The aim of this paper is to derive limits on various forms of “new physics” using atomic experimental data. Interactions with dark energy and dark matter fields can lead to space-time variations of fundamental constants, which can be detected through atomic spectroscopy. In this study, we examine the effects of a varying nuclear mass mN and nuclear radius rN on two transition ratios: the comparison of the two-photon transition in atomic hydrogen with the hyperfine transition in Cs133 based clocks, and the ratio of optical clock frequencies in Al+ and Hg+. The sensitivity of these frequency ratios to changes in mN and rN enables us to derive new limits on the variations of the proton mass, quark mass, and the QCD parameter θ. Additionally, we consider the scalar field generated by the Yukawa-type interaction of feebly interacting hypothetical scalar particles with Standard Model particles in the presence of massive bodies such as the Sun and Moon. Using the data from the Al+/Hg+, Yb+/Cs, and Yb+(E2)/Yb+(E3) transition frequency ratios, we place constraints on the interaction of the scalar field with photons, nucleons, and electrons for a range of scalar particle masses. We also investigate limits on the Einstein equivalence principle (EEP) violating term (c00) in the Standard Model extension (SME) Lagrangian and the dependence of fundamental constants on gravity. Published by the American Physical Society 2024