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I mean atoms are mostly electron clouds . So , all electron that hit a material should be taken up by the electrons of atom and the energy be used up by the electrons to go to a higher orbital and then eventually producing photons on going back to lower energy . How does some electron's energy convert into heat energy ?

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The thermal energy is simply energy randomly distributed in a sufficiently uniform manner among the many degrees of freedom of some large system as result of many interactions. Any energy pumped to the system may become thermal provided that it is transmitted to other degrees of freedom sufficiently well.

When electron hits the atom part it not only excites it but also gives it as a whole some velocity. This kinetic energy may be transmitted to other atoms through collisions just like in the ideal gas. During those collisions the energy of electrons in excited state may be transmitted to the electrons of other atom. Finally the photons produced by excited atom may be absorbed by other atoms instead of flying away. This distributes the energy obtained by a single atom among all the atoms in the material and raises thermal energy.

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