Energy Transfer Dynamics in Biomaterial Systems (eBook)

Irene Burghardt, V. May, David A. Micha, E. R. Bittner (Herausgeber)

eBook Download: PDF

2009 | 2009
XVI, 476 Seiten
Springer Berlin (Verlag)
978-3-642-02306-4 (ISBN)

Infos

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.

Inhalt

Preface 6
Contents 9
List of Contributors 11
Excitation Energy Transfer in Complex Molecular and Biological Systems 16
Electronic Energy Transfer in Photosynthetic Antenna Systems 17
1 Introduction 17
2 Overview of photosynthetic organisms and theirLight-Harvesting Antenna complexes 18
2.1 Introduction 18
2.2 Antenna complexes: evolutionary point of view 19
2.3 Classes of Antenna: structure and function 24
LH1 and LH2 antenna complexes 25
Chlorosomes and FMO protein 26
LHC family 27
Phycobiliproteins and Phycobilisomes (PBS) 28
Peridinin-Chl a-protein (PCP) 29
2.4 Dynamics of EET: an example 29
3 The mechanism of EET: Perspective from theory 33
3.1 Introduction 33
3.2 F orster theory for donor-acceptor pairs 34
3.3 Electronic coupling 36
3.4 Solvent screening 40
3.5 Spectral Overlap 42
3.6 Special attributes of multichromophoric systems 43
4 Summary and conclusions 43
Acknowledgements 44
References 44
Mixed Quantum Classical Simulations of Electronic Excitation Energy Transfer and Related Optical Spectra: Supramolecular Pheophorbide {a Complexes in Solution 49
1 Introduction 49
2 The Model for the Chromophore Complex in a Solvent 54
2.1 The Chromophore Complex Hamiltonian 54
2.2 Standard Exciton Hamiltonian 57
2.3 The Coulomb Interaction Matrix Element 58
2.4 Inclusion of Solvent Molecules 59
2.5 Adiabatic Exciton States 60
3 Full Quantum Dynamical Description 61
3.1 Excitation Energy Transfer 61
3.2 Linear Absorption Spectra 62
3.3 Spectra of Time and Frequency Resolved Luminescence 63
Density Matrix Theory of Excitation Energy Motion Including Radiative Decay 65
4 Mixed Quantum Classical Description 67
4.1 MD Simulations of the CC in a Solvent 68
4.2 Coulomb Interactions 70
4.3 Inuence of Intra Chromophore Vibrations 70
5 Mixed Description of Excitation Energy Transfer Dynamics 72
6 Mixed Description of Linear Absorption Spectra 73
6.1 Linear Response Theory Approach 74
6.2 Inclusion of Intra Chromophore Vibrations 75
6.3 Estimate of the Absorbance Using Adiabatic Exciton States 77
7 Mixed Description of Time and Frequency Resolved Emission 80
8 Conclusions 81
Acknowledgments 82
References 82
Conformational Structure and Dynamics from Single-Molecule FRET 86
1 Introduction 86
2 Measurement of conformational structure and dynamics via single-molecule FRET 88
2.1 Conformational structure 88
2.2 Conformational dynamics 90
2.3 Correlation between conformational structure and dynamics 92
3 Application to a model of a two-stranded coiled-coilpolypeptide 92
3.2 Conformational structure 96
3.3 Conformational dynamics 97
3.4 Correlation between conformational structure and dynamics 103
4 Discussion 109
Acknowledgement 111
References 111
The Many Facets of DNA 114
Quantum Mechanics in Biology: Photoexcitations in DNA 115
1 Quantum Biology 115
2 Excited state dynamics in DNA 117
3 Justi cation for a purely Exciton Model 119
3.1 Exciplexes, Excimers, and Excitons 120
3.2 Onsager criteria for intrachain charge-separated species. 123
3.3 Exciton coupling matrix elements 124
3.4 Exciton localization: disorder 126
4 Role of proton transfer 129
5 Summary 136
Acknowledgements 137
References 137
Energy Flow in DNA Duplexes 139
1 Motivations and simplifications 139
2 Absorption spectra: the sine qua non starting point 141
