Quantum process tomography of excitonic dimers from two-dimensional electronic spectroscopy. I. General theory and application to homodimers

Yuen-Zhou, Joel; Aspuru‐Guzik, Alán

doi:10.1063/1.3569694

Cited by 57 publications

(65 citation statements)

References 112 publications

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“…In this work, we have shown the application of CS to the calculation of a few types of spectra, but the method most likely can be applied to other quantities as well, such as nonlinear optical response (14,15), magnetic CD (34), semiclassical nuclear dynamics (35), and two-dimensional spectroscopy (36,37). Of course, the method is not limited to atomistic simulations and could be applied to simulations in all scientific fields.…”

Section: Discussionmentioning

confidence: 99%

Application of compressed sensing to the simulation of atomic systems

Andrade

Sanders

Aspuru‐Guzik

2012

Proc. Natl. Acad. Sci. U.S.A.

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Compressed sensing is a method that allows a significant reduction in the number of samples required for accurate measurements in many applications in experimental sciences and engineering. In this work, we show that compressed sensing can also be used to speed up numerical simulations. We apply compressed sensing to extract information from the real-time simulation of atomic and molecular systems, including electronic and nuclear dynamics. We find that, compared to the standard discrete Fourier transform approach, for the calculation of vibrational and optical spectra the total propagation time, and hence the computational cost, can be reduced by approximately a factor of five.sparse signal reconstruction | molecular dynamics | electron dynamics A recent development in the field of data analysis is the compressed sensing (CS) (or compressive sampling) method (1, 2). The foundation of the method is the concept of sparsity: A signal expanded in a certain basis is said to be sparse when most of the expansion coefficients are zero. This extra information can be used by the CS method to significantly reduce the number of measurements needed to reconstruct a signal. CS has been successfully applied to data acquisition in many different areas (3), including the improvement of the resolution of medical magnetic resonance imaging (4) and the experimental study of atomic and quantum systems (5-7).In this article we show that CS can also be an invaluable tool for some numerical simulations with a considerable reduction of the computational cost. We focus on atomistic simulations of nanoscopic systems by using CS to extract frequency-resolved information from real-time methods such as molecular dynamics (MD) and real-time electron dynamics.MD (8, 9) is one of the most widely used methods to study atomistic systems computationally as it can be used to compute many static and dynamical properties. In MD the trajectory of the atomic nuclei is obtained by integrating their equations of motion either with parametrized force fields or else by explicitly modeling the electrons (10). Given the importance of MD, developing methods that can improve the precision and reduce the computational cost of this method, especially for ab initio MD, can have a large impact in the field of atomistic simulation.Real-time electron dynamics, in particular real-time timedependent density functional theory (TDDFT) (11), plays a similarly important role in the study of linear and nonlinear electronic properties (12-15). Because of its scalability and parallelizability, real-time TDDFT is particularly efficient for large electronic systems (16), so an additional reduction in the computational cost can extend the boundaries of the system sizes that can be studied.Many physical properties are represented by frequency-dependent quantities. To obtain these from real-time information, usually a discrete Fourier transform (FT) is used. Our approach is to replace this FT by a calculation of the Fourier coefficients based on the CS method. To obtain a given ...

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Section: Discussionmentioning

confidence: 99%

Application of compressed sensing to the simulation of atomic systems

Andrade

Sanders

Aspuru‐Guzik

2012

Proc. Natl. Acad. Sci. U.S.A.

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“…It thus seems unlikely that the situation in real systems is as restrictive as the simple correlated site energy fluctuation model would suggest and more work both from the experimental and theoretical directions to elucidate the nature of such correlations and their influence on dynamics needs to be done with the aim to begin to design environments that can be self-assembled to take advantage of these correlations as a mechanism to control energy and charge transport in fluctuating nano-structured environments. Powerful new approaches, like quantum process tomography, 52 are in principle capable of combining advanced multidimensional electronic spectroscopies with quantum dynamical theoretical methods to enable extraction of the detailed quantum information necessary to build more realistic models that can accurately parameterize the more general classes of models for correlated fluctuations that we have begun exploring in this paper.…”

Section: Discussionmentioning

confidence: 99%

Influence of environment induced correlated fluctuations in electronic coupling on coherent excitation energy transfer dynamics in model photosynthetic systems

