How about the units in CC3D?

3 months ago by
Hi, I wonder what is the unit in a CC3D simulation?  Is it dimensionless? How to make the simulation agree with the experiment?
Community: CompuCell3D

1 Answer

3 months ago by
The lattice in CC3D represents a coordinate space in which you can measure positions. or measurements in length (in voxels). The other thing you can visualize from your simulation are measurements in time (in mcs) by observing how your configuration is changing. These length or time values are only a representation . For example, I could have a cell which measures 15 microns in diameter. To represent it I can construct a cell in CC3D with a diameter of 15 voxels and now my scale would be 1 voxel=1 micron. I could also pick a smaller or larger simulation diameter and scale accordingly.

Similarly I could have a problem in which my cell grows, reaches twice its volume and divides. If I know experimentally that the cell division time is 100 minutes, I would from my simulation check how long it takes for its growth and division and relate that mcs value to 100 minutes.
Thank you, I understand that. I still have a question. Can I use the boundary energy to resemble the adhesion between cells? How to make the J(energy) agree with the strength of adhesion i.e. the amount of E-cadherin?
written 3 months ago by Yuan  
So what you can use for this is the adhesion flex plugin (for more details please see the manual). This plugin allows you to specify the adhesion molecule density for each cell (in terms of E-cadherin etc) and writes the resultant surface energy in terms of products of different adhesion molecule concentrations in all the cells. It also allows you to specify the strength of interactions between these surface molecules.
written 3 months ago by priyomadhyapok  
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