When a physical change occurs, the arrangement of particles within the substance may change, but the atoms in the molecules remain bonded together.
I would say the correct answer would probably be that to explain the approx 100 years between Dalton (early 1800's) atomic theory and JJ Thomson's discovery of the smaller particle the electron was that Thomson had the use of a cathode ray tube that helped to determine the existence of negatively charged particles about 2000 times lighter than a hydrogen atom and therefore a smaller particle than the atom. The cathode ray tube was not invented until 1897, when Thomson began experimenting with it.