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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Efficient energy transfer in light-harvesting systems: Quantum-classical comparison, flux network, and robustness analysis

Following the calculation of optimal energy transfer in thermal environment in our first paper [J. L. Wu, F. Liu, Y. Shen, J. S. Cao, and R. J. Silbey, New J. Phys. 12, 105012 (2010)], full quantum dynamics and leading-order 'classical' hopping kinetics are compared in the seven-site Fenna-Matthews-Olson (FMO) protein complex. The difference between these two dynamic descriptions is due to higher-order quantum corrections. Two thermal bath models, classical white noise (the Haken-Strobl-Reineker (HSR) model) and quantum Debye model, are considered. In the seven-site FMO model, we observe that higher-order corrections lead to negligible changes in the trapping time or in energy transfer efficiency around the optimal and physiological conditions (2% in the HSR model and 0.1% in the quantum Debye model for the initial site at BChl 1). However, using the concept of integrated flux, we can identify significant differences in branching probabilities of the energy transfer network between hopping kinetics and quantum dynamics (26% in the HSR model and 32% in the quantum Debye model for the initial site at BChl 1). This observation indicates that the quantum coherence can significantly change the distribution of energy transfer pathways in the flux network with the efficiency nearly the same. The quantum-classical comparison of the average trapping time with the removal of the bottleneck site, BChl 4, demonstrates the robustness of the efficient energy transfer by the mechanism of multi-site quantum coherence. To reconcile with the latest eight-site FMO model which is also investigated in the third paper [J. Moix, J. L. Wu, P. F. Huo, D. F. Coker, and J. S. Cao, J. Phys. Chem. Lett. 2, 3045 (2011)], the quantum-classical comparison with the flux network analysis is summarized in Appendix C. The eight-site FMO model yields similar trapping time and network structure as the seven-site FMO model but leads to a more disperse distribution of energy transfer pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

On the alternatives for bath correlators and spectral densities from mixed quantum-classical simulations

We investigate on the procedure of extracting a 'spectral density' from mixed QM/MM calculations and employing it in open quantum systems models. In particular, we study the connection between the energy gap correlation function extracted from ground state QM/MM and the bath spectral density used as input in open quantum system approaches. We introduce a simple model which can give intuition on when the ground state QM/MM propagation will give the correct energy gap. We also discuss the role of higher order correlators of the energy-gap fluctuations which can provide useful information on the bath. Further, various semiclassical corrections to the spectral density, are applied and investigated. Finally, we apply our considerations to the photosynthetic Fenna-Matthews-Olson complex. For this system, our results suggest the use of the Harmonic prefactor for the spectral density rather than the Standard one, which was employed in the simulations of the system carried out to date.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Geometrical effects on energy transfer in disordered open quantum systems

We explore various design principles for efficient excitation energy transport in complex quantum systems. We investigate energy transfer efficiency in randomly disordered geometries consisting of up to 20 chromophores to explore spatial and spectral properties of small natural/artificial Light-Harvesting Complexes (LHC). We find significant statistical correlations among highly efficient random structures with respect to ground state properties, excitonic energy gaps, multichromophoric spatial connectivity, and path strengths. These correlations can even exist beyond the optimal regime of environment-assisted quantum transport. For random configurations embedded in spatial dimensions of 30 Å or 50 Å, we observe that the transport efficiency saturates to its maximum value if the systems contain around 7 or 14 chromophores, respectively. Remarkably, these optimum values coincide with the number of chlorophylls in the Fenna-Matthews-Olson protein complex and LHC II monomers, respectively, suggesting a potential natural optimization with respect to chromophoric density.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Energy-scales convergence for optimal and robust quantum transport in photosynthetic complexes

Underlying physical principles for the high efficiency of excitation energy transfer in light-harvesting complexes are not fully understood. Notably, the degree of robustness of these systems for transporting energy is not known considering their realistic interactions with vibrational and radiative environments within the surrounding solvent and scaffold proteins. In this work, we employ an efficient technique to estimate energy transfer efficiency of such complex excitonic systems. We observe that the dynamics of the Fenna-Matthews-Olson (FMO) complex leads to optimal and robust energy transport due to a convergence of energy scales among all important internal and external parameters. In particular, we show that the FMO energy transfer efficiency is optimum and stable with respect to important parameters of environmental interactions including reorganization energy λ, bath frequency cutoff γ, temperature T, and bath spatial correlations. We identify the ratio of k{sub B}λT/ℏγ⁢g as a single key parameter governing quantum transport efficiency, where g is the average excitonic energy gap.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Excitation transfer pathways in excitonic aggregates revealed by the stochastic Schrödinger equation

