1
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Sharma D, Bose A. Impact of Loss Mechanisms on Linear Spectra of Excitonic and Polaritonic Aggregates. J Chem Theory Comput 2024; 20:9522-9532. [PMID: 39401084 DOI: 10.1021/acs.jctc.4c00825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2024]
Abstract
The presence of loss mechanisms governed by empirical timescales can profoundly affect the dynamics in molecular systems, leading to changes in their spectra. However, incorporation of these effects along with the system's interaction with the thermal dissipative environments proves to be challenging. In this work, we demonstrate the possibility of utilizing the recently developed path integral Lindblad dynamics (PILD) method to study the linear spectra of molecular aggregates. PILD presents a uniquely powerful simulation technique for retaining the effects of the vibrations in a numerically exact manner through the Feynman-Vernon influence functional while incorporating the effects of losses in an empirical manner using the Lindbald master equation. As illustrations of this technique, we provide examples taken from chiral excitonic and polaritonic aggregates for which we simulate both the absorption spectra and circular dichroism (CD) spectra. We demonstrate that the effect of loss on particular states can differ not just on the basis of the symmetries of the state but also on the basis of complicated "interactions" of the structured dissipative environments with the system and its loss mechanisms. Due to the different selection rules between the absorption and CD spectra and the relative intensities and broadening of the peaks, the two linear spectra together give an interesting insight into the contributions of the various eigenstates to the correlation functions. While the focus here is on linear spectroscopy, it should be possible in the future to use PILD to study multidimensional spectra under loss mechanisms as well.
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Affiliation(s)
- Devansh Sharma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Amartya Bose
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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2
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Cai X, Feng Y, Ren J, Peng Y, Zheng Y. Quantum decoherence dynamics in stochastically fluctuating environments. J Chem Phys 2024; 161:044106. [PMID: 39041876 DOI: 10.1063/5.0217863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
We theoretically study the decoherence of a two-level quantum system coupled to noisy environments exhibiting linear and quadratic fluctuations within the framework of a stochastic Liouville equation. It is shown that the intrinsic energy levels of the quantum system renormalize under either the linear or quadratic influence of the environmental noise. In the case of quadratic dependence, the renormalization of the energy levels of the system emerges even if the environmental noise exhibits stationary statistical properties. This is in contrast to the case under linear influence, where the intrinsic energy levels of the system renormalize only if the environmental noise displays nonstationary statistics. We derive the analytical expressions of the decoherence function in the cases where the fluctuation of the frequency difference depends linearly and quadratically on the nonstationary Ornstein-Uhlenbeck noise (OUN) and random telegraph noise (RTN) processes, respectively. In the case of the linear dependence of the OUN, the environmental nonstationary statistical property can enhance the dynamical decoherence. However, the nonstationary statistics of the environmental noise can suppress the quantum decoherence in this case under the quadratic influence of the OUN. In the presence of the RTN, the quadratic influence of the environmental noise does not give rise to decoherence but only causes a determinate frequency renormalization in dynamical evolution. The environmental nonstationary statistical property can suppress the quantum decoherence of the case under the linear influence of the RTN.
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Affiliation(s)
- Xiangji Cai
- School of Science, Shandong Jianzhu University, Jinan 250101, China
| | - Yanyan Feng
- School of Science, Shandong Jianzhu University, Jinan 250101, China
| | - Jing Ren
- School of Science, Shandong Jianzhu University, Jinan 250101, China
| | - Yonggang Peng
- School of Physics, Shandong University, Jinan 250100, China
| | - Yujun Zheng
- School of Physics, Shandong University, Jinan 250100, China
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3
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London N, Bu S, Johnson B, Ananth N. Mean-Field Ring Polymer Rates Using a Population Dividing Surface. J Phys Chem A 2024; 128:5730-5739. [PMID: 38976564 DOI: 10.1021/acs.jpca.4c00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Mean-field ring polymer molecular dynamics offers a computationally efficient method for the simulation of reaction rates in multilevel systems. Previous work has established that, to model a nonadiabatic state-to-state reaction accurately, it is necessary to ensure reactive trajectories form kinked ring polymer configurations at the dividing surface. Building on this idea, we introduce a population difference coordinate and a reactive flux expression modified to only include contributions from kinked configurations. We test the accuracy of the resulting mean-field rate theory on a series of linear vibronic coupling model systems. We demonstrate that this new kMF-RP rate approach is efficient to implement and quantitatively accurate for models over a wide range of driving forces, coupling strengths, and temperatures.
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Affiliation(s)
- Nathan London
- Department of Chemistry, Cornell University, Ithaca, New York 14853, United States
| | - Siyu Bu
- Department of Chemistry, Cornell University, Ithaca, New York 14853, United States
| | - Britta Johnson
- Department of Chemistry, Cornell University, Ithaca, New York 14853, United States
| | - Nandini Ananth
- Department of Chemistry, Cornell University, Ithaca, New York 14853, United States
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4
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Koyanagi S, Tanimura Y. Classical and quantum thermodynamics described as a system-bath model: The dimensionless minimum work principle. J Chem Phys 2024; 160:234112. [PMID: 38904216 DOI: 10.1063/5.0205771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024] Open
Abstract
We formulate a thermodynamic theory applicable to both classical and quantum systems. These systems are depicted as thermodynamic system-bath models capable of handling isothermal, isentropic, thermostatic, and entropic processes. Our approach is based on the use of a dimensionless thermodynamic potential expressed as a function of the intensive and extensive thermodynamic variables. Using the principles of dimensionless minimum work and dimensionless maximum entropy derived from quasi-static changes of external perturbations and temperature, we obtain the Massieu-Planck potentials as entropic potentials and the Helmholtz-Gibbs potentials as free energy. These potentials can be interconverted through time-dependent Legendre transformations. Our results are verified numerically for an anharmonic Brownian system described in phase space using the low-temperature quantum Fokker-Planck equations in the quantum case and the Kramers equation in the classical case, both developed for the thermodynamic system-bath model. Thus, we clarify the conditions for thermodynamics to be valid even for small systems described by Hamiltonians and establish a basis for extending thermodynamics to non-equilibrium conditions.
