Resonance energy flow dynamics of coherently delocalized excitons in biological and macromolecular systems: Recent theoretical advances and open issues

Wiley Interdisciplinary Reviews: Computational Molecular Science

Volumn 3, Issue 1, 2013, Pages 84-104

  Jang, Seogjoo ^a   Cheng, Yuan Chung ^b  

^a CITY UNIVERSITY OF NEW YORK   (United States)

^b NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84871402154     PISSN: 17590876     EISSN: 17590884     Source Type: Journal    
DOI: 10.1002/wcms.1111     Document Type: Review

References (161)

1. Davydov AS. Theory of Molecular Excitons. New York: Plenum Press; 1971.
2. Förster Th. In Sinanoglu, O., Ed., Modern Quantum Chemistry, Part III. New York: Academic Press; 1965.
3. Silbey R. Electronic-energy transfer in molecular-crystals. Annu Rev Phys Chem 1976, 27:203.
4. Rashba EI, Sturge MD, Eds. Modern Problems in Condensed Matter Sciences: Vol. 2, Excitons. Amsterdam, The Netherlands: North-Holland; 1982.
5. Reineker P, Haken H, Wolf HC, Eds. Organic Molecular Aggregates. Berlin: Springer-Verlag; 1983.
6. Kenkre VM, Reineker P. Exciton Dynamics in Molecular Crystals and Aggregates. Berlin: Springer; 1982.
7. Sundstrom V, Pullerits T, van Grondelle R. Photosynthetic light-harvesting: reconciling dynamics and structure of purple bacteria LH2 reveals function of photosynthetic unit. J Phys Chem B 1999, 103:2327.
8. Hu X, Ritz T, Damjanovic A, Autenrieth F, Schulten K. Photosynthetic apparatus of purple bacteria. Quar Rev Biophys 2002, 35:1.
9. Renger T, May V, and Kühn O. Ultrafast excitation energy transfer dynamics in photosynthetic pigment-protein complexes. Phys Rep 2001, 343:137.
10. Cogdell RJ, Gali A, and Köhler J. The architecture and function of the light-harvesting apparatus of purple bacteria: from single molecules to in vivo membranes. Quart Rev Biophys 2006, 39:227.
11. Heeger AJ. Semiconducting and metallic polymers: The fourth generation of polymeric materials. Rev Mod Phys 2000, 73:681.
12. Bittner ER. Exciton dynamics-simplifying organic complexity. Nature Phys 2006, 2:591.
13. Gaab KM, Bardeen CJ. Wavelength and temperature dependence of the femtosecond pump-probe anisotropies in the conjugated polymer MEH-PPV: implications for energy transfer dynamics. J Phys Chem B 2004, 108:4619-4626.
14. Lim SH, Bjorklund TG, Gaab KM, Bardeen CJ. The role of long-lived dark states in the photoluminescence dynamics of phenylene vinylene conjugated polymers. J Chem Phys 2002, 117:454.
15. Beljonne D, Hennebicq E, Daniel C, Herz LM, Silva C, Scholes GD, Hoeben FJM, Jonkheijm P, Schenning APHJ, Meskers SCJ, et al. Excitation migration along oligophenylenevinylene-based chiral stacks: delocalization effects on transport dynamics. J Phys Chem B 2005, 109:10594.
16. Collini E, Scholes GD. Coherent intrachain energy migration in a conjugated polymer at room temperature. Science 2009, 323:369-373.
17. Spano FC. Excitons in conjugated oligomer aggregates, films, and crystals. Annu Rev Phys Chem 2006, 57:217.
18. Cao J, Silbey RJ. Optimization of exciton trapping in energy transfer processes. J Phys Chem A 2009, 113:13825-13838.
19. Frenkel J. On the transformation of light into heat in solids. I. Phys Rev 1931, 37:17-44.
20. Förster Th. Intermolecular energy migration and fluorescence. Ann Phys 1948, 6:55.
21. Dexter DL. A theory of sensitized luminescence in solids. J Chem Phys 1953, 21:836-850.
22. Gochanour CR, Andersen C, Fayer MD. Electronic excited state transport in solution. J Chem Phys 1979, 70:4254-4271.
23. Haan SW, Zwanzig R. Förster migration of electronic excitation between randomly distributed molecules. J Chem Phys 1978, 68:1879-1883.
