1
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Lorenzoni N, Cho N, Lim J, Tamascelli D, Huelga SF, Plenio MB. Systematic Coarse Graining of Environments for the Nonperturbative Simulation of Open Quantum Systems. PHYSICAL REVIEW LETTERS 2024; 132:100403. [PMID: 38518302 DOI: 10.1103/physrevlett.132.100403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/22/2024] [Accepted: 02/13/2024] [Indexed: 03/24/2024]
Abstract
Conducting precise electronic-vibrational dynamics simulations of molecular systems poses significant challenges when dealing with realistic environments composed of numerous vibrational modes. Here, we introduce a technique for the construction of effective phonon spectral densities that capture accurately open-system dynamics over a finite time interval of interest. When combined with existing nonperturbative simulation tools, our approach can reduce significantly the computational costs associated with many-body open-system dynamics.
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Affiliation(s)
- Nicola Lorenzoni
- Institut für Theoretische Physik und IQST, Albert-Einstein-Allee 11, Universität Ulm, D-89081 Ulm, Germany
| | - Namgee Cho
- Institut für Theoretische Physik und IQST, Albert-Einstein-Allee 11, Universität Ulm, D-89081 Ulm, Germany
| | - James Lim
- Institut für Theoretische Physik und IQST, Albert-Einstein-Allee 11, Universität Ulm, D-89081 Ulm, Germany
| | - Dario Tamascelli
- Institut für Theoretische Physik und IQST, Albert-Einstein-Allee 11, Universität Ulm, D-89081 Ulm, Germany
- Dipartimento di Fisica "Aldo Pontremoli," Università degli Studi di Milano, Via Celoria 16, 20133 Milano, Italy
| | - Susana F Huelga
- Institut für Theoretische Physik und IQST, Albert-Einstein-Allee 11, Universität Ulm, D-89081 Ulm, Germany
| | - Martin B Plenio
- Institut für Theoretische Physik und IQST, Albert-Einstein-Allee 11, Universität Ulm, D-89081 Ulm, Germany
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2
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Dong JY, Kitahama Y, Fujita T, Adachi M, Shigeta Y, Ishizaki A, Tanaka S, Xiao TH, Goda K. Manipulation of photosynthetic energy transfer by vibrational strong coupling. J Chem Phys 2024; 160:045101. [PMID: 38284659 DOI: 10.1063/5.0183383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
Uncovering the mystery of efficient and directional energy transfer in photosynthetic organisms remains a critical challenge in quantum biology. Recent experimental evidence and quantum theory developments indicate the significance of quantum features of molecular vibrations in assisting photosynthetic energy transfer, which provides the possibility of manipulating the process by controlling molecular vibrations. Here, we propose and theoretically demonstrate efficient manipulation of photosynthetic energy transfer by using vibrational strong coupling between the vibrational state of a Fenna-Matthews-Olson (FMO) complex and the vacuum state of an optical cavity. Specifically, based on a full-quantum analytical model to describe the strong coupling effect between the optical cavity and molecular vibration, we realize efficient manipulation of energy transfer efficiency (from 58% to 92%) and energy transfer time (from 20 to 500 ps) in one branch of FMO complex by actively controlling the coupling strength and the quality factor of the optical cavity under both near-resonant and off-resonant conditions, respectively. Our work provides a practical scenario to manipulate photosynthetic energy transfer by externally interfering molecular vibrations via an optical cavity and a comprehensible conceptual framework for researching other similar systems.
