Re:Simulation of a 2B-atom cell that metabolizes and grows l...
by blix on Friday January 28, 2022 @11:12PM
(#30123713)
> It does represent that many atoms.
It also represents even more electrons and even more quarks than that. I think it would be silly to characterize this system by the number of constituent quarks, but that's just me. To me, the important number is the number of degrees of freedom within the model. In a force-field model this scales linearly in with the number of atoms. In the model presented in the paper, this depends on voxel resolution and number of molecular species. Sadly, this is omitted in the press release.
Thanks for your links :) I work in inorganic materials but I really should understand more about models for more complex systems.
Yes, this is not the standard "force field" pairwise stuff you're used to when you heard "simulation" of biomolecular systems. I don't know if it's quite disingenuous, just not what we expect based on what the vast, vast majority of the field does! It does represent that many atoms. We shouldn't include atoms for the sake of having them, right? It should depend on what questions we're asking of the system.
I like seeing other (simulation or analytic) methods get attention. Lattice methods --(HP models[0], for hydrophobicity[1], lattice-boltzmann even. field theoretic (see polymer physics, melts, old theory[2], new theory, and even newer simulation[3]). Even the simplest shit like springs[4]!
[0] https://scholar.google.com/citations?view_op=view_citation&h... [1] https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.11... [2]https://www.google.com/books/edition/Renormalization_Group_T... [3]The Equilibrium Theory of Inhomogeneous Polymers (International Series of Monographs on Physics) https://www.amazon.com/dp/0199673799/ref=cm_sw_r_apan_glt_i_... (numerical scft) [4] https://en.m.wikipedia.org/wiki/Gaussian_network_model