Improve Actinomycin D behaviour

lhilbert / active-microemulsion

Package for the lattice-based simulation of active polymer microemulsions, such as dense DNA suspensions

BSD 2-Clause "Simplified" License

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Improve Actinomycin D behaviour #10

Closed churli closed 6 years ago

churli commented 6 years ago

Currently Actinomycin D simulation are represented by setting:

kChromPlus
kChromMinus
kRnaPlus

to 0.

This however doesn't fully represent the effects of the drug, especially now that we have RNA accumulation. To fill this gap we would also need to:

Set the kRnaTransfer rate to 0.
Set the kRnaMinus rate to 0, but only for TXN sites.

churli commented 6 years ago

Regarding the kRnaMinus change only for one type of sites: We decided to split this parameter into 2: kRnaMinusRbp (which applies to RBP sites) and kRnaMinusTxn (which applies to TXN sites). Usually they should be set to the same value, but when Actinomycin D is applied, kRnaMinusTxn must be switched to 0.