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Affiliation(s)
- Jun-Yu Dong
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yasutaka Kitahama
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- LucasLand, Tokyo 101-0052, Japan
| | - Takatoshi Fujita
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Motoyasu Adachi
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Akihito Ishizaki
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
| | - Shigenori Tanaka
- Department of Computational Science, Graduate School of System Informatics, Kobe University, Kobe 657-8501, Japan
| | - Ting-Hui Xiao
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
- Henan Key Laboratory of Diamond Optoelectronic Materials and Devices, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou 450052, China
- Institute of Quantum Materials and Physics, Henan Academy of Sciences, Zhengzhou 450046, China
| | - Keisuke Goda
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- LucasLand, Tokyo 101-0052, Japan
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
- Institute of Technological Sciences, Wuhan University, Hubei 430072, China
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
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3
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Borrelli R, Gelin MF. Finite temperature quantum dynamics of complex systems: Integrating
thermo‐field
theories and
tensor‐train
methods. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1539] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Maxim F. Gelin
- School of Sciences Hangzhou Dianzi University Hangzhou China
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4
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Wang H, Meyer HD. Importance of Appropriately Regularizing the ML-MCTDH Equations of Motion. J Phys Chem A 2021; 125:3077-3087. [DOI: 10.1021/acs.jpca.0c11221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haobin Wang
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217-3364, United States
| | - Hans-Dieter Meyer
- Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany
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5
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Dunnett AJ, Chin AW. Simulating Quantum Vibronic Dynamics at Finite Temperatures With Many Body Wave Functions at 0 K. Front Chem 2021; 8:600731. [PMID: 33505954 PMCID: PMC7831969 DOI: 10.3389/fchem.2020.600731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/24/2020] [Indexed: 11/16/2022] Open
Abstract
For complex molecules, nuclear degrees of freedom can act as an environment for the electronic “system” variables, allowing the theory and concepts of open quantum systems to be applied. However, when molecular system-environment interactions are non-perturbative and non-Markovian, numerical simulations of the complete system-environment wave function become necessary. These many body dynamics can be very expensive to simulate, and extracting finite-temperature results—which require running and averaging over many such simulations—becomes especially challenging. Here, we present numerical simulations that exploit a recent theoretical result that allows dissipative environmental effects at finite temperature to be extracted efficiently from a single, zero-temperature wave function simulation. Using numerically exact time-dependent variational matrix product states, we verify that this approach can be applied to vibronic tunneling systems and provide insight into the practical problems lurking behind the elegance of the theory, such as the rapidly growing numerical demands that can appear for high temperatures over the length of computations.
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Affiliation(s)
- Angus J Dunnett
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, Paris, France
| | - Alex W Chin
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, Paris, France
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6
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Dunnett AJ, Chin AW. Matrix Product State Simulations of Non-Equilibrium Steady States and Transient Heat Flows in the Two-Bath Spin-Boson Model at Finite Temperatures. ENTROPY (BASEL, SWITZERLAND) 2021; 23:E77. [PMID: 33419175 PMCID: PMC7825558 DOI: 10.3390/e23010077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/21/2020] [Accepted: 12/25/2020] [Indexed: 01/01/2023]
Abstract
Simulating the non-perturbative and non-Markovian dynamics of open quantum systems is a very challenging many body problem, due to the need to evolve both the system and its environments on an equal footing. Tensor network and matrix product states (MPS) have emerged as powerful tools for open system models, but the numerical resources required to treat finite-temperature environments grow extremely rapidly and limit their applications. In this study we use time-dependent variational evolution of MPS to explore the striking theory of Tamascelli et al. (Phys. Rev. Lett. 2019, 123, 090402.) that shows how finite-temperature open dynamics can be obtained from zero temperature, i.e., pure wave function, simulations. Using this approach, we produce a benchmark dataset for the dynamics of the Ohmic spin-boson model across a wide range of coupling strengths and temperatures, and also present a detailed analysis of the numerical costs of simulating non-equilibrium steady states, such as those emerging from the non-perturbative coupling of a qubit to baths at different temperatures. Despite ever-growing resource requirements, we find that converged non-perturbative results can be obtained, and we discuss a number of recent ideas and numerical techniques that should allow wide application of MPS to complex open quantum systems.
