Coherent Control of Retinal Isomerization in Bacteriorhodopsin

Direct observation of the coherent nuclear response after the absorption of a photon

How molecules convert light energy to perform a specific transformation is a fundamental question in photophysics. Ultrafast spectroscopy reveals the kinetics associated with electronic energy flow, but little is known about how absorbed photon energy drives nuclear motion. Here we used ultrabroadband transient absorption spectroscopy to monitor coherent vibrational energy flow after photoexcitation of the retinal chromophore. In the proton pump bacteriorhodopsin, we observed coherent activation of hydrogen-out-of-plane wagging and backbone torsional modes that were replaced by unreactive coordinates in the solution environment, concomitant with a deactivation of the reactive relaxation pathway.

Mechanisms in environmentally assisted one-photon phase control

The ability of an environment to assist in one-photon phase control relies upon entanglement between the system and bath and on the breaking of the time reversal symmetry. Here, one-photon phase control is examined analytically and numerically in a model system, allowing an analysis of the relative strength of these contributions. Further, the significant role of non-Markovian dynamics and of moderate system-bath coupling in enhancing one-photon phase control is demonstrated, and an explicit role for quantum mechanics is noted in the existence of initial non-zero stationary coherences. Finally, desirable conditions are shown to be required to observe such environmentally assisted control, since the system will naturally equilibrate with its environment at longer times, ultimately resulting in the loss of phase control.

Dynamic dimensionality identification for quantum control

The control of quantum systems with shaped laser pulses presents a paradox since the relative ease with which solutions are discovered appears incompatible with the enormous variety of pulse shapes accessible with a standard pulse shaper. Quantum landscape theory indicates that the relevant search dimensionality is not dictated by the number of pulse shaper elements, but rather is related to the number of states participating in the controlled dynamics. The actual dimensionality is encoded within the sensitivity of the observed yield to all of the pulse shaper elements. To investigate this proposition, the Hessian matrix is measured for controlled transitions amongst states of atomic rubidium, and its eigendecomposition reveals a dimensionality consistent with that predicted by landscape theory. Additionally, this methodology furnishes a low-dimensional picture that captures the essence of the light-matter interaction and the ensuing system dynamics.

Laboratory transferability of optimally shaped laser pulses for quantum control

Optimal control experiments can readily identify effective shaped laser pulses, or "photonic reagents," that achieve a wide variety of objectives. An important additional practical desire is for photonic reagent prescriptions to produce good, if not optimal, objective yields when transferred to a different system or laboratory. Building on general experience in chemistry, the hope is that transferred photonic reagent prescriptions may remain functional even though all features of a shaped pulse profile at the sample typically cannot be reproduced exactly. As a specific example, we assess the potential for transferring optimal photonic reagents for the objective of optimizing a ratio of photoproduct ions from a family of halomethanes through three related experiments. First, applying the same set of photonic reagents with systematically varying second- and third-order chirp on both laser systems generated similar shapes of the associated control landscape (i.e., relation between the objective yield and the variables describing the photonic reagents). Second, optimal photonic reagents obtained from the first laser system were found to still produce near optimal yields on the second laser system. Third, transferring a collection of photonic reagents optimized on the first laser system to the second laser system reproduced systematic trends in photoproduct yields upon interaction with the homologous chemical family. These three transfers of photonic reagents are demonstrated to be successful upon paying reasonable attention to overall laser system characteristics. The ability to transfer photonic reagents from one laser system to another is analogous to well-established utilitarian operating procedures with traditional chemical reagents. The practical implications of the present results for experimental quantum control are discussed.

