Qubits built out of Majorana zero modes constitute the primary path toward topologically protected quantum computing. Simulating the braiding process of multiple Majorana zero modes corresponds to the quantum dynamics of a superconducting many-body system. It is crucial to study the Majorana dynamics both in the presence of all other quasiparticles and for reasonably large system sizes. We present a method to calculate arbitrary many-body wave functions as well as their expectation values, correlators, and overlaps from time evolved single-particle states of a superconductor, allowing for significantly larger system sizes. We calculate the fidelity, transition probabilities, and joint parities of Majorana pairs to track the quality of the braiding process. We show how the braiding success depends on the speed of the braid. Moreover, we demonstrate the topological CNOT two-qubit gate as an example of two-qubit entanglement. Our Letter opens the path to test and analyze the many theoretical implementations of Majorana qubits. Moreover, this method can be used to study the dynamics of any noninteracting superconductor.
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