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A learning algorithm was used to manipulate optical pulse shapes and optimize retinal isomerization in bacteriorhodopsin, for excitation levels up to 1.8 ؋ 10 16 photons per square centimeter. Below 1/3 the maximum excitation level, the yield was not sensitive to pulse shape. Above this level the learning algorithm found that a Fourier-transform-limited (TL) pulse maximized the 13-cis population. For this optimal pulse the yield increases linearly with intensity well beyond the saturation of the first excited state. To understand these results we performed systematic searches varying the chirp and energy of the pump pulses while monitoring the isomerization yield. The results are interpreted including the influence of 1-photon and multiphoton transitions. The population dynamics in each intermediate conformation and the final branching ratio between the all-trans and 13-cis isomers are modified by changes in the pulse energy and duration.coherent control ͉ photoisomerization ͉ ultrafast science B acteriorhodopsin (bR) is a photosynthetic protein found in the purple membrane of Halobacterium salinarum and capable of conversion of solar energy into chemical energy. This energy conversion is efficient (1-3) and has several possible applications (4-12). A retinal chromophore is responsible for photon absorption. After photoexcitation retinal undergoes ultrafast isomerization from the all-trans to a 13-cis configuration, accompanied by additional changes in the conformation of bR (3,8). The initial steps of the bR photocycle (see Fig. 1) have been studied intensively (11, 13-33), but there are still unanswered questions regarding the electronic potential energy surfaces (PES) of retinal, the interaction with its surroundings in the protein, and related ultrafast vibrational coupling. A number of models have been proposed, each explaining parts of the large number of experiments (4,13,14,16,(34)(35)(36)(37)(38)(39)(40). Attempts have been made to reconcile the differences between these models (4).We aim to understand how the optical pulse shape and intensity affect the all-trans 3 13-cis yield and to explore potential pathways for producing high photoproduct yields on an ultrafast time scale. This is relevant for energy storage using bio-molecular machines (9, 32). Recently, Prokhorenko et al. showed that the isomerization yield of retinal in bR could be manipulated in a low intensity, biologically relevant regime through the use of phase and amplitude shaped optical fields (25). Modifications of as much as Ϯ20% were observed compared with unshaped pulses capable of exciting an equal number of molecules. Yet the ultimate yields remain small as photon flux was restricted to excite Ϸ0.3% of the chromophores in the excitation volume. In a different experiment, Vogt et al. used much higher intensity, shorter wavelength pump pulses to excite bR and a shaped 800-nm dump pulse to study the evolution of the molecule on the excited state PES (30). They found that the excited population is transferred most effectively back to t...

This paper discusses different routes to gaining insight from closed loop learning control experiments. We focus on the role of the basis in which pulse shapes are encoded and the algorithmic search is performed. We demonstrate that a physically motivated, nonlinear basis change can reduce the dimensionality of the phase space to one or two degrees of freedom. The dependence of the control goal on the most important degrees of freedom can then be mapped out in detail, leading toward a better understanding of the control mechanism. We discuss simulations and experiments in selective molecular fragmentation using shaped ultrafast laser pulses.