Physics of Life: The Physicist's Road to Biology
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Table of contents
- Cover
- Contentsv
- Prefaceix
- Part I: General introduction1
- 1. Introduction: The aim and the Scope of the Book1
- 2. The Physics of Life: Physics at Several Levels5
- Part II: The physics basis17
- 3. Concepts and Numerical Reference17
- 3A Numerical values18
- 4. Basics of Classical (Newtonian) Dynamics19
- 5. Electricity: The Core of Reductionism Basis26
- 5A General electrostatics26
- 5B Formalism of electrostatics29
- 5C Magnetism37
- 5D Relations between electric and magnetic fields: Maxwell’s equations40
- 5E Radiation42
- 6. Quantum Mechanics44
- 6A The thermodynamic path to quantum mechanics45
- 6B Basic principles of quantum mechanics48
- 6C The hydrogen atom53
- 6D The strange features of quantum mechanics58
- 7 Basic Thermodynamics: Introduction63
- 7A Thermodynamic concepts63
- 7B Energy and entropy64
- 7C The second law of thermodynamics67
- 7D Free energies and chemical potential68
- 8 Statistical Thermodynamics71
- 8A Basic assumption and statistical entropy71
- 8B Energy distribution76
- 8C More on micro- and macrostates78
- Part III: The general trends and objects81
- 9. Some Trends in 20th Century Physics81
- 10 From the Simple Equilibrium to the Complex85
- 11. Theoretical Physics Models: Important Analogies92
- 12. The Biological Molecules96
- 12A General properties of proteins and amino acids96
- 12B Sugars104
- 12C Nucleic acids105
- 12D The genetic code108
- 12E Energy-storing substances111
- 12F Lipids: membranes112
- 13 What is Life?113
- Part IV: Going further with thermodynamics117
- 14. Thermodynamics Formalism and Examples: Combinatorial Expressions and Stirling’s Formula117
- 14A General formalism: energy concepts118
- 14B Mixing entropy123
- 14C Water: solubility125
- 14D Formalism of mixing and solutions126
- 14E Chemical thermodynamics129
- 14F Non-equilibrium thermodynamics132
- 15 Examples of Entropy and Order/Disorder138
- 15A Shuffling cards139
- 15B The monkey library and DNA140
- 15C Order and disorder142
- 15D The relation to the second law144
- 16. Statistical Thermodynamics Models146
- 16A Magnetic analogies and molecule conformations146
- 16B Ising-type models of 1D systems156
- 16C Renormalisation methods163
- 16D Spin glass169
- Part V: Stochastic dynamics173
- 17. Probability Concepts173
- 17A Examples174
- 17B Normal distribution: approximation of binomial distribution177
- 18. Stochastic Processes178
- 18A Introduction: general account178
- 18B Terminology and formal basis180
- 18C Ergodicity in biology181
- 19. Random Walk182
- 19A Formalism183
- 19B Absorbing and reflecting boundaries186
- 19C First passage time188
- 19D Non-intersecting random walk190
- 20. Step Processes: Master Equations191
- 20A Poisson process193
- 20B Processes with a small number of states and constant transition probabilities194
- 20C Formalism: matrix method195
- 20D A process with constant average and extinction possibility201
- 20E Birth–death process with extinction203
- 20F Reaction kinetics as step processes206
- 20G Diffusion-controlled reaction as step process209
- 20H Barrier passage as step process212
- 20I When an average picture goes wrong: mutations and exponential growth214
- 21. Brownian Motion: First Description216
- 21A Introduction216
- 21B Formalism217
- 21C Brownian motion in linear force fields: fluctuation–dissipation theorem220
- 22. Diffusion and Continuous Stochastic Processes221
- 22A Diffusion221
- 22B Diffusion-controlled reactions224
- 22C Gaussian processes225
- 22D Fokker–Planck equations226
- 22E Examples: comparisons between master equations and Fokker–Planck equations230
- 23. Brownian Motion and Continuation234
- 23A Fokker–Planck equations for Brownian motion235
- 23B Brownian motion in potentials238
- 23C Brownian motion description of the passage over a potential barrier239
- 23D Low-friction situation243
- 23E Brownian motion description of stochastic resonance245
- Part VI: Macromolecular applications249
- 24 Protein Folding and Structure Dynamics249
- 24A General discussion249
- 24B Protein folding as stochastic process252
- 24C Stretched kinetics253
- 25 Enzyme Kinetics255
- 25A Enzyme actions: organisation255
- 25B Formalism: basic enzyme kinetics259
- 25C Allosteric action261
- Part VII: Non-linearity267
- 26. What Does Non-Linearity do?267
- 26A Non-linearity in cells: oscillations, pulses and waves271
- 27 Oscillations and Space Variation273
- 27A Electric circuit273
- 27B Chemical oscillating systems275
- 27C Neural signal generation278
- 27D Diffusion–reaction equations and spatial structures281
- 27E Non-linear waves284
- 28 Deterministic Chaos288
- 28A General features of irregular sequences289
- 28B Chaotic differential equations295
- 28C Characteristics of chaos298
- 28D Unstable orbits: control of chaos307
- 29 Noise and Non-Linear Phenomena310
- 29A General remarks310
- 29B Stochastic resonance311
- 29C Non-linear stochastic equations312
- Part VIII: Applications321
- 30 Recognition and Selection in Biological Synthesis321
- 30A Introduction: recognition321
- 30B Selection in nucleic acid synthesis323
- 30C Selection in protein synthesis326
- 30D Formalism in non-branched processes without proofreading329
- 30E Formalism of proofreading kinetics332
- 30F Further features of selection: error propagation338
- 31 Brownian Ratchet: Unidirectional Processes340
- 32 The Neural System343
- 32A General discussion343
- 32B Spin-glass analogy346
- 32C More on network features348
- 32D Noise in the neural system349
- 33 Origin of Life350
- 33A Ideas about early molecular evolution350
- 33B Thoughts on stability of co-operative systems362
- 33C The dynamics of replicating objects in the origin of life364
- 33D Errors and mutations367
- 33E Autocatalytic growth: hypercycles371
- Part IX: Going further377
- 34. Physics Aspects of Evolution377
- 35. Determinism and Randomness383
- 35A General discussion384
- 35B Game of life387
- 35C Laplace’s formula389
- 35D Macroscopic world390
- 35E Final words392
- 36 Higher Functions of Life392
- 36A Thinking, memory and the mind392
- 36B The free will and determinism396
- 37 About the Direction of Time401
- 38 We Live in the Best of Worlds:The Anthropic Principle406
- References411
- Index421
The purpose of the book is to give a survey of the physics that is relevant for biological applications, and also to discuss what kind of biology needs physics. The book gives a broad account of basic physics, relevant for the applications and various applications from properties of proteins to processes in the cell to wider themes such as the brain, the origin of life and evolution. It also considers general questions of common interest such as reductionism, determinism and randomness, where the physics view often is misunderstood. The subtle balance between order and disorder is a repeated theme appearing in many contexts. There are descriptive parts which shall be sufficient for the comprehension of general ideas, and more detailed, formalistic parts for those who want to go deeper, and see the ideas expressed in terms of mathematical formulas.
- Describes how physics is needed for understanding basic principles of biology
- Discusses the delicate balance between order and disorder in living systems
- Explores how physics play a role high biological functions, such as learning and thinking
- Describes how physics is needed for understanding basic principles of biology
- Discusses the delicate balance between order and disorder in living systems
- Explores how physics play a role high biological functions, such as learning and thinking