Simulation of the two-dimensional electronic spectra of the Fenna-Matthews-Olson complex using the hierarchical equations of motion method.

We apply the Liouville space hierarchical equations of motion method to calculate the linear and two-dimensional (2D) electronic spectra of the Fenna-Matthews-Olson (FMO) protein complex from Chlorobium tepidum, using a widely used model Hamiltonian. The absorption and linear dichroism spectra of the FMO complex, as well as the main features of the 2D spectra are well reproduced. However, comparison with the recent experimental 2D spectra reveals several limitations of the current model: (1) The homogeneous and inhomogeneous broadening seems to be overestimated for the first exciton peak, but may be underestimated for several other exciton peaks. (2) The calculated oscillations of the diagonal and off-diagonal peaks in the 2D spectra are much weaker than the experimental observations, which indicates that an improved model is needed for the excitonic dynamics of the FMO complex.

[1]  S. Mukamel,et al.  Quantum oscillatory exciton migration in photosynthetic reaction centers. , 2010, The Journal of chemical physics.

[2]  Gregory D. Scholes,et al.  Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature , 2010, Nature.

[3]  Justin R. Caram,et al.  Long-lived quantum coherence in photosynthetic complexes at physiological temperature , 2010, Proceedings of the National Academy of Sciences.

[4]  Qiang Shi,et al.  Two-dimensional electronic spectra from the hierarchical equations of motion method: Application to model dimers. , 2010, The Journal of chemical physics.

[5]  W. Domcke,et al.  Efficient and accurate simulations of two-dimensional electronic photon-echo signals: Illustration for a simple model of the Fenna-Matthews-Olson complex. , 2010, The Journal of chemical physics.

[6]  R. Silbey,et al.  Optimization of exciton trapping in energy transfer processes. , 2009, The journal of physical chemistry. A.

[7]  Seogjoo J. Jang.  Theory of coherent resonance energy transfer for coherent initial condition. , 2009, The Journal of chemical physics.

[8]  G. Fleming,et al.  Quantum coherence enabled determination of the energy landscape in light-harvesting complex II. , 2009, The journal of physical chemistry. B.

[9]  G. Fleming,et al.  Theoretical examination of quantum coherence in a photosynthetic system at physiological temperature , 2009, Proceedings of the National Academy of Sciences.

[10]  Qiang Shi,et al.  Hierarchical quantum master equation with semiclassical Drude dissipation. , 2009, The Journal of chemical physics.

[11]  Qiang Shi,et al.  Optical line shapes of molecular aggregates: hierarchical equations of motion method. , 2009, The Journal of chemical physics.

[12]  G. Fleming,et al.  Two-dimensional electronic spectroscopy of molecular aggregates. , 2009, Accounts of chemical research.

[13]  S. Mukamel,et al.  Excitonic couplings and interband energy transfer in a double-wall molecular aggregate imaged by coherent two-dimensional electronic spectroscopy. , 2009, The Journal of chemical physics.

[14]  Midori Tanaka,et al.  Quantum Dissipative Dynamics of Electron Transfer Reaction System: Nonperturbative Hierarchy Equations Approach , 2009 .

[15]  G. Fleming,et al.  On the adequacy of the Redfield equation and related approaches to the study of quantum dynamics in electronic energy transfer. , 2009, The Journal of chemical physics.

[16]  G. Fleming,et al.  Unified treatment of quantum coherent and incoherent hopping dynamics in electronic energy transfer: reduced hierarchy equation approach. , 2009, The Journal of chemical physics.

[17]  S. Mukamel,et al.  Lindblad equations for strongly coupled populations and coherences in photosynthetic complexes. , 2009, The Journal of chemical physics.

[18]  D. Tronrud,et al.  The structural basis for the difference in absorbance spectra for the FMO antenna protein from various green sulfur bacteria , 2009, Photosynthesis Research.

[19]  Darius Abramavicius,et al.  Coherent multidimensional optical spectroscopy of excitons in molecular aggregates; quasiparticle versus supermolecule perspectives. , 2009, Chemical reviews.