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Affiliation(s)
- Angus J. Dunnett
- Institut des NanoSciences de Paris, CNRS, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France;
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7
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Mass OA, Wilson CK, Roy SK, Barclay MS, Patten LK, Terpetschnig EA, Lee J, Pensack RD, Yurke B, Knowlton WB. Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds. J Phys Chem B 2020; 124:9636-9647. [PMID: 33052691 DOI: 10.1021/acs.jpcb.0c06480] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Exciton delocalization plays a prominent role in the photophysics of molecular aggregates, ultimately governing their particular function or application. Deoxyribonucleic acid (DNA) is a compelling scaffold in which to template molecular aggregates and promote exciton delocalization. As individual dye molecules are the basis of exciton delocalization in molecular aggregates, their judicious selection is important. Motivated by their excellent photostability and spectral properties, here, we examine the ability of squaraine dyes to undergo exciton delocalization when aggregated via a DNA Holliday junction (HJ) template. A commercially available indolenine squaraine dye was chosen for the study given its strong structural resemblance to Cy5, a commercially available cyanine dye previously shown to undergo exciton delocalization in DNA HJs. Three types of DNA-dye aggregate configurations-transverse dimer, adjacent dimer, and tetramer-were investigated. Signatures of exciton delocalization were observed in all squaraine-DNA aggregates. Specifically, strong blue shift and Davydov splitting were observed in steady-state absorption spectroscopy and exciton-induced features were evident in circular dichroism (CD) spectroscopy. Strongly suppressed fluorescence emission provided additional, indirect evidence for exciton delocalization in the DNA-templated squaraine dye aggregates. To quantitatively evaluate and directly compare the excitonic Coulombic coupling responsible for exciton delocalization, the strength of excitonic hopping interactions between the dyes was obtained by simultaneously fitting the experimental steady-state absorption and CD spectra via a Holstein-like Hamiltonian, in which, following the theoretical approach of Kühn, Renger, and May, the dominant vibrational mode is explicitly considered. The excitonic hopping strength within indolenine squaraines was found to be comparable to that of the analogous Cy5 DNA-templated aggregate. The squaraine aggregates adopted primarily an H-type (dyes oriented parallel to each other) spatial arrangement. Extracted geometric details of the dye mutual orientation in the aggregates enabled a close comparison of aggregate configurations and the elucidation of the influence of dye angular relationship on excitonic hopping interactions in squaraine aggregates. These results encourage the application of squaraine-based aggregates in next-generation systems driven by molecular excitons.
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Affiliation(s)
| | | | | | | | | | - Ewald A Terpetschnig
- SETA BioMedicals, LLC, 2014 Silver Court East, Urbana, Illinois 61801, United States
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8
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Kim CW, Rhee YM. Toward monitoring the dissipative vibrational energy flows in open quantum systems by mixed quantum-classical simulations. J Chem Phys 2020; 152:244109. [PMID: 32610983 DOI: 10.1063/5.0009867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In open quantum system dynamics, rich information about the major energy relaxation channels and corresponding relaxation rates can be elucidated by monitoring the vibrational energy flow among individual bath modes. However, such calculations often become tremendously difficult as the complexity of the subsystem-bath coupling increases. In this paper, we attempt to make this task feasible by using a mixed quantum-classical method, the Poisson-bracket mapping equation with non-Hamiltonian modification (PBME-nH) [H. W. Kim and Y. M. Rhee, J. Chem. Phys. 140, 184106 (2014)]. For a quantum subsystem bilinearly coupled to harmonic bath modes, we derive an expression for the mode energy in terms of the classical positions and momenta of the nuclei, while keeping consistency with the energy of the quantum subsystem. The accuracy of the resulting expression is then benchmarked against a numerically exact method by using relatively simple models. Although our expression predicts a qualitatively correct dissipation rate for a range of situations, cases involving a strong vibronic resonance are quite challenging. This is attributed to the inherent lack of quantum back reaction in PBME-nH, which becomes significant when the subsystem strongly interacts with a small number of bath modes. A rigorous treatment of such an effect will be crucial for developing quantitative simulation methods that can handle generic subsystem-bath coupling.
