Statistical Mechanics of Biopolymers / Part I: |
Random Walk Models for the Conformation / 1: |
The Freely Jointed Chain / 1.1: |
Entropic Elasticity / 1.1.1: |
Force-Extension Relation / 1.1.2: |
Two-Component Model / 1.2: |
Two-Component Model with Interactions / 1.2.1: |
Problems |
Flory-Huggins Theory for Biopolymer Solutions / 2: |
Monomeric Solution / 2.1: |
Polymeric Solution / 2.2: |
Phase Transitions / 2.3: |
Stability Criterion / 2.3.1: |
Critical Coupling / 2.3.2: |
Phase Diagram / 2.3.3: |
Protein Electrostatics and Solvation / Part II: |
Implicit Continuum Solvent Models / 3: |
Potential of Mean Force / 3.1: |
Dielectric Continuum Model / 3.2: |
Born Model / 3.3: |
Charges in a Protein / 3.4: |
Generalized Born Models / 3.5: |
Debye-Hückel Theory / 4: |
Electrostatic Shielding by Mobile Charges / 4.1: |
1-1 Electrolytes / 4.2: |
Charged Sphere / 4.3: |
Charged Cylinder / 4.4: |
Charged Membrane (Goüy-Chapman Double Layer) / 4.5: |
Stern Modification of the Double Layer / 4.6: |
Protonation Equilibria / 5: |
Protonation Equilibria in Solution / 5.1: |
Protonation Equilibria in Proteins / 5.2: |
Protonation Enthalpy / 5.2.1: |
Protonation Enthalpy Relative to the Uncharged State / 5.2.3: |
Statistical Mechanics of Protonation / 5.2.4: |
Abnormal Titration Curves of Coupled Residues / 5.3: |
Reaction Kinetics / Part III: |
Formal Kinetics / 6: |
Elementary Chemical Reactions / 6.1: |
Reaction Variable and Reaction Rate / 6.2: |
Reaction Order / 6.3: |
Zero-Order Reactions / 6.3.1: |
First-Order Reactions / 6.3.2: |
Second-Order Reactions / 6.3.3: |
Dynamical Equilibrium / 6.4: |
Competing Reactions / 6.5: |
Consecutive Reactions / 6.6: |
Enzymatic Catalysis / 6.7: |
Reactions in Solutions / 6.8: |
Diffusion-Controlled Limit / 6.8.1: |
Reaction-Controlled Limit / 6.8.2: |
Kinetic Theory: Fokker-Planck Equation / 7: |
Stochastic Differential Equation for Brownian Motion / 7.1: |
Probability Distribution / 7.2: |
Diffusion / 7.3: |
Sharp Initial Distribution / 7.3.1: |
Absorbing Boundary / 7.3.2: |
Fokker-Planck Equation for Brownian Motion / 7.4: |
Stationary Solution to the Focker-Planck Equation / 7.5: |
Diffusion in an External Potential / 7.6: |
Large Friction Limit: Smoluchowski Equation / 7.7: |
Master Equation / 7.8: |
Kramers' Theory / 8: |
Kramers' Model / 8.1: |
Kramers' Calculation of the Reaction Rate / 8.2: |
Dispersive Kinetics / 9: |
Dichotomous Model / 9.1: |
Fast Solvent Fluctuations / 9.1.1: |
Slow Solvent Fluctuations / 9.1.2: |
Numerical Example (Fig. 9.3) / 9.1.3: |
Continuous Time Random Walk Processes / 9.2: |
Formulation of the Model / 9.2.1: |
Exponential Waiting Time Distribution / 9.2.2: |
Coupled Equations / 9.2.3: |
Power Time Law Kinetics / 9.3: |
Transport Processes / Part IV: |
Nonequilibrium Thermodynamics / 10: |
Continuity Equation for the Mass Density / 10.1: |
Energy Conservation / 10.2: |
Entropy Production / 10.3: |
Phenomenological Relations / 10.4: |
Stationary States / 10.5: |
Simple Transport Processes / 11: |
Heat Transport / 11.1: |
Diffusion in an External Electric Field / 11.2: |
Ion Transport Through a Membrane / 12: |
Diffusive Transport / 12.1: |
Goldman-Hodgkin-Katz Model / 12.2: |
Hodgkin-Huxley Model / 12.3: |
Reaction-Diffusion Systems / 13: |
Derivation / 13.1: |
Linearization / 13.2: |
Fitzhugh-Nagumo Model / 13.3: |
Reaction Rate Theory / Part V: |
Equilibrium Reactions / 14: |
Arrhenius Law / 14.1: |
Statistical Interpretation of the Equilibrium Constant / 14.2: |
Calculation of Reaction Rates / 15: |
Collision Theory / 15.1: |
Transition State Theory / 15.2: |
Comparison Between Collision Theory and Transition State Theory / 15.3: |
Thermodynamical Formulation of TSt / 15.4: |
Kinetic Isotope Effects / 15.5: |
General Rate Expressions / 15.6: |
The Flux Operator / 15.6.1: |
Marcus Theory of Electron Transfer / 16: |
Phenomenological Description of ET / 16.1: |
