目次

1. Introduction : Biological Systems, and Physical ApproachesBring Physics to Life, Bring Life to Physics. Part A: Equilibrium Structures and Properties. 2. Basic Concepts of Relevant Thermodynamics. 2.1 The First Law and Thermodynamic Potentials. 2.2 The Second Law and Thermodynamic Variational Principles. 3. Basic Methods of Equilibrium Statistical Physics. 3.1 Boltzmann’s Entropy and Probability, Microcanonical Ensemble Theory for Thermodynamics. 3.2 Canonical Ensemble Theory. 3.3 The Gibbs Canonical Ensemble. 3.4 Grand Canonical Ensemble Theory. 4. Statistical Mechanics of Fluids and Solutions. 4.1 Phase-space Description of Fluids. 4.2 Fluids of Non-interacting Particles. 4.3 Fluids of Interacting Particles. 4.4 Extension to Solutions: Coarse-grained Descriptions. 5. The Coarse-grained Descriptions for Biological Complexes. 6. Water and Weak Electrostatic Interactions. 6.1 Thermodynamic Properties of Water. 6.2 The Weak Electrostatic Interactions in Water. 6.3 Screened Coulomb Interaction. 7. Law of Chemical Forces: Reaction, Transitions, and Self-assembly. 7.1 Law of Mass Action (LMA). 7.2 Self-Assembly. 8. Lattice and Ising Models. 8.1 Adsorption and Aggregation of Molecules. 8.2 Mixing and Phase Separation of Binary Mixtures. 8.3 The 1-D Ising Model and Applications. 9. Response, Fluctuations, Correlations, and Scatterings. 9.1 Linear Responses and Fluctuations: Fluctuation-Response Theorem. 9.2 Scatterings, Fluctuations, and Structures of Matter. 10. Mesoscopic model for Polymers: Flexible Chains. 10.1 Random Walk Model for a Flexible Chain. 10.2 The Flexible Chain under External Fields and Confinements. 10.3 Effects of Segmental Interactions: Polymer Exclusion and Condensation. 10.4 Scaling Theory. 11. Mesoscopic model for Polymers: Semi-flexible Chain Model and Polyelectrolytes. 11.1 Worm-like chain model. 11.2 Fluctuations in nearly straight semiflexible chains and the force-extension relation. 11.3 Polyelecrolytes. 12. Membranes and Elastic Surfaces. 12.1 Membrane Self-assembly and Phase Transition. 12.2 Mesoscopic Model for Elastic Energies and Shapes. 12.3 Effects of Thermal Undulations. Part B: Non-equilibrium Phenomena. 13.Brownian Motions. 13.1 Brownian Motion/Diffusion Equation. 13.2 Diffusive Transport in Cells. 13.3 Brownian Motion/Langevin Equation Theory. 14. Stochastic Processes, Markov Chains and Master Equations. 14.1 Markov Processes. 14.2 Master Equation. 15. Theory of Markov Processes & The Fokker-Planck Equations. 15.1 Fokker-Planck Equation (FPE). 15.2 The Langevin and Fokker-Planck Equations from Phenomenology and Effective Hamiltonian. 15.3 Solutions of Fokker-Planck Equations, Transition Probabilities and Correlation Functions. 16. The Mean-First Passage Times and Barrier Crossing Rates. 16.1 First Passage Time. 16.2 Rate Theory: Flux-over Population Method. 17. Dynamic Linear Responses and Time Correlation Functions. 17.1 Time-dependent Linear Response Theory. 17.2 Applications of the Fluctuation–dissipation Theorem. 18. Noise-induced Resonances: Stochastic Resonance and Resonant Activation. 18.1 Stochastic Resonance. 18.2 Resonant Activation (RA) and Stochastic Ratchet. 18.3 Stochastic ratchet. 19. Transport Phenomena and Fluid Dynamics. 19.1 Hydrodynamic Transport Equations. 19.2 Dynamics of Viscous Flow. 20. Dynamics of Polymers and Membranes. 20.1 Dynamics of Flexible Polymers. 20.2 Dynamics of a Semiflexible Chain. 20.3 Dynamics of Membrane Undulation. 20.4 A Unified View. 21. Epilogue.