Photosynthetic light harvesting: Excitons and coherence

Journal of the Royal Society Interface

Volumn 11, Issue 92, 2014, Pages

  Fassioli, Francesca ^a   Dinshaw, Rayomond ^a   Arpin, Paul C ^a   Scholes, Gregory D ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

Coherence; Energy transfer; Exciton; Light harvesting

Indexed keywords

COHERENT LIGHT; ELECTRIC EXCITATION; ENERGY TRANSFER; EXCITONS; QUANTUM THEORY;

COHERENT ENERGY TRANSFER; ELECTRONIC EXCITATION; ELECTRONIC EXCITED STATE; ELECTRONICALLY EXCITED STATE; EXCITED ELECTRONIC STATE; EXPERIMENTAL TECHNIQUES; LIGHT-HARVESTING; PIGMENT-PROTEIN COMPLEXES;

HARVESTING;

PIGMENT; EXCITON;

ABSORPTION SPECTROSCOPY; ANALYTICAL PARAMETERS; ANTENNA; BIOENERGY; BIOPHYSICS; CHROMATOPHORE; DYNAMICS; ELECTRON; ENERGY TRANSFER; ENVIRONMENTAL TEMPERATURE; EQUILIBRIUM CONSTANT; EXCITATION; EXCITON; EXPERIMENTATION; LANGUAGE; LIGHT ABSORPTION; LIGHT HARVESTING SYSTEM; MEASUREMENT; NONHUMAN; PHONON; PHOTOSYNTHESIS; PHOTOSYNTHETIC LIGHT HARVESTING; PROTEIN STRUCTURE; REVIEW; SPECTROSCOPY; SPECTRUM; SUNLIGHT; THEORETICAL STUDY; TWO DIMENSIONAL ELECTRONIC SPECTROSCOPY; ULTRAFAST SPECTROSCOPIC MEASUREMENT; CHEMICAL MODEL; COHERENCE; LIGHT; LIGHT HARVESTING; METABOLISM; PHYSIOLOGY; QUANTUM THEORY;

COHERENCE; ENERGY TRANSFER; EXCITON; LIGHT HARVESTING;

ENERGY TRANSFER; LIGHT; LIGHT-HARVESTING PROTEIN COMPLEXES; MODELS, CHEMICAL; PHOTOSYNTHESIS; PIGMENTS, BIOLOGICAL; QUANTUM THEORY;

EID: 84893123422     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2013.0901     Document Type: Review

References (179)

