D by simulating cell sorting by difference in contact energies in a hexagonal lattice.

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Version 1.1 - published on 31 Jul 2020

doi:10.21981/3414-RD17 cite this

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2D cell sorting using CompuCell3D in a hexagonal lattice. Showcases Hexagonal lattice use in CompuCell3D.

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CompuCell3D is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in-silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials. CompuCell3D models have been used to solve basic biological problems, to develop medical therapies, to assess modes of action of toxicants and to design engineered tissues. CompuCell3D intuitive and make Virtual Tissue modeling accessible to users without extensive software development or programming experience. It uses Cellular Potts Model to model cell behavior.


Part of the nanoBio group


Compucell3D is led by Maciej Swat (IU), TJ Sego (IU), Andy Somogyi (IU), Juliano Gianlupi (IU), and James Glazier (IU) in collabration with Dr. David Umulis (PU) and team.

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This project is currently funded by generous support from the U.S. National Science Foundation (NSF) and National Institutes of Health (NIH). Grants: NSF- 1720625, “Network for Computational Nanotechnology - Engineered nanoBIO Node” and NIH- R01 GM122424, “Competitive Renewal of Development and Improvement of the Tissue Simulation Toolkit”.

Cite this work

Researchers should cite this work as follows:

  • Multi-Scale Modeling of Tissues Using CompuCell3D – M. Swat, Gilberto L. Thomas, Julio M. Belmonte, A. Shirinifard, D.Hmeljak, J. A. Glazier, Computational Methods in Cell Biology, Methods in Cell Biology 110: 325-366 (2012)

  • Juliano Ferrari Gianlupi, T.J. Sego (2020), "CompuCell3d cell sorting in a hexagonal lattice," (DOI: 10.21981/3414-RD17).

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