The fundamental mistake in physics is the theory of atomic structure.

Atoms must be incompressible solid objects/spheres, therefore solid and incompressible matters are able to exist. 

If atoms are made from electrons orbiting/clouding/waving/whatever around a nucleus, what is the precise mechanism?  How can atoms be incompressible solid stuff?

If 1 electron and 1 proton can form into a stable hydrogen atom, what is the structure? How electron orbits/waves/clouds around the proton? What is the precise mechanism? Why electrons and protons don't stick together under Coulomb's force?

 If carbon atoms are made from 6 electrons waving/clouding/orbiting a nuclear and having 99,9999% empty space, how can diamond cut glass?

How atoms emit light? What is energy?  How atoms carry energy? What is the energy level? How electrons flow in the conductor? Why electrons don't flow to the positively charged nucleus?