1. Connolly JS, Janzen AF, Samuel EB. 1982 Fluorescence lifetimes of chlorophyll a: solvent, concentration and oxygen dependence. Photochem. Photobiol. 36, 559-563. (doi:10.1111/j.1751-1097. 1982.tb04416.x)
2. Mullineaux CW, Pascal AA, Horton P, Holzwarth AR. 1993 Excitation-energy quenching in aggregates of the LHC II chlorophyll-protein complex: a time-resolved fluorescence study. Biochim. Biophys. Acta - Bioenerg. 1141, 23-28. (doi:10.1016/0005-2728(93)90184-H)
3. Bowers PG, Porter G. 1967 Quantum yields of triplet formation in solutions of chlorophyll. Proc. R. Soc. A Math. Phys. Eng. Sci. 296, 435-441. (doi:10.1098/rspa.1967.0036)
4. Peterman EJ, Dukker FM, van Grondelle R, van Amerongen H. 1995 Chlorophyll a and carotenoid triplet states in light-harvesting complex II of higher plants. Biophys. J. 69, 2670-2678. (doi:10.1016/S0006-3495(95)80138-4)
5. Blankenship RE. 2002 Molecular mechanisms of photosynthesis. Oxford, UK: Blackwell Science Ltd.
6. Jursinic P, Govindjee. 1977 Temperature dependence of delayed light emission in the 6 to 340 microsecond range after a single flash in chloroplasts. Photochem. Photobiol. 26, 617-628. (doi:10.1111/j.1751-1097.1977.tb07541.x)
7. Wientjes E, van Amerongen H, Croce R. 2013 Quantum yield of charge separation in photosystem II: functional effect of changes in the antenna size upon light acclimation. J. Phys. Chem. B 117, 11 200-11 208. (doi:10.1021/jp401663w)
8. Sundstrom V, Pullerits T, Van Grondelle R. 1999 Photosynthetic light-harvesting: reconciling dynamics and structure of purple bacterial LH2 reveals function of phyotosynthetic unit. J. Phys. Chem. B 103, 2327-2346. (doi:10.1021/jp983722+)
9. Van Grondelle R, Novoderezhkin VI. 2006 Energy transfer in photosynthesis: experimental insights and quantitative models. Phys. Chem. Chem. Phys. 8, 793-807. (doi:10.1039/b514032c)
10. Novoderezhkin VI, van Grondelle R. 2010 Physical origins and models of energy transfer in photosynthetic light-harvesting. Phys. Chem. Chem. Phys. 12, 7352-7365. (doi:10.1039/c003025b)
11. Scholes GD, Fleming GR, Olaya-Castro A, van Grondelle R. 2011 Lessons from nature about solar light harvesting. Nat. Chem. 3, 763-774. (doi:10.1038/nchem.1145)
12. Renger T, Müh F. 2013 Understanding photosynthetic light-harvesting: a bottom up theoretical approach. Phys. Chem. Chem. Phys. 15, 3348-3371. (doi:10.1039/c3cp43439g)
13. Cheng Y-C, Fleming GR. 2009 Dynamics of light harvesting in photosynthesis. Annu. Rev. Phys. Chem. 60, 241-262. (doi:10.1146/annurev. physchem.040808.090259)
14. Iwata S, Barber J. 2004 Structure of photosystem II and molecular architecture of the oxygen-evolving centre. Curr. Opin. Struct. Biol. 14, 447-453. (doi:10.1016/j.sbi.2004.07.002)
15. Nield J, Barber J. 2006 Refinement of the structural model for the photosystem II supercomplex of higher plants. Biochim. Biophys. Acta 1757, 353-361. (doi:10.1016/j.bbabio.2006.03.019)
16. Standfuss J, Terwisscha van Scheltinga AC, Lamborghini M, Kühlbrandt W. 2005 Mechanisms of photoprotection and nonphotochemical quenching in pea light-harvesting complex at 2.5 Å resolution. EMBO J. 24, 919-928. (doi:10.1038/sj.emboj.7600585)
17. Guskov A, Kern J, Gabdulkhakov A, Broser M, Zouni A, Saenger W. 2009 Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride. Nat. Struct. Mol. Biol. 16, 334-342. (doi:10.1038/nsmb.1559)
18. Schlau-Cohen GS, Calhoun TR, Ginsberg NS, Read EL, Ballottari M, Bassi R, van Grondelle R, Fleming GR. 2009 Pathways of energy flow in LHCII from two-dimensional electronic spectroscopy. J. Phys. Chem. B 113, 15 352-15 363. (doi:10.1021/jp9066586)
19. Croce R, van Amerongen H. 2011 Light-harvesting and structural organization of photosystem II: from individual complexes to thylakoid membrane. J. Photochem. Photobiol. B. 104, 142-153. (doi:10.1016/j.jphotobiol.2011.02. 015)
20. Andrews DL, Curutchet C, Scholes GD. 2011 Resonance energy transfer: beyond the limits. Laser Photon. Rev. 5, 114-123. (doi:10.1002/lpor.201000004)
21. Renger T. 2009 Theory of excitation energy transfer: from structure to function. Photosynth. Res. 102, 471-485. (doi:10.1007/s11120-009-9472-9)
22. Scholes GD. 2003 Long-range resonance energy transfer in molecular systems. Annu. Rev. Phys. Chem. 54, 57-87. (doi:10.1146/annurev.physchem. 54.011002.103746)
23. Andrews DL. 1989 A unified theory of radiative and radiationless molecular energy transfer. Chem. Phys. 135, 195-201. (doi:10.1016/0301-0104(89) 87019-3)
24. Beljonne D, Curutchet C, Scholes GD, Silbey RJ. 2009 Beyond Förster resonance energy transfer in biological and nanoscale systems. J. Phys. Chem. B 113, 6583-6599. (doi:10.1021/jp900708f)
25. Van Grondelle R, Dekker JP, Gillbro T, Sundstrom V. 1994 Energy transfer and trapping in photosynthesis. Biochim. Biophys. Acta Bioenerg. 1187, 1-65. (doi:10.1016/0005-2728(94)90166-X)
26. Selvin PR. 2000 The renaissance of fluorescence resonance energy transfer. Nat. Struct. Biol. 7, 730-734. (doi:10.1038/78948)
27. Förster T. 1948 Zwischenmolekulare energiewanderung und fluoreszenz. Ann. Phys. 2, 55-75. (doi:10.1002/andp.19484370105)