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Affiliation(s)
- Shoki Koyanagi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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5
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Warman H, Slocombe L, Sacchi M. How proton transfer impacts hachimoji DNA. RSC Adv 2023; 13:13384-13396. [PMID: 37143915 PMCID: PMC10152326 DOI: 10.1039/d3ra00983a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/23/2023] [Indexed: 05/06/2023] Open
Abstract
Hachimoji DNA is a synthetic nucleic acid extension of DNA, formed by an additional four bases, Z, P, S, and B, that can encode information and sustain Darwinian evolution. In this paper, we aim to look into the properties of hachimoji DNA and investigate the probability of proton transfer between the bases, resulting in base mismatch under replication. First, we present a proton transfer mechanism for hachimoji DNA, analogous to the one presented by Löwdin years prior. Then, we use density functional theory to calculate proton transfer rates, tunnelling factors and the kinetic isotope effect in hachimoji DNA. We determined that the reaction barriers are sufficiently low that proton transfer is likely to occur even at biological temperatures. Furthermore, the rates of proton transfer of hachimoji DNA are much faster than in Watson-Crick DNA due to the barrier for Z-P and S-B being 30% lower than in G-C and A-T. Suggesting that proton transfer occurs more frequently in hachimoji DNA than canonical DNA, potentially leading to a higher mutation rate.
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Affiliation(s)
- Harry Warman
- School of Physics and Maths, University of Surrey Guildford GU2 7XH UK
| | - Louie Slocombe
- School of Chemistry and Chemical Engineering, University of Surrey Guildford GU2 7XH UK
| | - Marco Sacchi
- School of Chemistry and Chemical Engineering, University of Surrey Guildford GU2 7XH UK
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6
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Prada A, Pós ES, Althorpe SC. Comparison of Matsubara dynamics with exact quantum dynamics for an oscillator coupled to a dissipative bath. J Chem Phys 2023; 158:114106. [PMID: 36948794 DOI: 10.1063/5.0138250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
We report the first numerical calculations in which converged Matsubara dynamics is compared directly with exact quantum dynamics with no artificial damping of the time-correlation functions (TCFs). The system treated is a Morse oscillator coupled to a harmonic bath. We show that, when the system-bath coupling is sufficiently strong, the Matsubara calculations can be converged by explicitly including up to M = 200 Matsubara modes, with the remaining modes included as a harmonic "tail" correction. The resulting Matsubara TCFs are in near-perfect agreement with the exact quantum TCFs, for non-linear as well as linear operators, at a temperature at which the TCFs are dominated by quantum thermal fluctuations. These results provide compelling evidence that incoherent classical dynamics can arise in the condensed phase at temperatures at which the statistics are dominated by quantum (Boltzmann) effects, as a result of smoothing of imaginary-time Feynman paths. The techniques developed here may also lead to efficient methods for benchmarking system-bath dynamics in the overdamped regime.
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Affiliation(s)
- Adam Prada
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Eszter S Pós
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Stuart C Althorpe
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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7
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Chen ZH, Wang Y, Xu RX, Yan Y. Open quantum systems with nonlinear environmental backactions: Extended dissipaton theory vs core-system hierarchy construction. J Chem Phys 2023; 158:074102. [PMID: 36813728 DOI: 10.1063/5.0134700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In this paper, we present a comprehensive account of quantum dissipation theories with the quadratic environment couplings. The theoretical development includes the Brownian solvation mode embedded hierarchical quantum master equations, a core-system hierarchy construction that verifies the extended dissipaton equation of motion (DEOM) formalism [R. X. Xu et al., J. Chem. Phys. 148, 114103 (2018)]. Developed are also the quadratic imaginary-time DEOM for equilibrium and the λ(t)-DEOM for nonequilibrium thermodynamics problems. Both the celebrated Jarzynski equality and Crooks relation are accurately reproduced, which, in turn, confirms the rigorousness of the extended DEOM theories. While the extended DEOM is more numerically efficient, the core-system hierarchy quantum master equation is favorable for "visualizing" the correlated solvation dynamics.
