Contents
1 Physics in the Origin of Life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1
1.1 Origin of Life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1
1.1.1
Chemical Evolution on the Earth . . . . . . . . . . . . . . . . . . .
1
1.1.2
Origin of Catalytic Activity of Enzymes . . . . . . . . . . . . .
4
1.1.3
Development of Genetic Information
and RNA World . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4
1.1.4
Evolution as Progress of Energy Metabolic System . . . . .
6
1.2 Thermodynamics of Biological System . . . . . . . . . . . . . . . . . . . .
9
1.2.1
Kinetics of Chemical Reaction . . . . . . . . . . . . . . . . . . . .
9
1.2.2
Enzyme as Protein Catalyst and Its Kinetics . . . . . . . . . . . 11
1.2.3
Change of Free Energy in Chemical Reaction . . . . . . . . . 11
1.2.4
Coupling Reaction for Synthetic Chemical Reaction . . . . . 12
1.2.5
Non-equilibrium Thermodynamics and Living State . . . . . 12
1.3 Stationary State of Living Organism . . . . . . . . . . . . . . . . . . . . . . 13
1.3.1
Stationary State and Principle of Minimum Entropy
Production . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
1.3.2
Nonequilibrium Thermodynamics . . . . . . . . . . . . . . . . . . 15
1.3.3
Principle of Minimum Entropy Production . . . . . . . . . . . . 16
1.3.4
Derivation of Generation Rate of Entropy Production . . . . 17
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2 Cells and Biomembranes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.1 Cells and Biomembranes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.2 Thermodynamics of Lipid Assemblies . . . . . . . . . . . . . . . . . . . . . 20
2.3 Shape of Lipid Molecule and Structure of Lipid Assembly . . . . . . 22
2.4 Basic Structure of Biomembrane . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.5 Proteins and Functions of a Cell . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.6 Cell as a Device of Information Processing . . . . . . . . . . . . . . . . . . 24
2.7 Membrane Potential . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
ix
1 Physics in the Origin of Life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1
1.1 Origin of Life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1
1.1.1
Chemical Evolution on the Earth . . . . . . . . . . . . . . . . . . .
1
1.1.2
Origin of Catalytic Activity of Enzymes . . . . . . . . . . . . .
4
1.1.3
Development of Genetic Information
and RNA World . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4
1.1.4
Evolution as Progress of Energy Metabolic System . . . . .
6
1.2 Thermodynamics of Biological System . . . . . . . . . . . . . . . . . . . .
9
1.2.1
Kinetics of Chemical Reaction . . . . . . . . . . . . . . . . . . . .
9
1.2.2
Enzyme as Protein Catalyst and Its Kinetics . . . . . . . . . . . 11
1.2.3
Change of Free Energy in Chemical Reaction . . . . . . . . . 11
1.2.4
Coupling Reaction for Synthetic Chemical Reaction . . . . . 12
1.2.5
Non-equilibrium Thermodynamics and Living State . . . . . 12
1.3 Stationary State of Living Organism . . . . . . . . . . . . . . . . . . . . . . 13
1.3.1
Stationary State and Principle of Minimum Entropy
Production . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
1.3.2
Nonequilibrium Thermodynamics . . . . . . . . . . . . . . . . . . 15
1.3.3
Principle of Minimum Entropy Production . . . . . . . . . . . . 16
1.3.4
Derivation of Generation Rate of Entropy Production . . . . 17
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2 Cells and Biomembranes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.1 Cells and Biomembranes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.2 Thermodynamics of Lipid Assemblies . . . . . . . . . . . . . . . . . . . . . 20
2.3 Shape of Lipid Molecule and Structure of Lipid Assembly . . . . . . 22
2.4 Basic Structure of Biomembrane . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.5 Proteins and Functions of a Cell . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.6 Cell as a Device of Information Processing . . . . . . . . . . . . . . . . . . 24
2.7 Membrane Potential . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
ix