24. Godzik K, Jortner J. Electronic energy transfer in impurity band. Chem Phys 1979, 38:227-237.
25. Huber DL. Fluorescence in the presence of traps. Phys Rev B 1979, 20:2307.
26. Blumen A, Klafter J, Silbey R. Energy transfer in disordered media. J Chem Phys 1980, 72:5320-5332.
27. Loring RF, Andersen HC, Fayer MD. Electronic excited state transport and trapping in solution. J Chem Phys 1982, 76:2015-2027.
28. Fedorenko SG, Burshtein AI. Binary theory of impurity quenching accelerated by resonant excitation migration in a disordered system. Chem Phys 1988, 128:185.
29. Jang S, Shin KJ, Lee S. Effects of excitation migration and translational diffusion in luminescence quenching dynamics. J Chem Phys 1995, 102:815.
30. Grover M, Silbey R. Exciton migration in molecular crystals. J Chem Phys 1971, 54:4843.
31. Kenkre VM, Knox RS. Generalized master equation theory of excitation transfer. Phys Rev B 1974, 9:5279.
32. Cogdell RJ, Gardiner AT, Hashimoto H, Brotosudarmo THP. A comparative look at the first few milliseconds of the light reactions of photosynthesis. Photochem Photobiol Sci 2008, 7:1150-1158.
33. Kopelman R, Shortreed M, Shi ZY, Tan W, Xu Z, Moore JS, Bar-Haim A, Klafter J. Spectroscopic evidence for excitonic localization in fractal antenna supermolecules. Phys Rev Lett 1997, 78:1239.
34. Hofkens J, Maus M, Gensch T, Vosch T, Cotlet M, Köhn F, Hermann A, Müllen K, Schryver FCD. Probing photophysical processes in individual multichromophoric dendrimers by single molecule spectroscopy. J Am Chem Soc 2000, 122:9278.
35. Ranasinghe MI, Wang Y, Goodson T III. Excitation energy transfer in branched dendritic macromolecules at low (4 K) temperatures. J Am Chem Soc 2003, 125:5258-5259.
36. Ahn TA, Nantalaksakul A, Dasari RR, Al Kaysi RO, Müller AM, Thayumanavan S, Bardeen CJ. Energy and charge transfer dynamics in fully decorated benzyl ether dendrimers and their disubstituted analogues. J Phys Chem B 2006, 110:24331.
37. Peng Z, Melinger J, Kleiman V. Light harvesting unsymmetrical conjugated dendrimers as photosynthetic mimics. Photosyn Res 2006, 87:115.
38. Kleiman VD, Melinger JS, McMorrow D. Ultrafast dynamics of electronic excitations in a light harvesting phenylactylene dendrimer. J Phys Chem B 2001, 105:5595.
39. Varnavski OP, Ostrowski J, Sukhomlinova L, Twieg RJ, Bazan GC, Goodson T III. Coherent effects in energy transport in model dendritic structures investigated by ultrafast fluorescence anisotropy spectroscopy. J Am Chem Soc 2002, 124:1736-1743.
40. Kim D, Osuka A. Directly linked prophyrin arrays with tunable excitonic interactions. Acc Chem Res 2004, 37:735.
41. Yang M, Agarwal R, Fleming GR. The mechanism of energy transfer in the antenna of photosynthetic purple bacteria. J Photochem Photobiol A: Chem 2001, 142:107.
42. Yang M, Damjanović A, Vaswani HM, and Fleming GR. Energy transfer in photosystem I of cyanobacteria Synechococcus elongatus: model study with structure based semi-empirical Hamiltonian and experimental spectral density. Biophys J 2003, 85:140.
43. Jang S, Newton MD, Silbey RJ. Multichromophoric Förster resonance energy transfer. Phys Rev Lett 2004, 92:218301.
44. Jang S, Newton MD, Silbey RJ. 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 2007, 111:6807.
45. Brédas JL, Norton JE, Cornil J, Coropceanu V. Molecular understanding of organic solar cells: The Challenges. Acc Chem Res 2009, 42:1691-1699.
46. Chasteen SV, Sholin V, Carter SA, Rumbles G. Towards optimization of device performance in conjugated polymer photovoltaics: charge generation, transfer and transport in poly(p-phenylene-vinylene) polymer heterojunctions. Solar Energy Mater Solar Cells 2008, 92:651.
47. Bolinger JC, Traub MC, Adachi T, Barbara PF. Ultralong-range polaron-induced quenching of excitons in isolated conjugated polymers. Science 2011, 331:565-567.
