CompuCell3D v4 - Bacterium Macrophage simulation

Macrophage hunts bacterium in a maze

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Version 1.0.2 - published on 03 Aug 2020

doi:10.21981/WEXN-9E85 cite this

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Abstract

Macrophage hunting bacterium through a maze using CompuCell3D v4.

 

In this tool we simulate a bacterium secreting a diffusive chemical signal, the macrophage is able to detect the gradient of this signal and thus hunt the macrophase. In CompuCell3D the default view is of the cells, we can change the view to observe the chemical field by selecting the drop-down menu in the "Graphics 0" window and selecting it (in the case of this tool the chemical is named ATTR). If you don't see the cells anymore when changing to this view make sure that cell borders is selected under Visualizations option menu.

 

On the left hand side there is a Model Editor with most simulation properties presented. You can open each of the properties and change them, changing the simulated behavior on the fly. For instance, to change how strongly the macrophage feels the gradient we can change the value of λ (lambda) in Plugin Chemotaxis → Chemotaxis → Chemotaxis By Type → lambda (note, if the value presented is an integer you must enter an integer, if it is a float you must enter a float).

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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.

Bio

Part of the nanoBio group https://nanohub.org/groups/nanobio

Credits

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.

Sponsored by

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 v4 - Bacterium Macrophage simulation," https://nanohub.org/resources/bacmacrocc3d4. (DOI: 10.21981/WEXN-9E85).

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