We propose a scheme for the initialization of a quantum computer based on neutral atoms trapped in an optical lattice with large lattice constant. Our focus is the development of a compacting scheme to prepare a perfect optical lattice of simple orthorhombic structure with unit occupancy. Compacting is accomplished by sequential application of two types of operations: a flip operator that changes the internal state of the atoms, and a shift operator that moves them along the lattice principal axis. We propose physical mechanisms for realization of these operations and we study the effects of motional heating of the atoms. We carry out an analysis of the complexity of the compacting scheme and show that it scales linearly with the number of lattice sites per row of the lattice, thus showing good scaling behavior with the size of the quantum computer.
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