Simple Explanation of Marcus Theory / 16.2: |
Free Energy Contribution of the Nonequilibrium Polarization / 16.3: |
Activation Energy / 16.4: |
Simple Model Systems / 16.5: |
Charge Separation / 16.5.1: |
Charge Shift / 16.5.2: |
The Energy Gap as the Reaction Coordinate / 16.6: |
Inner-Shell Reorganization / 16.7: |
The Transmission Coefficient for Nonadiabatic Electron Transfer / 16.8: |
Elementary Photophysics / Part VI: |
Molecular States / 17: |
Born-Oppenheimer Separation / 17.1: |
Nonadiabatic Interaction / 17.2: |
Optical Transitions / 18: |
Dipole Transitions in the Condon Approximation / 18.1: |
Time Correlation Function Formalism / 18.2: |
The Displaced Harmonic Oscillator Model / 19: |
The Time Correlation Function in the Displaced Harmonic Oscillator Approximation / 19.1: |
High-Frequency Modes / 19.2: |
The Short-Time Approximation / 19.3: |
Spectral Diffusion / 20: |
Dephasing / 20.1: |
Gaussian Fluctuations / 20.2: |
Long Correlation Time / 20.2.1: |
Short Correlation Time / 20.2.2: |
Markovian Modulation / 20.3: |
Crossing of Two Electronic States / 21: |
Adiabatic and Diabatic States / 21.1: |
Semiclassical Treatment / 21.2: |
Application to Diabatic Et / 21.3: |
Crossing in More Dimensions / 21.4: |
Dynamics of an Excited State / 22: |
Green's Formalism / 22.1: |
Ladder Model / 22.2: |
A More General Ladder Model / 22.3: |
Application to the Displaced Oscillator Model / 22.4: |
Elementary Photoinduced Processes / Part VII: |
Photophysics of Chlorophylls and Carotenoids / 23: |
MO Model for the Electronic States / 23.1: |
The Free Electron Model for Polyenes / 23.2: |
The LCAO Approximation / 23.3: |
Hückel Approximation / 23.4: |
Simplified CI Model for Polyenes / 23.5: |
Cyclic Polyene as a Model for Porphyrins / 23.6: |
The Four Orbital Model for Porphyrins / 23.7: |
Energy Transfer Processes / 23.8: |
Incoherent Energy Transfer / 24: |
Excited States / 24.1: |
Interaction Matrix Element / 24.2: |
Multipole Expansion of the Excitonic Interaction / 24.3: |
Energy Transfer Rate / 24.4: |
Spectral Overlap / 24.5: |
Energy Transfer in the Triplet State / 24.6: |
Coherent Excitations in Photosynthetic Systems / 25: |
Coherent Excitations / 25.1: |
Strongly Coupled Dimers / 25.1.1: |
Excitonic Structure of the Reaction Center / 25.1.2: |
Circular Molecular Aggregates / 25.1.3: |
Dimerized Systems of LH2 / 25.1.4: |
Influence of Disorder / 25.2: |
Symmetry-Breaking Local Perturbation / 25.2.1: |
Periodic Modulation / 25.2.2: |
Diagonal Disorder / 25.2.3: |
Off-Diagonal Disorder / 25.2.4: |
Ultrafast Electron Transfer Processes in the Photosynthetic Reaction Center / 26: |
Proton Transfer in Biomolecules / 27: |
The Proton Pump Bacteriorhodopsin / 27.1: |
Nonadiabatic Proton Transfer (Small Coupling) / 27.2: |
Strongly Bound Protons / 27.4: |
Adiabatic Proton Transfer / 27.5: |
Molecular Motor Models / Part VIII: |
Continuous Ratchet Models / 28: |
Transport Equations / 28.1: |
Chemical Transitions / 28.2: |
The Two-State Model / 28.3: |
The Chemical Cycle / 28.3.1: |
The Fast Reaction Limit / 28.3.2: |
The Fast Diffusion Limit / 28.3.3: |
Operation Close to Thermal Equilibrium / 28.4: |
Discrete Ratchet Models / 29: |
Linear Model with Two Internal States / 29.1: |
Appendix / Part IX: |
The Grand Canonical Ensemble / A: |
Grand Canonical Distribution / A.l: |
Connection to Thermodynamics / A.2: |
Time Correlation Function of the Displaced Harmonic Oscillator Model / B: |
Evaluation of the Time Correlation Function / B.l: |
Boson Algebra / B.2: |
Derivation of Theorem 1 / B.2.1: |
Derivation of Theorem 2 / B.2.2: |
Derivation of Theorem 3 / B.2.3: |
Derivation of Theorem 4 / B.2.4: |
The Saddle Point Method / C: |
Solutions |
References |
Index |
Statistical Mechanics of Biopolymers / Part I: |
Random Walk Models for the Conformation / 1: |
The Freely Jointed Chain / 1.1: |