This is a README file for the Mathematica notebook "MT conc prediction.nb". 
The notebook takes the derived parameters {k1, k2, k3, k4, k5, k6, k7} and estimates the dimer formed [MN] with time for the dimerization reaction discussed in Supplementary note 14.

The following set of ODEs are solved.
ML + T ⇌[k₁/k₂] MT + L
MT + P ⇌[k₃/k₄] MP + T
MP + RQ ⇌[k₅/k₆] MPR + Q
P + RQ →[k₇] PR + Q
MT + N ⇌[k₈/k₉] MN + T
MN + RQ ⇌[k₁₀/k₁₁] MNR + Q

For extracting the dimer concentration, all reporter reaction rates are 0, i.e. k5=k6=k7=k10=k11=0

The following variables are used interchangably:
M1: B1
M2: B1a
M3: B1b

P5-6: P29-5
P5-7: P28-5
P5-8: P27-5


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Box 1 runs an iteration across all the 9 files for different combination of monomer-proofreader combination.
Here's what it does:

Extracts the reaction rates {k1, k2, k3, k4, k5, k6, k7} and assumes the rates
k8=0.021 S.U.
k9=k10=k11=0.
All the symbols and constants assumed are given in the notebook.
Saves the concentration of dimer for different initial [T] in the folder named "Dimer Prediction"



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Box 2 runs an iteration across all the 9 files for different combination of monomer-proofreader combination when no proofreader is present.
Here's what it does:

Extracts the reaction rates {k1, k2, k3, k4, k5, k6, k7} and assumes the rates k8 to k11 as 0. All the symbols and constants assumed are given in the notebook.



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Box 3 : Plots the concentration of MT, MP, MPR, MN, ML for any specific case. 
Use Parameter Ii to iterate through the choice of monomer, and J to iterate through the proofreader.