We study the effect of flux noise on the Cooper pair current of a superconducting charge pump. We generalize the definition of the current in order to take into account the contribution induced by the environment. It turns out that this dissipative current vanishes for charge noise but it is finite in general for noise operators that do not commute with the charge operator. We discuss in a generic framework the effect of flux noise and present a way to engineer it by coupling the system to an additional external circuit. We calculate numerically the pumped charge through the device by solving the master equation for the reduced density matrix of the system and show how it depends on the coupling to the artificial environment.
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