PHYSICS OF LIFE: THE PHYSICIST'S ROAD TO BIOLOGY
CONTENTS PART I GENERAL INTRODUCTION INTRODUCTION: THE AIM AND THE SCOPE OF THE BOOK THE PHYSICS OF LIFE: PHYSICS AT SEVERAL LEVELS PART II THE PHYSICS BASIS CONCEPTS AND NUMERICAL REFERENCE 3A NUMERICAL VALUES BASICS OF CLASSICAL (NEWTONIAN) DYNAMICS ELECTRICITY: THE CORE OF REDUCTIONISM BASIS 5A GENERAL ELECTROSTATICS 5B FORMALISM OF ELECTROSTATICS* 5C MAGNETISM 5D RELATIONS BETWEEN ELECTRIC AND MAGNETIC FIELDS: MAXWELL’S EQUATIONS* 5E RADIATION QUANTUM MECHANICS 6A THE THERMODYNAMIC PATH TO QUANTUM MECHANICS 6B BASIC PRINCIPLES OF QUANTUM MECHANICS 6C THE HYDROGEN ATOM* 6D THE STRANGE FEATURES OF QUANTUM MECHANICS BASIC THERMODYNAMICS: INTRODUCTION 7A THERMODYNAMIC CONCEPTS 7B ENERGY AND ENTROPY 7C THE SECOND LAW OF THERMODYNAMICS 7D FREE ENERGIES AND CHEMICAL POTENTIAL STATISTICAL THERMODYNAMICS 8A BASIC ASSUMPTION AND STATISTICAL ENTROPY 8B ENERGY DISTRIBUTION* 8C MORE ON MICRO- AND MACROSTATES PART III THE GENERAL TRENDS AND OBJECTS SOME TRENDS IN 20TH CENTURY PHYSICS FROM THE SIMPLE EQUILIBRIUM TO THE COMPLEX THEORETICAL PHYSICS MODELS: IMPORTANT ANALOGIES THE BIOLOGICAL MOLECULES 12A GENERAL PROPERTIES OF PROTEINS AND AMINO ACIDS 12B SUGARS 12C NUCLEIC ACIDS 12D THE GENETIC CODE 12E ENERGY-STORING SUBSTANCES 12F LIPIDS: MEMBRANES WHAT IS LIFE? PART IV GOING FURTHER WITH THERMODYNAMICS THERMODYNAMICS FORMALISM AND EXAMPLES: COMBINATORIAL EXPRESSIONS AND STIRLING’S FORMULA 14A GENERAL FORMALISM: ENERGY CONCEPTS 14B MIXING ENTROPY 14C WATER: SOLUBILITY 14D FORMALISM OF MIXING AND SOLUTIONS* 14E CHEMICAL THERMODYNAMICS* 14F NON-EQUILIBRIUM THERMODYNAMICS* EXAMPLES OF ENTROPY AND ORDER/DISORDER 15A SHUFFLING CARDS 15B THE MONKEY LIBRARY AND DNA 15C ORDER AND DISORDER 15D THE RELATION TO THE SECOND LAW STATISTICAL THERMODYNAMICS MODELS 16A MAGNETIC ANALOGIES AND MOLECULE CONFORMATIONS 16B ISING-TYPE MODELS OF 1D SYSTEMS* 16C RENORMALISATION METHODS* 16D SPIN GLASS PART V STOCHASTIC DYNAMICS PROBABILITY CONCEPTS 17A EXAMPLES 17B NORMAL DISTRIBUTION: APPROXIMATION OF BINOMIAL DISTRIBUTION STOCHASTIC PROCESSES 18A INTRODUCTION: GENERAL ACCOUNT 18B TERMINOLOGY AND FORMAL BASIS 18C ERGODICITY IN BIOLOGY RANDOM WALK* 19A FORMALISM 19B ABSORBING AND REFLECTING BOUNDARIES 19C FIRST PASSAGE TIME 19D NON-INTERSECTING RANDOM WALK STEP PROCESSES: MASTER EQUATIONS* 20A POISSON PROCESS 20B PROCESSES WITH A SMALL NUMBER OF STATES AND CONSTANT TRANSITION PROBABILITIES 20C FORMALISM: MATRIX METHOD 20D A PROCESS WITH CONSTANT AVERAGE AND EXTINCTION POSSIBILITY 20E BIRTH–DEATH PROCESS WITH EXTINCTION 20F REACTION KINETICS AS STEP PROCESSES 20G DIFFUSION-CONTROLLED REACTION AS STEP PROCESS 20H BARRIER PASSAGE