The future of quantum information is scaling to a ever larger number of qubits. Doing so will require advances in the approach for all aspects of current experimental systems. The QuantumION project is a large step in this direction. This project will provide an open-access trapped ion quantum processor for the research community. The necessary innovations for how QuantumION will be controlled and assembled represents a paradigm shift from ad-hock disparate systems running the experiment to a well engineered, integrated, quantum platform. These innovations will require coordinated work from many contributors, and this thesis covers a few specific aspects of QuantumION to which the author has contributed.

In this thesis laser cooling is numerically investigated with special attention paid to external heating rates, laser linewidths, power limitations, and laser direction. Considering all these imperfections a set of laser parameters are presented for both quenched resolved sideband cooling and electromagnetically induced transparency cooling that in concert will cool all motional modes to the ground state. A novel individual addressing (IA) scheme is presented with detailed simulation showing 10⁻⁵ intensity cross talk and the first attempt at realizing this IA scheme is presented. The design philosophy for opto-mechanical assemblies in QuantumION is discussed and an example assembly is walked through the design process.