Quantum technology with atomic, molecular and optical systems has advanced to a stage that single particles can be manipulated precisely so that quantum information processing is no longer elusive. In fact, a great number of quantum information protocols have been demonstrated with small scaled systems. The remaining task is to build large scale practical devices. However it turns out that scaling up is highly nontrivial in the quantum world. A protocol valid in principle could face enormous technical challenges when the system size is increased. Therefore new ideas and smart designs that bypass the technical obstacles are extremely useful in this field. In this dissertation we tackle several specific problems in quantum information processing with trapped ions and cold atomics gases. For ions, we first present a scalable implementation scheme for the recently proposed concept of Boson sampling, which holds the promise of outperforming classical computers in the near future. The scheme is based on the technically mature linear Paul trap and the transverse motional phonons of the ions are manipulated with laser to perform sampling. A complete recipe is provided and the technical requirements are discussed. Then we go back to the conventional circuit model for computation and discuss a method to perform individual ion addressing quantum gates with Gaussian beams. We describe the so-called spatial refocusing technique to significantly narrow down the beams with coherent interference. We also extend the original quantum gate formalism to include the effect of micromotion. We demonstrate high fidelity gates in the presence of significant micromotion. This paves the way to the development of a two dimensional ion crystal quantum processor with hundreds of ions inside a single trap. On the other hand, we explore precision measurement with a cold atom interferometer. Combining a spin-spin interaction Hamiltonian and coherent spin rotation pulses, we construct optimized pulse sequences for spin squeezing to approach the Heisenberg limit of noise. Finally we investigate the general problem of state detection with faulty detectors. We develop a statistical procedure to recover the true correlation from noisy data.
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