Statistical Mechanics of Cellular Systems and Processes

Cover......Page 1
Half-title......Page 3
Title......Page 5
Copyright......Page 6
Contents......Page 7
Contributors......Page 9
Preface......Page 13
Introduction......Page 15
Intrinsic protein stability......Page 16
Non-directional protein–protein interactions......Page 18
Directional protein–protein interactions......Page 20
Simulation methods......Page 23
Effects of protein concentration: uniform vs. patchy proteins......Page 25
Does the nature of the crowding species matter?......Page 30
Conclusions and open questions......Page 32
References......Page 34
Introduction......Page 40
Forced separation of a molecular bond......Page 41
A model of bond breaking......Page 42
The state of the bond......Page 46
The probability distribution…......Page 48
Implications......Page 52
Stability of bonds constraining a membrane......Page 56
Model problem with a single bond......Page 57
Membrane fluctuations and bending resistance......Page 59
The bonding potential......Page 60
Stability of the molecular bond......Page 62
The influence of membrane tension......Page 64
References......Page 66
Introduction......Page 68
Model system......Page 71
Cell–matrix interaction with immobilized ligands......Page 72
Cell–matrix interaction with mobile ligands......Page 76
Receptor clustering and implications for signaling......Page 81
Concluding remarks and future directions......Page 83
References......Page 84
Deterministic physical approaches......Page 88
Landscape framework of biological networks......Page 89
MAPK signal transduction......Page 90
Method......Page 91
Average kinetics......Page 92
Potential energy landscape in fluctuating environments......Page 93
Results and discussions......Page 94
Budding yeast cell cycle......Page 105
Methods......Page 107
Results......Page 111
Discussions......Page 118
Toggle switch of gene regulatory network......Page 119
Methods......Page 120
Mean-field approximation of the master equation......Page 121
Quantum field theoretic description......Page 123
Ritz’s variational method with coherent state ansatz......Page 124
Interpretation of the solutions......Page 126
Results......Page 127
Poisson and moment equation solutions of master equations......Page 128
Mono- versus bi-stability for symmetric toggle switch......Page 129
Potential energy landscape: mono-stability to bi-stability......Page 132
Discussions......Page 134
References......Page 135
Introduction......Page 139
Deterministic methods......Page 141
Autoactivation......Page 143
Mutual repression......Page 145
Natural lineage specification......Page 149
Understanding reprogramming experiments......Page 152
Stochastic models and their treatment......Page 154
Stochastic description of a bi-stable switch......Page 159
Elaborations on bi-stability......Page 162
Summary and outlook......Page 166
References......Page 167
Introduction......Page 173
Metabolic networks......Page 174
Protein–protein interaction networks......Page 176
Gene regulatory networks......Page 177
Overall leitmotif......Page 178
Dynamics of regulatory networks......Page 180
Boolean modeling of regulatory networks......Page 182
Modeling through differential equations......Page 185
Network modules......Page 189
Large regulatory networks......Page 191
Conclusions......Page 192
References......Page 193
7.1 Introduction......Page 195
7.2 Brief description of the immune system......Page 198
B cell model......Page 200
T Cell Model......Page 204
Original antigenic sin......Page 209
A new order parameter to describe antigenic distance......Page 212
Glassy dynamics suppresses autoimmune disease......Page 216
Dengue fever and polytopic vaccination......Page 222
References......Page 227
Index......Page 232