Dr. Who said:
Now consider a capacitor powered toy car. Here no biological or chemical reactions are taking place to run the car, simply the electric potential energy stored in the charged plates is converted into Kinetic energy. How do you account for the change in mass here?
There isn't one. Stored electrical potential energy gets converted to kinetic energy. The total energy, with respect to a fixed frame, is constant; therefore so is the mass, by the definition of "mass" we are using here (where it is just another name for "total energy").
What does change in this process is the
rest mass of the car. Before the car starts moving, the electrical potential energy stored in the capacitor is part of the rest mass of the car. After the car is moving, that energy is kinetic energy and is not part of the car's rest mass. So if the car were brought to rest again (for example, by pushing against a spring that slowed it to a stop and stored the energy in the compression of the spring), its mass would be smaller than before, by the amount of energy that was converted to kinetic energy.
Dr. Who said:
would I not be correct in assuming that the energy/mass that comes from within a system is not responsible for changing the total energy of the system.
Yes, that's correct. But, as above, if the system changes its state of motion, its
rest mass can change even if no external source of energy/mass is present.
Dr. Who said:
in a chemical reaction taking place in an isolated system, the masses of reactants and products should remain conserved. It is the bond energy or internal energy alone that gets converted into heat and other forms. Doesn't it?
Now you're using "mass" in a different sense. In chemical reactions in an isolated system (say a closed reactor vessel with perfect thermal insulation that remains at rest throughout the reaction), the total mass/energy of the system as a whole never changes, and since we've ruled out changes in the system's state of motion, its rest mass never changes either. However, the same is not necessarily true of individual constituents of the system.
For example, suppose we start out with a reactor vessel filled with two moles of hydrogen gas and one mole of oxygen gas, and we end up with a reactor vessel filled with one mole of water. Two water molecules are formed from two H2 molecules and one O2 molecule. But the mass of the water molecule is not the same as the mass of two H2 molecules plus the mass of one O2 molecule; it is slightly less. The difference shows up as heat--the temperature inside the reactor vessel goes up.
Now, can we say that this extra heat comes only from the change in bond energy? Sort of, but not really. The problem is that the mass of one H2 molecule, say, is not the same as the mass of two H atoms; it is slightly less. (If it weren't, H2 molecules would not exist; hydrogen would occur in nature as a gas of H atoms, not a gas of H2 molecules.) And similarly for one O2 molecule vs. two O atoms. So the H2 and O2 molecules already, as bound systems, have less energy/mass than their constituent atoms. So if we had started with H and O atoms inside our reactor vessel, in a 2-to-1 ratio, we would end up with a larger change in temperature inside the reactor vessel than the case above, where we started with H2 and O2 molecules.
But, you say, how about the H and O atoms? Well, first of all, they are still composite systems. An H atom is composed of a proton and electron. If we take a proton and electron that are not bound, and make an H atom from them, energy is given off (13.6 electron volts of it); so the mass of the H atom is smaller by that amount than the mass of a proton + the mass of an electron.
Also, H and O nuclei can participate in nuclear reactions, so clearly there is some portion of their masses that is really binding energy. For example, if we took a quantity of H and O atoms and ran them through nuclear reactions to form a quantity of iron nuclei with the same total number of nucleons, a considerable amount of heat would be given off, orders of magnitude more than in the chemical reactions above (so the temperature inside our reactor vessel would go up a lot more).
And if we dig still deeper, we find that nucleons themselves are composite systems, made up of quarks; but much of the observed mass of nucleons is believed to be energy associated with the strong interaction between the quarks rather than the masses of the quarks themselves. So even at the most fundamental level, we really don't have a sharp dividing line between "mass" and "binding energy". The simplest thing is to just lump them all together as "energy" and keep track of how energy changes in different reactions, and not worry about what part of it is "mass" and what part is something else.