Many low-energy, particle-physics experiments seek to reveal new fundamental physics by searching for very rare scattering events on atomic nuclei. The interpretation of their results requires quantifying the non-linear effects of the strong interaction on the spin-independent couplings of this new physics to protons and neutrons. Here we present a fully-controlled, ab-initio calculation of these couplings to the quarks within those constituents of nuclei. We use lattice quantum chromodynamics computations for the four lightest species of quarks and heavy-quark expansions for the remaining two. We determine each of the six quark contributions with an accuracy better than 15%. Our results are especially important for guiding and interpreting experimental searches for our universes dark matter.