Does modern physics contradict transubstantiation?

According to modern physics, all physical things are reducible to atoms, and that's all they are. In the doctrine of transubstantiation, the piece of bread's substance is transformed into Jesus, while its accidents remain the bread. If the accidents are the atoms, then this implies there is more to the bread, i.e. its 'substance', than just the atoms, and this substance is changed. If this is true, then is modern physics wrong, and there is something more to what bread is than just the atoms it is made of? Additionally, what is this 'more' thing if we were to remove all the atoms from the bread, what would be left that provides the substance of the bread? Alternatively, if the atoms constitute the entirety of the bread, then what changes about the bread during the Eucharist? UPDATE: I've asked a related question in the philosophy stackexchange. I'm not sure if I should close this question in the Christianity SE, since it has a couple answers.