Here is a new draft in which I have connected the RNA energy world and nucleotide bonds to the first 3 laws of physics as part of a connection to statics and then mechanics of materials. It also explains the ensemble and how the pairing probabilities form it, or at least it is the start of that. its at 19 pages now… Please let me know what you think. I am pretty close to explaining how RNA behaves in its entirety. I go through and show data from NUPACK and then go through a detailed walkthrough on what it shows.
Google Doc:
[A mechanical overview of RNA in an energy focused world - Draft rev3-shared - Google Docs]
PDF:
A mechanical overview of RNA in an energy focused world - Draft rev3-shared.pdf (2.0 MB)
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Thanks for the town hall presentation!
Following up on what I mentioned at the town hall - looking at the values provided by Thermo Fisher, I think the mass values that you might want to use in the force equations would be the ones used under “Nucleic Acid Molecular Weight Conversions,” which I will summarize here for convenience:
A: 329.2 g/mol
U: 306.2 g/mol
C: 305.2 g/mol
G: 345.2 g/mol
Specifically, I believe these values might correspond to the mass of the entire nucleotide base (which consists of a nucleobase, the phosphate group, and the sugar).
(One thing that is slightly confusing is that these values are different than the masses presented in the “ribonucleotide monophosphates” section, which I thought also corresponded to the mass of the entire nucleotide base but obviously doesn’t match . . . I haven’t figured out why this discrepancy exists yet.)