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Affiliation(s)
- Chang Woo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
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9
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Duan HG, Nalbach P, Miller RJD, Thorwart M. Intramolecular vibrations enhance the quantum efficiency of excitonic energy transfer. PHOTOSYNTHESIS RESEARCH 2020; 144:137-145. [PMID: 32306173 PMCID: PMC7203599 DOI: 10.1007/s11120-020-00742-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
We study the impact of underdamped intramolecular vibrational modes on the efficiency of the excitation energy transfer in a dimer in which each state is coupled to its own underdamped vibrational mode and, in addition, to a continuous background of environmental modes. For this, we use the numerically exact hierarchy equation of motion approach. We determine the quantum yield and the transfer time in dependence of the vibronic coupling strength, and in dependence of the damping of the incoherent background. Moreover, we tune the vibrational frequencies out of resonance with the excitonic energy gap. We show that the quantum yield is enhanced by up to 10% when the vibrational frequency of the donor is larger than at the acceptor. The vibronic energy eigenstates of the acceptor acquire then an increased density of states, which leads to a higher occupation probability of the acceptor in thermal equilibrium. We can conclude that an underdamped vibrational mode which is weakly coupled to the dimer fuels a faster transfer of excitation energy, illustrating that long-lived vibrations can, in principle, enhance energy transfer, without involving long-lived electronic coherence.
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Affiliation(s)
- Hong-Guang Duan
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, 20355, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Peter Nalbach
- Westfälische Hochschule, Münsterstr. 265, 46397, Bocholt, Germany
| | - R J Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
- The Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, M5S 3H6, Canada
| | - Michael Thorwart
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, 20355, Hamburg, Germany.
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany.
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10
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Li W, Ren J, Shuai Z. Numerical assessment for accuracy and GPU acceleration of TD-DMRG time evolution schemes. J Chem Phys 2020; 152:024127. [PMID: 31941314 DOI: 10.1063/1.5135363] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The time dependent density matrix renormalization group (TD-DMRG) has become one of the cutting edge methods of quantum dynamics for complex systems. In this paper, we comparatively study the accuracy of three time evolution schemes in the TD-DMRG, the global propagation and compression method with the Runge-Kutta algorithm (P&C-RK), the time dependent variational principle based methods with the matrix unfolding algorithm (TDVP-MU), and with the projector-splitting algorithm (TDVP-PS), by performing benchmarks on the exciton dynamics of the Fenna-Matthews-Olson complex. We show that TDVP-MU and TDVP-PS yield the same result when the time step size is converged and they are more accurate than P&C-RK4, while TDVP-PS tolerates a larger time step size than TDVP-MU. We further adopt the graphical processing units to accelerate the heavy tensor contractions in the TD-DMRG, and it is able to speed up the TDVP-MU and TDVP-PS schemes by up to 73 times.
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Affiliation(s)
- Weitang Li
- MOE Key Laboratory of Organic Optoelectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, People's Republic of China
| | - Jiajun Ren
- MOE Key Laboratory of Organic Optoelectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, People's Republic of China
| | - Zhigang Shuai
- MOE Key Laboratory of Organic Optoelectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, People's Republic of China
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11
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Chin A, Mangaud E, Chevet V, Atabek O, Desouter-Lecomte M. Visualising the role of non-perturbative environment dynamics in the dissipative generation of coherent electronic motion. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.110392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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12
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Schulze J, Shibl MF, Al-Marri MJ, Kuhn O. High-dimensional exciton-vibrational wave-packet dynamics in the FMO complex. influence of site-specific spectral densities. EPJ WEB OF CONFERENCES 2019. [DOI: 10.1051/epjconf/201920510010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The correlated exciton-vibrational dynamics of the Fenna-Matthews-Olson (FMO) complex is studied using Multi-layer Multi-configuration Time-dependent Hartree (ML-MCTDH) wavepacket propagation. Exciton populations and coherences are shown to be sensitive to the details of the spectral density.
