Atomic magnetometers are highly sensitive detectors of magnetic fields that monitor the evolution of the macroscopic magnetic moment of atomic vapors, and opening new applications in biological, physical, and chemical science. However, the performance of atomic magnetometers is often limited by hidden systematic effects that may cause misdiagnosis for a variety of applications, e.g., in NMR and in biomagnetism. In this work, we uncover a hitherto unexplained interference effect in atomic magnetometers, which causes an important systematic effect to greatly deteriorate the accuracy of measuring magnetic fields. We present a standard approach to detecting and characterizing the interference effect in, but not limited to, atomic magnetometers. As applications of our work, we consider the effect of the interference in NMR structural determination and locating the brain electrophysiological symptom, and show that it will help to improve the measurement accuracy by taking interference effects into account. Through our experiments, we indeed find good agreement between our prediction and the asymmetric amplitudes of resonant lines in ultralow-field NMR spectra -- an effect that has not been understood so far. We anticipate that our work will stimulate interesting new researches for magnetic interference phenomena in a wide range of magnetometers and their applications.
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