1;Preface;6 2;Contents;9 3;List of Contributors;11 4;Excitation Energy Transfer in Complex Molecular and Biological Systems;16 4.1;Electronic Energy Transfer in Photosynthetic Antenna Systems;17 4.1.1;1 Introduction;17 4.1.2;2 Overview of photosynthetic organisms and theirLight-Harvesting Antenna complexes;18 4.1.2.1;2.1 Introduction;18 4.1.2.2;2.2 Antenna complexes: evolutionary point of view;19 4.1.2.3;2.3 Classes of Antenna: structure and function;24 4.1.2.3.1;LH1 and LH2 antenna complexes;25 4.1.2.3.2;Chlorosomes and FMO protein;26 4.1.2.3.3;LHC family;27 4.1.2.3.4;Phycobiliproteins and Phycobilisomes (PBS);28 4.1.2.3.5;Peridinin-Chl a-protein (PCP);29 4.1.2.4;2.4 Dynamics of EET: an example;29 4.1.3;3 The mechanism of EET: Perspective from theory;33 4.1.3.1;3.1 Introduction;33 4.1.3.2;3.2 F orster theory for donor-acceptor pairs;34 4.1.3.3;3.3 Electronic coupling;36 4.1.3.4;3.4 Solvent screening;40 4.1.3.5;3.5 Spectral Overlap;42 4.1.3.6;3.6 Special attributes of multichromophoric systems;43 4.1.4;4 Summary and conclusions;43 4.1.5;Acknowledgements;44 4.1.6;References;44 4.2;Mixed Quantum Classical Simulations of Electronic Excitation Energy Transfer and Related Optical Spectra: Supramolecular Pheophorbide {a Complexes in Solution;49 4.2.1;1 Introduction;49 4.2.2;2 The Model for the Chromophore Complex in a Solvent;54 4.2.2.1;2.1 The Chromophore Complex Hamiltonian;54 4.2.2.2;2.2 Standard Exciton Hamiltonian;57 4.2.2.3;2.3 The Coulomb Interaction Matrix Element;58 4.2.2.4;2.4 Inclusion of Solvent Molecules;59 4.2.2.5;2.5 Adiabatic Exciton States;60 4.2.3;3 Full Quantum Dynamical Description;61 4.2.3.1;3.1 Excitation Energy Transfer;61 4.2.3.2;3.2 Linear Absorption Spectra;62 4.2.3.3;3.3 Spectra of Time and Frequency Resolved Luminescence;63 4.2.3.3.1;Density Matrix Theory of Excitation Energy Motion Including Radiative Decay;65 4.2.4;4 Mixed Quantum Classical Description;67 4.2.4.1;4.1 MD Simulations of the CC in a Solvent;68 4.2.4.2;4.2 Coulomb Interactions;70 4.2.4.3;4.3 Inuence of Intra Chromophore Vibrations;70 4.2.5;5 Mixed Description of Excitation Energy Transfer Dynamics;72 4.2.6;6 Mixed Description of Linear Absorption Spectra;73 4.2.6.1;6.1 Linear Response Theory Approach;74 4.2.6.2;6.2 Inclusion of Intra Chromophore Vibrations;75 4.2.6.3;6.3 Estimate of the Absorbance Using Adiabatic Exciton States;77 4.2.7;7 Mixed Description of Time and Frequency Resolved Emission;80 4.2.8;8 Conclusions;81 4.2.9;Acknowledgments;82 4.2.10;References;82 4.3;Conformational Structure and Dynamics from Single-Molecule FRET;86 4.3.1;1 Introduction;86 4.3.2;2 Measurement of conformational structure and dynamics via single-molecule FRET;88 4.3.2.1;2.1 Conformational structure;88 4.3.2.2;2.2 Conformational dynamics;90 4.3.2.3;2.3 Correlation between conformational structure and dynamics;92 4.3.3;3 Application to a model of a two-stranded coiled-coilpolypeptide;92 4.3.3.1;3.2 Conformational structure;96 4.3.3.2;3.3 Conformational dynamics;97 4.3.3.3;3.4 Correlation between conformational structure and dynamics;103 4.3.4;4 Discussion;109 4.3.5;Acknowledgement;111 4.3.6;References;111 5;The Many Facets of DNA;114 5.1;Quantum Mechanics in Biology: Photoexcitations in DNA;115 5.1.1;1 Quantum Biology;115 5.1.2;2 Excited state dynamics in DNA;117 5.1.3;3 Justi cation for a purely Exciton Model;119 5.1.3.1;3.1 Exciplexes, Excimers, and Excitons;120 5.1.3.2;3.2 Onsager criteria for intrachain charge-separated species.;123 5.1.3.3;3.3 Exciton coupling matrix elements;124 5.1.3.4;3.4 Exciton localization: disorder;126 5.1.4;4 Role of proton transfer;129 5.1.5;5 Summary;136 5.1.6;Acknowledgements;137 5.1.7;References;137 5.2;Energy Flow in DNA Duplexes;139 5.2.1;1 Motivations and simplifications;139 5.2.2;2 Absorption spectra: the sine qua non starting point;141 5.2.3;3 Time-resolved uorescence: one laser, two detection techniques;144 5.2.4;4 The unbearable complexity of the emission decays;145 5.2.5;5 Fluorescence anisotropy: a precious witness;