3 Time-resolved uorescence: one laser, two detection techniques 144
4 The unbearable complexity of the emission decays 145
5 Fluorescence anisotropy: a precious witness 147
6 Just a qualitative picture 150
Acknowledgements 152
References 152
Anharmonic Vibrational Dynamics of DNA Oligomers 155
1 Introduction 155
2 Microsolvated AT Base Pairs 158
2.1 Fundamental Transitions Using a Dual Level Approach 158
2.2 Anharmonic Coupling Patterns 163
3 Experimental Section 165
3.1 Methods 165
3.2 Experimental Results 166
4 Discussion 172
Acknowledgment 173
References 173
Simulation Study of the Molecular Mechanism of Intercalation of the Anti-Cancer Drug Daunomycin into DNA 177
1 Introduction 177
2 Simulation Details 179
2.1 Construction of the Intercalated and the Minor Groove-bound States 179
2.2 Force eld and Equilibration 180
2.3 Simulation Approach 182
3 Results and Discussion 183
3.1 Structural Changes in DNA during Intercalation: Rise and Roll 184
3.2 Potential of Mean Force of Intercalation 185
3.3 Minor Groove-bound State Analysis 186
3.4 Minor Groove-bound to Intercalated State Transition 186
3.5 Two dimensional (2D) Free Energy Landscape of Daunomycin Intercalation 187
3.6 Comparison with Experimental Kinetics Results 188
4 Concluding Remarks 190
Acknowledgment 190
References 190
Quantum Dynamics and Transport atInterfaces and Junctions 193
Ultrafast Photophysics of Organic Semiconductor Junctions 194
1 Introduction 194
2 Overview of interfacial electronic states of polymer heterojunctions 197
2.1 Energetics of a type-II heterojunction 197
2.2 Electronic structure calculations of interfacial singlet states 199
2.3 Triplet states at the heterojunction 201
3 Electron-phonon Hamiltonian 202
3.1 Two-band con guration interaction lattice model 203
3.2 Diabatic representation 204
4 Vibronic coupling in many dimensions: conicalintersections and e ective modes 205
4.1 LVC model and e ective modes 205
4.2 Hierarchical electron-phonon (HEP) representation 207
4.3 Dissipative closure of the HEP model 209
4.4 Generalization to three and more states 210
5 Quantum dynamics of exciton dissociation at a polymer heterojunction 211
5.1 Two-state XT-CT model 212
5.2 Three-state XT-CT-IS model 215
6 Discussion and Conclusions 218
Acknowledgments 220
References 220
Green Function Techniques in the Treatment of Quantum Transport at the Molecular Scale 224
1 Introduction 224
Recent experiments 225
Theoretical methods 225
General nanoscale quantum transport theory 227
Atomistic transport theory 230
Outline 230
2 From coherent transport to sequential tunneling (basics) 231
2.1 Coherent transport: single-particle Green functions 231
2.2 Interacting nanosystems and master equation method 240
Tunneling and master equation 241
Vibrons and Franck-Condon blockade 254
3 Nonequilibrium Green function theory of transport 266
3.1 Standard transport model: a nanosystem between ideal leads 266
3.2 Nonequilibrium Green functions: definition and properties 270
Spectral - retarded (GR) and advanced (GA) functions 270
Kinetic - lesser (G< ) and greater (G>
Interaction representation 278
Schwinger-Keldysh time contour and contour functions 281
3.3 Current through a nanosystem: Meir-Wingreen-Jauho formula 284
3.4 Nonequilibrium equation of motion method 286
3.5 Kadano -Baym-Keldysh method 289
4 Applications 296
4.1 Coulomb blockade 296
Nonequilibrium EOM formalism 297
Anderson impurity model (single site) 299
Double quantum dot (two sites) 304
4.2 Nonequilibrium vibrons 310
Nonequilibrium Dyson-Keldysh method 311
Single-level model: spectroscopy of vibrons 314