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Affiliation(s)
- Zi-Hao Chen
- Hefei National Research Center for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yao Wang
- Hefei National Research Center for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Rui-Xue Xu
- Hefei National Research Center for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - YiJing Yan
- Hefei National Research Center for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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8
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Takahashi H, Tanimura Y. Discretized hierarchical equations of motion in mixed Liouville-Wigner space for two-dimensional vibrational spectroscopies of liquid water. J Chem Phys 2023; 158:044115. [PMID: 36725520 DOI: 10.1063/5.0135725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A model of a bulk water system describing the vibrational motion of intramolecular and intermolecular modes is constructed, enabling analysis of its linear and nonlinear vibrational spectra as well as the energy transfer processes between the vibrational modes. The model is described as a system of four interacting anharmonic oscillators nonlinearly coupled to their respective heat baths. To perform a rigorous numerical investigation of the non-Markovian and nonperturbative quantum dissipative dynamics of the model, we derive discretized hierarchical equations of motion in mixed Liouville-Wigner space, with Lagrange-Hermite mesh discretization being employed in the Liouville space of the intramolecular modes and Lagrange-Hermite mesh discretization and Hermite discretization in the Wigner space of the intermolecular modes. One-dimensional infrared and Raman spectra and two-dimensional terahertz-infrared-visible and infrared-infrared-Raman spectra are computed as demonstrations of the quantum dissipative description provided by our model.
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Affiliation(s)
- Hideaki Takahashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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9
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Fay TP. A simple improved low temperature correction for the hierarchical equations of motion. J Chem Phys 2022; 157:054108. [DOI: 10.1063/5.0100365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
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 the 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-Metthews-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.
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Affiliation(s)
- Thomas Patrick Fay
- Department of Chemistry, University of California Berkeley Department of Chemistry, United States of America
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10
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Xing T, Li T, Yan Y, Bai S, Shi Q. Application of the imaginary time hierarchical equations of motion method to calculate real time correlation functions. J Chem Phys 2022; 156:244102. [DOI: 10.1063/5.0095790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We investigate the application of the imaginary time hierarchical equations of motion method to calculate real time quantum correlation functions. By starting from the path integral expression for the correlated system–bath equilibrium state, we first derive a new set of equations that decouple the imaginary time propagation and the calculation of auxiliary density operators. The new equations, thus, greatly simplify the calculation of the equilibrium correlated initial state that is subsequently used in the real time propagation to obtain the quantum correlation functions. It is also shown that a periodic decomposition of the bath imaginary time correlation function is no longer necessary in the new equations such that different decomposition schemes can be explored. The applicability of the new method is demonstrated in several numerical examples, including the spin-Boson model, the Holstein model, and the double-well model for proton transfer reaction.
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Affiliation(s)
- Tao Xing
- 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
| | - Tianchu Li
- 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
| | - Shuming Bai
- 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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11
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Ikeda T, Nakayama A. Collective bath coordinate mapping of "hierarchy" in hierarchical equations of motion. J Chem Phys 2022; 156:104104. [DOI: 10.1063/5.0082936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Akira Nakayama
- Department of Chemical System Engineering, University of Tokyo, Japan
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12
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Computational Characterization of Nanosystems. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2111233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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13
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Liu Y, Yan Y, Xing T, Shi Q. Understanding the Large Kinetic Isotope Effect of Hydrogen Tunneling in Condensed Phases by Using Double-Well Model Systems. J Phys Chem B 2021; 125:5959-5970. [PMID: 34033714 DOI: 10.1021/acs.jpcb.1c02851] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, many experiments have shown large kinetic isotope effects (KIEs) for hydrogen transfer reactions in condensed phases as evidence of strong quantum tunneling effects. Since accurate calculation of the tunneling dynamics in such systems still present significant challenges, previous studies have employed different types of approximations to estimate the tunneling effects and KIEs. In this work, by employing model systems consisting of a double-well coupled to a harmonic bath, we calculate the tunneling effects and KIEs using the numerically exact hierarchical equations of motion (HEOM) method. It is found that hydrogen and deuterium transfer reactions in the same system may show rather different behaviors, where hydrogen transfer is dominated by tunneling between the two lowest vibrational states and deuterium transfer is controlled by excited vibrational states close to the barrier top. The simulation results are also used to test the validity of various approximate methods. It is shown that the Wolynes theory of dissipative tunneling gives a good estimation of rate constants in the over-the-barrier regime, while the nonadiabatic reaction rate theory based on the Landau-Zener formula is more suitable for deep tunneling reactions.
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Affiliation(s)
- 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.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, 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.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
| | - Tao Xing
- 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.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, 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.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
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14
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Gelin MF, Borrelli R, Chen L. Hierarchical Equations-of-Motion Method for Momentum System-Bath Coupling. J Phys Chem B 2021; 125:4863-4873. [PMID: 33929205 PMCID: PMC8279550 DOI: 10.1021/acs.jpcb.1c02431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For a broad class of quantum models of practical interest, we demonstrate that the Hamiltonian of the system nonlinearly coupled to a harmonic bath through the system and bath coordinates can be equivalently mapped into the Hamiltonian of the system bilinearly coupled to the bath through the system and bath momenta. We show that the Hamiltonian with bilinear system-bath momentum coupling can be treated by the hierarchical equations-of-motion (HEOM) method and present the corresponding proof-of-principle simulations. The developed methodology creates the opportunity to scrutinize a new family of nonlinear quantum systems by the numerically accurate HEOM method.
