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Can superstring theory give a good reason of why the Yukawa coupling to the top quark is almost "natural" while the remaining leptons and quarks have negligible couplings to the Higgs? I mean, is there any symmetry principle based in superstring theories/M-Theory which shed light to the natural top mass quark but the unnatural masses of the remaining particles?

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In field theory, one often talks about the yukawa matrices in terms of "textures", patterns of zeroes in the yukawa matrix. So one might posit a particular zero texture at grand unification scale, and then try to obtain the standard model yukawas, with their specific hierarchical structure, from a zero texture plus corrections.

Apparently heterotic string model builders have known for some time that stringy yukawas will often equal zero when calculated, but for no obvious reason. There's now some preliminary work on "Generalized Vanishing Theorems for Yukawa Couplings in Heterotic Compactifications", building on earlier work which explained these yukawa "vanishing conditions" by embedding "structures on the Calabi-Yau manifold" in "a larger ambient space". The authors write:

the physical quark masses in the Standard Model require a comparatively heavy top quark. Such a mass hierarchy could be achieved by topological vanishings that left only one family with perturbatively non-zero couplings, leaving the remainder to be generated by non-perturbative effects

But string theory is big, and there is room for many possible explanations. The masses of the top and the Higgs combine to place the standard model at the edge of metastability, Abel and Dienes relate the Higgs mass to the cosmological constant, Abel and Stewart relate the yukawas to the cosmological constant... It would be nice if this could all tie up together!

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