In 1999, as a researcher at NEC, Nakamura and collaborators Yuri Pashkin and Jaw-Shen Tsai demonstrated "electrical coherent control of a qubit in a solid-state electronic device"[3] and in 2001 "realized the first measurement of the Rabi oscillations associated with the transition between two Josephson levels in the Cooper pair box"[13][14] in a configuration developed by Michel Devoret and colleagues in 1998.

[13][15] In 2000, Nakamura was featured as a "Younger Scientist" by the Japan Society of Applied Physics for his work at NEC in "quantum-state control of nanoscale superconducting devices.

[17][18][19] In 2003, he was named one of MIT Technology Review's top innovators under 35 years old, in which editors noted that "Nakamura and a collaborator got two qubits to interact in a manner that had been predicted but never demonstrated" at the time.

In past years, Nakamura and collaborators have published their findings on the efficient detection of single microwave frequency photons,[25] the suppression of quasiparticles in superconducting quantum computing environments for the improvement of qubit coherence times,[26] the development of "a deterministic scheme to generate maximal entanglement between remote superconducting atoms, using a propagating microwave photon as a flying qubit",[27] and the realization of a hybrid quantum system by the strong, coherent coupling between a collective magnetic mode of a ferromagnetic sphere and a superconducting qubit.

[1] More recently, results have been published in which superconducting qubits were used to resolve quanta of magnon number states,[28][29] to create a quantitatively non-classical photon number distribution,[30] to measure fluctuations in a surface acoustic wave (SAW) resonator,[31] and to measure an itinerant microwave photon in a quantum nondemolition (QND) detection experiment.