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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 inter rogation 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 measure ment 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 …