Divergent positive selection in rhodopsin from lake and riverine cichlid fishes

Studies of cichlid evolution have highlighted the importance of visual pigment genes in the spectacular radiation of the African rift lake cichlids. Recent work, however, has also provided strong evidence for adaptive diversification of riverine cichlids in the Neotropics, which inhabit environments of markedly different spectral properties from the African rift lakes. These ecological and/or biogeographic differences may have imposed divergent selective pressures on the evolution of the cichlid visual system. To test these hypotheses, we investigated the molecular evolution of the dim-light visual pigment, rhodopsin. We sequenced rhodopsin from Neotropical and African riverine cichlids and combined these data with published sequences from African cichlids. We found significant evidence for positive selection using random sites codon models in all cichlid groups, with the highest levels in African lake cichlids. Tests using branch-site and clade models that partitioned the data along ecological (lake, river) and/or biogeographic (African, Neotropical) boundaries found significant evidence of divergent selective pressures among cichlid groups. However, statistical comparisons among these models suggest that ecological, rather than biogeographic, factors may be responsible for divergent selective pressures that have shaped the evolution of the visual system in cichlids. We found that branch-site models did not perform as well as clade models for our data set, in which there was evidence for positive selection in the background. One of our most intriguing results is that the amino acid sites found to be under positive selection in Neotropical and African lake cichlids were largely nonoverlapping, despite falling into the same three functional categories: spectral tuning, retinal uptake/release, and rhodopsin dimerization. Taken together, these results would imply divergent selection across cichlid clades, but targeting similar functions. This study highlights the importance of molecular investigations of ecologically important groups and the flexibility of clade models in explicitly testing ecological hypotheses.

Ultrafast dynamics of single molecules

Room-temperature studies of single molecules at femtosecond timescales provide detailed observation and control of ultrafast electronic and vibrational dynamics of organic dyes and photosynthetic complexes, probing quantum dynamics at ambient conditions and elucidating its role in chemistry and biology.

Coherent-control of linear signals: frequency-domain analysis

The dependence of various types of linear signals on the phase profile of broadband optical pulses is examined using fundamental time translation invariance symmetry of multipoint correlation functions. The frequency-domain wave-mixing analysis presented here unifies several arguments made earlier with respect to the conditions whereby coherent control schemes may be used.

Coherent one-photon phase control in closed and open quantum systems: a general master equation approach

The underlying mechanisms for one photon phase control are revealed through a master equation approach. Specifically, two mechanisms are identified, one operating on the laser time scale and the other on the time scale of the system-bath interaction. The effects of the secular and non-secular Markovian approximations are carefully examined.

Coherent fiber supercontinuum for biophotonics

Biophotonics and nonlinear fiber optics have traditionally been two independent fields. Since the discovery of fiber-based supercontinuum generation in 1999, biophotonics applications employing incoherent light have experienced a large impact from nonlinear fiber optics, primarily because of the access to a wide range of wavelengths and a uniform spatial profile afforded by fiber supercontinuum. However, biophotonics applications employing coherent light have not benefited from the most well-known techniques of supercontinuum generation for reasons such as poor coherence (or high noise), insufficient controllability, and inadequate portability. Fortunately, a few key techniques involving nonlinear fiber optics and femtosecond laser development have emerged to overcome these critical limitations. Despite their relative independence, these techniques are the focus of this review, because they can be integrated into a low-cost portable biophotonics source platform. This platform can be shared across many different areas of research in biophotonics, enabling new applications such as point-of-care coherent optical biomedical imaging.

Quantum coherent energy transfer over varying pathways in single light-harvesting complexes

The initial steps of photosynthesis comprise the absorption of sunlight by pigment-protein antenna complexes followed by rapid and highly efficient funneling of excitation energy to a reaction center. In these transport processes, signatures of unexpectedly long-lived coherences have emerged in two-dimensional ensemble spectra of various light-harvesting complexes. Here, we demonstrate ultrafast quantum coherent energy transfer within individual antenna complexes of a purple bacterium under physiological conditions. We find that quantum coherences between electronically coupled energy eigenstates persist at least 400 femtoseconds and that distinct energy-transfer pathways that change with time can be identified in each complex. Our data suggest that long-lived quantum coherence renders energy transfer in photosynthetic systems robust in the presence of disorder, which is a prerequisite for efficient light harvesting.

