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Choose an isolated pair of energy levels, with ground state $|g⟩=(0,1{)}^T$ and excited state $|e⟩=(1,0{)}^T$. Use the Pauli matrices in the ordered basis $(|e⟩,|g⟩)$, so ${\sigma }_z=\mathrm{diag}(1,-1)$. After subtracting the mean energy, prescribe the laboratory Hamiltonian operatorThe unperturbed energy gap is $\hslash {\omega }_0$, the drive has angular frequency $\omega$, and $\varphi$ fixes its oscillation phase at the chosen time origin. All of ${\omega }_0$, $\omega$, the Rabi angular frequency $\Omega$ and the Rabi detuning $\delta$ are in radians per second; ordinary frequency is angular frequency divided by $2\pi$. In particular, $\Omega$ here is the coefficient multiplying the cosine in $H_{\mathrm{lab}}/\hslash$, not twice that coefficient.

Write $|{\psi }_{\mathrm{lab}}⟩=R(t)|{\psi }_{\mathrm{rot}}⟩$ with $R(t)=\exp (-i\omega t{\sigma }_z/2)$. Transforming the Schrödinger equation gives $H_{\mathrm{rot}}=R^{†}{H}_{\mathrm{lab}}R-i\hslash R^{†}\dot{R}$. The rotating-wave approximation drops terms at angular frequency $2\omega$, leavingThis approximation requires $\Omega ,|\delta |\ll {\omega }_0,\omega$, and an interaction duration over which omitted corrections remain small. It also assumes that other energy levels can be neglected. Resonance alone does not justify either assumption. An exactly co-rotating drive has no discarded counter-rotating component; the linearly oscillating laboratory drive above does.

The Pauli matrix multiplication law gives $K^2={\Omega }_{\mathrm{eff}}^{2}I$. Separating even and odd terms of the matrix exponential therefore proveswith the continuous limit $U=I$ when $\Omega =\delta =0$. Starting from $|g⟩$, the upper probability amplitude is $-i{e}^{-i\varphi }(\Omega /{\Omega }_{\mathrm{eff}})\sin ({\Omega }_{\mathrm{eff}}t/2)$. The Born rule givesThe rotating transformation only changes the quantum phases of these basis states, so their laboratory populations are the same. Rabi detuning tilts the rotation axis of the Bloch vector: it increases the oscillation rate to ${\Omega }_{\mathrm{eff}}$ but caps the transferred population at ${\Omega }^2/({\Omega }^2+{\delta }^2)$. A fixed drive oscillation phase cancels from this single-pulse population when the initial state is $|g⟩$. It still fixes the relative quantum phase of a resulting quantum superposition and matters when another pulse supplies a phase reference.

Use the Driven two-level Rabi model in the ordered basis $(|e⟩,|g⟩)$, with Pauli matrices satisfying ${\sigma }_z=\mathrm{diag}(1,-1)$. Let the Rabi detuning be $\delta ={\omega }_0-\omega =2\pi ({\nu }_0-\nu )$, in angular frequency, while ${\nu }_0$ and $\nu$ are ordinary frequencies in hertz. Assume two identical square pulses, equal drive oscillation phases, constant positive Rabi angular frequency $\Omega$, constant $\delta$ during pulses and flight, and no quantum decoherence or loss. The rotating-wave approximation and isolation of the chosen two-level system are required, just as for the Driven two-level Rabi model. Free flight means no transverse drive; the reference oscillator continues running.

The pulse and free-flight Hamiltonian operators in the rotating frame areThe Pauli matrix multiplication law gives $(\delta {\sigma }_z+\Omega {\sigma }_x{)}^2=q^{2}I$. Thus the exact special unitary group $\mathrm{SU}(2)$ pulse matrix for this effective Hamiltonian operator, and the flight matrix, areThe sequence is $U_p{U}_f{U}_p$. Starting in $|g⟩$, matrix multiplication and the Born rule giveThis retains the tilted rotation axis and quantum phase accumulated during each finite pulse. At resonance it gives $P_{g\to e}(0)={\sin }^2(\Omega \tau )$; with no flight it reduces to the single square-pulse response for duration $2\tau$. Both checks would fail if arbitrary ideal $\pi /2$ rotations were silently substituted at nonzero Rabi detuning.

