mechanism_id part_id param_name param_val comments
e coli Ribo 120 uM assuming ~72000 Ribosomes / e. coli with a volume 1 um^3
e coli RNAP 15 uM assuming ~10000 RNAP molecules / e. coli with a volume 1 um^3
e coli RNAase 30 uM assuming ~20000 RNAP molecules / e. coli with a volume 1 um^4
e coli extract 1 Ribo 24 1/5 th the Ribosome concentration of E. Coli
e coli extract 1 RNAP 3 1/5 th the rnap concentration of E. Coli
e coli extract 1 RNAase 6 1/5 th the rnaase concentration of E. Coli
e coli extract 2 Ribo 12
e coli extract 2 RNAP 6
e coli extract 2 RNAase 3
ktx 0.05 transcripts / second per polymerase assuming 50nt/s and transcript length of 1000
ktl 0.05 proteins / second per ribosome assuming 15aa/s and protein length of 300
cooperativity 2 Seems like a good default
kb 100 assuming 10ms to diffuse across 1um (characteristic cell size)
ku 10 """90% binding"""
kdil 0.001 assuming half life of ~20 minutes for everything (e coli doubling time)
rna_degredation_mm kdeg 0.000555556 assuming a half life of ~10 minutes for mRNA and 30uM of RNAase
rna_degredation kdil 0.002 assuming a half life of ~10 minutes for mRNA
simple_transcription ktx 0.1875 Assuming 25% of e coli rnap working at ktx above
simple_translation ktl 1.5 Assuming 25% of e coli ribosomes working at ktx above
gene_expression kexpress 0.28125 The product of the above two rates
negativehill_transcription k 0.01875 Estimates from Repressilator paper and the above numbers
negativehill_transcription K 10 Estimates from Repressilator paper and the above numbers
negativehill_transcription n 2 Estimates from Repressilator paper and the above numbers
negativehill_transcription kleak 0.000001 Estimates from Repressilator paper and the above numbers
J23103 ku 588.2352941 Anderson promoter (17x) strengths are proportional but gain factor is arbitrary
J23116 ku 25.25252525 Anderson promoter (396x) strengths are proportional but gain factor is arbitrary
J23107 ku 11.01321586 Anderson promoter (908x) strengths are proportional but gain factor is arbitrary
J23106 ku 8.438818565 Anderson promoter (1185x) strengths are proportional but gain factor is arbitrary
J23102 ku 4.589261129 Anderson promoter (2179x) strengths are proportional but gain factor is arbitrary
J23100 ku 3.926187672 Anderson promoter (2547x) strengths are proportional but gain factor is arbitrary
simple_transcription J23103 ktx 0.0031875 Above rescaled by ktx for simple transcription
simple_transcription J23116 ktx 0.07425 Above rescaled by ktx for simple transcription
simple_transcription J23107 ktx 0.17025 Above rescaled by ktx for simple transcription
simple_transcription J23106 ktx 0.2221875 Above rescaled by ktx for simple transcription
simple_transcription J23102 ktx 0.4085625 Above rescaled by ktx for simple transcription
simple_transcription J23100 ktx 0.4775625 Above rescaled by ktx for simple transcription
BCD2 ku 0.5 Strong BCD param value made up
BCD8 ku 10 Weak BCD param value made up
BCD12 ku 5 medium BCD param value made up
simple_translation BCD2 ktl 3 Above rescaled by ktl for simple translation
simple_translation BCD8 ktl 0.15 Above rescaled by ktl for simple translation
simple_translation BCD12 ktl 0.3 Above rescaled by ktl for simple translation