Inverting pump-probe spectroscopy for state tomography of excitonic systems

We propose a two-step protocol for inverting ultrafast spectroscopy experiments on a molecular aggregate to extract the time-evolution of the excited state density matrix. The first step is a deconvolution of the experimental signal to determine a pump-dependent response function. The second step inverts this response function to obtain the quantum state of the system, given a model for how the system evolves following the probe interaction. We demonstrate this inversion analytically and numerically for a dimer model system, and evaluate the feasibility of scaling it to larger molecular aggregates such as photosynthetic protein-pigment complexes. Our scheme provides a direct alternative to the approach of determining all Hamiltonian parameters and then simulating excited state dynamics.

Control Mechanisms of Photoisomerization in Protonated Schiff Bases

We performed ab initio excited-state molecular dynamics simulations of a gas-phase photoexcited protonated Schiff base (C1-N2═C3-C4═C5-C6) to search for control mechanisms of its photoisomerization. The excited molecule twists by ∼90° around either the N2C3 bond or the C4C5 bond and relaxes to the ground electronic state through a conical intersection with either a trans or cis outcome. We show that a large initial distortion of several dihedral angles and a specific normal vibrational mode combining pyramidalization and double-bond twisting can lead to a preferential rotation of atoms around the C4C5 bond. We also show that selective pretwisting of several dihedral angles in the initial ground state thermal ensemble (by analogy to a protein pocket) can significantly increase the fraction of photoreactive (cis → trans) trajectories. We demonstrate that new ensembles with higher degrees of control over the photoisomerization reaction can be obtained by a computational directed evolution approach on the ensembles of molecules with the pretwisted geometries.

Coherent High-Frequency Vibrational Dynamics in the Excited Electronic State of All-Trans Retinal Derivatives

Coherent vibrational dynamics of retinal in excited electronic states are of primary importance in the understanding of photobiology. Using pump-DFWM, we demonstrate for the first time the existence of coherent double-bond high-frequency modulations (>1300 cm(-1)) in the excited electronic state of different retinal derivatives. All-trans retinal as well as retinal Schiff bases exhibit a partial frequency downshift of the C═C double-bond mode from ∼1580 cm(-1) in the ground state to 1510 cm(-1) in the excited state. In addition, a new vibrational band at ∼1700 cm(-1) assigned to the C═N stretching mode in retinal Schiff bases in the excited state is detected. The newly reported bands are observed only in specific spectral regions of excited-state absorption. Implications regarding the observation of vibrational coherences in naturally occurring retinal protonated Schiff bases in rhodopsins are discussed.

Molecular response in one-photon absorption via natural thermal light vs. pulsed laser excitation

Photoinduced biological processes occur via one-photon absorption in natural light, which is weak, continuous wave, and incoherent, but are often studied in the laboratory using pulsed coherent light. Here, we compare the response of a molecule to these two very different sources within a quantized radiation field picture. The latter is shown to induce coherent time evolution in the molecule, whereas the former does not. As a result, the coherent time dependence observed in the laboratory experiments will not be relevant to the natural biological process. Emphasis is placed on resolving confusions regarding this issue that are shown to arise from aspects of quantum measurement and from a lack of appreciation of the proper description of the absorbed photon.

Solvation Stokes-Shift Dynamics Studied by Chirped Femtosecond Laser Pulses

The early optical dynamic response, resulting population, and electronic coherence are investigated experimentally and modeled theoretically for IR144 in solution. The fluorescence and stimulated emission response are studied systematically as a function of chirp. The magnitude of the chirp effect on fluorescence and stimulated emission is found to depend quadratically on pulse energy, even where excitation probabilities range from 0.02 to 5%, in the so-called "linear excitation regime". Interestingly, the shape of the chirp dependence on fluorescence and stimulated emission is found to be independent of pulse energy. The chirp dependence reveals dynamics related to solvent rearrangement following excitation and also depends on electronic relaxation of the chromophore. The experimental results are successfully simulated using a four-level model in the presence of inhomogeneous broadening of the electronic transitions.