For resonant pulse area $\Omega \tau =\pi /2$, $|\delta |/\Omega \ll 1$ and $\tau \ll T$, the central fringe approachesIts half-height points are $|\nu -{\nu }_0|=1/(4T)$, so the central peak's full width at half maximum is $1/(2T)$ in hertz, or $\pi /T$ in angular frequency. This width assumes an effectively flat pulse envelope across that central peak, one flight time and unit contrast; it is neither a universal finite-pulse width nor a frequency uncertainty. Longer flight lets a smaller frequency difference accumulate the same observable quantum phase.

The two pulses here have the same sign and the plotted outcome is transfer to $|e⟩$. The earlier Ramsey interferometry example uses an inverse analysis pulse and reports return to its initial label. Specifying the measured outcome and pulse oscillation phases reconciles the two conventions. In a beam the lengths and speed determine $\tau$ and $T$; in the Quantronium Ramsey interference experiment electronics set the pulse times for a stationary circuit.

A motional sideband is a transition that changes internal excitation and a motional quantum number together. Define the internal energy gap as $\hslash {\omega }_0>0$. A carrier drives $|g,n⟩\leftrightarrow |e,n⟩$; the first red sideband drives $|g,n⟩\leftrightarrow |e,n-1⟩$; the first blue sideband drives $|g,n⟩\leftrightarrow |e,n+1⟩$. Their resonant drive angular frequencies follow by subtracting these energy levels. For a Raman transition, the drive is a beam-difference frequency with a sign fixed by the selected internal transition.

Choose a real carrier Rabi angular frequency $\Omega$ defined so that resonant carrier excitation is ${\sin }^2(\Omega t/2)$. In the Lamb-Dicke regime, isolated first-sideband Hamiltonians in a rotating frame can be written, after choosing the pulse phase, asThese formulas use a rotating-wave approximation: neglected carrier and other-sideband terms oscillate rapidly compared with the retained coupling. The drive's effective width and sideband coupling must be small compared with $\nu$; sufficient suppression of off-resonant carrier excitation must also be checked. The red interaction is a Jaynes-Cummings model with a motional quantum replacing a cavity photon. The blue interaction creates internal excitation and a motional quantum together; the external laser supplies energy. The driven-system rotating-frame Hamiltonian alone is not the total laboratory energy.

Use the isolated nuclear spin Zeeman effect implied by the supplied nuclear magnetic moment, with hyperfine structure neglected. The proton gyromagnetic ratio isThe two spin levels are separated by $g_p{\mu }_N{B}_0$. Resonant nuclear magnetic resonance therefore requires the Larmor frequency

The duration is a Rabi pi pulse: in a frame rotating with the resonant transverse magnetic field, the spin must rotate through $\pi$. If $B_1$ denotes the magnitude of a circularly rotating field with the correct sense of rotation, the Rabi angular frequency is ${\Omega }_R={\gamma }_p{B}_1$. The shortest pulse is then

There is an amplitude convention to specify. If the applied transverse magnetic field is instead the linearly oscillating $B_1\cos (\omega t)\hat{\mathbf{x}}$, its resonant circular component has magnitude $B_1/2$. The rotating-wave approximation gives ${\Omega }_R={\gamma }_p{B}_1/2$ and henceThe wording does not specify this polarization convention, so the two pulse durations should be distinguished. Odd multiples of either shortest Rabi pi pulse also invert the spin within the corresponding ideal model.

Write ${\omega }_z=\gamma B_z$ and use the ordered spin basis $(|\uparrow ⟩,|\downarrow ⟩)$. The free Hamiltonian operator is $H_0=-\hslash {\omega }_z{\sigma }_z/2$, soResolving the cosine into its two complex exponentials gives the exact upper off-diagonal factorwith the complex conjugate in the lower entry. Choose the field orientation with ${\omega }_z>0$, as implicit in the printed near-resonance condition, and put $\delta =\omega -{\omega }_z$. The rotating-wave approximation discards the terms at $\omega +{\omega }_z$, retaining the slow terms at $\delta$. The resulting interaction picture equations areThe factor $1/4$ contains $1/2$ from $S_x=\hslash {\sigma }_x/2$ and $1/2$ from the cosine decomposition. This is a Driven two-level Rabi model, with signed on-resonance coupling $\Omega =\gamma B_x/2$ and generalized Rabi angular frequency ${\omega }_R=\sqrt{{\delta }^2+{\Omega }^2}$. Here the Rabi detuning uses the paper's convention, drive minus free frequency.

