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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RNA accumulation #8

Closed churli closed 6 years ago

churli commented 6 years ago

Allow for RNA to accumulate in several units in RBP and Transcribed Chromatin cells. Production should work as follows:

  1. For each TXN site, we produce a certain amount of RNA units (TBC how much)
  2. For each TXN site and for each RNA unit: compute the probability of this unit to be transferred to a neighbouring RBP site (depending on a transfer rate), perform the random choice and choose a neighbour to which the RNA unit should be transferred.
  3. Do a "Decay round": for each RNA-containing site and for each RNA unit, perform a random choice if it must decay, with probability based on the RNA decay rate.

At this point, the energy cost used for phase separation should be "binary", in the sense that it should be: