Various embodiments of the present invention provide methods for allocating nanowire junctions in a nanowire crossbar having one or more randomly distributed non-functional crossbar nanowire junctions. In certain embodiments, the method constructs a circuit graph based on the circuit and constructs a crossbar graph based on the nanowire crossbar. A search is then conducted, in the embodiments, in order to determine a monomorphism that respectively maps the nodes and edges of the circuit graph to a subset of nodes and a subset of edges of the crossbar graph. The subset of nodes and subset of edges of the crossbar graph can then be used to allocate nanowire junctions in the nanowire crossbar.