Burghardt / May Energy Transfer Dynamics in Biomaterial Systems

1. Auflage 2009
ISBN: 978-3-642-02306-4
Verlag: Springer
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 476 Seiten

The role of quantum coherence in promoting the e ciency of the initial stages of photosynthesis is an open and intriguing question. Lee, Cheng, and Fleming, Science 316, 1462 (2007) The understanding and design of functional biomaterials is one of today’s grand challenge areas that has sparked an intense exchange between biology, materials sciences, electronics, and various other disciplines. Many new - velopments are underway in organic photovoltaics, molecular electronics, and biomimetic research involving, e. g. , arti cal light-harvesting systems inspired by photosynthesis, along with a host of other concepts and device applications. In fact, materials scientists may well be advised to take advantage of Nature’s 3. 8 billion year head-start in designing new materials for light-harvesting and electro-optical applications. Since many of these developments reach into the molecular domain, the - derstanding of nano-structured functional materials equally necessitates f- damental aspects of molecular physics, chemistry, and biology. The elementary energy and charge transfer processes bear much similarity to the molecular phenomena that have been revealed in unprecedented detail by ultrafast op- cal spectroscopies. Indeed, these spectroscopies, which were initially developed and applied for the study of small molecular species, have already evolved into an invaluable tool to monitor ultrafast dynamics in complex biological and materials systems. The molecular-level phenomena in question are often of intrinsically quantum mechanical character, and involve tunneling, non-Born- Oppenheimer e ects, and quantum-mechanical phase coherence.

Autoren/Hrsg.

Burghardt, Irene

May, V.

