This PR resolves #1372 by activating fewer ribosomes to resolve overcrowding when rescaling protein_init_prob (which can be thought of as pushing more ribosomes onto mRNAs that aren't overcrowded) fails. The failure of the rescaling does not happen often but has been observed in a handful of seeds for a few parameter combinations that lead to high levels of new gene expression. In these cases where rescaling fails, the new reduced number of ribosomes activated is chosen to be such that no genes are overcrowded.
Along with this change to the polypeptide initiation process comes a few updates to analysis scripts:
model/ecoli/analysis/single/inter_rnap_dist.pymodel/ecoli/analysis/single/inter_ribosome_dist.pymodel/ecoli/analysis/single/ppgpp_concentration.py
Example plot outputs attached for a single generation wildtype simulation.
PR_reduced_ribos.pdf
(You may notice that a couple of monomers have average inter-ribosome distances slightly below the footprint size, but since the mRNA counts for these proteins are very small and this is averaged over only a single generation, this is okay. These monomer ids are marked with a * .)
This PR resolves #1372 by activating fewer ribosomes to resolve overcrowding when rescaling
protein_init_prob(which can be thought of as pushing more ribosomes onto mRNAs that aren't overcrowded) fails. The failure of the rescaling does not happen often but has been observed in a handful of seeds for a few parameter combinations that lead to high levels of new gene expression. In these cases where rescaling fails, the new reduced number of ribosomes activated is chosen to be such that no genes are overcrowded.Along with this change to the polypeptide initiation process comes a few updates to analysis scripts:
model/ecoli/analysis/single/inter_rnap_dist.pymodel/ecoli/analysis/single/inter_ribosome_dist.pymodel/ecoli/analysis/single/ppgpp_concentration.pyExample plot outputs attached for a single generation wildtype simulation. PR_reduced_ribos.pdf (You may notice that a couple of monomers have average inter-ribosome distances slightly below the footprint size, but since the mRNA counts for these proteins are very small and this is averaged over only a single generation, this is okay. These monomer ids are marked with a * .)