Optical control of the primary step of photoisomerization of the retinal molecule in bacteriorhodopsin from the all-trans to the 13-cis state was demonstrated under weak field conditions (where only 1 of 300 retinal molecules absorbs a photon during the excitation cycle) that are relevant to understanding biological processes. By modulating the phases and amplitudes of the spectral components in the photoexcitation pulse, we showed that the absolute quantity of 13-cis retinal formed upon excitation can be enhanced or suppressed by +/-20% of the yield observed using a short transform-limited pulse having the same actinic energy. The shaped pulses were shown to be phase-sensitive at intensities too low to access different higher electronic states, and so these pulses apparently steer the isomerization through constructive and destructive interference effects, a mechanism supported by observed signatures of vibrational coherence. These results show that the wave properties of matter can be observed and even manipulated in a system as large and complex as a protein.

We performed a series of successful experiments for the optimization of the population transfer from the ground to the first excited state in a complex solvated molecule (rhodamine 101 in methanol) using shaped excitation pulses at very low intensities (1 absorbed photon per 100-500 molecules per pulse). We found that the population transfer can be controlled and significantly enhanced by applying excitation laser pulses with crafted pulse shapes. The optimal shape was found in feedback-controlled experiments using a genetic search algorithm. The temporal profile of the optimal excitation pulse corresponds to a comb of subpulses regularly spaced by approximately 150 fs, whereas its spectrum consists of a series of well-resolved peaks spaced apart by approximately 6.5 nm corresponding to a frequency of 220 cm(-1). This frequency matches very well with the frequency modulation of the population kinetics (period of approximately 150 fs), observed by excitation with a short (approximately 20 fs) transform-limited laser pulse directly after excitation. In addition, an antioptimization experiment was performed under the same conditions. The difference in the population of the excited state for the optimal and antioptimal pulses reaches approximately 30% even at very weak excitation. The results of optimization are reproducible and have clear physical meaning.

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Joffre attempts to show that the linear response of any quantum system to an external perturbation is phase insensitive, but he uses incorrect mathematical assumptions, misinterprets the time invariance principle, and ignores causality. We argue that the opposite case-an explicit phase dependence for a signal measured in the linear excitation regime-can equally be shown using Joffre's approach and assumptions.T he comment by Joffre (1) claims to make a general statement covering all possible cases of the field-matter interaction in which the measured signal is governed by a twofield interaction. The photoisomerization of retinal in bacteriorhodopsin under question (2), is an example of a strongly coupled system (retinal) to a bath (protein). The system response with respect to photoinduced isomerization necessarily involves at least four modes: a coupling mode, the primary torsional or reactive mode, and dissipation to two accepting modes of the system-bath interaction (3). Joffre attempts to illustrate the general properties of an inherently multilevel problem with a simple two-level system. By definition, this model system cannot properly capture the photoisomerization process. Effectively, Joffre has attempted to treat a multilevel quantum problem without involving quantum mechanics. The derivation and strong assertions of complete generality for a "global system response" function (1) raise many questions that require a more detailed analysis than given to establish their validity.As we show, the outcome for a stationary signal given by equation 3 in (1) is not a unique solution to the problem as formulated (Eq. 1). The method proposed by Joffre allows one to derive an alternative result showing explicitly a phase sensitivity for the measured response. Let us start from equation 1 in (1) for the stationary value of the signal S. In accordance with Joffre, and making use of the hypothesis of time invariance, we replace E(t) by E(t + T), where T is an arbitrary time delay.According to (1), "this relation holds for any values of t 1 , t 2 , and T, and can thus be applied to the particular case" where T = −t 2 (4) that results in S ¼ Eð0Þ ZZRðt 1 ,t 2 ÞEðt 1 − t 2 Þdt 1 dt 2 ð2ÞExpressing R(t 1 ,t 2 ), E(t) as functions of their Fourier transforms R(w 1 ,w 2 ), E(w) ≡ A(w)e if(w)