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Is a complex torus $A$ of dimension 2 always isomorphic to its dual torus (i.e. the torus obtained by taking the dual lattice), or are there counterexamples to this?

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For non-algebraic tori, $T$ and $T^*$ are (usually) not isomorphic; for algebraic ones, they are isogeneous, and for the principally polarized abelian varieties, $T$ and $T^*$ are isomorphic.

This is obvious if you realize that a complex torus is a totally imaginary 2-dimensional complex subspace in ${\Bbb C}^4$ up to $GL(4,Z)$-action, and dual torus is a dual subspace in dual ${\Bbb C}^4$.

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