The quantum internet enables distribution of quantum states across distant nodes, supporting secure communication, distributed computing, and quantum sensing. Unlike classical networks, it is constrained by the no cloning theorem, probabilistic entanglement generation, decoherence, and hardware drift, making classical abstractions inadequate. Scalable quantum networking therefore requires new architectures, protocols, and optimisation methods that explicitly account for these limitations. This thesis studies the architecture, routing, and operation of quantum networks under realistic constraints, focusing on bipartite entanglement distribution over quantum repeater networks. Key metrics include end to end fidelity, throughput, scalability, and fairness. At the network layer, routing strategies are developed beyond assumptions of homogeneous nodes and full network knowledge. Routing under heterogeneous repeater efficiencies shows how partial knowledge of node quality improves fidelity and reduces path blocking. A grey box routing approach is then introduced, where path selection relies only on topology and end to end estimates, achieving robustness and fairness without detailed link information. At the link layer, calibration and hardware drift are addressed through a calibration aware model separating activation and calibration phases. For linear repeater chains, an optimal calibration schedule is derived to balance operation time and calibration overhead. This is extended to general topologies with shared links, where a greedy orchestration heuristic is proposed. Finally, the thesis connects network protocols with hardware via an instruction set architecture for programmable quantum repeater nodes based on NV centers, enabling coherent programmability and linking physical operations to higher layer protocols.

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