We theoretically investigate the process of splitting two-ion crystals in segmented Paul traps, i.e. the structural transition from two ions confined in a common well to ions confined in separate wells. The precise control of this process by application of suitable voltage ramps to the trap segments is non-trivial, as the harmonic confinement transiently vanishes during the process. This makes the ions strongly susceptible to background electric field noise, and to static offset fields in the direction of the trap axis. We analyze the reasons why large energy transfers can occur, which are impulsive acceleration, the presence of residual background fields and enhanced anomalous heating. For the impulsive acceleration, we identify the diabatic and adiabatic regimes, which are characterized by different scaling behavior of the energy transfer with respect to time. We propose a suitable control scheme based on experimentally accessible parameters. Simulations are used to verify both the high sensitivity of the splitting result and the performance of our control scheme. Finally, we analyze the impact of trap geometry parameters on the crystal splitting process.
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