48. Bardeen C. Exciton quenching and migration in single conjugated polymers. Science 2011, 331:544.
49. Mukamel S, Principles of Nonlinear Spectroscopy. New York: Oxford University Press; 1995.
50. Jonas DM. Two-dimensional femtosecond spectroscopy. Annu Rev Phys Chem 2003, 54:425.
51. Cho M, Vaswani HM, Brixner T, Stenger J, Fleming GR. Exciton analysis in 2D electronic spectroscopy. J Phys Chem B 2005, 109:10542.
52. Cho M. Coherent two-dimensional optical spectroscopy. Chem Rev 2008, 108:1331.
53. Engel GS, Calhoun TR, Read EL, Ahn TK, Mancal T, Cheng YC, Blankenship RE, Fleming GR. Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. Nature 2007, 446:782-786.
54. Collini E, Wong CY, Wilk KE, Curmi PMG, Brumer P, Scholes GD. Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature. Nature 2010, 463:644-647.
55. Panitchayangkoon G, Hayes D, Fransted KA, Caram JR, Harel E, Wen J, Blankenship RE, Engel GS. Long-lived quantum coherence in photosynthetic complexes at physiological temperature. Proc Natl Acad Sci USA 2010, 107:12766.
56. Schlau-Cohen GS, Ishizaki A, Fleming GR. Two-dimensional electronic spectroscopy and photosynthesis: fundamentals and applications to photosynthetic light-harvesting. Chem Phys 2011, 386:1-22.
57. Palmieri B, Abramvicius D, Mukamel S. Interplay of slow bath fluctuations and energy transfer in 2D spectroscopy of the FMO light-harvesting complex: benchmarking of simulation protocols. Phys Chem Chem Phys 2010, 12:108-114.
58. Sharp LZ, Egorova D, Domcke W. Efficient and accurate simulations of two-dimensional electronic photon-echo signals: illustration for a simple model of the Fenna-Matthews-Olson complex. J Chem Phys 2010, 132:014501.
59. Abramvicius D, Mukamel S. Quantum oscillatory exciton migration in photosynthetic reaction centers. J Chem Phys 2010, 133:064510.
60. Olbrich C, Jansen TLC, Liebers J, Aghtar M, Strümpfer J, Schulten K, Knoester J, Kleinekathöfer U. From atomistic modeling to excitation transfer and two-dimensional spectra of the FMO light-harvesting complex. J Phys Chem B 2011, 115:8609-8621.
61. Chen L, Zheng R, Jing Y, Shi Q. Simulation of the two-dimensional electronic spectra of the Fenna-Matthews-Olson complex using the hierarchical equations of motion method. J Chem Phys 2011, 134:194508.
62. Agranovich VM, Galanin MD, Modern Problems in Condensed Matter Sciences: Vol.3, Electronic Excitation Energy Transfer in Condensed Matter. Amsterdam: North-Holland; 1982.
63. Birks JB, ed. Excited States of Biological Molecules. London: John Wiley & Sons; 1976.
64. Andrews DL, Demidov AA, eds. Resonance Energy Transfer. Chichester, UK: John Wiley & Sons; 1999.
65. Scholes GD. Long range resonance energy transfer in molecular systems. Annu Rev Phys Chem 2003, 54:57.
66. Ha T, Enderle T, Ogletree DF, Chemla DS, Selvin PR, Weiss S. Probing the interaction between two single molecules: Fluorescence resonance energy transfer between a single donor and a single acceptor. Proc Natl Acad Sci 1996, 93:6264.
67. Lipman EA, Schuler B, Bakajin O, Eaton WA. Single-molecule measurement of protein folding kinetics. Science 2003, 301:1233.
68. Thompson AL, Gaab KM, Xu J, Bardeen CJ, Martínez TJ. Variable electronic coupling in phenylacetylene dendrimers: the role of Förster, Dexter, and charge-transfer interactions. J Phys Chem A 2004, 108:671.
69. Wong KF, Bagchi B, Rossky PJ. Distance and orientational dependence of excitation transfer rates in conjugated systems: beyond the Förster theory. J Phys Chem A 2004, 108:5752.
70. Russo V, Curutchet C, Mennucci B. Towards a molecular scale interpretation of excitation energy transfer in solvated bichromophoric systems. II. The through-bond contribution. J Phys Chem B 2007, 111:853.
