Blomberg Physics of Life

The Physicist's Road to Biology
1. Auflage 2007
ISBN: 978-0-08-055464-8
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 436 Seiten

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

Born 1936, Clas Blomberg has a PhD in theoretical physics at the Royal Institute of Technology in Stockholm 1966. He has been a Professor there since 1986. He started studies in statistical mechanics, and since mid-70:s worked with theoretical physics problems with relevance to biology. He built up a successful research group at the Royal Institute of Technology, Stockholm.

Autoren/Hrsg.

Blomberg, Clas

Inhaltsverzeichnis

1;Cover;1
2;Contents;4
3;Preface;8
4;Part I: General introduction;10
4.1;1. Introduction: The aim and the Scope of the Book;10
4.2;2. The Physics of Life: Physics at Several Levels;14
5;Part II: The physics basis;26
5.1;3. Concepts and Numerical Reference;26
5.1.1;3A Numerical values;27
5.2;4. Basics of Classical (Newtonian) Dynamics;28
5.3;5. Electricity: The Core of Reductionism Basis;35
5.3.1;5A General electrostatics;35
5.3.2;5B Formalism of electrostatics;38
5.3.3;5C Magnetism;46
5.3.4;5D Relations between electric and magnetic fields: Maxwell’s equations;49
5.3.5;5E Radiation;51
5.4;6. Quantum Mechanics;53
5.4.1;6A The thermodynamic path to quantum mechanics;54
5.4.2;6B Basic principles of quantum mechanics;57
5.4.3;6C The hydrogen atom;62
5.4.4;6D The strange features of quantum mechanics;67
5.5;7 Basic Thermodynamics: Introduction;72
5.5.1;7A Thermodynamic concepts;72
5.5.2;7B Energy and entropy;73
5.5.3;7C The second law of thermodynamics;76
5.5.4;7D Free energies and chemical potential;77
5.6;8 Statistical Thermodynamics;80
5.6.1;8A Basic assumption and statistical entropy;80
5.6.2;8B Energy distribution;85
5.6.3;8C More on micro- and macrostates;87
6;Part III: The general trends and objects;90
6.1;9. Some Trends in 20th Century Physics;90
6.2;10 From the Simple Equilibrium to the Complex;94
6.3;11. Theoretical Physics Models: Important Analogies;101
6.4;12. The Biological Molecules;105
6.4.1;12A General properties of proteins and amino acids;105
6.4.2;12B Sugars;113
6.4.3;12C Nucleic acids;114
6.4.4;12D The genetic code;117
6.4.5;12E Energy-storing substances;120
6.4.6;12F Lipids: membranes;121
6.5;13 What is Life?;122
7;Part IV: Going further with thermodynamics;126
7.1;14. Thermodynamics Formalism and Examples: Combinatorial Expressions and Stirling’s Formula;126
7.1.1;14A General formalism: energy concepts;127
7.1.2;14B Mixing entropy;132
7.1.3;14C Water: solubility;134
7.1.4;14D Formalism of mixing and solutions;135
7.1.5;14E Chemical thermodynamics;138
7.1.6;14F Non-equilibrium thermodynamics;141
7.2;15 Examples of Entropy and Order/Disorder;147
7.2.1;15A Shuffling cards;148
7.2.2;15B The monkey library and DNA;149
7.2.3;15C Order and disorder;151
7.2.4;15D The relation to the second law;153
7.3;16. Statistical Thermodynamics Models;155
7.3.1;16A Magnetic analogies and molecule conformations;155
7.3.2;16B Ising-type models of 1D systems;165
7.3.3;16C Renormalisation methods;172
7.3.4;16D Spin glass;178
8;Part V: Stochastic dynamics;182
8.1;17. Probability Concepts;182
8.1.1;17A Examples;183
8.1.2;17B Normal distribution: approximation of binomial distribution;186
8.2;18. Stochastic Processes;187
8.2.1;18A Introduction: general account;187
8.2.2;18B Terminology and formal basis;189
8.2.3;18C Ergodicity in biology;190
8.3;19. Random Walk;191
8.3.1;19A Formalism;192
8.3.2;19B Absorbing and reflecting boundaries;195
8.3.3;19C First passage time;197
8.3.4;19D Non-intersecting random walk;199
8.4;20. Step Processes: Master Equations;200
8.4.1;20A Poisson process;202
8.4.2;20B Processes with a small number of states and constant transition probabilities;203
8.4.3;20C Formalism: matrix method;204