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13
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Sala M, Egorova D. Quantum dynamics of multi-dimensional rhodopsin photoisomerization models: Approximate versus accurate treatment of the secondary modes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Wertnik M, Chin A, Nori F, Lambert N. Optimizing co-operative multi-environment dynamics in a dark-state-enhanced photosynthetic heat engine. J Chem Phys 2018; 149:084112. [PMID: 30193490 DOI: 10.1063/1.5040898] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We analyze the role of coherent, non-perturbative system-bath interactions in a photosynthetic heat engine. Using the reaction-coordinate formalism to describe the vibrational phonon-environment in the engine, we analyze the efficiency around an optimal parameter regime predicted in earlier studies. We show that, in the limit of high-temperature photon irradiation, the phonon-assisted population transfer between bright and dark states is suppressed due to dephasing from the photon environment, even in the Markov limit where we expect the influence of each bath to have an independent and additive effect on the dynamics. Manipulating the phonon bath properties via its spectral density enables us to identify both optimal low- and high-frequency regimes where the suppression can be removed. This suppression of transfer and its removal suggests that it is important to consider carefully the non-perturbative and cooperative effects of system-bath environments in designing artificial photosynthetic systems and also that manipulating inter-environmental interactions could provide a new multidimensional "lever" by which photocells and other types of quantum devices can be optimized.
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Affiliation(s)
- Melina Wertnik
- Theoretical Quantum Physics Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Saitama 351-0198, Japan
| | - Alex Chin
- Institut des NanoSciences de Paris, Sorbonne Université, 4 Place Jussieu, Bote Courrier 840, 75252 Paris Cedex 05, France
| | - Franco Nori
- Theoretical Quantum Physics Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Saitama 351-0198, Japan
| | - Neill Lambert
- Theoretical Quantum Physics Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Saitama 351-0198, Japan
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15
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Affiliation(s)
- Haobin Wang
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217-3364, USA and Beijing Computational Science Research Center, No. 10 East Xibeiwang Road, Haidian District, Beijing 100193, China
| | - Hans-Dieter Meyer
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, D-69120 Heidelberg, Germany
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16
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Wang L, Fujihashi Y, Chen L, Zhao Y. Finite-temperature time-dependent variation with multiple Davydov states. J Chem Phys 2018; 146:124127. [PMID: 28388128 DOI: 10.1063/1.4979017] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Dirac-Frenkel time-dependent variational approach with Davydov Ansätze is a sophisticated, yet efficient technique to obtain an accurate solution to many-body Schrödinger equations for energy and charge transfer dynamics in molecular aggregates and light-harvesting complexes. We extend this variational approach to finite temperature dynamics of the spin-boson model by adopting a Monte Carlo importance sampling method. In order to demonstrate the applicability of this approach, we compare calculated real-time quantum dynamics of the spin-boson model with that from numerically exact iterative quasiadiabatic propagator path integral (QUAPI) technique. The comparison shows that our variational approach with the single Davydov Ansätze is in excellent agreement with the QUAPI method at high temperatures, while the two differ at low temperatures. Accuracy in dynamics calculations employing a multitude of Davydov trial states is found to improve substantially over the single Davydov Ansatz, especially at low temperatures. At a moderate computational cost, our variational approach with the multiple Davydov Ansatz is shown to provide accurate spin-boson dynamics over a wide range of temperatures and bath spectral densities.
