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When someone says that a system is 'fundamentally a quantum system', does this mean that it is somehow different from a classical system ?
If so, what is the fundamental difference ?
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It just means it's a system where quantum effects make significant contribution to the system's behaviour. Classical mechanics follows from quantum mechanics but not vice versa. In other words, classical mechanics is a special case of quantum mechanics. If a system does not fall into that special case then I guess it's fair to say that it's a fundamentally quantum system.