28. Renger T, Klinger A, Steinecker F, Schmidt am Busch M, Numata J, Müh F. 2012 Normal mode analysis of the spectral density of the Fenna-Matthews-Olson light-harvesting protein: how the protein dissipates the excess energy of excitons. J. Phys. Chem. B 116, 14 565-14 580. (doi:10.1021/jp3094935)
29. Ishizaki A, Fleming GR. 2012 Quantum coherence in photosynthetic light harvesting. Annu. Rev. Condens. Matter Phys. 3, 333-361. (doi:10.1146/annurev- conmatphys-020911-125126)
30. Novoderezhkin VI, Doust AB, Curutchet C, Scholes GD, van Grondelle R. 2010 Excitation dynamics in phycoerythrin 545: modeling of steady-state spectra and transient absorption with modified Redfield theory. Biophys. J. 99, 344-352. (doi:10.1016/j.bpj.2010.04.039)
31. Jimenez R, Dikshit SN, Bradforth SE, Fleming GR. 1996 Electronic excitation transfer in the LH2 complex of Rhodobacter sphaeroides. J. Phys. Chem. 100, 6825-6834. (doi:10.1021/jp953074j)
32. Pullerits T, Chachisvilis M, Sundstrom V. 1996 Exciton delocalization length in the B850 antenna of Rhodobacter sphaeroides. J. Phys. Chem. 100, 10 787-10 792. (doi:10.1021/jp953639b)
33. Nagarajan V, Alden RG, Williams JC, Parson WW. 1996 Ultrafast exciton relaxation in the B850 antenna complex of Rhodobacter sphaeroides. Proc. Natl Acad. Sci. USA 93, 13 774-13 779. (doi:10.1073/pnas.93.24.13774)
34. Novoderezhkin VI, Razjivin VI. 1995 Excitation delocalization over the whole core antenna of photosynthetic purple bacteria evidenced by non-linear pump-probe spectroscopy. FEBS Lett. 368, 370-372. (doi:10.1016/0014-5793(95) 00663-T)
35. Leupold D, Stiel H, Teuchner K, Nowak F, Sandner W, Ucker B, Scheer H. 1996 Size enhancement of transition dipoles to one- and two-exciton bands in a photosynthetic antenna. Phys. Rev. Lett. 77, 4675-4678. (doi:10.1103/ PhysRevLett.77.4675)
36. Kuhn O, Sundstrom V. 1997 Pump-probe spectroscopy of dissipative energy transfer dynamics in photosynthetic antenna complexes: a density matrix approach. J. Chem. Phys. 107, 4154-4164. (doi:10.1063/1.474803)
37. Novoderezhkin V, Monshouwer R, van Grondelle R. 1999 Exciton (de)localization in the LH2 antenna of Rhodobacter sphaeroides as revealed by relative difference absorption measurements of the LH2 antenna and the B820 subunit. J. Phys. Chem. A 103, 10 540-10 548. (doi:10.1021/jp9844415)
38. Book LD, Ostafin AE, Ponomarenko N, Norris JR, Scherer NF. 2000 Exciton delocalization and initial dephasing dynamics of purple bacterial LH2. J. Phys. Chem. B 104, 8295-8307. (doi:10.1021/jp000485d)
39. Monshouwer R, Abrahamsson M, van Mourik F, van Grondelle R. 1997 Superradiance and exciton delocalization in bacterial photosynthetic light-harvesting systems. J. Phys. Chem. B 101, 7241-7248. (doi:10.1021/ jp963377t)
40. Cogdell RJ, Gall A, Köhler J. 2006 The architecture and function of the light-harvesting apparatus of purple bacteria: from single molecules to in vivo membranes. Q. Rev. Biophys. 39, 227-324. (doi:10.1017/S0033583506004434)
41. Van Oijen AM, Ketelaars M, Kohler J, Aartsma TJ, Schmidt J. 1999 Unraveling the electronic structure of individual photosynthetic pigment-protein complexes. Science 285, 400-402. (doi:10.1126/science.285.5426.400)
42. Sumi H. 1999 Theory on rates of excitation-energy transfer between molecular aggregates through distributed transition dipoles with application to the antenna system in bacterial photosynthesis. J. Phys. Chem. B 103, 252-260. (doi:10.1021/jp983477u)
43. Scholes GD, Fleming GR. 2000 On the mechanism of light harvesting in photosynthetic purple bacteria: B800 to B850 energy transfer. J. Phys. Chem. B 104, 1854-1868. (doi:10.1021/jp993435l)
44. Scholes GD, Jordanides XJ, Fleming GR. 2001 Adapting the Forster theory of energy transfer for modeling dynamics in aggregated molecular assemblies. J. Phys. Chem. B 105, 1640-1651. (doi:10.1021/jp003571m)
45. Jang S, Newton M, Silbey R. 2004 Multichromophoric Förster resonance energy transfer. Phys. Rev. Lett. 92, 218301. (doi:10.1103/PhysRevLett.92. 218301)
46. Scholes GD. 2002 Designing light-harvesting antenna systems based on superradiant molecular aggregates. Chem. Phys. 275, 373-386. (doi:10.1016/S0301-0104(01)00533-X)
47. Olaya-Castro A, Lee C-F, Fassioli Olsen F, Johnson NF. 2008 Efficiency of energy transfer in a light-harvesting system under quantum coherence. Phys. Rev. B 78, 085115. (doi:10.1103/PhysRevB.78.085115)
48. Cao J, Silbey RJ. 2009 Optimization of exciton trapping in energy transfer processes. J. Phys. Chem. A 113, 13 825-13 838. (doi:10.1021/jp9032589)
49. Fassioli F, Nazir A, Olaya-Castro A. 2010 Quantum state tuning of energy transfer in a correlated environment. J. Phys. Chem. Lett. 1, 2139-2143. (doi:10.1021/jz100717d)
50. Scholak T, Mintert F, Wellens T, Buchleitner A. 2010 Transport and entanglement. In Quantum efficiency in complex systems, part I: biomolecular systems (eds ER Weber, M Thorwart, U Würfel), pp. 1-38. Amsterdam, The Netherlands: Elsevier Inc.
51. Scholak T, De Melo F, Wellens T, Mintert F, Buchleitner A. 2011 Efficient and coherent excitation transfer across disordered molecular networks. Phys. Rev. E 83, 021912. (doi:10.1103/PhysRevE.83.021912)