71. Nguyen TQ, Wu J, Doan V, Schwartz BJ, Tolbert SH. Control of energy transfer in oriented conjugated polymer-mesoporous silica composites. Science 2000, 288:652.
72. Hsiao JS, Krueger B, Wagner W, Johonson TE, Delaney JK, Mazuerall D, Fleming GR, Lindsey JS, Bocian DF, Donohoe RJ. Soluble synthetic multiporphyrin arrays. 2. Phtodynamics of energy-transfer processes. J Am Chem Soc 1996, 118:11181-11193.
73. Yang SI, Lammi RK, Seth J, Riggs JA, Arai T, Kim D, Bocian D, Holten D, Lindsey J. Excited-state energy transfer and ground-state hole/electron hopping in p-phenylene-linked porphyrin dimers. J Phys Chem B 1998, 102:9426.
74. Serin JM, Brousmiche DW, Fréchet JMJ. Cascade energy transfer in a conformationally mobile multichromophoric dendrimer. Chem Commun 2002, 22:2605.
75. Gronheid R, Hofkens J, Kohn F, Weil T, Reuther E, Mullen K, Schryver FCD. Intramolecular Förster energy transfer in a dendritic system at the single molecule level. J Am Chem Soc 2002, 124:2418.
76. Aratani N, Cho HS, Ahn TK, Cho S, Kim D, Sumi H, Osuka A. Efficient excitation energy transfer in long meso-meso linked Zn(II) porphyrinarrays bearing a 5, 15-bisphenylethynylated Zn(II) porphyrin acceptor. J Am Chem Soc 2003, 125:9668.
77. Hindin E, Forties RA, Loewe RS, Ambroise A, Kirmaier C, Bocian D, Lindsey JS, Holten D, Knox RS. Excited-state energy flow in covalently linked multiporphyrin arrays: the essential contribution of energy transfer between nonadjacent chromophores. J Phys Chem B 2004, 108:12821.
78. Fan C, Wang S, Hong JW, Bazan GC, Plaxco KW, Heeger AJ. Beyond superquenching: hyper-efficient energy transfer from conjugated polymers to gold nanoparticles. Proc Natl Acad Sci 2003, 100:6297.
79. Chen CH, Liu KY, Sudhakar S, Lim TS, Fann W, Hsu CP, Luh TY. Efficient light harvesting and energy transfer in organic-inorganic hybrid multichromophoric materials. J Phys Chem B 2005, 109:17887.
80. Schlosser M, Lochbrunner S. Exciton migration by ultrafast Förster transfer in highly doped matrices. J Phys Chem B 2006, 110:6001.
81. Praveen VK, George SJ, Varghese R, Vijayakumar C, Ajayaghosh A. Self-assembled π-nanotapes as donor scaffolds for selective and thermally gated fluorescence resonance energy transfer (FRET). J Am Chem Soc 2002, 124:4436.
82. Stryer L, Haugland RP. Energy transfer: a spectroscopic ruler. Proc Natl Acad Sci USA 1967, 58:719.
83. Haugland RP, Yguerabide J, Stryer L. Dependence of the kinetics of singlet-singlet energy transfer on spectral overlap. Proc Natl Acad Sci USA 1969, 63:23.
84. Selvin PR. The renaissance of fluorescence resonance energy transfer. Nature Struct Biol 2000, 7:730.
85. Hillisch A, Lorenz M, Diekmann S. Recent advances in FRET: distance determination in protein-DNA complexes. Curr Opin Struct Biol 2001, 11:201.
86. Heyduk T. Measuring protein conformational changes by FRET/LRET. Curr Opin Biotechnol 2002, 13:292.
87. Koushik SV, Chen H, Thaler C, Puhl HL III, Vogel SS. Cerulean, Venus, and Venus (Y67C) FRET reference standards Biophys J 2006, 91:L99-L101.
88. Jang S. Generalization of the Förster resonance energy transfer theory for quantum mechanical modulation of the donor-acceptor coupling. J Chem Phys 2007, 127:174710.
89. Soules TF, Duke CB. Resonant energy transfer between localized electronic states in a crystal. Phys Rev B 1971, 3:262.
90. Jang S, Jung YJ, Silbey RJ. Nonequilibrium generalization of Förster-Dexter theory foor excitation energy transfer. Chem Phys 2002, 275:319-332.
91. Hennebicq E, Beljonne D, Curutchet C, Scholes GD, Silbey RJ. Shared-mode resonant energy transfer in the weak coupling regime. J Chem Phys 2009, 130:214505.
