1. The discovery of sub-particles like proton (positive charge and mass = unity), electron (negative charge and mass of 1/1840) and neutron (no charge and mass = unity) led to the nullification of 1st theory and hence atom is divisible.
2. Physical reaction disproves the 2nd theory since atoms can be created or destroyed on physical reaction.
3. Isotopy also nullifies the 3rd theory. Some Scientists like JJ Thomson, Ruther Ford, Bohr, Scinodinyer and many others worked very hard through their various experiments to describe the structure and arrangement of the atoms.