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An atomic clock system includes a magneto-optical trap (MOT) system that traps alkali metal atoms in a cell during a trapping stage of each of sequential coherent population trapping (CPT) cycles. The system also includes an interrogation system that generates an optical difference beam comprising a first optical beam having a first frequency and a second optical beam having a second frequency different from the first frequency. The interrogation system includes a direction controller that periodically alternates a direction of the optical difference beam through the cell during a CPT interrogation stage of each of the sequential clock measurement cycles to drive CPT interrogation of the trapped alkali metal atoms. The system also includes an oscillator system that adjusts a frequency of a local oscillator based on an optical response of the CPT interrogated alkali metal atoms during a state readout stage in each of the …