92. Sumi H. Theory of 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 1999, 103:252.
93. Lippitz M, Hübner CH, Christ T, Eichner H, Bordat P, Herrmann A, Müllen K, Basché T. Coherent electronic coupling versus localization in individual molecular dimers. Phys Rev Lett 2004, 92:103001.
94. Yamazaki I, Akimoto S, Yamazaki T, Sato S, Sakata Y. Oscillatory excitation transfer in dithiaanthracenophene: Quantum beat in a coherent photochemical process in solution. J Phys Chem A 2002, 106:2122-2128.
95. Collini E, Scholes GD. Electronic and vibrational coherences in resonance energy transfer along MEH-PPV chains at room temperature. J Phys Chem A 2009, 113:4223.
96. Jang S, Cheng YC, Reichman DR, Eaves JD. Theory of coherent resonance energy transfer. J Chem Phys 2008, 129:101104.
97. May V. Higher-order processes of excitation energy transfer in supramolecular complexes: Liouville space analysis of bridge molecule mediated transfer and direct photon exchange. J Chem Phys 2008, 129:114109.
98. Gilmore JB, McKenzie RH. Quantum dynamics of electronic excitations in biomolecular chromophores: role of the protein environment and solvent. J Phys Chem A 2008, 112:2162.
99. Yu ZG, Berding MA, Wang H. Spatially correlated fluctuations and coherence dynamics in photosynthesis. Phys Rev E 2008, 78:050902.
100. Palmieri B, Abramvicius D, Mukamel S. Lindblad equations for strongly coupled populations and coherences in photosynthetic complexes. J Chem Phys 2009, 130:204512.
101. Ishizaki A, Fleming GR. On the adequacy of the Redfield equation and related approaches to the study of quantum dynamics in electronic energy transfer. J Chem Phys 2009, 130:234110.
102. Ishizaki A, Fleming GR. Unified treatment of quantum coherent and incoherent hopping dynamics in electronic energy transfer: reduced hierarchy equation approach. J Chem Phys 2009, 130:234111.
103. Mohseni M, Rebentrost P, Loyd S, Aspuru-Guzik A. Environment-assisted quantum walks in photosynthetic energy transfer. J Chem Phys 2008, 129:174106.
104. Olaya-Castro A, Lee CF, Olsen FF, Johnson NF. Efficiency of energy transfer in a light-harvesting system under quantum coherence. Phys Rev B 2008, 78:085115.
105. Förster T. Transfer mechanisms of electronic excitation. Discuss Faraday Soc 1959, 27:7.
106. Jean JM, Fleming GR. Competition between energy and phase relaxation in electronic curve crossing processes. J Chem Phys 1995, 103:2092.
107. Wynne K, Hochstrasser RM. Anisotropy as an ultrafast probe of electronic coherence in degenerate systems exhibiting raman-scattering, fluorescence, transient absorption, and chemical-reacations. J Raman Spectrosc 1995, 26:561-569.
108. Yang M, Fleming GR. Influence of phonons on excitation transfer dynamics: comparison of the Redfield, Förster, and modified Redfield equations. Chem Phys 2002, 275:355.
109. Jang S. Theory of coherent resonance energy transfer for coherent initial condition. J Chem Phys 2009, 131:164101.
110. Jang S. Theory of multichromophoric coherent resonance energy transfer: a polaronic quantum master equation approach. J Chem Phys 2011, 135:034105.
111. Nazir A. Correlation-dependent coherent to incoherent transitions in resonant energy transfer dynamics. Phys Rev Lett 2009, 103:146404.
112. McCutcheon DPS, Nazir A. Consistent treatment of coherent and incoherent energy transfer dynamics using a variational master equation. J Chem Phys 2011, 135:114501.
113. Kolli A, Nazir A, Olaya-Castro A. Electronic excitation dynamics in multichromophoric systems described via polaron-representation master equation. J Chem Phys 2011, 135:154112.
114. Holstein T. Studies of polaron motion: Part I. The molecular-crystal model. Ann Phys 1959, 8:325-342; Studies of polaron motion: Part II. The "small" polaron. J Chem Phys 1959, 8:343-389.
115. Silbey R, Harris RA. On the calculation of transfer rates between impurity states in solids. J Chem Phys 1984, 80:2615.
