Theoretical Physics for Biological Systems

Cover......Page 1
Half Title......Page 2
Title Page......Page 4
Copyright Page......Page 5
Preface......Page 6
Table of Contents......Page 8
List of Figures......Page 10
List of Tables......Page 14
1.1 General Definitions......Page 16
1.2 The Time-independent Schrödinger Equation......Page 18
1.3 Time-dependent Schrödinger Equation......Page 23
1.5 Quantum Coherence and Entanglement......Page 25
1.6 Quantum Interference......Page 28
1.7 Quantum Effects in Biology......Page 29
2.1 Why Statistical Physics in Biology?......Page 40
2.2 Markov Processes......Page 42
2.3 The Chemical Master Equation......Page 44
2.4 Chemical Master Equation and Curse of Dimensionality......Page 47
2.5 Discrete Approach to Chemical Kinetics......Page 48
2.5.1 Effective Reactions are Inelastic Collisions......Page 49
2.5.2 Factors Affecting Reaction Rate......Page 53
2.6 Stochastic Simulation Algorithm......Page 56
2.7 An Example of Real Enzymatic Reactions Simulated with Gillespie Algorithm......Page 59
Chapter 3: Graph Theory and Physics Meet Network Biology......Page 66
3.1 Physics at the Birth of Network Biology......Page 67
3.2 Mutual Information-Based Network Inference......Page 70
3.3.1 Vibrational Centrality......Page 72
3.3.2 Network Entropy: A graph theory based definition......Page 75
3.4 Electronic Physics Applications in Network Analysis......Page 79
3.5 Assessment of Network Inference Methods and the Issue of Generation of Gold-Standard Data......Page 83
3.6 Network Biology is Transformed by Physics......Page 88
Chapter 4: Applied Descriptors for Complexity and Centrality to Network Biology......Page 94
4.1 Network Theory......Page 95
4.2 Measures for Network Complexity and Centrality......Page 97
4.2.1 Network Entropy: A statistical mechanics and quantum physics definition......Page 98
4.3 Comparative Network Analysis......Page 108
4.3.1 Maximum Likelihood Estimation and Model Selection......Page 109
4.3.2 Reducibility of Multiplex Networks......Page 111
4.4.1 Node Ranking in Biological Networks......Page 113
4.4.3 Entropy-Based Hallmark of Cancer......Page 114
5.1 Systems Theory and Quantum Physics......Page 120
5.2 Various Recapitulation Exercises......Page 125
References......Page 136
Index......Page 158
About the Authors......Page 160