It is well-known that some exotic phases in condensed matter physics are described by Schwarz-type TQFTs, such as Chern-Simons theory of quantum Hall states. My question is whether there are condensed matter systems that can realize Witten-type TQFTs?
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I don't think there are any Witten-type TQFTs which are directly relevant to condensed matter physics. Witten-type TQFTs are very strange beasts: they violate spin-statistics, they aren't unitary, etc. It'd be pretty tricky to find a physical system you could model with one in the usual way.
There are some indirect connections between Chern-Simons theory and Gromov-Witten theory, but that's all I can think of.