We derive the stochastic Schrödinger equation for the system wave vector and use it to describe the excitation energy transfer dynamics in molecular aggregates. We suggest a quantum-measurement based method of estimating the excitation transfer time. Adequacy of the proposed approach is demonstrated by performing calculations on a model system. The theory is then applied to study the excitation transfer dynamics in a photosynthetic pigment-protein Fenna-Matthews-Olson (FMO) aggregate using both the Debye spectral density and the spectral density obtained from earlier molecular dynamics simulations containing strong vibrational high-frequency modes. The obtained results show that the excitation transfer times in the FMO system are affected by the presence of the vibrational modes; however, the transfer pathways remain the same.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Simulated two-dimensional electronic spectroscopy of the eight-bacteriochlorophyll FMO complex

The Fenna-Matthews-Olson (FMO) protein-pigment complex acts as a molecular wire conducting energy between the outer antenna system and the reaction center; it is an important photosynthetic system to study the transfer of excitonic energy. Recent crystallographic studies report the existence of an additional (eighth) bacteriochlorophyll a (BChl a) in some of the FMO monomers. To understand the functionality of this eighth BChl, we simulated the two-dimensional electronic spectra of both the 7-site (apo form) and the 8-site (holo form) variant of the FMO complex from green sulfur bacteria, Prosthecochloris aestuarii. By comparing the spectrum, it was found that the eighth BChl can affect two different excitonic energy transfer pathways: (1) it is directly involved in the first apo form pathway (6 → 3 → 1) by passing the excitonic energy to exciton 6; and (2) it facilitates an increase in the excitonic wave function overlap between excitons 4 and 5 in the second pathway (7 → 4,5 → 2 → 1) and thus increases the possible downward sampling routes across the BChls.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Extending the applicability of Redfield theories into highly non-Markovian regimes

We present a new, computationally inexpensive method for the calculation of reduced density matrix dynamics for systems with a potentially large number of subsystem degrees of freedom coupled to a generic bath. The approach consists of propagation of weak-coupling Redfield-like equations for the high-frequency bath degrees of freedom only, while the low-frequency bath modes are dynamically arrested but statistically sampled. We examine the improvements afforded by this approximation by comparing with exact results for the spin-boson model over a wide range of parameter space. We further generalize the method to multi-site models and compare with exact results for a model of the Fenna–Matthews–Olson complex. The results from the method are found to dramatically improve Redfield dynamics in highly non-Markovian regimes, at a similar computational cost. Relaxation of the mode-freezing approximation via classical (Ehrenfest) evolution of the low-frequency modes results in a dynamical hybrid method. We find that this Redfield-based dynamical hybrid approach, which is computationally more expensive than bare Redfield dynamics, yields only a marginal improvement over the simpler approximation of complete mode arrest.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Multi-layer multi-configuration time-dependent Hartree (ML-MCTDH) approach to the correlated exciton-vibrational dynamics in the FMO complex

The coupled quantum dynamics of excitonic and vibrational degrees of freedom is investigated for high-dimensional models of the Fenna-Matthews-Olson complex. This includes a seven- and an eight-site model with 518 and 592 harmonic vibrational modes, respectively. The coupling between local electronic transitions and vibrations is described within the Huang-Rhys model using parameters that are obtained by discretization of an experimental spectral density. Different pathways of excitation energy flow are analyzed in terms of the reduced one-exciton density matrix, focussing on the role of vibrational and vibronic excitations. Distinct features due to both competing time scales of vibrational and exciton motion and vibronically assisted transfer are observed. The question of the effect of initial state preparation is addressed by comparing the case of an instantaneous Franck-Condon excitation at a single site with that of a laser field excitation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Near shot-noise limited time-resolved circular dichroism pump-probe spectrometer

We describe an optical near shot-noise limited time-resolved circular dichroism (TRCD) pump-probe spectrometer capable of reliably measuring circular dichroism signals in the order of $\mu$deg with nanosecond time resolution. Such sensitivity is achieved through a modification of existing TRCD designs and introduction of a new data processing protocol that eliminates approximations that have caused substantial nonlinearities in past measurements and allows the measurement of absorption and circular dichroism transients simultaneously with a single pump pulse. The exceptional signal-to-noise ratio of the described setup makes the TRCD technique applicable to a large range of non-biological and biological systems. Finally, the spectrometer was used to record, for the first time, weak TRCD kinetics associated with the triplet state energy transfer in the photosynthetic Fenna-Matthews-Olson antenna pigment-protein complex.

