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Normaly, a reactor is shut down by gradualy lowering the control rods into the core of the reactor, which is the opposite of starting the reactor up. The control rods are made from a neutron absorbing material, and they will "soak up" neutrons to diminish the chain reaction and eventually stop it. There is also what is called a "reactor scram" where the control rods are released from their drive mechanisms and allowed to fall into the core. They bottom out in just a couple of seconds, and with the rods in, the chain reaction comes to a screeching halt. In another type of emergency shutdown, certain chemicals that are neutron absorbers and are called "poisons" can be pumped into a fluid moderator (liquid or gas) to break the nuclear chain and shut the reactor down. As a final note, consider that a reactor which has been operating at even a moderate power level continues to generate a lot of heat after shutdown. A lot of it. If some kind of loss of coolant accident (LOCA) occurs, a shutdown is the least of the worries of the operating staff. The core will have to be continuously cooled for days and even weeks afterward to keep the fuel from melting its way out of its cladding. And with a loss of coolant because of, say, a major leak, things will get hairy as the operators scramble to get coolant circulating through the core, or at leasted pumped over it to keep the fuel elements from failing and releasing fission products into the coolant. Ruptured fuel elements are a disaster as they contaminate the primary plant enormously. And if containment fails, these highly radioactive materials get out into the environment.

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