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Dapen compiles every contract function to a Zero Knowledge Circuit, and generates a merkle tree where the hash of verifier data of each contract function's circuit is a leaf.
When we are generating a block in the QED protocol, we recursively prove/verify a bunch of transaction proofs. In particular, our block generation circuit allows state transitions in our global state tree can occur if and only if transaction proof's verifier data is a member of the contract circuit merkle tree which owns the part of the global state tree being modified.