52. Hossein-Nejad H, Olaya-Castro A, Scholes GD. 2012 Phonon-mediated path-interference in electronic energy transfer. J. Chem. Phys. 136, 024112. (doi:10.1063/1.3675844)
53. Lee H, Cheng Y-C, Fleming GR. 2007 Coherence dynamics in photosynthesis: protein protection of excitonic coherence. Science 316, 1462-1465. (doi:10.1126/science.1142188)
54. Nalbach P, Eckel J, Thorwart M. 2010 Quantum coherent biomolecular energy transfer with spatially correlated fluctuations. New J. Phys. 12, 065043. (doi:10.1088/1367-2630/12/6/065043)
55. Wu J, Liu F, Shen Y, Cao J, Silbey RJ. 2010 Efficient energy transfer in light-harvesting systems, I: optimal temperature, reorganization energy and spatial-temporal correlations. New J. Phys. 12, 105012. (doi:10.1088/1367-2630/ 12/10/105012)
56. Strümpfer J, Schulten K. 2011 The effect of correlated bath fluctuations on exciton transfer. J. Chem. Phys. 134, 095102. (doi:10.1063/1.3557042)
57. Ishizaki A, Fleming GR. 2009 Theoretical examination of quantum coherence in a photosynthetic system at physiological temperature. Proc. Natl Acad. Sci. USA 106, 17 255-17 260. (doi:10.1073/pnas.0908989106)
58. Olbrich C, Strümpfer J, Schulten K, Kleinekathöfer U. 2011 Quest for spatially correlated fluctuations in the FMO light-harvesting complex. J. Phys. Chem. B 115, 758-764. (doi:10.1021/jp1099514)
59. Hemelrijk PW, Kwa SLS, van Grondelle R, Dekker JP. 1992 Spectroscopic properties of LHC-II, the main light-harvesting chlorophyll a/b protein complex from chloroplast membranes. Biochim. Biophys. Acta Bioenerg. 1098, 159-166. (doi:10.1016/S0005-2728(05)80331-7)
60. Szalay L, Tombácz E, Singhal GS. 1974 Effect of solvent on the absorption spectra and Stokes' shift of absorption and fluorescence of chlorophylls. Acta Phys. Acad. Sci. Hungaricae 35, 29-36. (doi:10.1007/ BF03159738)
61. Scholes GD, Fleming GR. 2005 Energy transfer and photosynthetic light harvesting. Adv. Chem. Phys. 132, 57-129. (doi:10.1002/0471759309.ch2)
62. Ishizaki A, Calhoun TR, Schlau-Cohen GS, Fleming GR. 2010 Quantum coherence and its interplay with protein environments in photosynthetic electronic energy transfer. Phys. Chem. Chem. Phys. 12, 7319-7337. (doi:10.1039/C003389H)
63. Schröder M, Kleinekathöfer U, Schreiber M. 2006 Calculation of absorption spectra for light-harvesting systems using non-Markovian approaches as well as modified Redfield theory. J. Chem. Phys. 124, 084903. (doi:10.1063/1.2171188)
64. Doust AB, Marai CNJ, Harrop SJ, Wilk KE, Curmi PMG, Scholes GD. 2004 Developing a structure-function model for the cryptophyte phycoerythrin 545 using ultrahigh resolution crystallography and ultrafast laser spectroscopy. J. Mol. Biol. 344, 135-153. (doi:10.1016/j.jmb.2004.09.044)
65. Wendling M, Pullerits T, Przyjalgowski MA, Vulto SIE, Aartsma TJ, van Grondelle R, van Amerongen H. 2000 Electron-vibrational coupling in the Fenna-Matthews-Olson complex of Prosthecochloris aestuarii determined by temperature-dependent absorption and fluorescence line-narrowing measurements. J. Phys. Chem. B 104, 5825-5831. (doi:10.1021/jp000077)
66. Olbrich C, Strümpfer J, Schulten K, Kleinekathöfer U. 2011 Theory and simulation of the environmental effects on FMO electronic transitions. J. Phys. Chem. Lett. 2011, 1771-1776. (doi:10.1021/jz2007676)
67. Kolli A, Reilly EJO, Scholes GD, Olaya-castro A. 2012 The fundamental role of quantized vibrations in coherent light harvesting by cryptophyte algae. J. Chem. Phys. 137, 174109. (doi:10.1063/1.4764100)
68. Chin AW, Prior J, Rosenbach R, Caycedo-Soler F, Huelga SF, Plenio MB. 2013 The role of non-equilibrium vibrational structures in electronic coherence and recoherence in pigment-protein complexes. Nat. Phys. 9, 113-118. (doi:10.1038/nphys2515)
69. Cheng Y, Silbey R. 2006 Coherence in the B800 ring of purple bacteria LH2. Phys. Rev. Lett. 96, 028103. (doi:10.1103/PhysRevLett.96.028103)
70. Jang S, Newton MD, Silbey RJ. 2007 Multichromophoric Förster resonance energy transfer from B800 to B850 in the light harvesting complex 2: evidence for subtle energetic optimization by purple bacteria. J. Phys. Chem. B 111, 6807-6814. (doi:10.1021/jp070111l)
71. Hossein-Nejad H, Curutchet C, Kubica A, Scholes GD. 2011 Delocalization-enhanced long-range energy transfer between cryptophyte algae PE545 antenna proteins. J. Phys. Chem. A 115, 5243-5253. (doi:10.1021/jp108397a)
72. Brumer P, Shapiro M. 2012 Molecular response in one-photon absorption via natural thermal light vs. pulsed laser excitation. Proc. Natl Acad. Sci. USA 109, 19 575-19 578. (doi:10.1073/pnas.1211209109)
73. Fassioli F, Olaya-Castro A, Scholes GD. 2012 Coherent energy transfer under incoherent light conditions. J. Phys. Chem. Lett. 3, 3136-3142. (doi:10.1021/jz3010317)
74. Kassal I, Yuen-Zhou J, Rahimi-Keshari S. 2013 Does coherence enhance transport in photosynthesis? J. Phys. Chem. Lett. 4, 362-367. (doi:10.1021/jz301872b)
75. Davydov AS. 1948 Theory of absorption spectra of molecular crystals. Zhur. Eksptl. Teoret. Fiz. 18, 210-218.
