| Origins and Evolution of Life | p. 1 |
| Initiation | p. 1 |
| Machinery of prokaryotic cells | p. 3 |
| The photosynthetic revolution | p. 10 |
| Origins of diploidal eukaryotic cells | p. 15 |
| Summary: further stages of evolution | p. 19 |
| References | p. 21 |
| Structures of Biomolecules | p. 23 |
| Elementary building blocks | p. 23 |
| Generalized ester bonds | p. 26 |
| Directionality of chemical bonds | p. 30 |
| Weaker intratomic interactions | p. 39 |
| Ionic interactions | p. 40 |
| Covalent bonds | p. 42 |
| Free radicals | p. 46 |
| Van der Waals bonds | p. 46 |
| Hydrogen bonds and hydrophobic interactions | p. 52 |
| Polysaccharides | p. 59 |
| Amphiphilic molecules in water environments | p. 60 |
| Structures of proteins | p. 62 |
| Polypeptide chains | p. 67 |
| Proteins | p. 68 |
| Protein folding | p. 77 |
| Electrophoresis of proteins | p. 79 |
| Protein interactions with environment | p. 80 |
| Electron transfers in proteins | p. 81 |
| Structures of nucleic acids | p. 82 |
| Electrostatic potential of DNA | p. 86 |
| DNA: information and damage | p. 88 |
| Fluorescence in biomolecules | p. 89 |
| References | p. 93 |
| Dynamics of Biomolecules | p. 95 |
| Diffusion | p. 95 |
| Diffusional flow across membranes | p. 99 |
| Cells without sources | p. 100 |
| Cells with sources | p. 103 |
| Vibrations versus conformational transitions | p. 109 |
| Stochastic theory of reaction rates | p. 114 |
| Conformational transitions of proteins | p. 122 |
| Protein-glass model | p. 124 |
| Protein-machine model | p. 124 |
| Models of random walks on fractal lattices | p. 127 |
| Introduction to polymer biophysics | p. 132 |
| Elastic properties of polymers | p. 136 |
| Cellular automata | p. 137 |
| Conway's game of life | p. 137 |
| Bioenergetics: The Davydov model | p. 139 |
| Biological coherence: The Froehlich model | p. 142 |
| Ionic currents through electrolytes | p. 145 |
| Electron conduction and tunneling | p. 147 |
| Proton transport | p. 151 |
| Interactions with electromagnetic radiation | p. 152 |
| References | p. 156 |
| Structure of a Biological Cell | p. 159 |
| General characteristics of a cell | p. 159 |
| Membrane and membrane proteins | p. 161 |
| Elastic pressure of membrane | p. 165 |
| Mass diffusion across membranes | p. 165 |
| Membrane proteins | p. 166 |
| Electrical potentials of cellular membranes | p. 167 |
| Ion channels and ion pumps | p. 171 |
| Cytoplasm | p. 172 |
| Osmotic pressures of cells | p. 173 |
| Osmotic work | p. 175 |
| Cytoskeleton: the proteins participating in cytoskeletal organization | p. 176 |
| Cytoskeleton | p. 176 |
| Biopolymers of cytoskeleton | p. 176 |
| Tubulin | p. 178 |
| Microtubules | p. 180 |
| Microtubule-associated proteins | p. 187 |
| Microfilaments | p. 187 |
| Actin | p. 189 |
| Actin filaments | p. 189 |
| Actin-binding proteins | p. 190 |
| Intermediate filaments | p. 191 |
| Networks, stress fibers and tensegrity | p. 193 |
| Motor proteins and their roles in cellular processes | p. 195 |
| Myosin family | p. 197 |
| Kinesin family | p. 198 |
| NCD dimer structure | p. 201 |
| An overview of KN motion models | p. 201 |
| Dyneins | p. 202 |
| Centrioles, basal bodies, cilia, and flagella | p. 203 |
| Cilia and flagella | p. 203 |
| Cell energetics: chloroplasts and mitochondria | p. 206 |
| Cell as a thermodynamic machine | p. 209 |
| Active transport | p. 211 |
| Other organelles | p. 211 |
| Nucleus: nuclear chromatin, chromosomes, and nuclear lamina | p. 212 |
| Chromatin and chromosomes | p. 213 |
| Nucleolus | p. 213 |
| Nuclear envelope | p. 214 |
| Nuclear pores | p. 214 |
| Cell division | p. 214 |
| Centrioles, centrosomes, and aster formation | p. 216 |
| Chromosome segregation | p. 217 |
| Cytokinesis | p. 218 |
| Spindle and chromosome motility | p. 220 |
| Cell intelligence | p. 221 |
| Biological signaling | p. 222 |
| References | p. 225 |
| Nonequilibrium Thermodynamics and Biochemical Reactions | p. 229 |
| Second law of thermodynamics | p. 229 |
| Nonequilibrium thermodynamics | p. 233 |
| Rates of nonequilibrium thermodynamic processes | p. 241 |
| Single unimolecular chemical reaction | p. 244 |
| Bimolecular reactions: protolysis | p. 249 |
| Redox reactions | p. 253 |
| The steady state approximation: the theory of reaction rates | p. 257 |
| Chemical mechanisms of enzymatic catalysis | p. 260 |
| Michaelis-Menten kinetics | p. 264 |
| Control of enzymatic reactions | p. 269 |
| References | p. 275 |
| Molecular Biological Machines | p. 277 |
| Biological motion | p. 277 |
| Free energy transduction | p. 278 |
| Chemochemical machines | p. 282 |
| Biological machines as biased Maxwell's demons | p. 286 |
| Pumps and motors as chemochemical machines | p. 287 |
