Quantum computers offer great potential for significant speedup in executing certain algorithms compared to their classical counterparts. One of the most promising physical systems in which implementing such a device seems viable are trapped atomic ions. All of the fundamental operations needed for quantum information processing have already been experimentally demonstrated in trapped ion systems. Today, the remaining two obstacles are to improve the fidelities of these operations up to the point where quantum error correction techniques can be successfully applied, as well as to scale up the present systems to a higher number of quantum bits (qubits). This thesis addresses both issues. On the one hand, it decribes the experimental implementation of a high-fidelity two-qubit quantum logic gate, which is the most technically demanding fundamental operation to realise in practice. On the other hand, the presented work is carried out in a microfabricated surface ion trap - an architecture that holds the promise of scalability. The gate is applied directly to hyperfine "atomic clock" qubits in ⁴³Ca⁺ ions using the near-field microwave magnetic field gradient produced by an integrated trap electrode. To protect the gate against fluctuating energy shifts of the qubit states, as well as to avoid the need to null the microwave field at the position of the ions, a dynamically decoupled Mølmer-Sørensen scheme is employed. After accounting for state preparation and measurement errors, the achieved gate fidelity is 99.7(1)%. In previous work, the same apparatus has been used to demonstrate coherence times of T^*₂ ≈ 50 s and all single-qubit operations with fidelity > 99.95%. To gain access to the "atomic clock" qubit transition in ⁴³Ca⁺, a static magnetic field of 146G is applied. The resulting energy level Zeeman-structure is spread over many times the linewidth of the atomic transition used for Doppler cooling. This thesis presents a simple and robust method for Doppler cooling and obtaining high fluorescence from this qubit in spite of the complicated level structure. A temperature of 0.3mK, slightly below the Doppler limit, is reached.