The principle of coherence in multi-level brain information processing

Synchronisation has become one of the major scientific tools to explain biological order at many levels of organisation. In systems neuroscience, synchronised subthreshold and suprathreshold oscillatory neuronal activity within and between distributed neuronal assemblies is acknowledged as a fundamental mode of neuronal information processing. Coherent neuronal oscillations correlate with all basic cognitive functions, mediate local and long-range neuronal communication and affect synaptic plasticity. However, it remains unclear how the very fast and complex changes of functional neuronal connectivity necessary for cognition, as mediated by dynamic patterns of neuronal synchrony, could be explained exclusively based on the well-established synaptic mechanisms. A growing body of research indicates that the intraneuronal matrix, composed of cytoskeletal elements and their binding proteins, structurally and functionally connects the synapses within a neuron, modulates neurotransmission and memory consolidation, and is hypothesised to be involved in signal integration via electric signalling due to its charged surface. Theoretical modelling, as well as emerging experimental evidence indicate that neuronal cytoskeleton supports highly cooperative energy transport and information processing based on molecular coherence. We suggest that long-range coherent dynamics within the intra- and extracellular filamentous matrices could establish dynamic ordered states, capable of rapid modulations of functional neuronal connectivity via their interactions with neuronal membranes and synapses. Coherence may thus represent a common denominator of neurophysiological and biophysical approaches to brain information processing, operating at multiple levels of neuronal organisation, from which cognition may emerge as its cardinal manifestation.

Ultrafast dynamics in the power stroke of a molecular rotary motor

Light-driven molecular motors convert light into mechanical energy through excited-state reactions. Unidirectional rotary molecular motors based on chiral overcrowded alkenes operate through consecutive photochemical and thermal steps. The thermal (helix inverting) step has been optimized successfully through variations in molecular structure, but much less is known about the photochemical step, which provides power to the motor. Ultimately, controlling the efficiency of molecular motors requires a detailed picture of the molecular dynamics on the excited-state potential energy surface. Here, we characterize the primary events that follow photon absorption by a unidirectional molecular motor using ultrafast fluorescence up-conversion measurements with sub 50 fs time resolution. We observe an extraordinarily fast initial relaxation out of the Franck-Condon region that suggests a barrierless reaction coordinate. This fast molecular motion is shown to be accompanied by the excitation of coherent excited-state structural motion. The implications of these observations for manipulating motor efficiency are discussed.

Linear response in the strong field domain

We show that, while it is well-known that first-order perturbation theory leads to linear response (of, e.g., a material system to an external field), the reverse is not true: linear response does not necessarily imply the validity of first-order perturbation theory, nor does it follow from it that the external perturbation is weak. We do so by analyzing the intensity dependence in the photoexcitation followed by dissociation or isomerization of a bound molecular system by a shaped broadband laser pulse. We show that, in certain cases where strong field effects are definitely present, the observed photoexcitation yield as a function of intensity may exhibit linear dependence over a wide range of intensities. The behavior is shown to coexist with a rather extensive range of coherent control over the branching ratios, an effect that was shown in the past to be impossible in the single precursor state (e.g., in the first-order perturbation theory) domain. For example, we demonstrate computationally that when (flat continuum-mediated) Raman transitions are present, appropriate pulse shaping can lead to a linear yield with intensity over a wide range of intensities, while coherent control over the branching ratio is significant. Thus, it is not necessary to invoke external bath effects (as is currently being done) to explain present-day experiments where coherent control is observed in the linear response regime.

Reproducibility of observables and coherent control in molecular photoionization: from continuous wave to ultrashort pulsed radiation

One-photon single ionization of molecules has been at the focus of several discussions concerning the reconstruction of observables obtained with ultrashort pulses from those obtained from continuous wave radiation (and vice versa). A related controversy on the conditions and observables that allow for coherent control in one-photon processes has been recently revisited (Science 2006, 313, 1257; J. Chem. Phys. 2010, 133, 151101). Our benchmark to investigate these issues is photoionization of the hydrogen molecule, where the autoionization events are the time-dependent processes in field-free evolution that could serve as a target for coherent control. We show that the variation of one-photon ionization probabilities with pulse duration are solely due to spectral effects and thus cannot be coherently controlled. We then discuss for which observables and under which conditions phase control of autoionization dynamics is possible.