76. Davydov AS. 1962 Theory of molecular excitons. [translated by M. Kasha and M. Oppenheimer, Jr.]. New York, NY: McGraw-Hill Book Company.
77. Kasha M. 1959 Relation between exciton bands and conduction bands in molecular lamellar systems. Rev. Mod. Phys. 31, 162-169. (doi:10.1103/ RevModPhys.31.162)
78. Kasha M. 1963 Energy transfer mechanisms and the molecular exciton model for molecular aggregates. Radiat. Res. 20, 55-70. (doi:10.2307/3571331c)
79. Kasha M, Rawls HR, Ashraf El-Bayoumi M. 1965 The exciton model in molecular spectroscopy. Pure Appl. Chem. 11, 371-392. (doi:10.1351/ pac196511030371)
80. Shipman LL, Housman DL. 1979 Forster transfer rates for chlorophyll a. Photochem. Photobiol. 29, 1163-1167. (doi:10.1111/j.1751-1097.1979.tb07835.x)
81. Krueger BP, Scholes GD, Fleming GR. 1998 Calculation of couplings and energy-transfer pathways between the pigments of LH2 by the ab initio transition density cube method. J. Phys. Chem. B 102, 5378-5386. (doi:10.1021/jp9811171)
82. Scholes GD, Ghiggino KP, Oliver AM, Paddon-Row MN. 1993 Through-space and through-bond effects on exciton interactions in rigidly linked dinaphthyl molecules. J. Am. Chem. Soc. 115, 4345-4349. (doi:10.1021/ja00063a061)
83. May V, Kuhn O. 2005 Charge and energy transfer dynamics in molecular systems, 2nd edn. Weinheim, Germany: Wiley-VCH.
84. Stratt RM. 1995 The instantaneous normal modes of liquids. Acc. Chem. Res. 28, 201-207. (doi:10.1021/ar00053a001)
85. Read EL, Schlau-Cohen GS, Engel GS, Georgiou T, Papiz MZ, Fleming GR. 2009 Pigment organization and energy level structure in light-harvesting complex 4: insights from two-dimensional electronic spectroscopy. J. Phys. Chem. B 113, 6495-6504. (doi:10.1021/jp809713q)
86. Sauer K, Cogdell RJ, Prince SM, Freer A, Isaacs NW, Scheer H. 1996 Structure-based calculations of the optical spectra of the LH2 bacteriochlorophyllprotein complex from Rhodopseudomonas acidophila. Photochem. Photobiol. 64, 564-576. (doi:10.1111/j.1751-1097.1996.tb03106.x)
87. Yang M, Damjanović A, Vaswani HM, Fleming GR. 2003 Energy transfer in photosystem I of cyanobacteria Synechococcus elongatus: model study with structure-based semi-empirical Hamiltonian and experimental spectral density. Biophys. J. 85, 140-158. (doi:10.1016/S0006-3495(03)74461-0)
88. Doust AB, Wilk KE, Curmi PMG, Scholes GD. 2006 The photophysics of cryptophyte light-harvesting. J. Photochem. Photobiol. A Chem. 184, 1-17. (doi:10.1016/j.jphotochem.2006.06.006)
89. Marin A, Doust AB, Scholes GD, Wilk KE, Curmi PMG, van Stokkum IHM, van Grondelle R. 2011 Flow of excitation energy in the cryptophyte light-harvesting antenna phycocyanin 645. Biophys. J. 101, 1004-1013. (doi:10.1016/j.bpj.2011.07. 012)
90. Freiberg A, Godik VI, Pullerits T, Timpmann K. 1989 Picosecond dynamics of directed excitation transfer in spectrally heterogeneous light-harvesting antenna of purple bacteria. Biochim. Biophys. Acta 973, 93-104. (doi:10.1016/S0005-2728(89)80407-4)
91. Wientjes E, Roest G, Croce R. 2012 From red to blue to far-red in Lhca4: how does the protein modulate the spectral properties of the pigments? Biochim. Biophys. Acta 1817, 711-717. (doi:10.1016/j.bbabio.2012.02.030)
92. Van Amerongen H, Valkunas L, van Grondelle R. 2000 Photosynthetic excitons. Singapore: World Scientific Publishing.
93. Fowler GJ, Visschers RW, Grief GG, van Grondelle R, Hunter CN. 1992 Genetically modified photosynthetic antenna complexes with blueshifted absorbance bands. Nature 355, 848-850. (doi:10.1038/355848a0)
94. Novoderezhkin VI, Palacios MA, van Amerongen H, van Grondelle R. 2005 Excitation dynamics in the LHCII complex of higher plants: modeling based on the 2.72 Angstrom crystal structure. J. Phys. Chem. B 109, 10 493-10 504. (doi:10.1021/jp044082f)
95. Silbey R, Harris RA. 1984 Variational calculation of the dynamics of a two level system interacting with a bath. J. Chem. Phys. 80, 2615-2617. (doi:10.1063/1.447055)
96. Meier T, Zhao Y, Chernyak V, Mukamel S, Introduction I. 1997 Polarons, localization, and excitonic coherence in superradiance of biological antenna complexes. J. Chem. Phys. 107, 3876-3893. (doi:10.1063/1.474746)
97. Silbey R. 2011 Description of quantum effects in the condensed phase. Procedia Chem. 3, 188-197. (doi:10.1016/j.proche.2011.08.026)
98. Yena T-C, Cheng Y-C. 2011 Electronic coherence effects in photosynthetic light harvesting. Procedia Chem. 3, 211-221. (doi:10.1016/j.proche.2011.08.028)
99. Kolli A, Nazir A, Olaya-Castro A. 2011 Electronic excitation dynamics in multichromophoric systems described via a polaron-representation master equation. J. Chem. Phys. 135, 154112. (doi:10.1063/1.3652227)
100. Grondelle R, Van Novoderezhkin V. 2001 Dynamics of excitation energy transfer in the LH1 and LH2 light-harvesting complexes of photosynthetic bacteria. Biochemistry 40, 15 057-15 068. (doi:10.1021/bi0018943)
101. Novoderezhkin VI, Rutkauskas D, van Grondelle R. 2006 Dynamics of the emission spectrum of a single LH2 complex: interplay of slow and fast nuclear motions. Biophys. J. 90, 2890-2902. (doi:10.1529/biophysj.105.072652)
