We present results on the light, strange and charm nucleon scalar and tensor charges from lattice QCD, using simulations with $N_f=2$ flavors of twisted mass Clover-improved fermions with a physical value of the pion mass. Both connected and disconnected contributions are included, enabling us to extract the isoscalar, strange and charm charges for the first time directly at the physical point. Furthermore, the renormalization is computed non-perturbatively for both isovector and isoscalar quantities. We investigate excited state effects by analyzing several sink-source time separations and by employing a set of methods to probe ground state dominance. Our final results for the scalar charges are $g_S^u = 5.20(42)(15)(12)$, $g_S^d = 4.27(26)(15)(12)$, $g_S^s=0.33(7)(1)(4)$, $g_S^c=0.062(13)(3)(5)$ and for the tensor charges $g_T^u = 0.782(16)(2)(13)$, $g_T^d = -0.219(10)(2)(13)$, $g_T^s=-0.00319(69)(2)(22)$, $g_T^c=-0.00263(269)(2)(37)$ in the $overline{rm MS}$ scheme at 2~GeV. The first error is statistical, the second is the systematic error due to the renormalization and the third the systematic arising from possible contamination due to the excited states.
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