Binding energy
Mass–energy relation

A bound system is typically at a lower energy level than its unbound constituents because its mass must be less than the total mass of its unbound constituents. For systems with low binding energies, this "lost" mass after binding may be fractionally small, whereas for systems with high binding energies, the missing mass may be an easily measurable fraction. This missing mass may be lost during the process of binding as energy in the form of heat or light, with the removed energy corresponding to the removed mass through Einstein's equation E = mc. In the process of binding, the constituents of the system might enter higher energy states of the nucleus/atom/molecule while retaining their mass, and because of this, it is necessary that they are removed from the system before its mass can decrease. Once the system cools to normal temperatures and returns to ground states regarding energy levels, it will contain less mass than when it first combined and was at high energy. This loss of heat represents the "mass deficit", and the heat itself retains the mass that was lost (from the point of view of the initial system). This mass will appear in any other system that absorbs the heat and gains thermal energy.

For example, if two objects are attracting each other in space through their gravitational field, the attraction force accelerates the objects, increasing their velocity, which converts their potential energy (gravity) into kinetic energy. When the particles either pass through each other without interaction or elastically repel during the collision, the gained kinetic energy (related to speed) begins to revert into potential energy, driving the collided particles apart. The decelerating particles will return to the initial distance and beyond into infinity, or stop and repeat the collision (oscillation takes place). This shows that the system, which loses no energy, does not combine (bind) into a solid object, parts of which oscillate at short distances. Therefore, to bind the particles, the kinetic energy gained due to the attraction must be dissipated by resistive force. Complex objects in collision ordinarily undergo inelastic collision, transforming some kinetic energy into internal energy (heat content, which is atomic movement), which is further radiated in the form of photons – the light and heat. Once the energy to escape the gravity is dissipated in the collision, the parts will oscillate at a closer, possibly atomic, distance, thus looking like one solid object. This lost energy, necessary to overcome the potential barrier to separate the objects, is the binding energy. If this binding energy were retained in the system as heat, its mass would not decrease, whereas binding energy lost from the system as heat radiation would itself have mass. It directly represents the "mass deficit" of the cold, bound system.

Closely analogous considerations apply in chemical and nuclear reactions. Exothermic chemical reactions in closed systems do not change mass, but do become less massive once the heat of reaction is removed, though this mass change is too small to measure with standard equipment. In nuclear reactions, the fraction of mass that may be removed as light or heat, i.e. binding energy, is often a much larger fraction of the system mass. It may thus be measured directly as a mass difference between rest masses of reactants and (cooled) products. This is because nuclear forces are comparatively stronger than the Coulombic forces associated with the interactions between electrons and protons that generate heat in chemistry.
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