Multi State steric mass action - Problem with Rates

CADET Troubleshooting
1

Hi,

as the title says I got a problem getting my head around how the declaration of the MSSMA_rates works.

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I don’ manage to derive the order of rates from this entry of the Handbook.
I have a system with two components (salt(0), and protein (1)) and I want to implement two binding states for the protein.
Can someone maybe write out to me how the line has to look.
My best guess so far is that it its a double with either 4 / or 8 entries, though I am confused to what those 8 should be. ( is it like comp0 1-2 / comp0 2-1 / comp1 1-2 / comp1 2-1 ?)

Thanks for your help in advance

2

Hi David,

MSSMA_RATES needs to be of size five in your case, which is the sum of squared number of bound states per component. Since the array is component major, the first entry would be the conversion rate of the salt component (i.e. 1.0 since there is only one bound state), the trailing four entries specify the rates for the protein. Having a conversion rate matrix for the protein bound states, i.e.

\begin{pmatrix} rate_{0,0} rate_{0,1} \\ rate_{1,0} rate_{1,1} \end{pmatrix},

where rate_{0,1} specifies the conversion rate from bound state 0 to bound state 1, you’d get

MSSMA_RATES = [1.0,
               rate_{0,0}, rate_{0,1},
               rate_{1,0}, rate_{1,1}]

I hope this helps

1 Like
3

Thank you very much,

my problem seems to have been that I assumed the salt component would have multiple bound states as well ( hence how I ended up with 8 needed entries)

greetings
David