102. Fassioli F, Olaya-Castro A. 2010 Distribution of entanglement in light-harvesting complexes and their quantum efficiency. New J. Phys. 12, 085006. (doi:10.1088/1367-2630/12/8/085006)
103. Sarovar M, Ishizaki A, Fleming GR, Whaley KB. 2010 Quantum entanglement in photosynthetic light-harvesting complexes. Nat. Phys. 6, 462-467. (doi:10.1038/nphys1652)
104. Olaya-Castro A, Fassioli F. 2011 Characterizing quantum-sharing of electronic excitation in molecular aggregates. Procedia Chem. 3, 176-184. (doi:10.1016/j.proche.2011.08.024)
105. Whaley KB, Sarovar M, Ishizaki A. 2011 Quantum entanglement phenomena in photosynthetic light harvesting complexes. Procedia Chem. 3, 152-164. (doi:10.1016/j.proche.2011.08.021)
106. Smyth C, Fassioli F, Scholes GD. 2012 Measures and implications of electronic coherence in photosynthetic light-harvesting. Phil. Trans. R. Soc. A 370, 3728-3749. (doi:10.1098/rsta.2011.0420)
107. Tiersch M, Popescu S, Briegel HJ. 2012 A critical view on transport and entanglement in models of photosynthesis. Phil. Trans. R. Soc. A 370, 3771-3786. (doi:10.1098/rsta.2011.0202)
108. Breuer H-P, Petruccione F. 2002 The theory of open quantum systems. Oxford, UK: Oxford University Press.
109. Ritz T, Park S, Schulten K. 2001 Kinetics of excitation migration and trapping in the photosynthetic unit of purple bacteria. J. Phys. Chem. B 105, 8259-8267. (doi:10.1021/jp011032r)
110. Panitchayangkoon G, Hayes D, Fransted KA, Caram JR, Harel E, Wen J, Blankenship RE, Engel GS. 2010 Long-lived quantum coherence in photosynthetic complexes at physiological temperature. Proc. Natl Acad. Sci. USA 107, 12 766-12 770. (doi:10.1073/pnas.1005484107)
111. Ishizaki A, Fleming GR. 2009 Unified treatment of quantum coherent and incoherent hopping dynamics in electronic energy transfer: reduced hierarchy equation approach. J. Chem. Phys. 130, 234111. (doi:10.1063/1.3155372)
112. Roden J, Eisfeld A, Wolff W, Strunz WT. 2009 Influence of complex exciton-phonon coupling on optical absorption and energy transfer of quantum aggregates. Phys. Rev. Lett. 103, 058301. (doi:10. 1103/PhysRevLett.103.058301)
113. Nalbach P, Thorwart M. 2010 Multiphonon transitions in the biomolecular energy transfer dynamics. J. Chem. Phys. 132, 194111. (doi:10.1063/1.3428385)
114. Huo P, Coker DF. 2010 Iterative linearized density matrix propagation for modeling coherent excitation energy transfer in photosynthetic light harvesting. J. Chem. Phys. 133, 184108. (doi:10.1063/1.3498901)
115. Jang S. 2011 Theory of multichromophoric coherent resonance energy transfer: a polaronic quantum master equation approach. J. Chem. Phys. 135, 034105. (doi:10.1063/1.3608914)
116. Womick JM, Moran AM. 2011 Vibronic enhancement of exciton sizes and energy transport in photosynthetic complexes. J. Phys. Chem. B 115, 1347-1356. (doi:10.1021/jp106713q)
117. Nalbach P, Thorwart M. 2012 The role of discrete molecular modes in the coherent exciton dynamics in FMO. J. Phys. B At. Mol. Opt. Phys. 45, 154009. (doi:10.1088/0953-4075/45/15/154009)
118. Roden J, Strunz WT, Whaley KB, Eisfeld A. 2012 Accounting for intra-molecular vibrational modes in open quantum system description of molecular systems. J. Chem. Phys. 137, 204110. (doi:10.1063/1.4765329)
119. Shi Q, Chen L, Nan G, Xu R-X, Yan Y. 2009 Efficient hierarchical Liouville space propagator to quantum dissipative dynamics. J. Chem. Phys. 130, 084105. (doi:10.1063/1.3077918)
120. Kneip C, Parbel A, Foerstendorf H, Scheer H, Siebert F. 1998 Fourier transform near-infrared resonance Raman spectroscopic study of the a-subunit of phycoerythrocyanin and phycocyanin from the cyanobacterium Mastigocladus laminosus. J. Raman Spectrosc. 944, 939-944. (doi:10.1002/(SICI)1097- 4555(199810/11)29:10/11, 939::AID-JRS320.3.0.CO;2-X)
121. Hybl JD, Albrecht AW, Gallagher Faeder SM, Jonas DM. 1998 Two-dimensional electronic spectroscopy. Chem. Phys. Lett. 297, 307-313. (doi:10.1016/S0009- 2614(98)01140-3)
122. Cundiff ST, Bristow AD, Siemens M, Li H, Moody G, Karaiskaj D, Dai X, Zhang T. 2012 Optical 2-D Fourier transform spectroscopy of excitons in semiconductor nanostructures. IEEE J. Sel. Top. Quantum Electron. 18, 318-328. (doi:10.1109/JSTQE.2011.2123876)
123. Lewis KLM, Ogilvie JP. 2012 Probing photosynthetic energy and charge transfer with two-dimensional electronic spectroscopy. J. Phys. Chem. Lett. 3, 503-510. (doi:10.1021/jz201592v)
124. Anna JM, Song Y, Dinshaw R, Scholes GD. 2013 Two-dimensional electronic spectroscopy for mapping molecular photophysics. Pure Appl. Chem. 85, 1307-1319. (doi:10.1351/PAC-CON-12-10-21)
125. Tokmakoff A. 2000 Two-dimensional line shapes derived from coherent third-order nonlinear spectroscopy. J. Phys. Chem. A 104, 4247-4255. (doi:10.1021/jp993207r)
126. Hochstrasser RM. 2007 Two-dimensional spectroscopy at infrared and optical frequencies. Proc. Natl Acad. Sci. USA 104, 14 190-14 196. (doi:10.1073/pnas.0704079104)
127. Khalil M, Demirdoven N, Tokmakoff A. 2003 Obtaining absorptive line shapes in two-dimensional infrared vibrational correlation spectra. Phys. Rev. Lett. 90, 047401. (doi:10.1103/PhysRevLett.90.047401)