47 OTHER INSTRUMENTATION↗
DOE OSTI2019

A symmetrical quasi-classical windowing model for the molecular dynamics treatment of non-adiabatic processes involving many electronic states

In the previous work of Cotton and Miller [J. Chem. Phys. 145, 144108 (2016)], an improved symmetrical quasi-classical (SQC) windowing model for the molecular dynamics treatment of electronically non-adiabatic processes was developed in order to extend the original SQC approach to the regime of weak-coupling between the electronic states. Furthermore, the improved SQC model—based on triangular-shaped window functions—handled the weak-coupling limit as intended and, as a bonus, was shown to be universally superior to the original square/histogram SQC windowing model over all coupling regimes, but only for treating systems of two electronic states, as no higher-dimensional generalization was evident. This paper, therefore, provides a generalized version for treating an arbitrary number of electronic states. By construction, the benefits of the two-state triangle model—seamless treatment of weak-coupling and improved accuracy in all coupling regimes—carry over to the generalized version. Far more significant, however, is that the new model provides vastly improved windowing statistics in higher dimensions, enabling the SQC simulation of electronically non-adiabatic processes involving many more relevant electronic states than was previously practical. Capabilities are demonstrated with respect to a 24 pigment trimer model of the Fenna-Matthews-Olson light-harvesting complex, as well as treating similar 48- and 96-electronic state model problems, illustrating the scaling properties of the new method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Efficient construction of generalized master equation memory kernels for multi-state systems from nonadiabatic quantum-classical dynamics

Techniques derived from the generalized quantum master equation (GQME) framework have provided the basis for elucidating energy and charge transfer in systems ranging from molecular solids to photosynthetic complexes. Recently, the nonperturbative combination of the GQME with quantum-classical methods has resulted in approaches whose accuracy and efficiency exceed those of the original quantumclassical schemes while offering significant accuracy improvements over perturbative expansions of the GQME. In this work, we show that, while the non-Markovian memory kernel required to propagate the GQME scales quartically with the number of subsystem states, the number of trajectories required scales at most quadratically when using quantum-classical methods to construct the kernel. We then present an algorithm that allows further acceleration of the quantum-classical GQME by offering a way to selectively sample the kernel matrix elements that are most important to the process of interest. We demonstrate the utility of these advances by applying the combination of Ehrenfest mean field theory with the GQME (MF-GQME) to models of the Fenna-Matthews-Olson (FMO) complex and the light harvesting complex II (LHCII), with 7 and 14 states, respectively. This allows us to show that the MF-GQME is able to accurately capture all the relevant dynamical time scales in LHCII: the initial nonequilibrium population transfer on the femtosecond time scale, the steady state-type trapping on the picosecond time scale, and the long time population relaxation. Remarkably, all of these physical effects spanning tens of picoseconds can be encoded in a memory kernel that decays only after ~65 fs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A simple improved low temperature correction for the hierarchical equations of motion

The study of open system quantum dynamics has been transformed by the hierarchical equations of motion (HEOM) method, which gives the exact dynamics for a system coupled to a harmonic bath at arbitrary temperature and system–bath coupling strength. However, in its standard form, this method is only consistent with the weak-coupling quantum master equation at all temperatures when many auxiliary density operators are included in the hierarchy, even when low temperature corrections are included. Here, we propose a new low temperature correction scheme for the termination of the hierarchy based on Zwanzig projection, which alleviates this problem and restores consistency with the weak-coupling master equation with a minimal hierarchy. The utility of the new correction scheme is demonstrated on a range of model systems, including the Fenna–Matthews–Olson complex. The new closure is found to improve convergence of the HEOM even beyond the weak-coupling limit and is very straightforward to implement in existing HEOM codes.

Fay, Thomas P. (ORCID:000000030625731X)↗
DOE OSTI2024

PigmentHunter: A point-and-click application for automated chlorophyll-protein simulations

Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. Yet predicting CP optical and electronic properties remains a serious challenge, driven by the computational difficulty of treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. To address this challenge, we introduce here an analysis tool called PigmentHunter, which automates the process of preparing CP structures for molecular dynamics (MD), running short MD simulations on the nanoHUB.org science gateway, and then using electrostatic and steric analysis routines to predict optical absorption, fluorescence, and circular dichroism spectra within a Frenkel exciton model. Inter-pigment couplings are evaluated using point-dipole or transition-charge coupling models, while site energies can be estimated using both electrostatic and ring-deformation approaches. The package is built in a Jupyter Notebook environment, with a point-and-click interface that can be used either to manually prepare individual structures or to batch-process many structures at once. Here, we illustrate PigmentHunter’s capabilities with example simulations on spectral line shapes in the light harvesting 2 complex, site energies in the Fenna–Matthews–Olson protein, and ring deformation in photosystems I and II.