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Affiliation(s)
- Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | | | - Lipeng Chen
- Max Planck Institute for the Physics of Complex Systems, D-01187 Dresden, Germany
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15
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Cainelli M, Tanimura Y. Exciton transfer in organic photovoltaic cells: A role of local and nonlocal electron–phonon interactions in a donor domain. J Chem Phys 2021; 154:034107. [DOI: 10.1063/5.0036590] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mauro Cainelli
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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16
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Tanimura Y. Numerically "exact" approach to open quantum dynamics: The hierarchical equations of motion (HEOM). J Chem Phys 2021; 153:020901. [PMID: 32668942 DOI: 10.1063/5.0011599] [Citation(s) in RCA: 184] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
An open quantum system refers to a system that is further coupled to a bath system consisting of surrounding radiation fields, atoms, molecules, or proteins. The bath system is typically modeled by an infinite number of harmonic oscillators. This system-bath model can describe the time-irreversible dynamics through which the system evolves toward a thermal equilibrium state at finite temperature. In nuclear magnetic resonance and atomic spectroscopy, dynamics can be studied easily by using simple quantum master equations under the assumption that the system-bath interaction is weak (perturbative approximation) and the bath fluctuations are very fast (Markovian approximation). However, such approximations cannot be applied in chemical physics and biochemical physics problems, where environmental materials are complex and strongly coupled with environments. The hierarchical equations of motion (HEOM) can describe the numerically "exact" dynamics of a reduced system under nonperturbative and non-Markovian system-bath interactions, which has been verified on the basis of exact analytical solutions (non-Markovian tests) with any desired numerical accuracy. The HEOM theory has been used to treat systems of practical interest, in particular, to account for various linear and nonlinear spectra in molecular and solid state materials, to evaluate charge and exciton transfer rates in biological systems, to simulate resonant tunneling and quantum ratchet processes in nanodevices, and to explore quantum entanglement states in quantum information theories. This article presents an overview of the HEOM theory, focusing on its theoretical background and applications, to help further the development of the study of open quantum dynamics.
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Affiliation(s)
- Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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17
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Sakamoto S, Tanimura Y. Numerically "exact" simulations of entropy production in the fully quantum regime: Boltzmann entropy vs von Neumann entropy. J Chem Phys 2020; 153:234107. [PMID: 33353341 DOI: 10.1063/5.0033664] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a scheme to evaluate thermodynamic variables for a system coupled to a heat bath under a time-dependent external force using the quasi-static Helmholtz energy from the numerically "exact" hierarchical equations of motion (HEOM). We computed the entropy produced by a spin system strongly coupled to a non-Markovian heat bath for various temperatures. We showed that when changes to the external perturbation occurred sufficiently slowly, the system always reached thermal equilibrium. Thus, we calculated the Boltzmann entropy and the von Neumann entropy for an isothermal process, as well as various thermodynamic variables, such as changes in internal energies, heat, and work, for a system in quasi-static equilibrium based on the HEOM. We found that although the characteristic features of the system entropies in the Boltzmann and von Neumann cases as a function of the system-bath coupling strength are similar, those for the total entropy production are completely different. The total entropy production in the Boltzmann case is always positive, whereas that in the von Neumann case becomes negative if we chose a thermal equilibrium state of the total system (an unfactorized thermal equilibrium state) as the initial state. This is because the total entropy production in the von Neumann case does not properly take into account the contribution of the entropy from the system-bath interaction. Thus, the Boltzmann entropy must be used to investigate entropy production in the fully quantum regime. Finally, we examined the applicability of the Jarzynski equality.
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Affiliation(s)
- Souichi Sakamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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18
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Poudel H, Reid KM, Yamato T, Leitner DM. Energy Transfer across Nonpolar and Polar Contacts in Proteins: Role of Contact Fluctuations. J Phys Chem B 2020; 124:9852-9861. [PMID: 33107736 DOI: 10.1021/acs.jpcb.0c08091] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Molecular dynamics simulations of the villin headpiece subdomain HP36 have been carried out to examine relations between rates of vibrational energy transfer across non-covalently bonded contacts and equilibrium structural fluctuations, with focus on van der Waals contacts. Rates of energy transfer across van der Waals contacts vary inversely with the variance of the contact length, with the same constant of proportionality for all nonpolar contacts of HP36. A similar relation is observed for hydrogen bonds, but the proportionality depends on contact pairs, with hydrogen bonds stabilizing the α-helices all exhibiting the same constant of proportionality, one that is distinct from those computed for other polar contacts. Rates of energy transfer across van der Waals contacts are found to be up to 2 orders of magnitude smaller than rates of energy transfer across polar contacts.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Korey M Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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19
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Zhang J, Borrelli R, Tanimura Y. Proton tunneling in a two-dimensional potential energy surface with a non-linear system–bath interaction: Thermal suppression of reaction rate. J Chem Phys 2020; 152:214114. [DOI: 10.1063/5.0010580] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Jiaji Zhang
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Raffaele Borrelli
- DISAFA, University of Torino, Largo Paolo Braccini 2, I-10095 Grugliasco, Italy
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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20
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Zhang HD, Cui L, Gong H, Xu RX, Zheng X, Yan Y. Hierarchical equations of motion method based on Fano spectrum decomposition for low temperature environments. J Chem Phys 2020; 152:064107. [PMID: 32061227 DOI: 10.1063/1.5136093] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hierarchical equations of motion (HEOM) method has become one of the most popular methods for the studies of the open quantum system. However, its applicability to systems at ultra-low temperatures is largely restrained by the enormous computational cost, which is caused by the numerous exponential functions required to accurately characterize the non-Markovian memory of the reservoir environment. To overcome this problem, a Fano spectrum decomposition (FSD) scheme has been proposed recently [Cui et al., J. Chem. Phys. 151, 024110 (2019)], which expands the reservoir correlation functions using polynomial-exponential functions and hence greatly reduces the size of the memory basis set. In this work, we explicitly establish the FSD-based HEOM formalisms for both bosonic and fermionic environments. The accuracy and efficiency of the FSD-based HEOM are exemplified by the calculated low-temperature dissipative dynamics of a spin-boson model and the dynamic and static properties of a single-orbital Anderson impurity model in the Kondo regime. The encouraging numerical results highlight the practicality and usefulness of the FSD-based HEOM method for general open systems at ultra-low temperatures.
