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Report of the Referee -- AY11417/Chin
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The manuscript reports on an experimental investigation of
light-matter interaction for a single atom trapped in strong optical
tweezers and irradiated by tightly focused light. On resonance, the
authors observe 17% reduction of the light transmitted through the
atom and 0.6% enhancement of the light reflected by the atom. These
are impressive (although state-of-the-art) results, and the overall
study is interesting for all single-atom experiments. Particularly
interesting are the time dependence of the light extinction and the
dynamical light shift in figure 6. The manuscript might therefore be
publishable in the Physical Review. However, a few important questions
remain:

1) The observed extinction is only half as large as the expected
extinction (~17% compared to ~36%). This huge discrepancy is not
explained, although the reported work aims to be a careful and
systematic study of light-matter interaction (as stated in the
introduction of the manuscript). Which big effect is missing? Without
such effect being properly identified, the presented work is not very
useful for other groups in the field.

2) For tight focussing, the light polarization in the focus usually
differs from the polarization away from the focus.The authors do not
mention this at all. Is the effect irrelevant for circularly polarized
light as used in the experiment? Or could it explain the large
discrepancy between observed and expected transmission?

3) The heating model used to explain the measurements in figure 6
assumes that _each_ scattered photon changes the kinetic energy of the
atom by two recoil energies, as clearly stated towards the bottom of
page 4 right column (where the directionality of the heating is also .
discussed). However, absorption-emission cycles in which the absorbed
photon is emitted (almost) into the direction of the laser beam would
leave the momentum of the atom and, hence, its energy (almost)
unchanged. The heating model therefore seems incorrect which makes the
good agreement between experiment and simulation in figure 6a somewhat
obscure. The authors must resolve this issue.

4) Figure 4b claims to display results of a saturation experiment, and
serves to experimentally determine the saturation power. However, the
reflection continues to significantly increase even beyond power
levels as high as 4 times the saturation power. How can the saturation
power be determined from a measurement which shows no limit in the
amount of reflected light (although plotted on a logarithmic scale)?

I recommend that the authors clarify these points before publication
of the manuscript.