ArcA activation in aerobic conditions

[tahorst]

In certain simulation situations, ArcA can become active in aerobic conditions (minimal media). This should not happen because ArcA is active when phosphorylated. It is phosphorylated by ArcB which should only autophosphorylate in anaerobic conditions. This activation can be seen in the tf_binding.py multigen plot during the 4th gen of a wildtype sim from c1ce238 (red on the left decreases and blue on the right increases indicating fewer inactive TFs and more promoters being bound).

The activation only appears to happen when ArcA counts dip below a certain point (an issue that was fixed with #1017 so this does not appear to actively be an issue in current sims). This might indicate an unexpected interplay between equilibrium, two_component_system and tf_binding simulation processes that should be investigated and something might affect other transcription factors.

Steps to reproduce:

git checkout c1ce23848dab987b2856ab85b07becf00f5e52bb
python runscripts/manual/runParca.py arca-issue
python runscripts/manual/runSim.py arca-issue -g4
python runscripts/manual/analysisMultigen.py arca-issue -p tf_binding