[20]  Qiang Shi,et al.  Electron transfer dynamics: Zusman equation versus exact theory. , 2009, The Journal of chemical physics.

[21]  Graham R Fleming,et al.  Dynamics of light harvesting in photosynthesis. , 2009, Annual review of physical chemistry.

[22]  Qiang Shi,et al.  Efficient hierarchical Liouville space propagator to quantum dissipative dynamics. , 2009, The Journal of chemical physics.

[23]  S. Mukamel,et al.  Extracting single and two-exciton couplings in photosynthetic complexes by coherent two-dimensional electronic spectra. , 2009, Chemical physics.

[24]  Animesh Datta,et al.  Highly efficient energy excitation transfer in light-harvesting complexes: The fundamental role of n , 2009, 0901.4454.

[25]  Seogjoo J. Jang,et al.  Theory of coherent resonance energy transfer. , 2008, The Journal of chemical physics.

[26]  John H. Reina,et al.  Galactic Dynamics , 1995 .

[27]  S. Lloyd,et al.  Environment-assisted quantum walks in photosynthetic energy transfer. , 2008, The Journal of chemical physics.

[28]  Graham R Fleming,et al.  Coherence quantum beats in two-dimensional electronic spectroscopy. , 2008, The journal of physical chemistry. A.

[29]  Minhaeng Cho,et al.  Coherent two-dimensional optical spectroscopy. , 2008, Chemical reviews.

[30]  T. Renger,et al.  Calculation of pigment transition energies in the FMO protein , 2008, Photosynthesis Research.

[31]  S. Mukamel,et al.  Transport and correlated fluctuations in the nonlinear optical response of excitons , 2007 .

[32]  T. Pullerits,et al.  Non-perturbative calculation of 2D spectra in heterogeneous systems: Exciton relaxation in the FMO complex , 2007 .

[33]  Y. Tanimura,et al.  Ultrafast exciton-exciton coherent transfer in molecular aggregates and its application to light-harvesting systems. , 2007, The Journal of chemical physics.

[34]  Ying Chen,et al.  The quantum solvation, adiabatic versus nonadiabatic, and Markovian versus non-Markovian nature of electron-transfer rate processes. , 2007, The journal of physical chemistry. A.

[35]  Hohjai Lee,et al.  Coherence Dynamics in Photosynthesis: Protein Protection of Excitonic Coherence , 2007, Science.

[36]  T. Mančal,et al.  Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems , 2007, Nature.

[37]  W. Domcke,et al.  Analysis of cross peaks in two-dimensional electronic photon-echo spectroscopy for simple models with vibrations and dissipation. , 2007, The Journal of chemical physics.

[38]  T. Renger,et al.  How proteins trigger excitation energy transfer in the FMO complex of green sulfur bacteria. , 2006, Biophysical journal.

[39]  Igor V. Stiopkin,et al.  Heterogeneous exciton dynamics revealed by two-dimensional optical spectroscopy. , 2006, The journal of physical chemistry. B.

[40]  A. Ishizaki,et al.  Modeling vibrational dephasing and energy relaxation of intramolecular anharmonic modes for multidimensional infrared spectroscopies. , 2006, The Journal of chemical physics.

[41]  Y. Tanimura.  Stochastic Liouville, Langevin, Fokker–Planck, and Master Equation Approaches to Quantum Dissipative Systems , 2006 .

[42]  Andrei V. Pisliakov,et al.  Two-dimensional optical three-pulse photon echo spectroscopy. II. Signatures of coherent electronic motion and exciton population transfer in dimer two-dimensional spectra. , 2006, The Journal of chemical physics.

[43]  Andrei V. Pisliakov,et al.  Two-dimensional optical three-pulse photon echo spectroscopy. I. Nonperturbative approach to the calculation of spectra. , 2006, The Journal of chemical physics.

[44]  S. Mukamel,et al.  Optical coherence and theoretical study of the excitation dynamics of a highly symmetric cyclophane-linked oligophenylenevinylene dimer. , 2006, The Journal of chemical physics.

