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> His goal is nothing less than a digital twin of the real worm, accurate down to the molecule. I am nitpicking this: The state of computational chemistry is n

> His goal is nothing less than a digital twin of the real worm, accurate down to the molecule. I am nitpicking this: The state of computational chemistry is not at a level to support this. I'm optimistic we'll get there eventually; need to find novel approaches, and current ones are too imprecise, or too slow. I think the connectome aspect is more interesting, as it may be feasible to get there 100% without a computational chem breakthrough.

firtoz 2y ago
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?
- rsfern 2y ago
  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/meeting/presentations/view/2024-fall-meeting/2024-fall-meeting-4151737 https://www.mrs.org/meetings-events/annual-meetings/archive/...
  - kaferoni 2y ago
    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://arxiv.org/abs/2405.07898 - https://www.psc.edu/resources/anton/ https://www.psc.edu/resources/anton/
  - throwawaymaths 2y ago
    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
    - deleted 2y ago
      [deleted]
    - rsfern 2y ago
      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 https://arxiv.org/abs/1812.09976 1: https://arxiv.org/abs/2307.07067 https://arxiv.org/abs/2307.07067
      - throwawaymaths 2y ago
        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.
mkoubaa 2y ago
And I don't think we will get there with digital computers either.
- FrustratedMonky 2y ago
  Oh sure, because neurons totally get a free pass from determinism, right? They're obviously powered by tiny wizards flipping quantum coins, unlike boring digital computers just mindlessly following rules. Newsflash: neurons and digital computers both have to play by the universe's stubbornly deterministic rules—it's all just matter wiggling predictably, with neurons simply doing it in a squishier way.
  - dingnuts 2y ago
    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
    - FrustratedMonky 2y ago
      " 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"
      - nipah 2y ago
        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.

firtoz 2y ago

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?

rsfern 2y ago
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/meeting/presentations/view/2024-fall-meeting/2024-fall-meeting-4151737 https://www.mrs.org/meetings-events/annual-meetings/archive/...
- kaferoni 2y ago
  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://arxiv.org/abs/2405.07898 - https://www.psc.edu/resources/anton/ https://www.psc.edu/resources/anton/
- throwawaymaths 2y ago
  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
  - deleted 2y ago
    [deleted]
  - rsfern 2y ago
    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 https://arxiv.org/abs/1812.09976 1: https://arxiv.org/abs/2307.07067 https://arxiv.org/abs/2307.07067
    - throwawaymaths 2y ago
      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.

mkoubaa 2y ago

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

FrustratedMonky 2y ago
Oh sure, because neurons totally get a free pass from determinism, right? They're obviously powered by tiny wizards flipping quantum coins, unlike boring digital computers just mindlessly following rules. Newsflash: neurons and digital computers both have to play by the universe's stubbornly deterministic rules—it's all just matter wiggling predictably, with neurons simply doing it in a squishier way.
- dingnuts 2y ago
  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
  - FrustratedMonky 2y ago
    " 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"
    - nipah 2y ago
      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.