8.4.4;20D A process with constant average and extinction possibility;210
8.4.5;20E Birth–death process with extinction;212
8.4.6;20F Reaction kinetics as step processes;215
8.4.7;20G Diffusion-controlled reaction as step process;218
8.4.8;20H Barrier passage as step process;221
8.4.9;20I When an average picture goes wrong: mutations and exponential growth;223
8.5;21. Brownian Motion: First Description;225
8.5.1;21A Introduction;225
8.5.2;21B Formalism;226
8.5.3;21C Brownian motion in linear force fields: fluctuation–dissipation theorem;229
8.6;22. Diffusion and Continuous Stochastic Processes;230
8.6.1;22A Diffusion;230
8.6.2;22B Diffusion-controlled reactions;233
8.6.3;22C Gaussian processes;234
8.6.4;22D Fokker–Planck equations;235
8.6.5;22E Examples: comparisons between master equations and Fokker–Planck equations;239
8.7;23. Brownian Motion and Continuation;243
8.7.1;23A Fokker–Planck equations for Brownian motion;244
8.7.2;23B Brownian motion in potentials;247
8.7.3;23C Brownian motion description of the passage over a potential barrier;248
8.7.4;23D Low-friction situation;252
8.7.5;23E Brownian motion description of stochastic resonance;254
9;Part VI: Macromolecular applications;258
9.1;24 Protein Folding and Structure Dynamics;258
9.1.1;24A General discussion;258
9.1.2;24B Protein folding as stochastic process;261
9.1.3;24C Stretched kinetics;262
9.2;25 Enzyme Kinetics;264
9.2.1;25A Enzyme actions: organisation;264
9.2.2;25B Formalism: basic enzyme kinetics;268
9.2.3;25C Allosteric action;270
10;Part VII: Non-linearity;276
10.1;26. What Does Non-Linearity do?;276
10.1.1;26A Non-linearity in cells: oscillations, pulses and waves;280
10.2;27 Oscillations and Space Variation;282
10.2.1;27A Electric circuit;282
10.2.2;27B Chemical oscillating systems;284
10.2.3;27C Neural signal generation;287
10.2.4;27D Diffusion–reaction equations and spatial structures;290
10.2.5;27E Non-linear waves;293
10.3;28 Deterministic Chaos;297
10.3.1;28A General features of irregular sequences;298
10.3.2;28B Chaotic differential equations;304
10.3.3;28C Characteristics of chaos;307
10.3.4;28D Unstable orbits: control of chaos;316
10.4;29 Noise and Non-Linear Phenomena;319
10.4.1;29A General remarks;319
10.4.2;29B Stochastic resonance;320
10.4.3;29C Non-linear stochastic equations;321
11;Part VIII: Applications;330
11.1;30 Recognition and Selection in Biological Synthesis;330
11.1.1;30A Introduction: recognition;330
11.1.2;30B Selection in nucleic acid synthesis;332
11.1.3;30C Selection in protein synthesis;335
11.1.4;30D Formalism in non-branched processes without proofreading;338
11.1.5;30E Formalism of proofreading kinetics;341
11.1.6;30F Further features of selection: error propagation;347
11.2;31 Brownian Ratchet: Unidirectional Processes;349
11.3;32 The Neural System;352
11.3.1;32A General discussion;352
11.3.2;32B Spin-glass analogy;355
11.3.3;32C More on network features;357
11.3.4;32D Noise in the neural system;358
11.4;33 Origin of Life;359
11.4.1;33A Ideas about early molecular evolution;359
11.4.2;33B Thoughts on stability of co-operative systems;371
11.4.3;33C The dynamics of replicating objects in the origin of life;373
11.4.4;33D Errors and mutations;376
11.4.5;33E Autocatalytic growth: hypercycles;380
12;Part IX: Going further;386
12.1;34. Physics Aspects of Evolution;386
12.2;35. Determinism and Randomness;392
12.2.1;35A General discussion;393
12.2.2;35B Game of life;396
12.2.3;35C Laplace’s formula;398
12.2.4;35D Macroscopic world;399
12.2.5;35E Final words;401
12.3;36 Higher Functions of Life;401
12.3.1;36A Thinking, memory and the mind;401
12.3.2;36B The free will and determinism;405
12.4;37 About the Direction of Time;410
12.5;38 We Live in the Best of Worlds:The Anthropic Principle;415
13;References;420
14;Index;430