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Affiliation(s)
- Hou-Dao Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Lei Cui
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hong Gong
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Rui-Xue Xu
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiao Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - YiJing Yan
- Hefei National Laboratory for Physical Sciences at the Microscale, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
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21
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Erpenbeck A, Thoss M. Hierarchical quantum master equation approach to vibronic reaction dynamics at metal surfaces. J Chem Phys 2019; 151:191101. [DOI: 10.1063/1.5128206] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. Erpenbeck
- Institute of Physics, Albert-Ludwig University Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany
| | - M. Thoss
- Institute of Physics, Albert-Ludwig University Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany
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22
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Iwamoto Y, Tanimura Y. Open quantum dynamics of a three-dimensional rotor calculated using a rotationally invariant system-bath Hamiltonian: Linear and two-dimensional rotational spectra. J Chem Phys 2019; 151:044105. [DOI: 10.1063/1.5108609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yuki Iwamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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23
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Rahman H, Kleinekathöfer U. Chebyshev hierarchical equations of motion for systems with arbitrary spectral densities and temperatures. J Chem Phys 2019; 150:244104. [PMID: 31255062 DOI: 10.1063/1.5100102] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The time evolution in open quantum systems, such as a molecular aggregate in contact with a thermal bath, still poses a complex and challenging problem. The influence of the thermal noise can be treated using a plethora of schemes, several of which decompose the corresponding correlation functions in terms of weighted sums of exponential functions. One such scheme is based on the hierarchical equations of motion (HEOM), which is built using only certain forms of bath correlation functions. In the case where the environment is described by a complex spectral density or is at a very low temperature, approaches utilizing the exponential decomposition become very inefficient. Here, we utilize an alternative decomposition scheme for the bath correlation function based on Chebyshev polynomials and Bessel functions to derive a HEOM approach up to an arbitrary order in the environmental coupling. These hierarchical equations are similar in structure to the popular exponential HEOM scheme, but are formulated using the derivatives of the Bessel functions. The proposed scheme is tested up to the fourth order in perturbation theory for a two-level system and compared to benchmark calculations for the case of zero-temperature quantum Ohmic and super-Ohmic noise. Furthermore, the benefits and shortcomings of the present Chebyshev-based hierarchical equations are discussed.
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Affiliation(s)
- Hasan Rahman
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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24
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Ridley M, Gull E, Cohen G. Lead geometry and transport statistics in molecular junctions. J Chem Phys 2019; 150:244107. [DOI: 10.1063/1.5096244] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michael Ridley
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
- The Raymond and Beverley Sackler Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Emanuel Gull
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, USA
| | - Guy Cohen
- School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
- The Raymond and Beverley Sackler Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel
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25
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Hartmann R, Werther M, Grossmann F, Strunz WT. Exact open quantum system dynamics: Optimal frequency vs time representation of bath correlations. J Chem Phys 2019; 150:234105. [PMID: 31228905 DOI: 10.1063/1.5097158] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Richard Hartmann
- Max-Planck-Institut für Physik Komplexer Systeme, Nöthnitzer Str. 38, D-01187 Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Michael Werther
- Max-Planck-Institut für Physik Komplexer Systeme, Nöthnitzer Str. 38, D-01187 Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Frank Grossmann
- Institut für Theoretische Physik, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Walter T. Strunz
- Institut für Theoretische Physik, Technische Universität Dresden, D-01062 Dresden, Germany
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26
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Dunn IS, Tempelaar R, Reichman DR. Removing instabilities in the hierarchical equations of motion: Exact and approximate projection approaches. J Chem Phys 2019; 150:184109. [DOI: 10.1063/1.5092616] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ian S. Dunn
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
| | - Roel Tempelaar
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
| | - David R. Reichman
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
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27
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Ikeda T, Dijkstra AG, Tanimura Y. Modeling and analyzing a photo-driven molecular motor system: Ratchet dynamics and non-linear optical spectra. J Chem Phys 2019; 150:114103. [DOI: 10.1063/1.5086948] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tatsushi Ikeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Arend G. Dijkstra
- School of Chemistry and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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28
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Ikeda T, Tanimura Y. Low-Temperature Quantum Fokker–Planck and Smoluchowski Equations and Their Extension to Multistate Systems. J Chem Theory Comput 2019; 15:2517-2534. [DOI: 10.1021/acs.jctc.8b01195] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tatsushi Ikeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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29
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30
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Axelrod S, Brumer P. An efficient approach to the quantum dynamics and rates of processes induced by natural incoherent light. J Chem Phys 2018; 149:114104. [PMID: 30243280 DOI: 10.1063/1.5041005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In many important cases, the rate of excitation of a system embedded in an environment is significantly smaller than the internal system relaxation rates. An important example is that of light-induced processes under natural conditions, in which the system is excited by weak, incoherent (e.g., solar) radiation. Simulating the dynamics on the time scale of the excitation source can thus be computationally intractable. Here we describe a method for obtaining the dynamics of quantum systems without directly solving the master equation. We present an algorithm for the numerical implementation of this method and, as an example, use it to reconstruct the internal conversion dynamics of pyrazine excited by sunlight. Significantly, this approach also allows us to assess the role of quantum coherence on biological time scales, which is a topic of ongoing interest.