AS STEP PROCESS 20I WHEN AN AVERAGE PICTURE GOES WRONG: MUTATIONS AND EXPONENTIAL GROWTH BROWNIAN MOTION: FIRST DESCRIPTION* 21A INTRODUCTION 21B FORMALISM 21C BROWNIAN MOTION IN LINEAR FORCE FIELDS: FLUCTUATION–DISSIPATION THEOREM DIFFUSION AND CONTINUOUS STOCHASTIC PROCESSES* 22A DIFFUSION 22B DIFFUSION-CONTROLLED REACTIONS 22C GAUSSIAN PROCESSES 22D FOKKER–PLANCK EQUATIONS 22E EXAMPLES: COMPARISONS BETWEEN MASTER EQUATIONS AND FOKKER–PLANCK EQUATIONS BROWNIAN MOTION AND CONTINUATION* 23A FOKKER–PLANCK EQUATIONS FOR BROWNIAN MOTION 23B BROWNIAN MOTION IN POTENTIALS 23C BROWNIAN MOTION DESCRIPTION OF THE PASSAGE OVER A POTENTIAL BARRIER 23D LOW-FRICTION SITUATION 23E BROWNIAN MOTION DESCRIPTION OF STOCHASTIC RESONANCE PART VI MACROMOLECULAR APPLICATIONS PROTEIN FOLDING AND STRUCTURE DYNAMICS 24A GENERAL DISCUSSION 24B PROTEIN FOLDING AS STOCHASTIC PROCESS 24C STRETCHED KINETICS* ENZYME KINETICS 25A ENZYME ACTIONS: ORGANISATION 25B FORMALISM: BASIC ENZYME KINETICS 25C ALLOSTERIC ACTION* PART VII NON-LINEARITY WHAT DOES NON-LINEARITY DO? 26A NON-LINEARITY IN CELLS: OSCILLATIONS, PULSES AND WAVES OSCILLATIONS AND SPACE VARIATION* 27A ELECTRIC CIRCUIT 27B CHEMICAL OSCILLATING SYSTEMS 27C NEURAL SIGNAL GENERATION 27D DIFFUSION–REACTION EQUATIONS AND SPATIAL STRUCTURES 27E NON-LINEAR WAVES DETERMINISTIC CHAOS 28A GENERAL FEATURES OF IRREGULAR SEQUENCES 28B CHAOTIC DIFFERENTIAL EQUATIONS* 28C CHARACTERISTICS OF CHAOS* 28D UNSTABLE ORBITS: CONTROL OF CHAOS* NOISE AND NON-LINEAR PHENOMENA 29A GENERAL REMARKS 29B STOCHASTIC RESONANCE 29C NON-LINEAR STOCHASTIC EQUATIONS PART VIII APPLICATIONS RECOGNITION AND SELECTION IN BIOLOGICAL SYNTHESIS 30A INTRODUCTION: RECOGNITION 30B SELECTION IN NUCLEIC ACID SYNTHESIS 30C SELECTION IN PROTEIN SYNTHESIS 30D FORMALISM IN NON-BRANCHED PROCESSES WITHOUT PROOFREADING* 30E FORMALISM OF PROOFREADING KINETICS* 30F FURTHER FEATURES OF SELECTION: ERROR PROPAGATION BROWNIAN RATCHET: UNIDIRECTIONAL PROCESSES THE NEURAL SYSTEM 32A GENERAL DISCUSSION 32B SPIN-GLASS ANALOGY 32C MORE ON NETWORK FEATURES 32D NOISE IN THE NEURAL SYSTEM ORIGIN OF LIFE 33A IDEAS ABOUT EARLY MOLECULAR EVOLUTION 33B THOUGHTS ON STABILITY OF CO-OPERATIVE SYSTEMS 33C THE DYNAMICS OF REPLICATING OBJECTS IN THE ORIGIN OF LIFE* 33D ERRORS AND MUTATIONS* 33E AUTOCATALYTIC GROWTH: HYPERCYCLES* PART IX GOING FURTHER PHYSICS ASPECTS OF EVOLUTION DETERMINISM AND RANDOMNESS 35A GENERAL DISCUSSION 35B GAME OF LIFE 35C LAPLACE’S FORMULA 35D MACROSCOPIC WORLD 35E FINAL WORDS HIGHER FUNCTIONS OF LIFE 36A THINKING, MEMORY AND THE MIND 36B THE FREE WILL AND DETERMINISM ABOUT THE DIRECTION OF TIME WE LIVE IN THE BEST OF WORLDS: THE ANTHROPIC PRINCIPLE REFERENCES