116. Harris RA, Silbey R. Variational calculation of the tunneling system interacting with a heat bath. II. Dynamics of an asymmetric tunneling system. J Chem Phys 1985, 83:1069.
117. Suárez A, Silbey R. Hydrogen tunneling in condensed media. J Chem Phys 1991, 94:4809.
118. Rackovsky S, Silbey R. Electronic energy transfer in impure solids I. Two molecules embedded in a lattice. Mol Phys 1973, 25:61.
119. Jackson B, Silbey R. On the calculation of transfer rates between impurity states in solids. J Chem Phys 1983, 78:4193.
120. Cheng YC, Silbey RJ. A unified theory for charge-carrier transport in organic crystals. J Chem Phys 2008, 128:114713.
121. Yarkony DR, Silbey RJ. Comments on exciton phonon coupling -temperature-dependence. J Chem Phys 1976, 65:1042-1052.
122. Cheng YC, Silbey RJ. Coherence in the B800 ring of purple bacteria LH2. Phys Rev Lett 2006, 96:028103.
123. McDermott G, Prince SM, Freer AA, Hawthornthwaite-Lawless AM, Paplz MZ, Cogdell RJ, Issacs NW. Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria. Nature 1995, 374:517.
124. Jang S, Silbey RJ. Single complex line shapes of the B850 band of LH2. J Chem Phys 2003, 118:9324.
125. Jang S, Dempster SE, Silbey RJ. Characterization of the static disorder in the B850 band of LH2. J Phys Chem B 2001, 105:6655.
126. Renger T, Marcus RA. On the relation of protein dynamics and exciton relaxation in pigment-protein complexes: an estimate of the spectral density and a theory for the calculation of optical spectra. J Chem Phys 2002, 116:9997.
127. Pullerits T, Hess S, Herek JL, Sundström V. Temperature dependence of excitation transfer in LH2 of Rhodobacter sphaeroides. J Phys Chem B 1997, 101:10560.
128. Scherz A, Parson WW. Exciton interactions in dimers of bacteriochlorophyll and related molecules. Biochim Biophys Acta 1984, 766:666-678.
129. Monshouwer R, Abrahamsson M, van Mourik F, van Grondelle R. J. Superradiance and exciton delocalization in bacterial photosynthetic light-harvesting systems. Phys Chem B 1997, 101:7241-7248.
130. Mukai K, Abe S, Sumi H. Theory of rapid excitation-energy transfer from B800 to optically-forbidden exciton states of B850 in the antenna system LH2 of photosynthetic purple bacteria. J Phys Chem B 1999, 103:6096.
131. Scholes GD, Fleming GR. On the mechanism of light harvesting in photosynthetic purple bacteria: B800 to B850 energy transfer. J Phys Chem B 2000, 104:1854.
132. Salverda JM, van Mourik F, van der Zwan G, van Grondelle R. Energy transfer in the B800 rings of the peripheral bacterial light-harvesting complexes of Rhodopseudomonas acidophila and Rhodospirillum molischianum studied with photon echo techniques. J Phys Chem B 2000, 104:11395.
133. Agarwal, R, Yang, M, Xu, QH, Fleming, GR. Three pulse photon echo peak shift study of the B800 band of the LH2 complex of Rps. acidophila at room temperature: A coupled master equation and nonlinear optical response function approach. J. Phys. Chem. B 2001, 105:1887.
134. Krueger BP, Scholes GD, Fleming GR. Calculation of couplings and energy-transfer pathways between the pigments of LH2 by the ab initio transition density cube method. J Phys Chem B 1998, 102:5378-5386.
135. Scholes GD, Cogdell IRGRJ, Fleming GR. Ab initio molecular orbital calculations of electronic couplings in the LH2 bacterial light-harvesting complex of rps-acidophila. J Phys Chem B 1999, 103:2543-2553.
136. Kimura A, Kakitani T. Theoretical analysis of the energy gap dependence of the reconstituted B800 → B850 excitation energy transfer rate in bacterial LH2 complexes. J Phys Chem B 2003, 107:7932-7939.
137. Jang S, Silbey RJ, Kunz R, Hofmann C, Köhler J. Is there elliptic distortion in the light harvesting complex 2 of purple bacteria? J Phys Chem B 2011, 115: 12947.
138. Vos M, Breton J, Martin MJ. Electronic energy transfer within the hexamer cofactor system of bacterial reaction centers. J Phys Chem B 1997, 101:9820-9832.
