### how to model cell neucleus, cytoplasm and membrance?

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Dear all,

I wonder if i could model cell nucleus, cytoplasm and membrance according to attached paper. i dont know how to estimate proper values of target surface and target volume especially for membrance so that it dosnt get fragmented(for membrance, target surface gets biger than target volume!!! is that the reason of fragmentation?).

Another issue is that when subcellular adhesions got negative the membrance pixels start to come into cytoplasm area.

At the end, have i chosen FocalPointPlasticity parameters values properly?

sincerely,

Silvana

paper:

https://www.sciencedirect.com/science/article/pii/S0010482515001274

File attached: CancerCell.cc3d (267 Bytes)

I wonder if i could model cell nucleus, cytoplasm and membrance according to attached paper. i dont know how to estimate proper values of target surface and target volume especially for membrance so that it dosnt get fragmented(for membrance, target surface gets biger than target volume!!! is that the reason of fragmentation?).

Another issue is that when subcellular adhesions got negative the membrance pixels start to come into cytoplasm area.

At the end, have i chosen FocalPointPlasticity parameters values properly?

sincerely,

Silvana

paper:

https://www.sciencedirect.com/science/article/pii/S0010482515001274

File attached: CancerCell.cc3d (267 Bytes)

Community: CompuCell3D

### 2 Answers

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Marco and Luigi published another paper (they used CC3D for their simulations) where they give you parameter values

https://epubs.siam.org/doi/abs/10.1137/100812951

Take a look at it and this should give you some hints.

Regarding negative contact energies:

If you use them you have to use surface constraint plugin ("Surface"). Here is the reason: CC3D minimizes energy and if one of your contact energy coefficients is negative one way to accomplish this is to create as many cell-cell interfaces with negative coefficients as possible . And this is exactly what you see. In order to prevent this you need to add surface constraint for any cell (except Medium) that has negative contact energy coefficient

https://epubs.siam.org/doi/abs/10.1137/100812951

Take a look at it and this should give you some hints.

Regarding negative contact energies:

If you use them you have to use surface constraint plugin ("Surface"). Here is the reason: CC3D minimizes energy and if one of your contact energy coefficients is negative one way to accomplish this is to create as many cell-cell interfaces with negative coefficients as possible . And this is exactly what you see. In order to prevent this you need to add surface constraint for any cell (except Medium) that has negative contact energy coefficient

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So here is the explanation of what we mean by surface /volume in 2 and 3 dimensions

in 2D

volume is numerically equal to the surface area of the shape (because our cells have hight of 1 pixel)

Surface is numerically equal to the perimeter of the the shape

in 3D

volume is "true" 3D volume

surface is the surface of the 3D cell

Coming back to your question - when you increase target surface in surface constraint C#D will try to accommodate your request and will start creating single pixels (because isolated pixel brings 4 units of surface in 2D and 6 units in 3D).

to prevent this behavior you have two choices:

1. Use Connectivity constraint - not a bad idea and it will keep your cell connected . The downside is it slows your simulation to some extent

2. Use compartmentalized cells -this is a bit more sophisticated solutions but you can create big variety of cellular shapes shapes.

Let me know if this helps

in 2D

volume is numerically equal to the surface area of the shape (because our cells have hight of 1 pixel)

Surface is numerically equal to the perimeter of the the shape

in 3D

volume is "true" 3D volume

surface is the surface of the 3D cell

Coming back to your question - when you increase target surface in surface constraint C#D will try to accommodate your request and will start creating single pixels (because isolated pixel brings 4 units of surface in 2D and 6 units in 3D).

to prevent this behavior you have two choices:

1. Use Connectivity constraint - not a bad idea and it will keep your cell connected . The downside is it slows your simulation to some extent

2. Use compartmentalized cells -this is a bit more sophisticated solutions but you can create big variety of cellular shapes shapes.

Let me know if this helps

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I had considered surface constraint for all cell types but the membrance fluctuates. but my question is that when you calculate the target shape constranits for some thin objects(here, cell membrance), can the target perimeter gets higher than target surface? i think in this case the outer pixels start to fluctuate.