Huo

Coker

2012

The Journal of Chemical Physics

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Two-dimensional photon-echo experiments indicate that excitation energy transfer between chromophores near the reaction center of the photosynthetic purple bacterium Rhodobacter sphaeroides occurs coherently with decoherence times of hundreds of femtoseconds, comparable to the energy transfer time scale in these systems. The original explanation of this observation suggested that correlated fluctuations in chromophore excitation energies, driven by large scale protein motions could result in long lived coherent energy transfer dynamics. However, no significant site energy correlation has been found in recent molecular dynamics simulations of several model light harvesting systems. Instead, there is evidence of correlated fluctuations in site energy-electronic coupling and electronic coupling-electronic coupling. The roles of these different types of correlations in excitation energy transfer dynamics are not yet thoroughly understood, though the effects of site energy correlations have been well studied. In this paper, we introduce several general models that can realistically describe the effects of various types of correlated fluctuations in chromophore properties and systematically study the behavior of these models using general methods for treating dissipative quantum dynamics in complex multi-chromophore systems. The effects of correlation between site energy and inter-site electronic couplings are explored in a two state model of excitation energy transfer between the accessory bacteriochlorophyll and bacteriopheophytin in a reaction center system and we find that these types of correlated fluctuations can enhance or suppress coherence and transfer rate simultaneously. In contrast, models for correlated fluctuations in chromophore excitation energies show enhanced coherent dynamics but necessarily show decrease in excitation energy transfer rate accompanying such coherence enhancement. Finally, for a three state model of the Fenna-Matthews-Olsen light harvesting complex, we explore the influence of including correlations in inter-chromophore couplings between different chromophore dimers that share a common chromophore. We find that the relative sign of the different correlations can have profound influence on decoherence time and energy transfer rate and can provide sensitive control of relaxation in these complex quantum dynamical open systems.

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“…As we show next, 2d echo-spectra are not directly derivable from population dynamics and carry along additional information about the exciton dynamics [35]. To demonstrate this, we calculate the exciton-dynamics for the spectral densities J 11peaks (J 3peaks ) shown in Fig.…”

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confidence: 99%

Long-Lived Electronic Coherence in Dissipative Exciton Dynamics of Light-Harvesting Complexes

Kreisbeck

Kramer

2012

J. Phys. Chem. Lett.

236

320

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The observed prevalence of oscillatory signals in the spectroscopy of biological light-harvesting complexes at ambient temperatures has led to a search for mechanisms supporting coherent transport through larger molecules in noisy environments. We demonstrate a generic mechanism supporting long-lasting electronic coherence up to 0.3 ps at a temperature of 277 K. The mechanism relies on two properties of the spectral density: (i) a large dissipative coupling to a continuum of higherfrequency vibrations required for efficient transport and (ii) a small slope of the spectral density at zero frequency.PACS numbers: 03.65. Yz, 78.47.nj, 05.60.Gg Long-lasting oscillatory signals in optically excited light-harvesting complexes (LHCs) point towards the prevalence of a coherent electronic dynamics in molecular networks at physiological temperatures [2][3][4][5]. The experiments probe the electronic dynamics using twodimensional (2d) echo-spectroscopy for a series of delaytimes between the excitation pulse and the probe pulse. The 2d spectroscopy makes studies of the dynamics of dissipative systems possible and has found further applications in mesoscopic systems such as molecular nanotubes [6] and semiconductor devices [7]. Due to its known crystallographic structure and relative simplicity, the Fenna-Matthews-Olson (FMO) complex serves as the prototype system for studying the choreography of the energy transfer from the antenna to the reaction center of a light harvesting complex [8]. In 2d spectra long-lasting beatings are observed, ranging from 1.2 ps at T = 150 K to 0.3 ps at T = 277 K [9]. The interplay of coherent dynamics, which leads to a delocalization of an initial excitation arriving at the FMO network from the antenna, and the coupling to a vibronic environment with slow and fast fluctuations, has lead to studies of environmentally assisted transport in LHCs [10,11].An important open question is whether coherence plays a key-role in the functioning of light-harvesting complexes [8]. The theoretical understanding of the experiments is in its early stages and atomistic simulations based on molecular dynamics have not reached agreement [12,13]. A calculation of 2d echo-spectra based on the molecular dynamics simulation [14] does not show clear coherent oscillations at T = 277 K. One key ingredient for efficient transfer dynamics is the strong coupling to vibronic modes, which induces energy dissipation [10,11,15]. For the FMO complex the thermalization occurs within picoseconds and was observed by Brixner et al. by the decay of diagonal-peak amplitudes to lower energies [16]. It has been proposed that the inclusion of the finite time scale of the reorganization process gives rise to long-lasting coherence in LHCs [17]. While a sluggish bath relaxation leads to prolonged population beatings in the FMO network, calculations of 2d echo-spectra show oscillations of the exciton cross-peaks for only about 1/6th of the experimentally recorded time at T = 150 K [18]. For an even longer bath-relaxation cross-peak osci...

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Quantum process tomography of excitonic dimers from two-dimensional electronic spectroscopy. I. General theory and application to homodimers

Cited by 57 publications

References 112 publications

Application of compressed sensing to the simulation of atomic systems

Application of compressed sensing to the simulation of atomic systems

Influence of environment induced correlated fluctuations in electronic coupling on coherent excitation energy transfer dynamics in model photosynthetic systems

Long-Lived Electronic Coherence in Dissipative Exciton Dynamics of Light-Harvesting Complexes

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