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Affiliation(s)
- Simon Axelrod
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Paul Brumer
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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31
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Erpenbeck A, Hertlein C, Schinabeck C, Thoss M. Extending the hierarchical quantum master equation approach to low temperatures and realistic band structures. J Chem Phys 2018; 149:064106. [PMID: 30111120 DOI: 10.1063/1.5041716] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hierarchical quantum master equation (HQME) approach is an accurate method to describe quantum transport in interacting nanosystems. It generalizes perturbative master equation approaches by including higher-order contributions as well as non-Markovian memory and allows for the systematic convergence to the numerically exact result. As the HQME method relies on a decomposition of the bath correlation function in terms of exponentials, however, its application to systems at low temperatures coupled to baths with complexer band structures has been a challenge. In this publication, we outline an extension of the HQME approach, which uses re-summation over poles and can be applied to calculate transient currents at a numerical cost that is independent of temperature and band structure of the baths. We demonstrate the performance of the extended HQME approach for noninteracting tight-binding model systems of increasing complexity as well as for the spinless Anderson-Holstein model.
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Affiliation(s)
- A Erpenbeck
- Institute for Theoretical Physics and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 7/B2, D-91058 Erlangen, Germany
| | - C Hertlein
- Institute for Theoretical Physics and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 7/B2, D-91058 Erlangen, Germany
| | - C Schinabeck
- Institute for Theoretical Physics and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 7/B2, D-91058 Erlangen, Germany
| | - M Thoss
- Institute for Theoretical Physics and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 7/B2, D-91058 Erlangen, Germany
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32
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Han L, Zhang HD, Zheng X, Yan Y. On the exact truncation tier of fermionic hierarchical equations of motion. J Chem Phys 2018; 148:234108. [PMID: 29935503 DOI: 10.1063/1.5034776] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The hierarchical equations of motion (HEOM) theory is in principle exact for describing the dissipative dynamics of quantum systems linearly coupled to Gaussian environments. In practice, the hierarchy needs to be truncated at a finite tier. We demonstrate that, for general systems described by the fermionic HEOM, the (n+L̃)th-tier truncation with L̃=2NσNν yields the exact density operators up to the nth tier. Here, Nσ = 2 for fermionic systems and Nν is the system degrees of freedom. For noninteracting systems, L̃ is further reduced by half. Such an exact termination pattern originates from the Pauli exclusion principle for fermions, and it holds true regardless of the system-environment coupling strength, the number of coupling reservoirs, or the specific scheme employed to unravel the environment memory contents. The relatively small L̃ emphasizes the nonperturbative nature of the HEOM theory. We also propose a simplified HEOM approach to further reduce the memory cost for practical calculations.
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Affiliation(s)
- Lu Han
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hou-Dao Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiao Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - YiJing Yan
- Hefei National Laboratory for Physical Sciences at the Microscale and iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
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33
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Affiliation(s)
- Hou-Dao Zhang
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Rui-Xue Xu
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiao Zheng
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - YiJing Yan
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
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34
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Ye L, Zhang HD, Wang Y, Zheng X, Yan Y. Low-frequency logarithmic discretization of the reservoir spectrum for improving the efficiency of hierarchical equations of motion approach. J Chem Phys 2017; 147:074111. [DOI: 10.1063/1.4999027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- LvZhou Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hou-Dao Zhang
- Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yao Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiao Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - YiJing Yan
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
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35
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Ritschel G, Strunz WT, Eisfeld A. Closures of the functional expansion hierarchy in the non-Markovian quantum state diffusion approach. J Chem Phys 2017; 147:064113. [DOI: 10.1063/1.4986251] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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36
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Ikeda T, Tanimura Y. Probing photoisomerization processes by means of multi-dimensional electronic spectroscopy: The multi-state quantum hierarchical Fokker-Planck equation approach. J Chem Phys 2017; 147:014102. [DOI: 10.1063/1.4989537] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Tatsushi Ikeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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37
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Song K, Shi Q. Theoretical study of photoinduced proton coupled electron transfer reaction using the non-perturbative hierarchical equations of motion method. J Chem Phys 2017. [DOI: 10.1063/1.4982928] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Kai Song
- 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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38
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Mascherpa F, Smirne A, Huelga SF, Plenio MB. Open Systems with Error Bounds: Spin-Boson Model with Spectral Density Variations. PHYSICAL REVIEW LETTERS 2017; 118:100401. [PMID: 28339221 DOI: 10.1103/physrevlett.118.100401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Indexed: 06/06/2023]
Abstract
In the study of open quantum systems, one of the most common ways to describe environmental effects on the reduced dynamics is through the spectral density. However, in many models this object cannot be computed from first principles and needs to be inferred on phenomenological grounds or fitted to experimental data. Consequently, some uncertainty regarding its form and parameters is unavoidable; this in turn calls into question the accuracy of any theoretical predictions based on a given spectral density. Here, we focus on the spin-boson model as a prototypical open quantum system, find two error bounds on predicted expectation values in terms of the spectral density variation considered, and state a sufficient condition for the strongest one to apply. We further demonstrate an application of our result, by bounding the error brought about by the approximations involved in the hierarchical equations of motion resolution method for spin-boson dynamics.