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Affiliation(s)
- Lu Wang
- Department of Physics, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Yuta Fujihashi
- Division of Materials Science, Nanyang Technological University, Singapore 639798, Singapore
| | - Lipeng Chen
- Division of Materials Science, Nanyang Technological University, Singapore 639798, Singapore
| | - Yang Zhao
- Division of Materials Science, Nanyang Technological University, Singapore 639798, Singapore
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17
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Reprint of “The effect of site-specific spectral densities on the high-dimensional exciton-vibrational dynamics in the FMO complex”. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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18
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Correlated Protein Environments Drive Quantum Coherence Lifetimes in Photosynthetic Pigment-Protein Complexes. Chem 2018. [DOI: 10.1016/j.chempr.2017.12.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Mendive-Tapia D, Mangaud E, Firmino T, de la Lande A, Desouter-Lecomte M, Meyer HD, Gatti F. Multidimensional Quantum Mechanical Modeling of Electron Transfer and Electronic Coherence in Plant Cryptochromes: The Role of Initial Bath Conditions. J Phys Chem B 2017; 122:126-136. [DOI: 10.1021/acs.jpcb.7b10412] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David Mendive-Tapia
- Institut
Charles Gerhardt Montpellier, UMR 5253, CNRS-UM-ENSCM, CTMM, Université Montpellier, CC 15001, Place Eugène Bataillon, 34095 Montpellier, France
- Theoretische
Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, INF 229, D-69120 Heidelberg, Germany
| | - Etienne Mangaud
- Laboratoire
Collisions Agrégats Réactivité, UMR 5589, IRSAMC, Université Toulouse III Paul Sabatier, F-31062 Toulouse, France
| | - Thiago Firmino
- Laboratoire
de Chimie Physique, CNRS, Université Paris-Sud, Université Paris Saclay, Orsay F-91405, France
| | - Aurélien de la Lande
- Laboratoire
de Chimie Physique, CNRS, Université Paris-Sud, Université Paris Saclay, Orsay F-91405, France
| | - Michèle Desouter-Lecomte
- Laboratoire
de Chimie Physique, CNRS, Université Paris-Sud, Université Paris Saclay, Orsay F-91405, France
| | - Hans-Dieter Meyer
- Theoretische
Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, INF 229, D-69120 Heidelberg, Germany
| | - Fabien Gatti
- Institut
des Sciences Moléculaires d’Orsay, UMR-CNRS 8214, Université Paris-Sud, Université Paris Saclay, Orsay F-91405, France
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20
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Fujihashi Y, Wang L, Zhao Y. Direct evaluation of boson dynamics via finite-temperature time-dependent variation with multiple Davydov states. J Chem Phys 2017; 147:234107. [DOI: 10.1063/1.5017713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yuta Fujihashi
- Division of Materials Science, Nanyang Technological University, Singapore 639798, Singapore
| | - Lu Wang
- Division of Materials Science, Nanyang Technological University, Singapore 639798, Singapore
- Department of Physics, Zhejiang University, Hangzhou 310027, People’s Republic of China
| | - Yang Zhao
- Division of Materials Science, Nanyang Technological University, Singapore 639798, Singapore
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21
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Häse F, Kreisbeck C, Aspuru-Guzik A. Machine learning for quantum dynamics: deep learning of excitation energy transfer properties. Chem Sci 2017; 8:8419-8426. [PMID: 29619189 PMCID: PMC5863613 DOI: 10.1039/c7sc03542j] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 10/23/2017] [Indexed: 12/20/2022] Open
Abstract
Understanding the relationship between the structure of light-harvesting systems and their excitation energy transfer properties is of fundamental importance in many applications including the development of next generation photovoltaics. Natural light harvesting in photosynthesis shows remarkable excitation energy transfer properties, which suggests that pigment-protein complexes could serve as blueprints for the design of nature inspired devices. Mechanistic insights into energy transport dynamics can be gained by leveraging numerically involved propagation schemes such as the hierarchical equations of motion (HEOM). Solving these equations, however, is computationally costly due to the adverse scaling with the number of pigments. Therefore virtual high-throughput screening, which has become a powerful tool in material discovery, is less readily applicable for the search of novel excitonic devices. We propose the use of artificial neural networks to bypass the computational limitations of established techniques for exploring the structure-dynamics relation in excitonic systems. Once trained, our neural networks reduce computational costs by several orders of magnitudes. Our predicted transfer times and transfer efficiencies exhibit similar or even higher accuracies than frequently used approximate methods such as secular Redfield theory.