[45]  Rienk van Grondelle,et al.  Energy transfer in photosynthesis: experimental insights and quantitative models. , 2006, Physical chemistry chemical physics : PCCP.

[46]  T. Pullerits,et al.  Three-pulse photon echo of an excitonic dimer modeled via Redfield theory. , 2006, The Journal of chemical physics.

[47]  A. Ishizaki,et al.  Quantum Dynamics of System Strongly Coupled to Low-Temperature Colored Noise Bath: Reduced Hierarchy Equations Approach , 2005 .

[48]  Graham R Fleming,et al.  Exciton analysis in 2D electronic spectroscopy. , 2005, The journal of physical chemistry. B.

[49]  Graham R. Fleming,et al.  Two-dimensional spectroscopy of electronic couplings in photosynthesis , 2005, Nature.

[50]  P. Cui,et al.  Exact quantum master equation via the calculus on path integrals. , 2004, The Journal of chemical physics.

[51]  S. Mukamel,et al.  Many-body approaches for simulating coherent nonlinear spectroscopies of electronic and vibrational excitons. , 2004, Chemical reviews.

[52]  Andrei Tokmakoff,et al.  Coherent 2D IR Spectroscopy: Molecular Structure and Dynamics in Solution , 2003 .

[53]  M. Cho.  Nonlinear response functions for the three-dimensional spectroscopies , 2001 .

[54]  Thomas Renger,et al.  Ultrafast excitation energy transfer dynamics in photosynthetic pigment–protein complexes , 2001 .

[55]  J. Amesz,et al.  EXCITED STATE DYNAMICS IN FMO ANTENNA COMPLEXES FROM PHOTOSYNTHETIC GREEN SULFUR BACTERIA : A KINETIC MODEL , 1999 .

[56]  R. Louwe,et al.  Excited-State Structure and Dynamics in FMO Antenna Complexes from Photosynthetic Green Sulfur Bacteria , 1998 .

[57]  R. Louwe,et al.  Exciton simulations of optical spectra of the FMO complex from the green sulfur bacterium Chlorobium tepidum at 6 K. , 1998 .

[58]  S. Mukamel,et al.  Exciton-migration and three-pulse femtosecond optical spectroscopies of photosynthetic antenna complexes , 1998 .

[59]  R. Louwe,et al.  TOWARD AN INTEGRAL INTERPRETATION OF THE OPTICAL STEADY-STATE SPECTRA OF THE FMO-COMPLEX OF PROSTHECOCHLORIS AESTUARII. 2. EXCITON SIMULATIONS , 1997 .

[60]  S. Savikhin,et al.  Oscillating anisotropies in a bacteriochlorophyll protein: Evidence for quantum beating between exciton levels , 1997 .

[61]  Robert Eugene Blankenship,et al.  Crystal structure of the bacteriochlorophyll a protein from Chlorobium tepidum. , 1997, Journal of molecular biology.

[62]  S. Mukamel.  Principles of Nonlinear Optical Spectroscopy , 1995 .

[63]  Y. Tanimura,et al.  Nonperturbative expansion method for a quantum system coupled to a harmonic-oscillator bath. , 1990, Physical review. A, Atomic, molecular, and optical physics.

[64]  R. Kubo,et al.  Time Evolution of a Quantum System in Contact with a Nearly Gaussian-Markoffian Noise Bath , 1989 .

[65]  B. Matthews,et al.  Chlorophyll arrangement in a bacteriochlorophyll protein from Chlorobium limicola , 1975, Nature.

[66]  Milosz A. Przyjalgowski,et al.  The quantitative relationship between structure and polarized spectroscopy in the FMO complex of Prosthecochloris aestuarii: refining experiments and simulations , 2004, Photosynthesis Research.

[67]  Y. Tanimura,et al.  Two-dimensional Raman and infrared vibrational spectroscopy for a harmonic oscillator system nonlinearly coupled with a colored noise bath. , 2004, The Journal of chemical physics.

[68]  Robert Eugene Blankenship.  Molecular mechanisms of photosynthesis , 2002 .