Small detuning alone is insufficient to derive the printed equations. One also requires $|\gamma B_x|,|\delta |\ll \omega +{\omega }_z$, and an evolution time over which neglected terms stay small. At resonance this is the weak transverse-field regime $|B_x|\ll |B_z|$. The supplied solution is thus an approximate solution for the linearly oscillating field, not an exact one at arbitrary drive strength. If $\gamma B_z<0$, the other exponential is resonant and the physical positive resonance frequency is $|\gamma B_z|$.

The Rabi angular frequency is the on-resonance population oscillation rate in the specified Driven two-level Rabi model. The rotating-frame off-diagonal Hamiltonian operator entry has magnitude $\hslash \Omega /2$. Stating this convention avoids a factor-of-two ambiguity between drive coefficients and oscillation rates. The generalized rate off resonance is ${\Omega }_{\mathrm{eff}}=\sqrt{{\Omega }^2+{\delta }^2}$.

For an ideal single transit, let the oscillatory magnetic field occupy a region of length $L$, take the longitudinal speed $v$ constant, and neglect edge fields. Each molecule then experiences one square pulse of duration $\tau =L/v$. This is one contiguous interaction region, distinct from the two separated pulses of Ramsey interferometry. The static magnetic field sets the selected transition gap; the transverse drive sets Rabi angular frequency. A change of RF frequency or static magnetic field changes Rabi detuning.

For an original ideal detector model, suppose every successful transition removes an otherwise accepted molecule and the incident beam occupies the lower state of the selected pair. With accepted no-transition signal $S_0$, constant background $S_{\mathrm{bg}}$, and effective loss contrast $0\le \eta \le 1$, writeFor identical trajectories $\overline{P}=P_{g\to e}(L/v)$, giving an intensity dip where transfer is largest. For real trajectory variation, a normalized joint probability density $w(v,ϵ,{\Omega }^{\prime })$ gives the static-offset modelHere $ϵ$ is the trajectory's transition-frequency offset and ${\Omega }^{\prime }$ its drive strength, each in angular-frequency units. The weighting is for molecules accepted by the apparatus, rather than an assumed unfiltered oven distribution. In particular, designing $\Omega L/v_0=\pi$ does not produce a Rabi pi pulse for every speed: at $0.8v_0$ and $1.2v_0$ the resonant transfer probabilities are respectively ${\sin }^2(5\pi /8)\simeq 0.8536$ and ${\sin }^2(5\pi /12)\simeq 0.9330$.

Spread in transit times, static magnetic fields and drive amplitudes can reduce or smear oscillations without quantum decoherence on any individual trajectory. Even the single-transit square pulse has finite spectral width of order $1/\tau$ in angular frequency. If the magnetic field varies substantially along one path, its Hamiltonian operator changes during the passage and the constant-offset average above must be replaced by a time-ordered exponential. Actual molecules may also have several coupled energy levels; the isolated pair and perfect loss discriminator are explicit idealizations of this model.

In the Driven two-level Rabi model, the transition probability is $P(t)={\Omega }^2{\sin }^2(\sqrt{{\Omega }^2+{\delta }^2}t/2)/({\Omega }^2+{\delta }^2)$. Maximizing over time at each detuning gives a Lorentzian line shape, with first maximizing time $\pi /\sqrt{{\Omega }^2+{\delta }^2}$ and full width at half maximum $2|\Omega |$ in angular frequency. The amplitude parameter $\Omega$ must use the specified Rabi angular frequency convention.

This envelope differs from a spectrum obtained with a fixed pulse duration: optimizing the time separately removes the sine-squared factor, while fixing time retains it. A finite linewidth here describes detuning-limited transfer under coherent driving, without requiring dissipative decay.