139. Stanley R, King B, Boxer S. Excited state energy transfer pathways in photosynthetic reaction centers. 1. structural symmetry effects. J Phys Chem 1996, 100:12052-12059.
140. Jean J, Chan CK, Fleming GR. Electronic-energy transfer in photosynthetic bacterial reaction centers. Israel J Chem 1988, 28:169-175.
141. Jordanides XJ, Scholes GD, Fleming GR. The mechanism of energy transfer in the bacterial photosynthetic reaction center. J Phys Chem B 2001, 105:1652-1669.
142. King BA, Stanley R, Boxer S. Excited state energy transfer pathways in photosynthetic reaction centers. 2. heterodimer special pair. J Phys Chem B 1997, 101:3644-3648.
143. Lin S, Taguchi A, Woodbury N. Excitation wavelength dependence of energy transfer and charge separation in reaction centers from rhodobacter sphaeroides: Evidence for adiabatic electron transfer. J Phys Chem B 1996, 100:17067-17078.
144. Scholes GD, Jordanides XJ, Fleming GR. Adapting the Förster theory of energy transfer for modeling dynamics in aggregated molecular assemblies. J Phys Chem B 2001, 105:1640.
145. Raszewaski G, Renger T. Light harvesting in photosystem II core complexes is limited by the transfer to the trap: Can the core complex turn into a photoprotective mode? J Am Chem Soc 2008, 130:4431-4446.
146. Raszewaski G, Renger T. Theory of optical spectra of photosystem ii reaction centers: location of the triplet state and the identity of the primary electron donor. Biophys J 2005, 88:986-998.
147. Schlau-Cohen GS, Calhoun TR, Ginsberg NS, Read EL, Ballottari M, Bassi R, van Grondelle R, Fleming GR. Pathways of energy flow in lhcii from two-dimensional electronic spectroscopy. J Phys Chem B 2009, 113:15352-15363.
148. Munn R, Silbey RJ. Remarks on exciton - phonon coupling and exciton transport. Mol Cryst Liq Cryst 1980, 57:131.
149. Emelianova EV, Athanasopoulos S, Silbey RJ, Beljone D. 2d excitons as primary energy carriers in organic crystals: The case of oligoacenes. Phys Rev Lett 2010, 104:206405.
150. Kobayashi T. ed. J-Aggregates. Singapore: World Scientific; 1996.
151. Kasha M. Energy transfer mechanisms and molecular exciton model for molecular aggregates. Radiat Res 1963, 20:55.
152. Scholes GD. Designing light-harvesting antenna systems based on superradiant molecular aggregates. Chem Phys 2002, 275:373-386.
153. Yang L, Caprasecca S, Mennucci B, Jang S. Theoretical investigation of the mechanism and dynamics of intramolecular coherent resonance energy transfer in soft molecules: A case study of dithia-anthracenophane. J Am Chem Soc 2010, 132:16911-16921.
154. Huo P, Coker DF. Iterative linearized density matrix propagation for modeling coherent excitation energy transfer in photosynthetic light harvesting. J Chem Phys 2010, 133:184108.
155. Zhu J, Kais S, Rebentrost P, Aspuru-Guzik A. Modified scaled hierarchical equation of motion approach for the study of quantum coherence in photosynthetic complexes. J Phys Chem B 2011, 115:1531-1537.
156. Strümpfer J, Schulten K. The effect of correlated bath fluctuations on exciton transfer. J Chem Phys 2011, 134:095102.
157. Knox RS, van Amerongen H. Refractive index dependence of the Förster resonance excitation transfer rate. J Phys Chem B 2002, 106:5289-5293.
158. Juzeliũnas G, Andrews DL. Quantum electrodynamics of resonant energy transfer in condensed matter. Phys Rev B 1994, 49:8751.
159. Craig DP, Thirunamachandran T. Molecular Quantum Electrodynamics: An Introduction to Radiation-Molecule Interactions. London: Academic Press; 1984.
160. Curutchet C, Kongsted J, Muñoz-Losa AH, Hossein-Nejad GDS, Mennucci B. Photosynthetic light-harvesting is tuned by the heterogeneous polarizable environment of the protein. J Am Chem Soc 2011, 133:3078.
161. Olbrich C, Strümpfer J, Schulten K, Knoester J, Kleinekathöfer U. Theory and simulation of the environmental effects on fmo electronic transitions. J Phys Chem Lett 2011, 2:1771-1776.