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Currently, GPS satellites use atomic clocks as part of navigation systems, but there are limits to the approach. They rely on atoms confined by a gas cell to serve as a meter for the clock, but the long-term stability of gas-cell clocks can suffer when the atoms collide with the "walls" of the cell, causing drift. GPS systems get signals from earthbound atomic clocks to correct the instability. But that gets trickier the deeper you go into space.
Trapped-ion atomic clocks, in which charged atoms are prevented from colliding with walls by an electromagnetic cage, have been around since the early 2000s and are more accurate than earlier approaches to atomic time-keeping, which have been around since the 1950s. NASA's Deep Space Atomic Clock loses one second every 10 million years, as proven in controlled tests on Earth.