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Janković V, Mančal T. Self-consistent approach to the dynamics of excitation energy transfer in multichromophoric systems. J Chem Phys 2024; 161:204108. [PMID: 39589224 DOI: 10.1063/5.0237483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 11/12/2024] [Indexed: 11/27/2024] Open
Abstract
Computationally tractable and reliable, albeit approximate, methods for studying exciton transport in molecular aggregates immersed in structured bosonic environments have been actively developed. Going beyond the lowest-order (Born) approximation for the memory kernel of the quantum master equation typically results in complicated and possibly divergent expressions. Starting from the memory kernel in the Born approximation, and recognizing the quantum master equation as the Dyson equation of Green's functions theory, we formulate the self-consistent Born approximation to resum the memory-kernel perturbation series in powers of the exciton-environment interaction. Our formulation is in the Liouville space and frequency domain and handles arbitrary exciton-environment spectral densities. In a molecular dimer coupled to an overdamped oscillator environment, we conclude that the self-consistent cycle significantly improves the Born-approximation energy-transfer dynamics. The dynamics in the self-consistent Born approximation agree well with the solutions of hierarchical equations of motion over a wide range of parameters, including the most challenging regimes of strong exciton-environment interactions, slow environments, and low temperatures. This is rationalized by the analytical considerations of coherence-dephasing dynamics in the pure-dephasing model. We find that the self-consistent Born approximation is good (poor) at describing energy transfer modulated by an underdamped vibration resonant (off-resonant) with the exciton energy gap. Nevertheless, it reasonably describes exciton dynamics in the seven-site model of the Fenna-Matthews-Olson complex in a realistic environment comprising both an overdamped continuum and underdamped vibrations.
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Affiliation(s)
- Veljko Janković
- Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, 11080 Belgrade, Serbia
| | - Tomáš Mančal
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
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2
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Schultz JD, Yuly JL, Arsenault EA, Parker K, Chowdhury SN, Dani R, Kundu S, Nuomin H, Zhang Z, Valdiviezo J, Zhang P, Orcutt K, Jang SJ, Fleming GR, Makri N, Ogilvie JP, Therien MJ, Wasielewski MR, Beratan DN. Coherence in Chemistry: Foundations and Frontiers. Chem Rev 2024; 124:11641-11766. [PMID: 39441172 DOI: 10.1021/acs.chemrev.3c00643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
Coherence refers to correlations in waves. Because matter has a wave-particle nature, it is unsurprising that coherence has deep connections with the most contemporary issues in chemistry research (e.g., energy harvesting, femtosecond spectroscopy, molecular qubits and more). But what does the word "coherence" really mean in the context of molecules and other quantum systems? We provide a review of key concepts, definitions, and methodologies, surrounding coherence phenomena in chemistry, and we describe how the terms "coherence" and "quantum coherence" refer to many different phenomena in chemistry. Moreover, we show how these notions are related to the concept of an interference pattern. Coherence phenomena are indeed complex, and ambiguous definitions may spawn confusion. By describing the many definitions and contexts for coherence in the molecular sciences, we aim to enhance understanding and communication in this broad and active area of chemistry.
