One the hardest subjects I found, at least conceptually is using the standard model in particle physics to predict the output of over 100,000 different physical formulas. Instead of using constants such as speed of light, you can use the standard model of physics to predict well over 100,000 physical constants. These 32 measurements consist of wavelengths in light, the mass of a neutrino and energy emissions from photons. I find it conceptually difficult because many physical equations are giving an abstraction, such as e = mc^2 into more atomic propositions like van der waal forces, electron orbitals, centripedal and centrifugal forces and so much more (unfortunately, gravity hasn't been reduced to atomic forces yet).
It's like computers: People understand how to operate windows, but under that there's a GUI, an IDE, high level programming languages, low level programming languages, assembly code, logical cores in a processor, which process bits using binary bits of 1s and 0s, which are abstractions of electrical voltage and logical gates like AND,OR,XOR, NOR.... it's like peeling away at the abstractions that are an integral part of our reality and getting closer to the source code of the universe.