Add Simulations and Spike analysis to documentation

[jgallowa07]

As stated in #107 , we should move our documentation notebooks to be produced by MyST{nb} as it's got way better features as shown in the spike analysis web page.

As we'll be updating the spike analysis wrt reviewer comments and updated multidms versions, we should take the opportunity to merge in the simulations, and spike analysis to the official documentation.

TODO:

• final pass on simulations notebook.
• Add spike analysis
• Look into replacing sphinx with MyST.

[jgallowa07]

It's been decided that we'll keep the behemoth spike / simulation analysis notebooks out of the multidms repo and docs, as they will be made static and reproducible in the manuscript analysis repo -> https://github.com/matsengrp/SARS-CoV-2_spike_multidms