What's the latest and the best so far? Are they using GPGPU? Is quantum computing there yet, or would it help? Heuristics and sampling?

GPGPU is definitely mainstream for large scale quantum and molecular simulation. Quantum computing might help speed up electronic structure calculations, but my impression is that it’s still in its infancy

To give a sense of the scale of this problem, the largest frontier simulations I’m aware of are around the trillion atom scale. (On tens of thousands of GPUs [0])

Based on a quick web search, a c elegans cell is between 3 microns and 30 microns in diameter, so if we assume we can count atoms using the density of water then an all-atom simulation of a single neuron would need between 5e11 to 5e14 atoms. c. Elegans has 302 neurons so simulating the full neural network will be 2-5 orders of magnitude larger than current frontier simulations. Honestly more doable than I thought it would be, though all-atom simulation of a full organism still seems quite out of reach

This is all with classical force fields. Doing this simulation at the electronic structure level is much much harder with our current modeling capabilities

0: https://www.mrs.org/meetings-events/annual-meetings/archive/...

There's also interesting custom-made machines for molecular simulations that don't rely on GPGPUs and are significantly faster, e.g.: - https://arxiv.org/abs/2405.07898 - https://www.psc.edu/resources/anton/

is there any reasoning that for besides highly reductionistic and repetitive systems like crystals, quantum computing can compute quantum properties of molecules?

it seems to me "the quantum computer you seek" is the molecule + the medium (especially the medium) itself

So first I think I might need to apologize for some jargon collision - my background is mostly material simulation, and when I say “quantum simulation” I mostly mean using classical algorithms to solve the quantum mechanical wave equation describing a material or molecule.

I don’t pretend to have any particularly deep insight into quantum algorithms for chemistry, but [0] is a really nice review. It seems like there are a lot of possibilities for simulating general molecular and materials systems on quantum computers. The holy grail would be solving the exact quantum mechanical wave equation in sub-exponential time and space complexity. I don’t know how feasible that is, but it seems like people are making progress using quantum algorithms to accelerate approximate quantum simulation [1].

Back to all-atom c. elegans: I think quantum computing is more about accurate and scalable electronic structure modeling, and simulating enormous systems like this will still require fitting classical (meaning electrons are implicit) force fields and running them at scale for the foreseeable future. A lot of this is space complexity - I’m not sure how a quantum computer could do atomic simulations with sublinear scaling of qubits in the number of atoms being simulated, and were in the very early days of scaling quantum computers up

0: https://arxiv.org/abs/1812.09976

1: https://arxiv.org/abs/2307.07067

thanks for the reference.

yes. you nailed my point-that you will have to fit classical or quasi-classical fields, which is liable to require scads of qbits just to get close. qbits are just not "designed" to do that sort of thing.

in any case we ~solved protein folding heuristically and not using fields so i shouldn't be too pessimistic that it's impossible that quantum compute will help eventually.

And I don't think we will get there with digital computers either.

So, with what?

If we get there, and it's not guaranteed that we do, it will be a different kind of machine.

> flipping quantum coins...Newsflash: neurons and digital computers both have to play by the universe's stubbornly deterministic rules

I don't really understand what this means - you obviously know at the smallest level things happen by random probability - because you mention the quantum world - but then you say the universe is deterministic.

Computers can also include physics based random number generators so that's still simulatable. And analog computing also is possible. Quantum computing not really yet but theoretically possible.

Not sure if any other wizard hat things than those can extend classical digital computing

This is just partially a solution, because this assumes cognition as a whole is computable.

Because randomness does not introduce agency.

Bringing up 'Quantum' effects to somehow free us from determinism and somehow introduce free will, is completely false. Somehow using the word "Quantum" explains human consciousness is wrong.

A coin flip is still determined. You don't know which way it will flip, but also, you aren't deciding which way it will flip. The future is determined either way, determined one way, or determined the other way.

It does not introduce, but maybe the combination of both does (see Searle points in freedom and neurobiology). You also need to prove that the future is determined, simply assuming so is an error.

> you obviously know at the smallest level things happen by random probability

We don't actually know this. It is just what we observe that fits our map so far.

If you don't believe in God, actually you NEED to buy this, or buy into some other methaphysical eternalism that is as hard to prove as truly random events. The universe either started randomly or it was created, and the existence either existed eternally or it was created (both prospects are also problematic in some level, but at least it is something better than thinking you can not have a position on this and also assume that determinism is trivially true).

you're making a straw man argument and being an asshole about it to boot.

neurons aren't binary. who knows if they're special in a way digital computers can't simulate -- they aren't well understood.

nobody said anything about determinism besides you

" digital computers either".

Most of the time someone brings up the word 'Digital' they are talking about 1's and 0's, and how everything is known and determined, and thus looses the ineffable human quality.

"they're special in a way digital computers can't simulate"

I might be making a straw man, but you are literally just saying "something magical that exists outside physics must be going on"

This is a strawman, but it also could be the case of it being something supernatural. You don't have the skill to enter in a serious discussion about that either, so calling it "magic" is the unique thing will help you here (as people are usually scared of things they can't explain).

But it would be the case that the universe is non-computable, and if this is the case, even without "magic", you would not be able to reproduce certain kinds of things (even not conscious ones) with a computer.