128. Mukamel S. 1995 Principles of nonlinear optical spectroscopy. New York, NY: Oxford University Press.
129. Cho M. 2008 Coherent two-dimensional optical spectroscopy. Chem. Rev. 108, 1331-1418. (doi:10. 1021/cr078377b)
130. Mukamel S. 2000 Multidimensional femtosecond correlation spectroscopies of electronic and vibrational excitations. Annu. Rev. Phys. Chem. 51, 691-729. (doi:10.1146/annurev.physchem.51.1.691)
131. Abramavicius D, Palmieri B, Voronine DV, Sanda F, Mukamel S. 2009 Coherent multidimensional optical spectroscopy of excitons in molecular aggregates; quasiparticle versus supermolecule perspectives. Chem. Rev. 109, 2350-2408. (doi:10.1021/cr800268n)
132. Turner DB, Hassan Y, Scholes GD. 2012 Exciton superposition states in CdSe nanocrystals measured using broadband two-dimensional electronic spectroscopy. Nano Lett. 12, 880-886. (doi:10.1021/nl2039502)
133. Nemeth A, Milota F, Mančal T, Lukeš V, Hauer J, Kauffmann HF, Sperling J. 2010 Vibrational wave packet induced oscillations in two-dimensional electronic spectra. I. Experiments. J. Chem. Phys. 132, 184514. (doi:10.1063/1.3404404)
134. Mančal T, Nemeth A, Milota F, Lukeš V, Kauffmann HF, Sperling J. 2010 Vibrational wave packet induced oscillations in two-dimensional electronic spectra. II. Theory. J. Chem. Phys. 132, 184515. (doi:10.1063/1.3404405)
135. Egorova D. 2008 Detection of electronic and vibrational coherences in molecular systems by 2D electronic photon echo spectroscopy. Chem. Phys. 347, 166-176. (doi:10.1016/j.chemphys.2007.12.019)
136. Turner DB, Wilk KE, Curmi PMG, Scholes GD. 2011 Comparison of electronic and vibrational coherence measured by two-dimensional electronic spectroscopy. J. Phys. Chem. Lett. 2, 1904-1911. (doi:10.1021/jz200811p)
137. Hayes D, Wen J, Panitchayangkoon G, Blankenship RE, Engel GS. 2011 Robustness of electronic coherence in the Fenna-Matthews-Olson complex to vibronic and structural modifications. Faraday Discuss. 150, 459-469. (doi:10.1039/c0fd00030b)
138. Chachisvilis M, Kuhn O, Pullerits T, Sundstrom V. 1997 Excitons in photosynthetic purple bacteria: wavelike motion or incoherent hopping? J. Phys. Chem. B 101, 7275-7283. (doi:10.1021/jp963360a)
139. Savikhin S, Buck DR, Struve WS. 1997 Oscillating anisotropies in a bacteriochlorophyll protein: evidence for quantum beating between exciton levels. Chem. Phys. 223, 303-312. (doi:10.1016/S0301-0104(97)00223-1)
140. Engel GS, Calhoun TR, Read EL, Ahn T-K, Mancal T, Cheng Y-C, Blankenship RE, Fleming GR. 2007 Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. Nature 446, 782-786. (doi:10.1038/ nature05678)
141. Calhoun TR, Ginsberg NS, Schlau-Cohen GS, Cheng Y-C, Ballottari M, Bassi R, Fleming GR. 2009 Quantum coherence enabled determination of the energy landscape in light-harvesting complex II. J. Phys. Chem. B 113, 16 291-16 295. (doi:10.1021/jp908300c)
142. Collini E, Wong CY, Wilk KE, Curmi PMG, Brumer P, Scholes GD. 2010 Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature. Nature 463, 644-647. (doi:10.1038/nature08811)
143. Wong CY, Alvey RM, Turner DB, Wilk KE, Bryant DA, Curmi PMG, Silbey RJ, Scholes GD. 2012 Electronic coherence lineshapes reveal hidden excitonic correlations in photosynthetic light harvesting. Nat. Chem. 4, 396-404. (doi:10.1038/nchem.1302)
144. Wedemayer GJ, Kidd DG, Glazer AN. 1996 Cryptomonad biliproteins: bilin types and locations. Photosynth. Res. 48, 163-170. (doi:10.1007/BF00041006)
145. Harrop ASJ et al. Submitted. Evolution of cryptophyte light harvesting proteins: a structural switch that controls energy transfer.
146. Turner DB, Dinshaw R, Lee K-K, Belsley MS, Wilk KE, Curmi PMG, Scholes GD. 2012 Quantitative investigations of quantum coherence for a light-harvesting protein at conditions simulating photosynthesis. Phys. Chem. Chem. Phys. 14, 4857-4874. (doi:10.1039/c2cp23670b)
147. Christensson N, Milota F, Hauer J, Sperling J, Bixner O, Nemeth A, Kauffmann HF. 2011 High frequency vibrational modulations in two-dimensional electronic spectra and their resemblance to electronic coherence signatures. J. Phys. Chem. B 115, 5383-5391. (doi:10.1021/jp109442b)
148. Tiwari V, Peters WK, Jonas DM. 2013 Electronic resonance with anticorrelated pigment vibrations drives photosynthetic energy transfer outside the adiabatic framework. Proc. Natl Acad. Sci. USA 110, 1203-1208. (doi:10.1073/pnas.1211157110)
149. Cheng Y-C, Fleming GR. 2008 Coherence quantum beats in two-dimensional electronic spectroscopy. J. Phys. Chem. A 112, 4254-4260. (doi:10.1021/ jp7107889)
150. Butkus V, Zigmantas D, Valkunas L, Abramavicius D. 2012 Vibrational vs. electronic coherences in 2D spectrum of molecular systems. Chem. Phys. Lett. 545, 40-43. (doi:10.1016/j.cplett.2012.07.014)
151. Richards GH, Wilk KE, Curmi PMG, Quiney M, Davis JA. 2012 Coherent vibronic coupling in light-harvesting complexes from photosynthetic marine algae. J. Phys. Chem. Lett. 3, 272-277. (doi:10.1021/jz201600f)