Beating spatio-temporal coupling: implications for pulse shaping and coherent control experiments

Diffraction of finite sized laser beams imposes a limit on the control that can be exerted over ultrafast pulses. This limit manifests as spatio-temporal coupling induced in standard implementations of pulse shaping schemes. We demonstrate the influence this has on coherent control experiments that depend on finite excitation, sample, and detection volumes. Based on solutions used in pulse stretching experiments, we introduce a double-pass scheme that reduces the errors produced through spatio-temporal coupling by at least one order of magnitude. Finally, employing single molecules as nanoscale probes, we prove that such a double pass scheme is capable of artifact-free pulse shaping at dimensions two orders of magnitude smaller than the diffraction limit.

Invited article: The coherent optical laser beam recombination technique (COLBERT) spectrometer: coherent multidimensional spectroscopy made easier

We have developed an efficient spectrometer capable of performing a wide variety of coherent multidimensional measurements at optical wavelengths. The two major components of the largely automated device are a spatial beam shaper which controls the beam geometry and a spatiotemporal pulse shaper which controls the temporal waveform of the femtosecond pulse in each beam. We describe how to construct, calibrate, and operate the device, and we discuss its limitations. We use the exciton states of a semiconductor nanostructure as a working example. A series of complex multidimensional spectra-displayed in amplitude and real parts-reveals increasingly intricate correlations among the excitons.

Closed loop coherent control of electronic transitions in gallium arsenide

A genetic algorithm was used to control the photoluminesce-nce (PL) from GaAs(100). A spatial light modulator (SLM) used feedback from the emission to optimize the spectral phase profile of an ultrashort laser pulse. Most of the experiments were performed using a sine phase function to optimize the integrated PL spectrum over a specified wavelength range, with the amplitude and period of the phase function treated as genetic parameters. An order of magnitude increase in signal was achieved after only one generation, and an optimized waveform, consisting of three equally spaced pulses approximately 0.8 ps apart, was obtained after 15 generations. The effects of fluence, polarization, relative phase of the subpulses, and spectral range of the optimized PL were investigated. In addition, preliminary experiments were performed using the phases of individual pixels of the SLM as genetic variables. The PL spectrum is identified with recombination of electron-hole pairs in the L-valley of the Brillouin zone. Control is achieved by coherent manipulation of plasma electrons. It is proposed that hot electrons excite lattice phonons, which in turn scatter carriers into the L-valley.

Why is chemical synthesis and property optimization easier than expected?

Identifying optimal conditions for chemical and material synthesis as well as optimizing the properties of the products is often much easier than simple reasoning would predict. The potential search space is infinite in principle and enormous in practice, yet optimal molecules, materials, and synthesis conditions for many objectives can often be found by performing a reasonable number of distinct experiments. Considering the goal of chemical synthesis or property identification as optimal control problems provides insight into this good fortune. Both of these goals may be described by a fitness function J that depends on a suitable set of variables (e.g., reactant concentrations, components of a material, processing conditions, etc.). The relationship between J and the variables specifies the fitness landscape for the target objective. Upon making simple physical assumptions, this work demonstrates that the fitness landscape for chemical optimization contains no local sub-optimal maxima that may hinder attainment of the absolute best value of J. This feature provides a basis to explain the many reported efficient optimizations of synthesis conditions and molecular or material properties. We refer to this development as OptiChem theory. The predicted characteristics of chemical fitness landscapes are assessed through a broad examination of the recent literature, which shows ample evidence of trap-free landscapes for many objectives. The fundamental and practical implications of OptiChem theory for chemistry are discussed.