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In this paper, we will present some ideas to use 3D topology for quantum computing extending ideas from a previous paper. Topological quantum computing used "knotted" quantum states of topological phases of matter, called anyons. But anyons are connected with surface topology. But surfaces have (usually) abelian fundamental groups and therefore one needs non-Abelian anyons to use it for quantum computing. But usual materials are 3D objects which can admit more complicated topologies. Here, complements of knots do play a prominent role and are in principle the main parts to understand 3-manifold topology. For that purpose, we will construct a quantum system on the complements of a knot in the 3-sphere (see T. Asselmeyer-Maluga, Quantum Rep. 3 (2021) 153, arXiv:2102.04452 for previous work). The whole system is designed as knotted superconductor, where every crossing is a Josephson junction and the qubit is realized as flux qubit. We discuss the properties of this systems in particular the fluxion quantization by using the A-polynomial of the knot. Furthermore, we showed that 2-qubit operations can be realized by linked (knotted) superconductors again coupled via a Josephson junction. [ABSTRACT FROM AUTHOR]