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Atomic reactors do not always need to be cooled as some chemical reactions are endothermic or even have no or verry little enthalpy change.

Nuclear reactors on the other hand are difficult to cool for the follwign reasons:

Contamination of cooling medium: The medium used to cool the reactor, usually water or a gas, is subject to intense radiation which could decompose the substance and transport radiation around the building

Extreme temperatures: As nuclear reactors are extremely hot, many substances will undergo thermal decomosition and / or expand producing excess pressure.

In the recent meltdowns in Japan, primary cooling water has stopped because of the earthquake. Becasue the fuel rods are no longer fully submersed, the cooling water is turning to steam then decomposing into Hydrogen and Oxygen then combusting and exploding

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