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Affiliation(s)
- Jonathan D Schultz
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jonathon L Yuly
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Eric A Arsenault
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Kelsey Parker
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Sutirtha N Chowdhury
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Reshmi Dani
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Sohang Kundu
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Hanggai Nuomin
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Zhendian Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jesús Valdiviezo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Sección Química, Departamento de Ciencias, Pontificia Universidad Católica del Perú, San Miguel, Lima 15088, Peru
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Kaydren Orcutt
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Bioproducts Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 800 Buchanan Street, Albany, California 94710, United States
| | - Seogjoo J Jang
- Department of Chemistry and Biochemistry, Queens College, City University of New York, Queens, New York 11367, United States
- Chemistry and Physics PhD programs, Graduate Center, City University of New York, New York, New York 10016, United States
| | - Graham R Fleming
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Nancy Makri
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois, Urbana, Illinois 61801, United States
- Illinois Quantum Information Science and Technology Center, University of Illinois, Urbana, Illinois 61801, United States
| | - Jennifer P Ogilvie
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Michael J Therien
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Michael R Wasielewski
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
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Jang SJ. Fourth order expressions for the electronic absorption lineshape of molecular excitons. J Chem Phys 2019; 151:044110. [DOI: 10.1063/1.5100986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Seogjoo J. Jang
- Department of Chemistry and Biochemistry, Queens College, City University of New York, 65-30 Kissena Boulevard, Queens, New York 11367, USA and Ph.D. Programs in Chemistry and Physics, and Initiative for Theoretical Sciences, Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York 10016, USA
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4
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Seah S, Nimmrichter S, Scarani V. Nonequilibrium dynamics with finite-time repeated interactions. Phys Rev E 2019; 99:042103. [PMID: 31108604 DOI: 10.1103/physreve.99.042103] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Indexed: 11/07/2022]
Abstract
We study quantum dynamics in the framework of repeated interactions between a system and a stream of identical probes. We present a coarse-grained master equation that captures the system's dynamics in the natural regime where interactions with different probes do not overlap, but it is otherwise valid for arbitrary values of the interaction strength and mean interaction time. We then apply it to some specific examples. For probes prepared in Gibbs states, such channels have been used to describe thermalization: while this is the case for many choices of parameters, for others one finds out-of-equilibrium states including inverted Gibbs and maximally mixed states. Gapless probes can be interpreted as performing an indirect measurement, and we study the energy transfer associated with this measurement.
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Affiliation(s)
- Stella Seah
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542, Singapore
| | - Stefan Nimmrichter
- Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
| | - Valerio Scarani
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542, Singapore.,Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
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Liu YY, Yan YM, Xu M, Song K, Shi Q. Exact generator and its high order expansions in time-convolutionless generalized master equation: Applications to spin-boson model and excitation energy transfer. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1806146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Xu M, Yan Y, Liu Y, Shi Q. Convergence of high order memory kernels in the Nakajima-Zwanzig generalized master equation and rate constants: Case study of the spin-boson model. J Chem Phys 2018; 148:164101. [DOI: 10.1063/1.5022761] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Meng Xu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaming Yan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanying Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
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Ke Y, Zhao Y. Perturbation expansions of stochastic wavefunctions for open quantum systems. J Chem Phys 2017; 147:184103. [DOI: 10.1063/1.4996737] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yaling Ke
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yi Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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Sun KW, Gelin MF, Chernyak VY, Zhao Y. Davydov Ansatz as an efficient tool for the simulation of nonlinear optical response of molecular aggregates. J Chem Phys 2015; 142:212448. [DOI: 10.1063/1.4921575] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Ke-Wei Sun
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Maxim F. Gelin
- Department of Chemistry, Technische Universität München, Garching D-85747, Germany
| | - Vladimir Y. Chernyak
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - Yang Zhao
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
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Chen L, Gelin MF, Domcke W, Zhao Y. Theory of femtosecond coherent double-pump single-molecule spectroscopy: Application to light harvesting complexes. J Chem Phys 2015; 142:164106. [DOI: 10.1063/1.4919240] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lipeng Chen
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Maxim F. Gelin
- Department of Chemistry, Technische Universität München, Garching D-85747, Germany
| | - Wolfgang Domcke
- Department of Chemistry, Technische Universität München, Garching D-85747, Germany
| | - Yang Zhao
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
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Olšina J, Kramer T, Kreisbeck C, Mančal T. Exact stochastic unraveling of an optical coherence dynamics by cumulant expansion. J Chem Phys 2014; 141:164109. [DOI: 10.1063/1.4898354] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jan Olšina
- Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | - Tobias Kramer
- Mads Clausen Insitute, University of Southern Denmark, 6400 Sønderborg, Denmark
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Christoph Kreisbeck
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Tomáš Mančal
- Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
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Huynh TD, Sun KW, Gelin M, Zhao Y. Polaron dynamics in two-dimensional photon-echo spectroscopy of molecular rings. J Chem Phys 2014; 139:104103. [PMID: 24050324 DOI: 10.1063/1.4820135] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have developed a new approach to the computation of third-order spectroscopic signals of molecular rings, by incorporating the Davydov soliton theory into the nonlinear response function formalism. The Davydov D1 and D Ansätze have been employed to treat the interactions between the excitons and the primary phonons, allowing for a full description of arbitrary exciton-phonon coupling strengths. As an illustration, we have simulated a series of optical 2D spectra for two models of molecular rings.
