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Comment by sprash | Hacker News Reader

I still don't understand why we need such a thing. Every single interaction that is involved with protein folding or any chemical or molecular process can be calculated "ab initio" via QED (Quantum Electro Dynamics). So why not just build big computers and be done with it? If there is any macroscopic effect that can be exploited, we still can prove that the theory works and won't need a super powerful FEL for it.

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The main problem is scaling. In quantum chemistry, you need electron correlation to get accurate results (comparing your ab initio with experiments) and these methods scale quite badly. Somewhat state-of-the-art CCSD(T) (coupled cluster singles and doubles with triple excitations approximated by perturbation theory) scales formally as N^7, with N being the number of electrons in your system (somewhat simplified). Proteins are huge. Even with some of the newest nearly linear-scaling coupled-cluster methods (which utilize GPUs) running calculations on proteins takes extremely long time. And this is just electron correlation methods. We're still using the Born-Oppenheimer approximation, not taking all excitaions into account, using a finite size basis set, ignoring relativistic effects, not thinking about time evolution and (most of the time) not considering (explicit) solvent effects.

We are still a long way from modelling protein folding in solution with 100% quantum mechanics. Luckily, classical molecular dynamics are quite good at modelling biochemical systems (to a degree). There are a ton of errors that a much bigger than quantum (and relativistic) effects anyway.

Ok now I understand why we need such a thing, thank you very much. My knowledge does not go beyond good old Hatree-Fock on that matter. I thought this is a legitimate question because in theory this device is not build to discover any new physics which I would expect from such a facility.

Edit: Followup question, is it possible to build a ProteinFoldingCoin? Can the problems of theoretical chemistry formulated in a way that is hard to calculate and easy to verify, hence replacing the useless sha256 calculations in Bitcoin with something that makes sense?

>is it possible to build a ProteinFoldingCoin?

I've thought about it, but don't think it's possible. Basically quantum chemical methods like Hartree-Fock or Coupled Cluster is a question of finding eigenvalues to some very very large matrices and/or solving non-linear equation. Verifying a solution (such as electron correlation energy) can, to my knowledge, only be done by using the result and checking if the equations are still valid, which pretty much is just doing the whole work.

Your premise, while theoretically true, is not practicable in reality. To compute the realistic trajectory (more correctly: to estimate the probability of all the transitions between all the states to build up the PDF) would require multiple universe-lifetimes to calculate with enough accuracy to replace what an xFEL can tell you.

It's not just about building bigger computers. If it were, we would make that investment. If you look at the QED and QC calculations done on the world's largest supercomputers, they're not that inspiring.

Exactly. Outsourcing calculations to the rest of the universe is via such experiments is a better alternative

The economy is just made of humans and equipment, which also obey the rules of QED. We should get rid of all these useless economists taking data and just simulate everything!

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