Hi Jon,
You asked an excellent question following through on the half pulse manifestation of the self-referential operator. Let me first clear up some of your questions on the technical infrastructure in the Rubidium setup:
A laser whose output power is constant over time is called a continuous wave laser and this is what was used in the setup. This is opposed to pulsed operation in which the optical power appears in pulses of some duration at some repetition rate (such as in a Q-switching or mode-locking laser). For continuous wave operation it's required for the population inversion of the gain medium to be continually replenished by a steady pump source. Even a laser whose output is normally continuous can be intentionally turned on and off at some rate in order to create pulses of light (the modulation rate is on time scales much slower than the cavity lifetime and the time period over which energy can be stored in the lasing medium or pumping mechanism, and it's still classified as a modulated or pulsed yet nevertheless continuous wave laser) - it is this type of pulse that's being shined on the Rubidium atom in the setup. Pulse of laser light thus refers to a duration of time in which the laser is being shined on the atom, necessary to excite the electron to the excited state. The half pulse refers to shining the laser light for half this duration of time on the atom.
Now, one half pulse (i.e. shining this continuous wave laser on the Rubidium atom for this half-duration time) causes the electron to go into superposition of the ground and excited states. Another half pulse excites it to the definitive excited state. This corresponds to two self referential operators, but that's the key: whatever the physical mechanism is, it is one that manifests the self referential operator. In representing a qubit, the most general state of a quantum two-level system can be written in the form ∣ψ〉 = α ∣0〉 + β∣1〉 where α and β are complex numbers. The state has to be normalized, so ∣α∣^2 + ∣β∣^2 = 1, and an overall phase makes no difference, so either α or β can be chosen to be real. This leads to the parametrization ∣ψ 〉 = cos (θ/2)∣0〉+ (e^iφ) sin (θ/2)∣1〉 in terms of only two real numbers θ and φ, with ranges 0 ≤ θ ≤ π and 0 ≤ φ ≤ 2π. These are the same as the polar angles in 3-dimensional spherical coordinates, and this leads to the representation of the state as a point on a unit sphere called the Bloch sphere. The Bloch sphere can be traveled with pulses of different lengths and the system driven from the superposition state to the ground or excited states. But this can be done only during a certain amount of time which is called the coherence time. It can vary from several microseconds to several seconds depending on the particular system. When this period is over the system has to be initialized again in the ground state. If the phase of the driving field is fixed, the system will be going in one direction, but if phase is changed by π, the rotation axis in the Bloch representation is changed, and in that case the system might rotate in the reverse direction (for example around -x axis instead of the x-axis). One can also change the phase by π/2 which would result in a mirror image of the state. For example if a π/sqrt(2) pulse is shined and then the axis is changed from x to y, the coefficients of the two states in the superposition are reversed. So the physical manifestation for a self referential operator may not be the same half pulse but rather may change - but this makes sense: there are different physical paths as we see to get back to the ground state; hence there are different physical manifestations for the NOT operator. It then follows there would be different manifestations for the SQR (NOT) and thus for a self referential operator at that particular point. There's lots of research being done on these variations (and part of my own personal research) and I hope this can be shifted to the engineering of self-referential operator gates which would be an extremely fascinating field.