In some aspects, a control system interacts with a quantum system. In some instances, the quantum system includes qubits that respond to a control signal generated by the control system, and the control system is configured to generate the control signal in response to an input signal. A control sequence (which may include, for example, a sequence of values for the input signal) can be generated by a computing system based on a target operation to be applied to the qubits. The control sequence can be generated based on the target operation, a quantum system model, a distortion model and possibly other information. The quantum system model represents the quantum system and includes a control parameter representing the control signal. The distortion model represents a nonlinear relationship between the control signal and the input signal. The control sequence is applied to the quantum system by operation of the control system.