Establishing end-to-end quantum connections requires quantified link characteristics, and operations need to coordinate decision-making between nodes across a network. We introduce the RuleSet-based communication protocol for supporting quantum operations over distant nodes to minimize classical packet transmissions for guaranteeing synchronicity. RuleSets are distributed to nodes along a path at connection set up time, and hold lists of operations that need to be performed in real time. We simulate the RuleSet-based quantum link bootstrapping protocol, which consists of recurrent purifications and link-level tomography, to quantify the quantum link fidelity and its throughput. Our Markov-Chain Monte-Carlo simulation includes various error sources, such as the memory error, gate error and channel error, modeled on currently available hardware. We found that when two quantum nodes, each with 100 memory qubits capable of emitting photons ideally to the optical fiber, are physically connected with a 10km MeetInTheMiddle link, the Recurrent Single selection - Single error purification (RSs-Sp) protocol is capable of bringing up the fidelity from an average input $F_{r}=0.675$ to around $F_{r}=0.865$ with a generation rate of 1106 Bell pairs per second, as determined by simulated tomography. The system gets noisier with longer channels, in which case errors may develop faster than the purification gain. In such a situation, a stronger purification method, such as the double selection-based purification, shows an advantage for improving the fidelity. The knowledge acquired from bootstrapping can later be distributed to nodes within the same network, and used for other purposes such as route selection.
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