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The Yang-Mills matrix model admits self-dual and anti-self-dual instantons. When coupled to flavors of massless quarks, the Euclidean Dirac equation in an instanton background has positive and negative chirality zero modes. We show that the index is equal to a suitably defined instanton charge. Further, we show that the path integral measure is not invariant under a chiral rotation, and relate the non-invariance of the measure to the index of the Dirac operator. Axial symmetry is broken anomalously, with the residual symmetry being a finite group. For fundamental fermions, this residual symmetry is , whereas for adjoint quarks it is .

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