Physics of Life (eBook)

Cover 1
Contents 4
Preface 8
Part I: General introduction 10
1. Introduction: The aim and the Scope of the Book 10
2. The Physics of Life: Physics at Several Levels 14
Part II: The physics basis 26
3. Concepts and Numerical Reference 26
3A Numerical values 27
4. Basics of Classical (Newtonian) Dynamics 28
5. Electricity: The Core of Reductionism Basis 35
5A General electrostatics 35
5B Formalism of electrostatics 38
5C Magnetism 46
5D Relations between electric and magnetic fields: Maxwell’s equations 49
5E Radiation 51
6. Quantum Mechanics 53
6A The thermodynamic path to quantum mechanics 54
6B Basic principles of quantum mechanics 57
6C The hydrogen atom 62
6D The strange features of quantum mechanics 67
7 Basic Thermodynamics: Introduction 72
7A Thermodynamic concepts 72
7B Energy and entropy 73
7C The second law of thermodynamics 76
7D Free energies and chemical potential 77
8 Statistical Thermodynamics 80
8A Basic assumption and statistical entropy 80
8B Energy distribution 85
8C More on micro- and macrostates 87
Part III: The general trends and objects 90
9. Some Trends in 20th Century Physics 90
10 From the Simple Equilibrium to the Complex 94
11. Theoretical Physics Models: Important Analogies 101
12. The Biological Molecules 105
12A General properties of proteins and amino acids 105
12B Sugars 113
12C Nucleic acids 114
12D The genetic code 117
12E Energy-storing substances 120
12F Lipids: membranes 121
13 What is Life? 122
Part IV: Going further with thermodynamics 126
14. Thermodynamics Formalism and Examples: Combinatorial Expressions and Stirling’s Formula 126
14A General formalism: energy concepts 127
14B Mixing entropy 132
14C Water: solubility 134
14D Formalism of mixing and solutions 135
14E Chemical thermodynamics 138
14F Non-equilibrium thermodynamics 141
15 Examples of Entropy and Order/Disorder 147
15A Shuffling cards 148
15B The monkey library and DNA 149
15C Order and disorder 151
15D The relation to the second law 153
16. Statistical Thermodynamics Models 155
16A Magnetic analogies and molecule conformations 155
16B Ising-type models of 1D systems 165
16C Renormalisation methods 172
16D Spin glass 178
Part V: Stochastic dynamics 182
17. Probability Concepts 182
17A Examples 183
17B Normal distribution: approximation of binomial distribution 186
18. Stochastic Processes 187
18A Introduction: general account 187
18B Terminology and formal basis 189
18C Ergodicity in biology 190
19. Random Walk 191
19A Formalism 192
19B Absorbing and reflecting boundaries 195
19C First passage time 197
19D Non-intersecting random walk 199
20. Step Processes: Master Equations 200
20A Poisson process 202
20B Processes with a small number of states and constant transition probabilities 203
20C Formalism: matrix method 204
20D A process with constant average and extinction possibility 210
20E Birth–death process with extinction 212
20F Reaction kinetics as step processes 215
20G Diffusion-controlled reaction as step process 218
20H Barrier passage as step process 221
20I When an average picture goes wrong: mutations and exponential growth 223
21. Brownian Motion: First Description 225
21A Introduction 225
21B Formalism 226
21C Brownian motion in linear force fields: fluctuation–dissipation theorem 229
22. Diffusion and Continuous Stochastic Processes 230
22A Diffusion 230
22B Diffusion-controlled reactions 233
22C Gaussian processes 234
22D Fokker–Planck equations 235
22E Examples: comparisons between master equations and Fokker–Planck equations 239
23. Brownian Motion and Continuation 243
23A Fokker–Planck equations for Brownian motion 244
23B Brownian motion in potentials 247
23C Brownian motion description of the passage over a potential barrier 248
23D Low-friction situation 252
23E Brownian motion description of stochastic resonance 254
Part VI: Macromolecular applications 258
24 Protein Folding and Structure Dynamics 258
24A General discussion 258
24B Protein folding as stochastic process 261
24C Stretched kinetics 262
25 Enzyme Kinetics 264
25A Enzyme actions: organisation 264
25B Formalism: basic enzyme kinetics 268
25C Allosteric action 270
Part VII: Non-linearity 276
26. What Does Non-Linearity do? 276
26A Non-linearity in cells: oscillations, pulses and waves 280
27 Oscillations and Space Variation 282
27A Electric circuit 282
27B Chemical oscillating systems 284
27C Neural signal generation 287
27D Diffusion–reaction equations and spatial structures 290
27E Non-linear waves 293
28 Deterministic Chaos 297
28A General features of irregular sequences 298
28B Chaotic differential equations 304
28C Characteristics of chaos 307
28D Unstable orbits: control of chaos 316
29 Noise and Non-Linear Phenomena 319
29A General remarks 319
29B Stochastic resonance 320
29C Non-linear stochastic equations 321
Part VIII: Applications 330
30 Recognition and Selection in Biological Synthesis 330
30A Introduction: recognition 330
30B Selection in nucleic acid synthesis 332
30C Selection in protein synthesis 335
30D Formalism in non-branched processes without proofreading 338
30E Formalism of proofreading kinetics 341
30F Further features of selection: error propagation 347
31 Brownian Ratchet: Unidirectional Processes 349
32 The Neural System 352
32A General discussion 352
32B Spin-glass analogy 355
32C More on network features 357
32D Noise in the neural system 358
33 Origin of Life 359
33A Ideas about early molecular evolution 359
33B Thoughts on stability of co-operative systems 371
33C The dynamics of replicating objects in the origin of life 373
33D Errors and mutations 376
33E Autocatalytic growth: hypercycles 380
Part IX: Going further 386
34. Physics Aspects of Evolution 386
35. Determinism and Randomness 392
35A General discussion 393
35B Game of life 396
35C Laplace’s formula 398
35D Macroscopic world 399
35E Final words 401
36 Higher Functions of Life 401
36A Thinking, memory and the mind 401
36B The free will and determinism 405
37 About the Direction of Time 410
38 We Live in the Best of Worlds:The Anthropic Principle 415
References 420
Index 430