Control over physical systems at the quantum level is a goal shared by scientists in fields as diverse as metrology, information processing, simulation and chemistry. For trapped atomic ions, the quantized motional and internal degrees of freedom can be coherently manipulated with laser light. Similar control is difficult to achieve with radio frequency or microwave radiation because the essential coupling between internal degrees of freedom and motion requires significant field changes over the extent of the atoms' motion. The field gradients are negligible at these frequencies for freely propagating fields; however, stronger gradients can be generated in the near-field of microwave currents in structures smaller than the free-space wavelength. In the experiments reported here, we coherently manipulate the internal quantum states of the ions on time scales of 20 ns. We also generate entanglement between the internal degrees of freedom of two atoms with a gate operation suitable for general quantum computation. We implement both operations through the magnetic fields from microwave currents in electrodes that are integrated into the micro-fabricated trap structure and create an entangled state with fidelity 76(3) %. This approach, where the quantum control mechanism is integrated into the trapping device in a scalable manner, can potentially benefit quantum information processing, simulation and spectroscopy.Comment: 22 pages, 4 figures, accepted as a letter to Natur
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