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Affiliation(s)
- F Mascherpa
- Institut für Theoretische Physik, Universität Ulm, Ulm D-89069, Germany
| | - A Smirne
- Institut für Theoretische Physik, Universität Ulm, Ulm D-89069, Germany
| | - S F Huelga
- Institut für Theoretische Physik, Universität Ulm, Ulm D-89069, Germany
| | - M B Plenio
- Institut für Theoretische Physik, Universität Ulm, Ulm D-89069, Germany
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39
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Zhang HD, Qiao Q, Xu RX, Yan Y. Solvent-induced polarization dynamics and coherent two-dimensional spectroscopy: Dissipaton equation of motion approach. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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Welsch R, Song K, Shi Q, Althorpe SC, Miller TF. Non-equilibrium dynamics from RPMD and CMD. J Chem Phys 2016; 145:204118. [DOI: 10.1063/1.4967958] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Ralph Welsch
- Division of Chemistry and Chemical Engineering, California Institute of Technology,1200 E. California Blvd., Pasadena, California 91125, USA
| | - Kai Song
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Stuart C. Althorpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Thomas F. Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology,1200 E. California Blvd., Pasadena, California 91125, USA
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41
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Ye L, Wang X, Hou D, Xu RX, Zheng X, Yan Y. HEOM-QUICK: a program for accurate, efficient, and universal characterization of strongly correlated quantum impurity systems. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1269] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- LvZhou Ye
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics; University of Science and Technology of China; Hefei China
| | - Xiaoli Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics; University of Science and Technology of China; Hefei China
| | - Dong Hou
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics; University of Science and Technology of China; Hefei China
| | - Rui-Xue Xu
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics; University of Science and Technology of China; Hefei China
| | - Xiao Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information and Quantum Physics; University of Science and Technology of China; Hefei China
| | - YiJing Yan
- Hefei National Laboratory for Physical Sciences at the Microscale and iChEM (Collaborative Innovation Center of Chemistry for Energy Materials); University of Science and Technology of China; Hefei China
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42
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Jang S. Generalized quantum Fokker-Planck equation for photoinduced nonequilibrium processes with positive definiteness condition. J Chem Phys 2016; 144:214102. [PMID: 27276940 DOI: 10.1063/1.4952477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
This work provides a detailed derivation of a generalized quantum Fokker-Planck equation (GQFPE) appropriate for photo-induced quantum dynamical processes. The path integral method pioneered by Caldeira and Leggett (CL) [Physica A 121, 587 (1983)] is extended by utilizing a nonequilibrium influence functional applicable to different baths for the ground and the excited electronic states. Both nonequilibrium and non-Markovian effects are accounted for consistently by expanding the paths in the exponents of the influence functional up to the second order with respect to time. This procedure results in approximations involving only single time integrations for the exponents of the influence functional but with additional time dependent boundary terms that have been ignored in previous works. The boundary terms complicate the derivation of a time evolution equation but do not affect position dependent physical observables or the dynamics in the steady state limit. For an effective density operator with the boundary terms factored out, a time evolution equation is derived, through short time expansion of the effective action and Gaussian integration in analytically continued complex domain of space. This leads to a compact form of the GQFPE with time dependent kernels and additional terms, which renders the resulting equation to be in the Dekker form [Phys. Rep. 80, 1 (1981)]. Major terms of the equation are analyzed for the case of Ohmic spectral density with Drude cutoff, which shows that the new GQFPE satisfies the positive definiteness condition in medium to high temperature limit. Steady state limit of the GQFPE is shown to approach the well-known expression derived by CL in the high temperature and Markovian bath limit and also provides additional corrections due to quantum and non-Markovian effects of the bath.
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Affiliation(s)
- Seogjoo 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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43
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Zhang HD, Yan Y. Onsets of hierarchy truncation and self-consistent Born approximation with quantum mechanics prescriptions invariance. J Chem Phys 2016; 143:214112. [PMID: 26646874 DOI: 10.1063/1.4936831] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The issue of efficient hierarchy truncation is related to many approximate theories. In this paper, we revisit this issue from both the numerical efficiency and quantum mechanics prescription invariance aspects. The latter requires that the truncation approximation made in Schrödinger picture, such as the quantum master equations and their self-consistent-Born-approximation improvements, should be transferable to their Heisenberg-picture correspondences, without further approximations. We address this issue with the dissipaton equation of motion (DEOM), which is a unique theory for the dynamics of not only reduced systems but also hybrid bath environments. We also highlight the DEOM theory is not only about how its dynamical variables evolve in time, but also the underlying dissipaton algebra. We demonstrate this unique feature of DEOM with model systems and report some intriguing nonlinear Fano interferences characteristics that are experimentally measurable.
