Theory of even energy distribution – Why does RNA behave this way?

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Lately I have been thinking about my Theory of even energy distribution.

The good designs tend to have a fairly even energy distribution. And very uneven energy distribution always results in a bad design. Uneven energy distribution is not penalized in the Eterna energy model that the challenge and player puzzles are running on, again proving the energy model to be flawed and lacking the overall picture of how nature works. So far I have only found one element in lab RNA design that behaves different (the neckarea) and allow much higher and lower energy compared to the rest of the RNA design.

Nothing I have seen so far, contradicts my theory. In the beginning I didn't care about the why, just that the pattern was there. Now I want to know.

The backbone itself is more than 40 times stronger compared to the hydrogen bonds. But I think it is sort of out of the picture as explanation on why an area with high energy distribution absolutely have to split up and fuse with a low energy area, as the chain of RNA is not breaking and an energeticly pressurised design only cause the neck area to split open.

I have just read about Van der walls force – which is a weak energy force between atoms. But it should be much weaker than hydrogen bonds. So it can't be what cause the hydrogen bonds to split in high and low energy areas.

So now I'm thinking, that the splitting up might have something to do with the polarity of the atoms in the nucleotides. Or at least it is the only other force I'm left with, as far as my present chemical knowledge goes.

Is there something about the polarity of GC pairs, that is different to that of AU pairs? Espesially if there is many of the same kind together?

I would really like to know why even energy distribution takes place and why uneven energy distribution makes RNA pair up otherwise than planned.

I'm quite sure I see what I see. Each time a design have an uneven energy distribution, it scores bad. And all the winners I have checked, have a nice even energy distribution.

Here are some of the posts about my theory:

Energy, structure and symmetric colors
Even energy distribution continued
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Eli Fisker

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Posted 8 years ago

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Edward Lane

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perhaps it's stable and unstable equilibriums ?

with the energy model currently just looking for equilibrium

but not checking stability of that equilibrium

a coin is at rest (in an unstable equilibrium position) when it stands on it's edge - but just nudge it and it will mostly fall flat, into a more stable equilibrium position.

so a structure with a high energy area and a low energy area seems more likely to "fall" into an area where the energy overall is more stable - even if that's not the target shape.

would that make sense ?
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Eli Fisker

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Actually this makes a lot of sence, thanks Ed. Can see I need to look more into what equilibrium is and what it means to RNA.
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Eli Fisker

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Outline from what I said in the chat, yesterday.

I'm interested in Van der Waals forces at the moment. Mat posted this video to me: Van der Waals forces It is describing the different forces of Van der Waal. Yes - there are more, I only thought there were one. So right now I'm sticking to the hypothesis that there is some atom polarity involved in why there need to be an even energy distribution. I think London dispersion force and Van der Wall's force itself are too week to mess things up in a design with uneven energy distribution. It is something strong enough to break the hydrogen bonds that is at play.

Thought after Ed's comment: Equilibrium could be involved in this...
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Eli Fisker

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Latest thoughts on the subject:

Either a lot of GC-pairs does not like to be together (because of polarity) and thus rejects each other and pair up elsewhere where there is a local energy weak area, or RNA has a global sense that truimphs local imbalance.
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Demon0f1ight

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my thoery is about polarity but with codon. Codon are 3 nucleotide pair up together. like the first 3 nucleotides will be one codon 4-6 be the 2nd and so on. for design that got 100% complete has very close amount of nonpolar and polar amino acid. I have to do more research on the amino acids themselves. But with GC combination comes up with mostly bases. And the most succesful design contain only a 26% on avg. base. polar and non polar is always 33% on avg. and acidic with 3% on avg. With all this data they are very closely related with high succesful design. But i belive when the 3 nucleotide pair up in a chain they create a polarlity that bring the other side to it.
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Eli Fisker

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Hi Demon!

Thanks for posting your theory on polarity of codons. Codons and polarity I don't know much about yet. As I understand things so far, the order of amino acids have defines the structure of the protein. But I find the polarity thing it very interesting and I will love to hear what you find out.