### How to specify the values of the parameters in GGH model?

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Dear all, there are some puzzles for GGH model.

1. How to specify the values of parameters in the model? For example, adhesion energy J, elastic constants K. Can I set them according to the experiments? How to realize?

2. As for the time, the Monto Carol Step(MCS) is determined by the real-time. However, the values of the parameters in simulation based on the relationship of MCS and real-time and the values have an impact on the total MCSs, i.e. they are coupled. How to solve this?

3. How to specify the relative values of the parameters?

Thank you~

1. How to specify the values of parameters in the model? For example, adhesion energy J, elastic constants K. Can I set them according to the experiments? How to realize?

2. As for the time, the Monto Carol Step(MCS) is determined by the real-time. However, the values of the parameters in simulation based on the relationship of MCS and real-time and the values have an impact on the total MCSs, i.e. they are coupled. How to solve this?

3. How to specify the relative values of the parameters?

Thank you~

Community: CompuCell3D

### 2 Answers

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Hi Yuan,

If I understand the question correctly, the way I map MCS to real time is to look at the average square displacement of cells in experiments and simulations and then use this to directly map MCS to real time.

Mapping adhesion energy to experiments is more complicated, unless you can extract real values or find values in literature, it is very difficult, one possible way is to use ratios depending on the minimization or maximization of cell boundary interfaces, i.e if two cells in a non confluent environment in contact increase their shared contact area they more adhesive than cells that decrease their contact area.

best,

Daniel

If I understand the question correctly, the way I map MCS to real time is to look at the average square displacement of cells in experiments and simulations and then use this to directly map MCS to real time.

Mapping adhesion energy to experiments is more complicated, unless you can extract real values or find values in literature, it is very difficult, one possible way is to use ratios depending on the minimization or maximization of cell boundary interfaces, i.e if two cells in a non confluent environment in contact increase their shared contact area they more adhesive than cells that decrease their contact area.

best,

Daniel

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The mcs to time relationship can often be determined simply by inspecting your problem. How fast do things happen? Are cells moving and/or dividing? How long does it take to move or divide? You mcs to time relationship is typically set so that an mcs represents a small portion of your time domain. If it takes 2 hours for a cell to divide then a 1 second/mcs time scale might be OK since that means there are 7200 mcs over the course of the process, which is likely to be sufficient.

Alternatively, you can scan the mcs to time relationship. Compare the results of simulations with 1 mcs= 1 hour, 1 minute, 1 second, 1 millisecond, ... Usually there will be a range of time scales where the simulation output changes with the time scale and another range of time scales where the output doesn't change. You want your simulation to be running in the time step size independent domain.

Alternatively, you can scan the mcs to time relationship. Compare the results of simulations with 1 mcs= 1 hour, 1 minute, 1 second, 1 millisecond, ... Usually there will be a range of time scales where the simulation output changes with the time scale and another range of time scales where the output doesn't change. You want your simulation to be running in the time step size independent domain.

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Thanks for your answer. I still have two questions:

1. The MCS and real-time relationship can only be obtained after the simulation and experiment?

2. How to specify the relative size of the parameters?

Thank you~

Yuan