Concentration Dependency

Cofolding is an intermolecular process, therefore whether duplex formation will actually occur is concentration dependent. Trivially, if one of the molecules is not present, no dimers are going to be formed. The partition functions of the molecules give us the equilibrium constants: $$K_{AB} = \frac{[AB]}{[A][B]} = \frac{Z_{AB}}{Z_AZ_B}$$ with these and mass conservation, the equilibrium concentration of homodimers, heterodimers and monomers can be computed in dependence of the start concentrations of the two molecules. This is most easily done by creating a file with the initial concentrations of molecules $A$ and $B$ in two columns:

$$\begin{eqnarray*}[a_1]([mol/l]) & [b_1]([mol/l])\cr [a_2]([mol/l]) & [b_2]([mol/l])\cr \vdots & \cr [a_n]([mol/l]) & [b_n]([mol/l]) \end{eqnarray*}$$