Pulse 1 pushes all the molecules out of sync. Pulse 2 lets them do their biological business. Pulse 3 blows a whistle, telling them to reverse time and high-five each other. You measure the high-five.
A laser pulse hits your molecule. The electric field pushes the electrons around. Your molecule gets a temporary dipole moment. This is called polarization (P) . Pulse 1 pushes all the molecules out of sync
Mukamel spends pages on the RWA. Here is the translation: Laser fields oscillate at optical frequencies ((10^15) Hz). Your detector is slow. The RWA throws away terms that oscillate too fast to matter (at (2\omega) or sum frequencies) and keeps only the near-resonant terms ((\omega_signal \approx \omega_laser)). Pulse 1 pushes all the molecules out of sync