Inhaltsverzeichnis

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;147
5.2.6;6 Just a qualitative picture;150
5.2.7;Acknowledgements;152
5.2.8;References;152
5.3;Anharmonic Vibrational Dynamics of DNA Oligomers;155
5.3.1;1 Introduction;155
5.3.2;2 Microsolvated AT Base Pairs;158
5.3.2.1;2.1 Fundamental Transitions Using a Dual Level Approach;158
5.3.2.2;2.2 Anharmonic Coupling Patterns;163
5.3.3;3 Experimental Section;165
5.3.3.1;3.1 Methods;165
5.3.3.2;3.2 Experimental Results;166
5.3.4;4 Discussion;172
5.3.5;Acknowledgment;173
5.3.6;References;173
5.4;Simulation Study of the Molecular Mechanism of Intercalation of the Anti-Cancer Drug Daunomycin into DNA;177
5.4.1;1 Introduction;177
5.4.2;2 Simulation Details;179
5.4.2.1;2.1 Construction of the Intercalated and the Minor Groove-bound States;179
5.4.2.2;2.2 Force eld and Equilibration;180
5.4.2.3;2.3 Simulation Approach;182
5.4.3;3 Results and Discussion;183
5.4.3.1;3.1 Structural Changes in DNA during Intercalation: Rise and Roll;184
5.4.3.2;3.2 Potential of Mean Force of Intercalation;185
5.4.3.3;3.3 Minor Groove-bound State Analysis;186
5.4.3.4;3.4 Minor Groove-bound to Intercalated State Transition;186
5.4.3.5;3.5 Two dimensional (2D) Free Energy Landscape of Daunomycin Intercalation;187
5.4.3.6;3.6 Comparison with Experimental Kinetics Results;188
5.4.4;4 Concluding Remarks;190
5.4.5;Acknowledgment;190
5.4.6;References;190
6;Quantum Dynamics and Transport atInterfaces and Junctions;193
6.1;Ultrafast Photophysics of Organic Semiconductor Junctions;194
6.1.1;1 Introduction;194
6.1.2;2 Overview of interfacial electronic states of polymer heterojunctions;197
6.1.2.1;2.1 Energetics of a type-II heterojunction;197
6.1.2.2;2.2 Electronic structure calculations of interfacial singlet states;199
6.1.2.3;2.3 Triplet states at the heterojunction;201
6.1.3;3 Electron-phonon Hamiltonian;202
6.1.3.1;3.1 Two-band con guration interaction lattice model;203
6.1.3.2;3.2 Diabatic representation;204
6.1.4;4 Vibronic coupling in many dimensions: conicalintersections and e ective modes;205
6.1.4.1;4.1 LVC model and e ective modes;205
6.1.4.2;4.2 Hierarchical electron-phonon (HEP) representation;207
6.1.4.3;4.3 Dissipative closure of the HEP model;209
6.1.4.4;4.4 Generalization to three and more states;210
6.1.5;5 Quantum dynamics of exciton dissociation at a polymer heterojunction;211
6.1.5.1;5.1 Two-state XT-CT model;212
6.1.5.2;5.2 Three-state XT-CT-IS model;215
6.1.6;6 Discussion and Conclusions;218
6.1.7;Acknowledgments;220
6.1.8;References;220
6.2;Green Function Techniques in the Treatment of Quantum Transport at the Molecular Scale;224
6.2.1;1 Introduction;224
6.2.1.1;Recent experiments;225
6.2.1.2;Theoretical methods;225
6.2.1.3;General nanoscale quantum transport theory;227
6.2.1.4;Atomistic transport theory;230
6.2.1.5;Outline;230
6.2.2;2 From coherent transport to sequential tunneling (basics);231
6.2.2.1;2.1 Coherent transport: single-particle Green functions;231
6.2.2.2;2.2 Interacting nanosystems and master equation method;240
6.2.2.2.1;Tunneling and master equation;241
6.2.2.2.2;Vibrons and Franck-Condon blockade;254
6.2.3;3 Nonequilibrium Green function theory of transport;266
6.2.3.1;3.1 Standard transport model: a nanosystem between ideal leads;266
6.2.3.2;3.2 Nonequilibrium Green functions: definition and properties;270
6.2.3.2.1;Spectral - retarded (GR) and advanced (GA) functions;270
6.2.3.2.2;Kinetic - lesser (G<) and greater (G>) functions;274
6.2.3.2.3;Interaction representation;278
6.2.3.2.4;Schwinger-Keldysh time contour and contour functions;281
6.2.3.3;3.3 Current through a nanosystem: Meir-Wingreen-Jauho formula;284
6.2.3.4;3.4 Nonequilibrium equation of motion method;286
6.2.3.5;3.5 Kadano -Baym-Keldysh method;289
6.2.4;4 Applications;296
6.2.4.1;4.1 Coulomb blockade;296
6.2.4.1.1;Nonequilibrium EOM formalism;297
6.2.4.1.2;Anderson impurity model (single site);299
6.2.4.1.3;Double quantum dot (two sites);304
6.2.4.2;4.2 Nonequilibrium vibrons;310
6.2.4.2.1;Nonequilibrium Dyson-Keldysh method;311
6.2.4.2.2;Single-level model: spectroscopy of vibrons;314
6.2.4.2.3;Multi-level model: nonequilibrium vibrons;318
6.2.4.3;4.3 Coupling to a vibrational continuum: dissipation andrenormalization;323
6.2.4.3.1;The model Hamiltonian;323
6.2.4.3.2;Limiting cases;329
6.2.5;5 Conclusions and Perspectives;336
6.2.6;Acknowledgments;337
6.2.7;References;338
7;New Methods for Open Systems Dynamics;347
7.1;Time-Local Quantum Master Equations and their Applications to Dissipative Dynamics and Molecular Wires;348
7.1.1;1 Introduction;348
7.1.2;2 Spectral densities and correlations functions;349
7.1.2.1;2.1 Bosonic bath;350
7.1.2.2;2.2 Fermionic reservoirs;352
7.1.3;3 Dissipative dynamics;353
7.1.3.1;3.1 Model and quantum master equation;353
7.1.3.2;3.2 Time-independent systems;356
7.1.3.3;3.3 Time-dependent systems;356
7.1.3.4;3.4 Example: damped harmonic oscillator;357
7.1.3.5;3.5 Absorption spectra;360
7.1.4;4 Molecular wires;361
7.1.4.1;4.1 Model and quantum master equation;361
7.1.4.2;4.2 Auxiliary operators;363
7.1.4.3;4.3 Switching electron transport with laser pulses;363
7.1.5;5 Concluding remarks;365
7.1.5.1;Acknowledgement;366
7.1.5.2;Appendix;367
7.1.5.3;5.1 Nakajima-Zwanzig identity;367
7.1.5.4;5.2 Hashitsume-Shibata-Takahashi identity;368
7.1.6;References;369
7.2;Reduced Density Matrix Equations forCombined Instantaneous and Delayed Dissipation in Many-Atom Systems, and their Numerical Treatment;371
7.2.1;1 Introduction;371
7.2.2;2 Density operator treatment;374
7.2.2.1;2.1 Equation for the reduced density operator;374
7.2.2.2;2.2 Competing Instantaneous and Delayed Dissipation;377
7.2.2.2.1;Instantaneous dissipation;378
7.2.2.2.2;Delayed dissipation;379
7.2.3;3 Computational method;380
7.2.3.1;3.1 Matrix Equations in a Basis Set;380
7.2.3.2;3.2 Numerical Procedure;381
7.2.4;4 Application to adsorbates;382
7.2.4.1;4.1 A model for adsorbates;382
7.2.4.2;4.2 CO/Cu(001) dissipative dynamics;382
7.2.5;5 Conclusion;386
7.2.6;Acknowledgements;387
7.2.7;References;387
8;New Methods for Mixing Quantum and Classical Mechanics;389
8.1;Quantum Dynamics in Almost Classical Environments;390
8.1.1;1 Introduction;390
8.1.2;2 Quantum-Classical Liouville Dynamics;391
8.1.3;3 Representations and Solutions;394
8.1.3.1;3.1 The subsystem basis;395
8.1.3.2;3.2 The adiabatic basis;396
8.1.3.3;3.3 The force basis;399
8.1.3.4;3.4 The mapping basis;400
8.1.4;4 Approximations to the QCL equation;402
8.1.4.1;4.1 Mean eld theory;402
8.1.4.2;4.2 Surface-hopping dynamics;404
8.1.5;5 Observables and correlation functions;407
8.1.6;6 Example reaction rate calculation;410
8.1.7;6.1 Simulation results;411
8.1.8;7 Conclusions;415
8.1.9;Acknowledgements;416
8.1.10;References;416
8.2;Trajectory Based Simulations of Quantum-Classical Systems;421
8.2.1;1 Introduction;421
8.2.2;2 Quantum-Classical Liouville Dynamics;423
8.2.2.1;2.1 Evolution equation;423
8.2.2.2;2.2 Simulation of expectation values;424
8.2.3;3 Iterative Linearized Density Matrix Propagation;428
8.2.3.1;3.1 Theory;429
8.2.3.2;3.2 Implementation;432
8.2.4;4 Model Simulations;434
8.2.5;5 Conclusion;439
8.2.6;Acknowledgements;440
8.2.7;References;440
8.3;Do We Have a Consistent Non-Adiabatic Quantum-Classical Statistical Mechanics?;443
8.3.1;1 Introduction;443
8.3.2;2 Heisenberg group description;447
8.3.3;3 Quantum mechanics;452
8.3.4;4 Classical mechanics;455
8.3.5;5 Mixed quantum-classical dynamics;457
8.3.6;6 Comments;463
8.3.7;7 Conclusion;468
8.3.8;Appendix 1;469
8.3.9;Appendix 2;471
8.3.10;References;473
9;Index;474