14 SOLAR ENERGY↗
DOE OSTI2016

Evidence for a cysteine-mediated mechanism of excitation energy regulation in a photosynthetic antenna complex

Significance All photosynthetic organisms face the challenge of absorbing solar energy and regulating its flow through their light-harvesting antennas across widely varying photic conditions. For anoxygenic phototrophs, this process is complicated by the need to downregulate photosynthetic output when oxygen is encountered. The Fenna–Matthews–Olson protein from green sulfur bacteria is able to quench excitations in aerobic conditions effectively despite its apparent lack of photoprotective accessory molecules, indicating a previously unidentified type of energy transfer regulation. In this study, we provide evidence for a novel energy-quenching mechanism involving cysteine–bacteriochlorophyll photochemistry. This interaction should be able to be programed into other natural or bio-inspired antennas, opening new possibilities for regulating these systems in response to excess light.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer

Significance We have revisited the 2D spectroscopy of the excitation energy transfer in the Fenna–Matthews–Olson (FMO) protein. Based on 2D spectroscopic signatures, the energy transfer dynamics in the FMO protein has been argued to be supported by long-lived electronic quantum coherence on timescales up to 1.5 ps. In contrast, our analysis, based on experimental data and confirmed by theoretical calculations, shows that the electronic decoherence occurs within 60 fs, in agreement with typical dephasing times in systems under these conditions. Given the relatively well-defined structure of the FMO protein, and comparative couplings between chlorophylls to other photosynthetic systems, the observed extremely fast decoherence should be viewed as general, bringing to question any significant quantum coherent transport contributions to photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Photosynthesis tunes quantum-mechanical mixing of electronic and vibrational states to steer exciton energy transfer

Significance Photosynthetic light-harvesting antennae transfer energy toward reaction centers with high efficiency, but in high light or oxidative environments, the antennae divert energy to protect the photosynthetic apparatus. For a decade, quantum effects driven by vibronic coupling, where electronic and vibrational states couple, have been suggested to explain the energy transfer efficiency, but questions remain whether quantum effects are merely consequences of molecular systems. Here, we show evidence that biology tunes interpigment vibronic coupling, indicating that the quantum mechanism is operative in the efficient transfer regime and exploited by evolution for photoprotection. Specifically, the Fenna–Matthews–Olson complex uses redox-active cysteine residues to tune the resonance between its excitons and a pigment vibration to steer excess excitation toward a quenching site.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Quantum simulator of an open quantum system using superconducting qubits: exciton transport in photosynthetic complexes

Open quantum system approaches are widely used in the description of physical, chemical and biological systems. A famous example is electronic excitation transfer in the initial stage of photosynthesis, where harvested energy is transferred with remarkably high efficiency to a reaction center. This transport is affected by the motion of a structured vibrational environment, which makes simulations on a classical computer very demanding. Here we propose an analog quantum simulator of complex open system dynamics with a precisely engineered quantum environment. Our setup is based on superconducting circuits, a well established technology. As an example, we demonstrate that it is feasible to simulate exciton transport in the Fenna–Matthews–Olson photosynthetic complex. Our approach allows for a controllable single-molecule simulation and the investigation of energy transfer pathways as well as non-Markovian noise-correlation effects.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Generalized Master Equation with Non-Markovian Multichromophoric Förster Resonance Energy Transfer for Modular Exciton Densities

A generalized master equation (GME) governing quantum evolution of modular exciton density (MED) is derived for large scale light harvesting systems composed of weakly interacting modules of multiple chromophores. The GME-MED offers a practical framework to incorporate real time coherent quantum dynamics calculations of small length scales into dynamics over large length scales, and also provides a non-Markovian generalization and rigorous derivation of the Pauli master equation employing multichromophoric Förster resonance energy transfer rates. A test of the GME-MED for four sites of the Fenna-Matthews-Olson complex demonstrates how coherent dynamics of excitonic populations over coupled chromophores can be accurately described by transitions between subgroups (modules) of delocalized excitons. Application of the GME-MED to the exciton dynamics between a pair of light harvesting complexes in purple bacteria demonstrates its promise as a computationally efficient tool to investigate large scale exciton dynamics in complex environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