vilhelm_s t1_j51bk1j wrote on January 19, 2023 at 6:34 PM

I think it's not extremely "quantum". Of course proteins are molecules so they ultimately obey quantum mechanics, but I think for the folding problem people are not really treating that---they just consider the parts of the chain as having well-defined positions in 3d-space, and add up energy from pairwise interactions between the parts that end up close to each others. (Finding the minimal energy configuration here is already very difficult, even before starting to consider any quantum superpositions or trying to compute the pairwise interactions more exactly).

However, some people hope that quantum computers could still be helpful, e.g. this recent paper. The problem they are solving is still the classical, non-quantum setup, but there are quantum algorithms that are supposed to be good at searching for minimal-energy configurations, so it may still speed things up.

fuzzywolf23 t1_j51uz18 wrote on January 19, 2023 at 8:32 PM

> -they just consider the parts of the chain as having well-defined positions in 3d-space, and add up energy from pairwise interactions between the parts that end up close to each others.

Yes, but also if you want an accurate calculation of that energy, you need to use quantum mechanics. The nuclei of the atoms have definite positions, but electrons do not

prionprion OP t1_j52nptp wrote on January 19, 2023 at 11:41 PM

this is also my point, I know the whole folding is more classical, and the folding is mainly driven by thermodynamics, but I feel like how the change in shape happen as protein jump from one conformation to another is quantum mechanical

fuzzywolf23 t1_j52yn3z wrote on January 20, 2023 at 12:58 AM

The folding is driven by thermodynamics, but in a sense, so is everything!

All of nature tends to move from higher energy to lower energy states. You can approximately calculate the energy of a protein structure, but you'll be wrong by enough that your error is bigger than the difference between candidate structures. To calculate the energy with sufficient accuracy, you need to use quantum mechanics using, e.g., density functional theory.