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Affiliation(s)
- Hou-Dao Zhang
- Department of Chemistry, Hong Kong University of Science and Technology, Hong Kong, China
| | - YiJing Yan
- Department of Chemistry, Hong Kong University of Science and Technology, Hong Kong, China
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44
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Ito H, Tanimura Y. Simulating two-dimensional infrared-Raman and Raman spectroscopies for intermolecular and intramolecular modes of liquid water. J Chem Phys 2016; 144:074201. [DOI: 10.1063/1.4941842] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Hironobu Ito
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyoku, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyoku, Kyoto 606-8502, Japan
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45
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Chen L, Gelin MF, Chernyak VY, Domcke W, Zhao Y. Dissipative dynamics at conical intersections: simulations with the hierarchy equations of motion method. Faraday Discuss 2016; 194:61-80. [DOI: 10.1039/c6fd00088f] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of a dissipative environment on the ultrafast nonadiabatic dynamics at conical intersections is analyzed for a two-state two-mode model chosen to represent the S2(ππ*)–S1(nπ*) conical intersection in pyrazine (the system) which is bilinearly coupled to infinitely many harmonic oscillators in thermal equilibrium (the bath). The system–bath coupling is modeled by the Drude spectral function. The equation of motion for the reduced density matrix of the system is solved numerically exactly with the hierarchy equation of motion method using graphics-processor-unit (GPU) technology. The simulations are valid for arbitrary strength of the system–bath coupling and arbitrary bath memory relaxation time. The present computational studies overcome the limitations of weak system–bath coupling and short memory relaxation time inherent in previous simulations based on multi-level Redfield theory [A. Kühl and W. Domcke, J. Chem. Phys. 2002, 116, 263]. Time evolutions of electronic state populations and time-dependent reduced probability densities of the coupling and tuning modes of the conical intersection have been obtained. It is found that even weak coupling to the bath effectively suppresses the irregular fluctuations of the electronic populations of the isolated two-mode conical intersection. While the population of the upper adiabatic electronic state (S2) is very efficiently quenched by the system–bath coupling, the population of the diabatic ππ* electronic state exhibits long-lived oscillations driven by coherent motion of the tuning mode. Counterintuitively, the coupling to the bath can lead to an enhanced lifetime of the coherence of the tuning mode as a result of effective damping of the highly excited coupling mode, which reduces the strong mode–mode coupling inherent to the conical intersection. The present results extend previous studies of the dissipative dynamics at conical intersections to the nonperturbative regime of system–bath coupling. They pave the way for future first-principles simulations of femtosecond time-resolved four-wave-mixing spectra of chromophores in condensed phases which are nonperturbative in the system dynamics, the system–bath coupling as well as the field-matter coupling.
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Affiliation(s)
- Lipeng Chen
- Division of Materials Science
- Nanyang Technological University
- 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
- Singapore 639798
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46
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Kato A, Tanimura Y. Quantum heat transport of a two-qubit system: Interplay between system-bath coherence and qubit-qubit coherence. J Chem Phys 2015; 143:064107. [DOI: 10.1063/1.4928192] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Akihito Kato
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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47
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Chen L, Zhao Y, Tanimura Y. Dynamics of a One-Dimensional Holstein Polaron with the Hierarchical Equations of Motion Approach. J Phys Chem Lett 2015; 6:3110-3115. [PMID: 26267210 DOI: 10.1021/acs.jpclett.5b01368] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Dynamics of a one-dimensional Holstein molecular crystal model is investigated by making use of the hierarchical equations of motion (HEOM) introduced by Tanimura and Kubo [J. Phys. Soc. Jpn. 1989, 104, 101]. Our extended, numerically exact HEOM approach is capable of treating exciton-phonon coupling in a nonperturbative manner and is applicable to any temperature. It is revealed that strong exciton phonon coupling leads to excitonic localization, while a large exciton transfer integral facilitates exciton transport. Temperature effects on excitonic scattering have also been examined. A proof of concept, our work also serves as a benchmark for future comparisons with other numerical approaches to Holstein polaron dynamics.
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Affiliation(s)
- Lipeng Chen
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yang Zhao
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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48
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Alemi M, Loring RF. Two-Dimensional Vibrational Spectroscopy of a Dissipative System with the Optimized Mean-Trajectory Approximation. J Phys Chem B 2015; 119:8950-9. [PMID: 25275943 PMCID: PMC4383732 DOI: 10.1021/jp5076884] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/10/2014] [Indexed: 11/30/2022]
Abstract
The optimized mean-trajectory (OMT) approximation is a semiclassical method for computing vibrational response functions from action-quantized classical trajectories connected by discrete transitions representing radiation-matter interactions. Here we apply this method to an anharmonic chromophore coupled to a harmonic bath. A forward-backward trajectory implementation of the OMT method is described that addresses the numerical challenges of applying the OMT to large systems with disparate frequency scales. The OMT is shown to well reproduce line shapes and waiting time dynamics in the pure dephasing limit of weak coupling to an off-resonant bath. The OMT is also shown to describe a case where energy transfer is the predominant source of line broadening.
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Affiliation(s)
- Mallory Alemi
- Department
of Chemistry and
Chemical Biology, Baker Laboratory, Cornell
University, Ithaca, New York 14853, United
States
| | - Roger F. Loring
- Department
of Chemistry and
Chemical Biology, Baker Laboratory, Cornell
University, Ithaca, New York 14853, United
States
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49
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Wilkins DM, Dattani NS. Why Quantum Coherence Is Not Important in the Fenna–Matthews–Olsen Complex. J Chem Theory Comput 2015; 11:3411-9. [DOI: 10.1021/ct501066k] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- David M. Wilkins
- Physical and Theoretical
Chemistry Laboratory, Oxford University, South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Nikesh S. Dattani
- Quantum
Chemistry Laboratory,
Department of Chemistry, Kyoto University, 606-8502, Kyoto, Japan
- School of Materials Science
and Engineering, Nanyang Technological University, Block N4.1, Nanyang Avenue, Singapore 639798
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50
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Ikeda T, Ito H, Tanimura Y. Analysis of 2D THz-Raman spectroscopy using a non-Markovian Brownian oscillator model with nonlinear system-bath interactions. J Chem Phys 2015; 142:212421. [DOI: 10.1063/1.4917033] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tatsushi Ikeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Hironobu Ito
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitaka Tanimura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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