Title Theoretical molecular biophysics / Philipp Scherer and Sighart F. Fischer

Published Berlin ; Heidelberg : Springer-Verlag, ©2010

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Description 1 online resource (xiii, 371 pages) Series Biological and medical physics, biomedical engineering Biological and medical physics, biomedical engineering. Contents Note continued: 6.8.1. Diffusion-Controlled Limit -- 6.8.2. Reaction-Controlled Limit -- Problems -- 7. Kinetic Theory: Fokker -- Planck Equation -- 7.1. Stochastic Differential Equation for Brownian Motion -- 7.2. Probability Distribution -- 7.3. Diffusion -- 7.3.1. Sharp Initial Distribution -- 7.3.2. Absorbing Boundary -- 7.4. Fokker-Planck Equation for Brownian Motion -- 7.5. Stationary Solution to the Focker-Planck Equation -- 7.6. Diffusion in an External Potential -- 7.7. Large Friction Limit: Smoluchowski Equation -- 7.8. Master Equation -- Problems -- 8. Kramers' Theory -- 8.1. Kramers' Model -- 8.2. Kramers' Calculation of the Reaction Rate -- 9. Dispersive Kinetics -- 9.1. Dichotomous Model -- 9.1.1. Fast Solvent Fluctuations -- 9.1.2. Slow Solvent Fluctuations -- 9.1.3. Numerical Example (Fig. 9.3) -- 9.2. Continuous Time Random Walk Processes -- 9.2.1. Formulation of the Model -- 9.2.2. Exponential Waiting Time Distribution -- 9.2.3. Coupled Equations -- 9.3. Power Time Law Kinetics -- Problems -- pt. IV Transport Processes -- 10. Nonequilibrium Thermodynamics -- 10.1. Continuity Equation for the Mass Density -- 10.2. Energy Conservation -- 10.3. Entropy Production -- 10.4. Phenomenological Relations -- 10.5. Stationary States -- Problems -- 11. Simple Transport Processes -- 11.1. Heat Transport -- 11.2. Diffusion in an External Electric Field -- Problems -- 12. Ion Transport Through a Membrane -- 12.1. Diffusive Transport -- 12.2. Goldman-Hodgkin-Katz Model -- 12.3. Hodgkin-Huxley Model -- 13. Reaction -- Diffusion Systems -- 13.1. Derivation -- 13.2. Linearization -- 13.3. Fitzhugh-Nagumo Model -- pt. V Reaction Rate Theory -- 14. Equilibrium Reactions -- 14.1. Arrhenius Law -- 14.2. Statistical Interpretation of the Equilibrium Constant -- 15. Calculation of Reaction Rates Note continued: 15.1. Collision Theory -- 15.2. Transition State Theory -- 15.3. Comparison Between Collision Theory and Transition State Theory -- 15.4. Thermodynamical Formulation of TST -- 15.5. Kinetic Isotope Effects -- 15.6. General Rate Expressions -- 15.6.1. Flux Operator -- Problems -- 16. Marcus Theory of Electron Transfer -- 16.1. Phenomenological Description of ET -- 16.2. Simple Explanation of Marcus Theory -- 16.3. Free Energy Contribution of the Nonequilibrium Polarization -- 16.4. Activation Energy -- 16.5. Simple Model Systems -- 16.5.1. Charge Separation -- 16.5.2. Charge Shift -- 16.6. Energy Gap as the Reaction Coordinate -- 16.7. Inner-Shell Reorganization -- 16.8. Transmission Coefficient for Nonadiabatic Electron Transfer -- Problems -- pt. VI Elementary Photophysics -- 17. Molecular States -- 17.1. Born-Oppenheimer Separation -- 17.2. Nonadiabatic Interaction -- 18. Optical Transitions -- 18.1. Dipole Transitions in the Condon Approximation -- 18.2. Time Correlation Function Formalism -- Problems -- 19. Displaced Harmonic Oscillator Model -- 19.1. Time Correlation Function in the Displaced Harmonic Oscillator Approximation -- 19.2. High-Frequency Modes -- 19.3. Short-Time Approximation -- 20. Spectral Diffusion -- 20.1. Dephasing -- 20.2. Gaussian Fluctuations -- 20.2.1. Long Correlation Time -- 20.2.2. Short Correlation Time -- 20.3. Markovian Modulation -- Problems -- 21. Crossing of Two Electronic States -- 21.1. Adiabatic and Diabatic States -- 