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Affiliation(s)
- Florian Häse
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , 02138 , USA . ; ; Tel: +1-617-384-8188
| | - Christoph Kreisbeck
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , 02138 , USA . ; ; Tel: +1-617-384-8188
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , 02138 , USA . ; ; Tel: +1-617-384-8188
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22
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Farhat M, Kais S, Alharbi FH. Effect of Time-Delayed Feedback on the Interaction of a Dimer System with its Environment. Sci Rep 2017; 7:15468. [PMID: 29133789 PMCID: PMC5684406 DOI: 10.1038/s41598-017-15185-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/20/2017] [Indexed: 11/09/2022] Open
Abstract
In this work, we report modeling of non-Markovian open quantum systems, consisting of an excitonic dimer that displays memory effect due to time delayed interaction with its environment. We, indeed investigate the effect of these time delays on quantum coherence and excitation dynamical behavior in the time domain generally considered for photosynthetic experiments (few hundred femtoseconds). In particular, we show that the coherence is maintained for periods proportional to time delays. Additionally, if delay is taken into account, coupling to the environment can be tuned to lower values, unlike in previous studies. This kind of intriguing effect can, therefore, when generalized to complete systems, permit more control on the experimental parameters, which may lead to more accurate description of the photosynthetic energy transfer functioning and subsequent applications in artificial photovoltaic research.
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Affiliation(s)
- M Farhat
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.
| | - S Kais
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- Department of Chemistry, Department of Physics and Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - F H Alharbi
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
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23
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Chen L, Borrelli R, Zhao Y. Dynamics of Coupled Electron–Boson Systems with the Multiple Davydov D1 Ansatz and the Generalized Coherent State. J Phys Chem A 2017; 121:8757-8770. [DOI: 10.1021/acs.jpca.7b07069] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lipeng Chen
- Division
of Materials Science, Nanyang Technological University, 639798, Singapore
| | - Raffaele Borrelli
- Department
of Agricultural, Forestry and Food Science, Universitá di Torino, I-10095 Grugliasco, Turin, Italy
| | - Yang Zhao
- Division
of Materials Science, Nanyang Technological University, 639798, Singapore
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24
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Schulze J, Shibl MF, Al-Marri MJ, Kühn O. The effect of site-specific spectral densities on the high-dimensional exciton-vibrational dynamics in the FMO complex. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Borrelli R, Gelin MF. Simulation of Quantum Dynamics of Excitonic Systems at Finite Temperature: an efficient method based on Thermo Field Dynamics. Sci Rep 2017; 7:9127. [PMID: 28831074 PMCID: PMC5567225 DOI: 10.1038/s41598-017-08901-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/18/2017] [Indexed: 11/09/2022] Open
Abstract
Quantum electron-vibrational dynamics in molecular systems at finite temperature is described using an approach based on Thermo Field Dynamics theory. This formulation treats temperature effects in the Hilbert space without introducing the Liouville space. The solution of Thermo Field Dynamics equations with a novel technique for the propagation of Tensor Trains (Matrix Product States) is implemented and discussed. The methodology is applied to the study of the exciton dynamics in the Fenna-Mathews-Olsen complex using a realistic structured spectral density to model the electron-phonon interaction. The results of the simulations highlight the effect of specific vibrational modes on the exciton dynamics and energy transfer process, as well as call for careful modeling of electron-phonon couplings.
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Affiliation(s)
| | - Maxim F Gelin
- Department of Theoretical Chemistry, Technische Universität München, Garching, D-85747, Germany
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26
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Lee MH, Troisi A. Vibronic enhancement of excitation energy transport: Interplay between local and non-local exciton-phonon interactions. J Chem Phys 2017; 146:075101. [DOI: 10.1063/1.4976558] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Myeong H. Lee
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alessandro Troisi
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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27
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Schulze J, Shibl MF, Al-Marri MJ, Kühn O. Multi-layer multi-configuration time-dependent Hartree (ML-MCTDH) approach to the correlated exciton-vibrational dynamics in the FMO complex. J Chem Phys 2017; 144:185101. [PMID: 27179506 DOI: 10.1063/1.4948563] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
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.