| Flux-force dependence | p. 291 |
| Overview of motor protein biophysics | p. 296 |
| Biochemical energy currency: ATP molecules | p. 299 |
| Structure of ATP | p. 300 |
| Functions of ATP | p. 301 |
| Double energy packet | p. 302 |
| Methods of producing ATP | p. 303 |
| Chloroplasts | p. 304 |
| Assembly of microtubules | p. 304 |
| Assembly of actin filaments | p. 308 |
| Muscle contraction: biophysical mechanisms and contractile proteins | p. 313 |
| References | p. 316 |
| Nerve Cells | p. 319 |
| Anatomy of a nerve cell | p. 319 |
| Conducting properties of neurons | p. 321 |
| Action potential generation: Hodgkin-Huxley equations | p. 325 |
| Structure and function of synapse | p. 331 |
| Neural network models | p. 335 |
| Memory | p. 338 |
| References | p. 339 |
| Tissue and Organ Biophysics | p. 341 |
| Introduction | p. 341 |
| Pressure in human organs | p. 341 |
| Anatomy and physiology of human circulatory system | p. 342 |
| Circulation of blood | p. 342 |
| Cardiovascular system | p. 343 |
| Regulation of fluid between cells (interstitial fluid) | p. 349 |
| Gas exchange with circulatory system | p. 350 |
| Heart dynamics | p. 352 |
| Energy management in the human body | p. 353 |
| Respiration biophysics | p. 355 |
| Kidney physiology and dialysis | p. 360 |
| Muscle biophysics | p. 361 |
| Bone stiffness and strength | p. 367 |
| Vision biophysics | p. 368 |
| Wavelength responses | p. 370 |
| Optical properties | p. 371 |
| Light absorption and black-and-white vision | p. 372 |
| Color vision | p. 373 |
| Resolution of the human eye | p. 375 |
| Quantum response of the eye | p. 376 |
| Sound perception biophysics | p. 378 |
| Gross features of the nervous system | p. 380 |
| Bioelectricity and biomagnetism | p. 384 |
| Biological piezoelectricity | p. 388 |
| Biomagnetism | p. 388 |
| Immune system and its models | p. 389 |
| References | p. 392 |
| Biological Self-Regulation and Self-Organization | p. 395 |
| Introduction | p. 395 |
| Self-organization | p. 395 |
| Homeostasis | p. 397 |
| First law of thermodynamics and living organisms | p. 398 |
| Physics of animal thermoregulation | p. 399 |
| Allometric laws in physiology | p. 403 |
| Introductory scaling concepts | p. 403 |
| Overview of allometric laws of physiology | p. 404 |
| Fractals and living systems | p. 407 |
| Entropy and information | p. 408 |
| Entropy reduction in living systems | p. 409 |
| Biological information | p. 414 |
| Evolutionary theories | p. 416 |
| Punctuated equilibria | p. 416 |
| Mathematical modeling of evolution | p. 417 |
| Mathematical models of population genetics | p. 418 |
| Artificial life | p. 419 |
| References | p. 420 |
| Epilogue: Toward New Physics and New Biology | p. 425 |
| Toward new physics | p. 425 |
| Toward new biology | p. 426 |
| Biocomputing | p. 427 |
| Biophysics: the physics of animate matter or an experimental biological tool? | p. 430 |
| References | p. 431 |
| Random Walks and Diffusion | p. 433 |
| Introduction | p. 433 |
| Gaussian probability distributions | p. 438 |
| Diffusion equation | p. 440 |
| Probability of displacement for a three-dimensional random walk | p. 441 |
| Diffusion equation | p. 443 |
| Example | p. 445 |
| Diffusion equation (differential form) | p. 448 |
| Example | p. 450 |
| Particle conservation | p. 453 |
| Models of Phase Transitions and Criticality | p. 455 |
| Introduction | p. 455 |
| Ctystals | p. 455 |
| Structural phase trastions | p. 456 |
| Perroelectrictiy | p. 457 |
| Magnetic orderings | p. 457 |
| Ordering transitions in binary alloys | p. 457 |
| Subpeconductivity | p. 457 |
| Superfluidity | p. 458 |
| Liquid crystals | p. 458 |
| References | p. 478 |
| Foundations of Nonlinear Physics | p. 481 |
| Multistability and bifurcation | p. 481 |
| Stochastic analogue of a bifurcation | p. 484 |
| Harmonic versus anharmonic motion | p. 486 |
| External driving and dissipation | p. 487 |
| Relaxation dynamics and asymptotic stability | p. 491 |
| Coupled systems and limit cycles | p. 493 |
| Nonlinear waves and solitons | p. 496 |
| Pattern formation | p. 503 |
| Pattern formation in fluid dynamics | p. 503 |
| Pattern formation in liquid crystals | p. 503 |
| Pattern formation in polymers | p. 504 |
| Crystal growth and structural transitions | p. 504 |
| Chemical instabilities | p. 505 |
| Chaos and turbulence | p. 505 |
| Landau scenario | p. 506 |
| Ruelle-Takens-Newhouse scenario | p. 507 |
| Feigenbaum picture | p. 507 |
| Pomeau-Manneville scenario | p. 509 |
| Fractals | p. 509 |
| Self-organized criticality | p. 510 |
| References | p. 513 |
| Master Equations | p. 517 |
| References | p. 519 |
| Index | p. 521 |
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