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Affiliation(s)
- Thanh Duc Huynh
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798
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Mančal T. Excitation energy transfer in a classical analogue of photosynthetic antennae. J Phys Chem B 2013; 117:11282-91. [PMID: 23822554 DOI: 10.1021/jp402101z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We formulate a classical pure dephasing system-bath interaction model in a full correspondence to the well-studied quantum model of natural light-harvesting antennae. The equations of motion of our classical model not only represent the correct classical analogy to the quantum description of excitonic systems, but they also have exactly the same functional form. We demonstrate derivation of classical dissipation and relaxation tensor in second order perturbation theory. We find that the only difference between the classical and quantum descriptions is in the interpretation of the state and in certain limitations imposed on the parameters of the model by classical physics. The effects of delocalization, transfer pathway interference, and the transition from coherent to diffusive transfer can be found already in the classical realm. The only qualitatively new effect occurring in quantum systems is the preference for a downhill energy transfer and the resulting possibility of trapping the energy in the lowest energy state.
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Affiliation(s)
- Tomáš Mančal
- Faculty of Mathematics and Physics, Charles University in Prague , Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
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13
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Pouthier V. The reduced dynamics of an exciton coupled to a phonon bath: A new approach combining the Lang-Firsov transformation and the perturbation theory. J Chem Phys 2013; 138:044108. [DOI: 10.1063/1.4789017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Burghardt I, Martinazzo R, Hughes KH. Non-Markovian reduced dynamics based upon a hierarchical effective-mode representation. J Chem Phys 2012; 137:144107. [DOI: 10.1063/1.4752078] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Thingna J, Wang JS, Hänggi P. Generalized Gibbs state with modified Redfield solution: Exact agreement up to second order. J Chem Phys 2012; 136:194110. [DOI: 10.1063/1.4718706] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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18
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Gelin MF, Sharp LZ, Egorova D, Domcke W. Bath-induced correlations and relaxation of vibronic dimers. J Chem Phys 2012; 136:034507. [DOI: 10.1063/1.3676063] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Gelin MF, Egorova D, Domcke W. Exact quantum master equation for a molecular aggregate coupled to a harmonic bath. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:041139. [PMID: 22181119 DOI: 10.1103/physreve.84.041139] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/04/2011] [Indexed: 05/31/2023]
Abstract
We consider a molecular aggregate consisting of N identical monomers. Each monomer comprises two electronic levels and a single harmonic mode. The monomers interact with each other via dipole-dipole forces. The monomer vibrational modes are bilinearly coupled to a bath of harmonic oscillators. This is a prototypical model for the description of coherent exciton transport, from quantum dots to photosynthetic antennae. We derive an exact quantum master equation for such systems. Computationally, the master equation may be useful for the testing of various approximations employed in theories of quantum transport. Physically, it offers a plausible explanation of the origins of long-lived coherent optical responses of molecular aggregates in dissipative environments.
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Affiliation(s)
- Maxim F Gelin
- Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
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Olšina J, Mančal T. Electronic coherence dephasing in excitonic molecular complexes: Role of Markov and secular approximations. J Mol Model 2010; 16:1765-78. [DOI: 10.1007/s00894-010-0786-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 06/16/2010] [Indexed: 11/29/2022]
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