  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.
