I'm following Preskill's notes and he derives the Schmidt decomposition in the following way:
Let a bipartite state be ψAB=∑i,jλij|i⟩|j⟩=∑i|i⟩|˜i⟩, where I simply choose ∑jλij|j⟩=|˜i⟩.
I choose a set of basis vectors |i⟩ such that the partial state is diagonal, that is ρA=∑ipi|i⟩⟨i|. But I can also obtain ρA=TrB(ρAB)=TrB∑i,j|i⟩⟨j|⊗|˜i⟩⟨˜j|=∑ij⟨˜j|˜i⟩|i⟩⟨j|. The last part can be computed by explicitly writing out the trace over B and using the properties of an orthonormal basis.
Thus, we have ρA=∑ipi|i⟩⟨i|=∑ij⟨˜j|˜i⟩|i⟩⟨j|. That is ⟨˜j|˜i⟩=piδij. Suddenly, the |˜i⟩ are all orthogonal to each other.
Why does choosing the basis where ρA is diagonal also give you orthogonal vectors in B? This seemed to drop out of the sky for me although the math is clear. What is the physical meaning of this?
Answer
Let us start from the Schmidt decomposition |ψ⟩=∑si|ai⟩|bi⟩.
Now consider the reduced state of A: ρA=∑s2i|ai⟩⟨ai|. This is, the eigenbasis of A is exactly the basis you need for the Schmidt decomposition!
Thus, if you write your state using that eigenbasis of Alice, |ψ⟩=∑i|ai⟩(∑jλij|j⟩) , the part |˜bi⟩=∑jλij|j⟩ must be equal to si|bi⟩, since the Schmidt decomposition is unique (modulo degeneracies).
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