How to model CRISPR/Cas9 binding and cleavage using a generalized Kittel's zipper model?

Question

I am thinking about how to model the binding of a CRISPR/Cas9+guide-RNA complex to a double-stranded DNA that cause its cleavage.

This post describes four steps at which a CRISPR/Cas9 system binds and cuts a target DNA strand:

1. PAM Binding:
2. Phosphate Lock Loop
3. Guide RNA binding
4. Cleavage

I believe it is possible to develop a fairly simple model based on Kittel's zipper model or its generalization to estimate the propensity of a Cas9 and gRNA to cleave the DNA. Thus, I would appreciate some advice how to develop such a zipper-like model (e.g., maybe by having a double zipper).

Ultimately, I would like to compute the free energy of the different states based on the sgRNA sequence: $\Delta G_\text{bind}$, $\Delta G_\text{melt}$, $\Delta G_\text{cut}$.

Here is another schematic illustration by Addgene (in this illustration, the binding step includes the DNA melting and the binding of the RNA with the DNA):