21.2. Semiclassical Treatment -- 21.3. Application to Diabatic ET -- 21.4. Crossing in More Dimensions -- Problems -- 22. Dynamics of an Excited State -- 22.1. Green's Formalism -- 22.2. Ladder Model -- 22.3. More General Ladder Model -- 22.4. Application to the Displaced Oscillator Model -- Problems Note continued: pt. VII Elementary Photoinduced Processes -- 23. Photophysics of Chlorophylls and Carotenoids -- 23.1. MO Model for the Electronic States -- 23.2. Free Electron Model for Polyenes -- 23.3. LCAO Approximation -- 23.4. Hucker Approximation -- 23.5. Simplified CI Model for Polyenes -- 23.6. Cyclic Polyene as a Model for Porphyrins -- 23.7. Four Orbital Model for Porphyrins -- 23.8. Energy Transfer Processes -- Problems -- 24. Incoherent Energy Transfer -- 24.1. Excited States -- 24.2. Interaction Matrix Element -- 24.3. Multipole Expansion of the Excitonic Interaction -- 24.4. Energy Transfer Rate -- 24.5. Spectral Overlap -- 24.6. Energy Transfer in the Triplet State -- 25. Coherent Excitations in Photosynthetic Systems -- 25.1. Coherent Excitations -- 25.1.1. Strongly Coupled Dimers -- 25.1.2. Excitonic Structure of the Reaction Center -- 25.1.3. Circular Molecular Aggregates -- 25.1.4. Dimerized Systems of LH2 -- 25.2. Influence of Disorder -- 25.2.1. Symmetry-Breaking Local Perturbation -- 25.2.2. Periodic Modulation -- 25.2.3. Diagonal Disorder -- 25.2.4. Off-Diagonal Disorder -- Problems -- 26. Ultrafast Electron Transfer Processes in the Photosynthetic Reaction Center -- 27. Proton Transfer in Biomolecules -- 27.1. Proton Pump Bacteriorhodopsin -- 27.2. Born-Oppenheimer Separation -- 27.3. Nonadiabatic Proton Transfer (Small Coupling) -- 27.4. Strongly Bound Protons -- 27.5. Adiabatic Proton Transfer -- pt. VIII Molecular Motor Models -- 28. Continuous Ratchet Models -- 28.1. Transport Equations -- 28.2. Chemical Transitions -- 28.3. Two-State Model -- 28.3.1. Chemical Cycle -- 28.3.2. Fast Reaction Limit -- 28.3.3. Fast Diffusion Limit -- 28.4. Operation Close to Thermal Equilibrium -- Problems -- 29. Discrete Ratchet Models -- 29.1. Linear Model with Two Internal States Note continued: pt. IX Appendix -- A. Grand Canonical Ensemble -- A.1. Grand Canonical Distribution -- A.2. Connection to Thermodynamics -- B. Time Correlation Function of the Displaced Harmonic Oscillator Model -- B.1. Evaluation of the Time Correlation Function -- B.2. Boson Algebra -- B.2.1. Derivation of Theorem 1 -- B.2.2. Derivation of Theorem 2 -- B.2.3. Derivation of Theorem 3 -- B.2.4. Derivation of Theorem 4 -- C. Saddle Point Method Summary Theoretical Molecular Biophysics is an advanced study book for students, shortly before or after completing undergraduate studies, in physics, chemistry or biology. It provides the tools for an understanding of elementary processes in biology, such as photosynthesis on a molecular level. A basic knowledge in Mechanics, Electrostatics, Quantum Theory and Statistical Physics is desirable. The reader will be exposed to basic concepts in modern biophysics such as entropic forces, phase separation, potentials of mean force, proton and electron transfer, heterogeneous reactions coherent and incoherent energy transfer as well as molecular motors. --Book Jacket Analysis fysica physics biofysica biophysics engineering biomedische techniek biomedical engineering toegepaste wiskunde applied mathematics quantumfysica quantum physics Physics (General) Fysica (algemeen) Notes Print version record Subject Molecular biology. Molecular Biology molecular biology. Physique. Molecular biology Form Electronic book Author Fischer, Sighart F. ISBN 9783540856108 3540856102

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