1;Preface;7 2;Contents;10 3;1 Biophysics: An Experimental Tool of Biology or the Physics of Animate Matter?;14 4;2 Statistical Description of Matter;19 4.1;2.1 Molecular Structure of Matter;19 4.2;2.2 The Principle of Mechanical Determinism;21 4.3;2.3 Irreversibility of Macroscopic Processes;24 4.4;2.4 Instability of Motion as the Origin of Irreversibility;28 4.5;2.5 Statistical Ensembles.;30 4.6;2.6 Probability and Entropy.;34 4.7;2.7 The Law of Large Numbers.;38 4.8;2.8 The Relativity of Thermodynamic Equilibrium;44 5;3 Thermodynamic State;47 5.1;3.1 Global and Structural Thermodynamic Variables;47 5.2;3.2 The Clausius Entropy;51 5.3;3.3 Temperature and Thermodynamic Forces.;54 5.4;3.4 Energy Transformations: Work, Heat and Dissipation;60 5.5;3.5 Free Energy and Bound Energy;64 5.6;3.6 Open Thermodynamic Systems: Steady State versus Dissipative Structures;69 5.7;3.7 Rate of Nonequilibrium Thermodynamic Processes;74 6;4 Origins and Evolution of Life;77 6.1;4.1 History in Physics;77 6.2;4.2 Initiation;79 6.3;4.3 Origins of the Prokaryotic Cell Machinery;82 6.4;4.4 The Photosynthetic Revolution;88 6.5;4.5 Origins and Structure of the Eukaryotic Cell.;92 6.6;4.6 The Main Metabolic Pathways. Enzymes;97 7;5 Molecular Biology of the Eukaryotic Cell;102 7.1;5.1 The Eukaryotic Cell as a System of Compartments;102 7.2;5.2 Membrane Channels and Pumps;105 7.3;5.3 Substrate, Oxidative, and Photo Phosphorylation;111 7.4;5.4 Cytoskeleton and Cell Motility: Micro.laments;122 7.5;5.5 Cytoskeleton and Cell Motility: Microtubules;131 7.6;5.6 Regulation of Enzyme Activity;134 7.7;5.7 Receptors;138 7.8;5.8 The Cell Cycle;148 8;6 Chemical Reactions;151 8.1;6.1 Single Unimolecular Reactions.;151 8.2;6.2 Transport Across Membranes;158 8.3;6.3 Bimolecular Reactions;162 8.4;6.4 Protolysis Reactions;165 8.5;6.5 Redox Reactions;168 8.6;6.6 Fuel Cells and Photocells.;172 8.7;6.7 Two Successive Reactions.;176 8.8;6.8 Phenomenological Theory of Reaction Rates;179 9;7 Enzymatic Catalysis;182 9.1;7.1 Chemical Mechanisms of Enzymatic Catalysis;182 9.2;7.2 Steady-State Kinetics of Enzymatic Reactions with One Intermediate;186 9.3;7.3 Competitive and Noncompetitive Inhibition;192 9.4;7.4 Two-Substrate Enzyme;195 9.5;7.5 Allosteric Control of Enzymatic Activity;197 9.6;7.6 Oscillations in Enzymatic Reactions;201 10;8 Biological Free Energy Transduction;206 10.1;8.1 Isothermal Machines;206 10.2;8.2 Chemochemical Machines.;210 10.3;8.3 Universality of the Enzymatic Mechanism of Free Energy Transduction;213 10.4;8.4 Molecular Pumps and Motors;218 10.5;8.5 Flux-Force Dependence;221 10.6;8.6 Biological Signal Transduction;228 11;9 Lack of Partial Thermodynamic Equilibrium;234 11.1;9.1 Two Classes of Experiments;234 11.2;9.2 Intramolecular Dynamics of Biomolecules;239 11.3;9.3 Enzyme in a Multitude of Conformational States;245 11.4;9.4 Two Coupled Enzymatic Processes: Case of the Actomyosin Motor;249 11.5;9.5 Flux-Force Dependence for the Actomyosin Motor;258 11.6;9.6 Biological Molecular Machines as Biased Maxwell Demons;268 12;A Thermodynamic Supplement;272 12.1;A.1 Thermodynamics of Ideal Gases;272 12.2;A.2 Legendre Transformations;277 12.3;A.3 Capacities and Susceptibilities.;282 12.4;A.4 Canonical and Generalized Canonical Probability Distributions;285 12.5;A.5 Statistical Interpretation of Thermodynamics;290 13;B Stochastic Processes;294 13.1;B.1 From Liouville's Equation to the Di.usion Equation;294 13.2;B.2 Markov Processes;298 13.3;B.3 Stochastic Theory of Reaction Rates;305 13.4;B.4 Reaction Rate and the First-Passage Time Problem;311 13.5;B.5 One-Dimensional Di.usion in the Presence of a Sink;315 13.6;B.6 Diffusion in a Parabolic Potential;319 14;C Structure of Biomolecules;323 14.1;C.1 Elementary Building Blocks;323 14.2;C.2 Generalized Ester Bonds;327 14.3;C.3 Directionality of Chemical Bonds;331 14.4;C.4 Hydrogen Bond. Amphiphilic Molecules in Water Environments;340 14.5;C.5 Protein Structures;344 14.6;C.6 Nucleic Acid Structures;351 15;D Dynamics of Bi