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Affiliation(s)
- Jan Schulze
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Mohamed F Shibl
- Gas Processing Center, College of Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mohammed J Al-Marri
- Gas Processing Center, College of Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Oliver Kühn
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
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28
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Vibronic effects and destruction of exciton coherence in optical spectra of J-aggregates: A variational polaron transformation approach. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.06.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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30
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Cysteine-mediated mechanism disrupts energy transfer to prevent photooxidation. Proc Natl Acad Sci U S A 2016; 113:8562-4. [PMID: 27439861 DOI: 10.1073/pnas.1609372113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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31
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Monahan DM, Whaley-Mayda L, Ishizaki A, Fleming GR. Influence of weak vibrational-electronic couplings on 2D electronic spectra and inter-site coherence in weakly coupled photosynthetic complexes. J Chem Phys 2016; 143:065101. [PMID: 26277167 DOI: 10.1063/1.4928068] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Coherence oscillations measured in two-dimensional (2D) electronic spectra of pigment-protein complexes may have electronic, vibrational, or mixed-character vibronic origins, which depend on the degree of electronic-vibrational mixing. Oscillations from intrapigment vibrations can obscure the inter-site coherence lifetime of interest in elucidating the mechanisms of energy transfer in photosynthetic light-harvesting. Huang-Rhys factors (S) for low-frequency vibrations in Chlorophyll and Bacteriochlorophyll are quite small (S ≤ 0.05), so it is often assumed that these vibrations influence neither 2D spectra nor inter-site coherence dynamics. In this work, we explore the influence of S within this range on the oscillatory signatures in simulated 2D spectra of a pigment heterodimer. To visualize the inter-site coherence dynamics underlying the 2D spectra, we introduce a formalism which we call the "site-probe response." By comparing the calculated 2D spectra with the site-probe response, we show that an on-resonance vibration with Huang-Rhys factor as small as S = 0.005 and the most strongly coupled off-resonance vibrations (S = 0.05) give rise to long-lived, purely vibrational coherences at 77 K. We moreover calculate the correlation between optical pump interactions and subsequent entanglement between sites, as measured by the concurrence. At 77 K, greater long-lived inter-site coherence and entanglement appear with increasing S. This dependence all but vanishes at physiological temperature, as environmentally induced fluctuations destroy the vibronic mixing.
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Affiliation(s)
- Daniele M Monahan
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Lukas Whaley-Mayda
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Akihito Ishizaki
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
| | - Graham R Fleming
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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32
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Firmino T, Mangaud E, Cailliez F, Devolder A, Mendive-Tapia D, Gatti F, Meier C, Desouter-Lecomte M, de la Lande A. Quantum effects in ultrafast electron transfers within cryptochromes. Phys Chem Chem Phys 2016; 18:21442-57. [DOI: 10.1039/c6cp02809h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cryptochromes and photolyases are flavoproteins that may undergo ultrafast charge separation upon electronic excitation of their flavin cofactors.
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Affiliation(s)
- Thiago Firmino
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | - Etienne Mangaud
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | - Fabien Cailliez
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | - Adrien Devolder
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
| | | | - Fabien Gatti
- CTMM
- Institut Charles Gerhardt UMR 5253
- CNRS/Université de Montpellier
- France
| | - Christoph Meier
- Laboratoire Collisions Agrégats Réactivité
- UMR 5589
- IRSAMC
- Université Toulouse III Paul Sabatier
- Toulouse
| | | | - Aurélien de la Lande
- Laboratoire de Chimie Physique
- CNRS
- Université Paris-Sud
- Université Paris Saclay
- Orsay F-91405
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