Multi-level model: nonequilibrium vibrons 318
4.3 Coupling to a vibrational continuum: dissipation andrenormalization 323
The model Hamiltonian 323
Limiting cases 329
5 Conclusions and Perspectives 336
Acknowledgments 337
References 338
New Methods for Open Systems Dynamics 347
Time-Local Quantum Master Equations and their Applications to Dissipative Dynamics and Molecular Wires 348
1 Introduction 348
2 Spectral densities and correlations functions 349
2.1 Bosonic bath 350
2.2 Fermionic reservoirs 352
3 Dissipative dynamics 353
3.1 Model and quantum master equation 353
3.2 Time-independent systems 356
3.3 Time-dependent systems 356
3.4 Example: damped harmonic oscillator 357
3.5 Absorption spectra 360
4 Molecular wires 361
4.1 Model and quantum master equation 361
4.2 Auxiliary operators 363
4.3 Switching electron transport with laser pulses 363
5 Concluding remarks 365
Acknowledgement 366
Appendix 367
5.1 Nakajima-Zwanzig identity 367
5.2 Hashitsume-Shibata-Takahashi identity 368
References 369
Reduced Density Matrix Equations forCombined Instantaneous and Delayed Dissipation in Many-Atom Systems, and their Numerical Treatment 371
1 Introduction 371
2 Density operator treatment 374
2.1 Equation for the reduced density operator 374
2.2 Competing Instantaneous and Delayed Dissipation 377
Instantaneous dissipation 378
Delayed dissipation 379
3 Computational method 380
3.1 Matrix Equations in a Basis Set 380
3.2 Numerical Procedure 381
4 Application to adsorbates 382
4.1 A model for adsorbates 382
4.2 CO/Cu(001) dissipative dynamics 382
5 Conclusion 386
Acknowledgements 387
References 387
New Methods for Mixing Quantum and Classical Mechanics 389
Quantum Dynamics in Almost Classical Environments 390
1 Introduction 390
2 Quantum-Classical Liouville Dynamics 391
3 Representations and Solutions 394
3.1 The subsystem basis 395
3.2 The adiabatic basis 396
3.3 The force basis 399
3.4 The mapping basis 400
4 Approximations to the QCL equation 402
4.1 Mean eld theory 402
4.2 Surface-hopping dynamics 404
5 Observables and correlation functions 407
6 Example reaction rate calculation 410
6.1 Simulation results 411
7 Conclusions 415
Acknowledgements 416
References 416
Trajectory Based Simulations of Quantum-Classical Systems 421
1 Introduction 421
2 Quantum-Classical Liouville Dynamics 423
2.1 Evolution equation 423
2.2 Simulation of expectation values 424
3 Iterative Linearized Density Matrix Propagation 428
3.1 Theory 429
3.2 Implementation 432
4 Model Simulations 434
5 Conclusion 439
Acknowledgements 440
References 440
Do We Have a Consistent Non-Adiabatic Quantum-Classical Statistical Mechanics? 443
1 Introduction 443
2 Heisenberg group description 447
3 Quantum mechanics 452
4 Classical mechanics 455
5 Mixed quantum-classical dynamics 457
6 Comments 463
7 Conclusion 468
Appendix 1 469
Appendix 2 471
References 473
Index 474

Produkt-Details

• Erscheint lt. Verlag: 22.9.2009
• Reihe/Serie: Springer Series in Chemical Physics
• Zusatzinfo: XVI, 476 p. 133 illus., 51 illus. in color.
• Verlagsort: Berlin
• Sprache: englisch
• Themenwelt: Naturwissenschaften ► Biologie
• Themenwelt: Naturwissenschaften ► Chemie
• Themenwelt: Naturwissenschaften ► Physik / Astronomie
• Themenwelt: Technik ► Maschinenbau
• Schlagworte: Aster • Biomaterial • biomaterials • charge transfer • Condensed Matter • DNA • Electronics • Energy Transport • FRET • Molecular electronics • quantum dynamics • Reaction • semiconductor • spectroscopy • Transport
• ISBN-10: 3-642-02306-1 / 3642023061
• ISBN-13: 978-3-642-02306-4 / 9783642023064