6.4.3 The Noncrossing Rule -- 6.4.4 Landau-Zener Model -- 6.4.5 Berry's Phase or Geometric Phase -- 6.5 Photosynthetic Electron Transfer Controlledby Protein Relaxation -- 6.6 Model Hamiltonian -- 6.7 Dependence of the Rate Constant on Electron Position -- 6.8 Program 61, Matlab Code -- 6.9 Program 62, Matlab Code -- References -- 7 Entanglement, Coherence and Decoherence -- 7.1 Entanglement -- 7.2 Coherence and Decoherence -- 7.2.1 Experiment on Coherence -- 7.3 Example of Decoherence -- 7.3.1 The Quantum Langevin Equation -- 7.4 The Spin-Boson Model in Photosynthesis -- 7.4.1 Independent Boson Model -- 7.4.2 The Spectral Density Function -- 7.4.3 Time Evolution of the Density Matrix -- 7.5 The Liouville Equation for the Two-State Density Matrix -- 7.5.1 Obtention of the Parameters -- 7.5.2 Rabi Cycle -- 7.6 The Caldeira-Leggett Master Equation -- 7.6.1 Decoherence Time -- References -- 8 Excitons -- 8.1 Chlorophyll Excitations in the Fenna-Matthews-Olson Complex -- 8.2 Förster Theory of Fluorescent Resonance Energy in Pigment-Protein Complexes -- 8.3 Program 8.1, Matlab Code -- 8.4 Program 8.2, Matlab Code -- References -- 9 Long Wavelength Quantum Energy Exchange and Its Possible Role in Cellular Recognition and Communication -- 9.1 Introduction -- 9.2 Basic Ideas of Rytov's Theory -- 9.3 The Poynting Vector in Medium 3 -- 9.4 The Electric Field in Medium 3 -- 9.5 Integrations of the Electric Field Fourier's Squared Component -- 9.5.1 Preliminary Definitions -- 9.5.2 Another Computing Version -- 9.6 Program 9.1, Fortran Code -- 9.7 Program 9.2, Fortran Code -- 9.8 Program 9.3, Fortran Code -- References -- A Appendix -- A.1 Forced Oscillations -- A.2 Damped Oscillations -- A.2.1 Classification -- A.2.2 Summary -- A.2.2.1 (a) Overdamped Oscillations, γ2 ω0 -- A.2.2.2 (b) Underdamped Oscillations, γ2 < -- ω0. |