152. Yuen-Zhou J, Krich JJ, Aspuru-Guzik A. 2012 A witness for coherent electronic vs vibronic-only oscillations in ultrafast spectroscopy. J. Chem. Phys. 136, 234501. (doi:10.1063/1.4725498)
153. Fragnito HL, Bigot J-Y, Becker PC, Shank CV. 1989 Evolution of the vibronic absorption spectrum in a molecule following impulsive excitation with a 6 fs optical pulse. Chem. Phys. Lett. 160, 101-104. (doi:10.1016/0009-2614(89) 87564-5)
154. Pollard WT, Fragnito HL, Bigot J-Y, Shank CV, Mathies RA. 1990 Quantum-mechanical theory for 6 fs dynamic absorption spectroscopy and its application to nile blue. Chem. Phys. Lett. 168, 239-245. (doi:10.1016/0009- 2614(90)85603-A)
155. Jonas DM, Fleming GR. 1995 Vibrationally abrupt pulses in pump-probe spectroscopy. In Ultrafast processes in chemistry and photobiology (chemistry in the 21st century series IUPAC) (eds MA El-Sayed, I Tanaka, Y Molin), pp. 225-256. Oxford, UK: Blackwell Science.
156. Fulton RL, Gouterman M. 1961 Vibronic coupling. I. Mathematical treatment for two electronic states. J. Chem. Phys. 35, 1059. (doi:10.1063/1.1701181)
157. Christensson N, Kauffmann HF, Pullerits T, Mančal T. 2012 Origin of long-lived coherences in light-harvesting complexes. J. Phys. Chem. B 116, 7449-7454. (doi:10.1021/jp304649c)
158. Heid CG, Ottiger P, Leist R, Leutwyler S. 2011 The S1/S2 exciton interaction in 2-pyridone.6-methyl-2-pyridone: Davydov splitting, vibronic coupling, and vibronic quenching. J. Chem. Phys. 135, 154311. (doi:10.1063/1.3652759)
159. Ottiger P, Leutwyler S, Köppel H. 2012 Vibrational quenching of excitonic splittings in H-bonded molecular dimers: the electronic Davydov splittings cannot match experiment. J. Chem. Phys. 136, 174308. (doi:10.1063/1.4705119)
160. Mohseni M, Rebentrost P, Lloyd S, Aspuru-Guzik A. 2008 Environment-assisted quantum walks in photosynthetic energy transfer. J. Chem. Phys. 129, 174106. (doi:10.1063/1.3002335)
161. Plenio MB, Huelga SF. 2008 Dephasing-assisted transport: quantum networks and biomolecules. New J. Phys. 10, 113019. (doi:10.1088/1367-2630/10/11/113019)
162. Caruso F, Chin AW, Datta A, Huelga SF, Plenio MB. 2009 Highly efficient energy excitation transfer in light-harvesting complexes: the fundamental role of noise-assisted transport. J. Chem. Phys. 131, 105106. (doi:10.1063/1.3223548)
163. Fassioli F, Oblinsky DG, Scholes GD. 2013 Designs for molecular circuits that use electronic coherence. Faraday Discuss. 163, 341-351. (doi:10.1039/c3fd00009e)
164. Mančal T, Valkunas L. 2010 Exciton dynamics in photosynthetic complexes: excitation by coherent and incoherent light. New J. Phys. 12, 065044. (doi:10.1088/1367-2630/12/6/065044)
165. Jiang X, Brumer P. 1991 Creation and dynamics of molecular states prepared with coherent vs partially coherent pulsed light. J. Chem. Phys. 94, 5833-5843. (doi:10.1063/1.460467)
166. Kistiakowsky GB, Parmenter CS. 1965 Effects of pressure on fluorescence and intersystem crossing in benzene vapor. J. Chem. Phys. 42, 2942-2948. (doi:10.1063/1.1703267)
167. Watts RJ, Strickler SJ. 1966 Fluorescence and internal conversion in naphthalene vapor. J. Chem. Phys. 44, 2423-2426. (doi:10.1063/1. 1727059)
168. Bixon M, Jortner J. 1968 Intramolecular radiationless transitions. J. Chem. Phys. 48, 715-726. (doi:10.1063/1.1668703)
169. Englman R, Jortner J. 1970 The energy gap law for radiationless transitions in large molecules. Mol. Phys. 18, 145-164. (doi:10.1080/002689770 00100171)
170. Turner DB, Arpin PC, McClure SD, Ulness DJ, Scholes GD. 2013 Coherent multidimensional optical spectra measured using incoherent light. Nat. Commun. 4, 2298. (doi:10.1038/ncomms3298)
171. Turner DB, Howey DJ, Sutor EJ, Hendrickson RA, Gealy MW, Ulness DJ. 2013 Two-dimensional electronic spectroscopy using incoherent light: theoretical analysis. J. Phys. Chem. A 117, 5926-5954. (doi:10.1021/jp310477y)
172. Morita N, Yajima T. 1984 Ultrahigh-time-resolution coherent transient spectroscopy with incoherent light. Phys. Rev. A 30, 2525-2536. (doi:10.1103/PhysRevA.30.2525)
173. Beach R, Hartmann S. 1984 Incoherent photon echoes. Phys. Rev. Lett. 53, 663-666. (doi:10.1103/PhysRevLett.53.663)
174. 3+-doped silicate glass. Phys. Rev. A 29, 2286-2289. (doi:10.1103/PhysRevA.29.2286)
175. Tomita M, Matsuoka M. 1986 Ultrafast pump-probe measurement using intensity correlation of incoherent light. J. Opt. Soc. Am. B 3, 560-563. (doi:10.1364/JOSAB.3.000560)
176. Ulness DJ. 2003 On the role of classical field time correlations in noisy light spectroscopy: color locking and a spectral filter analogy. J. Phys. Chem. A 107, 8111-8123. (doi:10.1021/jp0222494)
177. Hildner R, Brinks D, van Hulst NF. 2010 Femtosecond coherence and quantum control of single molecules at room temperature. Nat. Phys. 7, 172-177. (doi:10.1038/nphys1858)
178. Hildner R, Brinks D, Nieder JB, Cogdell RJ, van Hulst NF. 2013 Quantum coherent energy transfer over varying pathways in single light-harvesting complexes. Science 340, 1448-1451. (doi:10.1126/science.1235820)
179. Dong H, Fleming GR. 2013 Three-pulse photon echo of finite numbers of molecules: single-molecule traces. J. Phys. Chem. B 117, 11 318-11 325. (doi:10.1021/jp402768c)