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xxii | |
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3 | (12) |
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1.1 Big science and the inner frontier |
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3 | (2) |
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1.2 What is a complex system? |
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5 | (2) |
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1.3 The science of sciences? |
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7 | (2) |
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1.4 Universality and individuality |
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9 | (1) |
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1.5 Relevant and irrelevant details |
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10 | (2) |
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1.6 The gifts we neither understand nor deserve |
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12 | (2) |
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14 | (1) |
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15 | (19) |
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15 | (1) |
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2.2 The common threads of Complexity |
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15 | (1) |
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16 | (5) |
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2.3.1 The superposition principle |
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19 | (1) |
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2.3.2 Multiscale coupling |
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20 | (1) |
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21 | (6) |
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2.4.1 Memory, history, and hierarchy |
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23 | (1) |
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24 | (2) |
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2.4.3 Chicken-egg causality |
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26 | (1) |
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2.5 Hyperland and ultradimensions |
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27 | (5) |
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28 | (3) |
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31 | (1) |
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32 | (2) |
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3 Competition and Cooperation |
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34 | (14) |
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34 | (1) |
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34 | (2) |
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3.3 Symmetry and broken symmetry |
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36 | (1) |
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3.4 Equilibrium & non-equilibrium |
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37 | (4) |
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3.4.1 The ever-shifting battle |
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37 | (1) |
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3.4.2 Stable and unstable equilibria |
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38 | (1) |
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3.4.3 Conditional equilibrium |
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39 | (1) |
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3.4.4 One, none, or many equilibria? |
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40 | (1) |
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41 | (5) |
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3.5.1 Zeno's paradox: Achilles and the tortoise |
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42 | (1) |
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3.5.2 A new beauty in town: Fractals |
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43 | (2) |
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3.5.3 Computer simulation |
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45 | (1) |
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46 | (1) |
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3.7 Appendix 3.1: Summing series |
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47 | (1) |
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4 Nonlinearity, the Mother of Complexity |
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48 | (12) |
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48 | (1) |
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48 | (2) |
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50 | (1) |
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50 | (2) |
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52 | (1) |
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4.4 Pitagora's theorem and beyond |
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52 | (2) |
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54 | (1) |
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4.6 Butterflies and elephants |
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55 | (3) |
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58 | (1) |
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4.8 Appendix 4.1: Nonlinear functions |
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58 | (1) |
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4.9 Appendix 4.2: How much is it two plus two? |
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59 | (1) |
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5 The Dark Side of Nonlinearity |
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60 | (16) |
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60 | (3) |
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5.1.1 Surprises over lunchtime |
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61 | (2) |
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5.2 A closer look at chaos |
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63 | (1) |
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5.2.1 Population dynamics |
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63 | (1) |
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5.3 Entry competition: The logistic map |
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64 | (2) |
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5.4 Chaos: Lost and found |
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66 | (4) |
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5.4.1 Are maps realistic? |
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69 | (1) |
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5.5 From chaos to turbulence |
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70 | (3) |
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71 | (1) |
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5.5.2 The Reynolds number |
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72 | (1) |
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5.6 The pleasure of being unpredictable |
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73 | (1) |
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5.7 Appendix 5.1: More on the logistic map |
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74 | (2) |
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6 The Bright Side of Nonlinearity |
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76 | (12) |
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76 | (1) |
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6.2 Nonlinear cooperation |
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77 | (1) |
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6.3 Moving information across scales |
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77 | (1) |
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6.4 From large to small: Breakup |
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77 | (2) |
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6.5 From small to large: Coalescence |
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79 | (3) |
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6.6 Morphogenesis: The Turing model |
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82 | (3) |
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85 | (1) |
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6.8 Appendix 6.1 Breakup and coalescence |
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86 | (1) |
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6.9 Appendix 6.2 Wave steepening |
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86 | (2) |
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7 Networks, the Fabric of Complexity |
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88 | (25) |
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88 | (1) |
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88 | (1) |
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7.3 Dismantling Zeno's trick: The lattice world |
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89 | (1) |
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7.4 Hamletic fluids: Lattice gas cellular automata |
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90 | (3) |
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7.5 Probabilistic fluids: Lattice Boltzmann |
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93 | (2) |
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7.6 A new kind of science? |
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95 | (1) |
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7.7 Is the Universe a gigantic self-computing automaton? |
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96 | (2) |
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7.7.1 The take-home lesson of lattice fluids |
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98 | (1) |
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7.8 From lattices to general networks |
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98 | (1) |
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99 | (1) |
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7.9.1 Statistical properties |
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100 | (1) |
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7.10 Metric versus topological networks |
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100 | (1) |
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101 | (2) |
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103 | (3) |
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7.12.1 Tolerance to outliers |
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104 | (1) |
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7.12.2 The Matthew effect |
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105 | (1) |
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106 | (2) |
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108 | (1) |
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7.14 Complex adaptive networks |
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108 | (2) |
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110 | (3) |
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Part II The Science of Change |
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8 Old but Gold: Thermodynamics |
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113 | (23) |
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8.1 The science of (slow) change |
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113 | (1) |
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8.2 The cosmic prima donnas |
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114 | (1) |
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8.3 Energy: Transformation and conservation |
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114 | (5) |
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8.3.1 The many faces of potential energy |
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117 | (2) |
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119 | (3) |
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8.4.1 Work and zero temperature |
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120 | (2) |
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8.5 Much ado about something: The Carnot cycle |
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122 | (3) |
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8.6 The mirage of perfect efficiency |
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125 | (2) |
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127 | (1) |
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128 | (3) |
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8.9 The Second Principle of Thermodynamics |
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131 | (1) |
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132 | (2) |
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8.11 The rules of the game |
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134 | (1) |
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135 | (1) |
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9 The Man Who Trusted Atoms |
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136 | (23) |
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9.1 The microscopic roots of thermodynamics |
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136 | (1) |
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137 | (2) |
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9.2.1 Kinetic theory of gases |
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137 | (2) |
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139 | (1) |
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9.4 Local and global equilibria |
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139 | (5) |
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9.4.1 Maxwell-Boltzmann local equilibrium distribution |
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141 | (2) |
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9.4.2 The fatal attraction of conservation laws |
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143 | (1) |
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9.5 From molecules to entropy |
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144 | (1) |
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145 | (2) |
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9.6.1 Entropy and happiness |
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147 | (1) |
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9.7 Temperature: The entropic trigger |
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147 | (1) |
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148 | (2) |
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9.9 The microscopic face of dissipation |
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150 | (2) |
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152 | (3) |
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152 | (1) |
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9.10.2 Entropy, information, and scrambled eggs |
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153 | (2) |
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9.10.3 Caveat: Entropy and Disorder |
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155 | (1) |
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155 | (1) |
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9.12 Appendix 9.1: Boltzmann's kinetic theory |
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156 | (3) |
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159 | (16) |
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159 | (1) |
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159 | (1) |
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160 | (2) |
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162 | (2) |
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10.5 Dissipative structures |
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164 | (1) |
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10.6 Conduction and convection |
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165 | (1) |
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166 | (1) |
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10.8 Where is nonlinearity? |
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167 | (2) |
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169 | (1) |
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169 | (2) |
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171 | (1) |
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10.12 Summary: Life on borrowed time |
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172 | (1) |
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10.13 Appendix 10.1: Rayleigh-Benard equations |
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173 | (2) |
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175 | (20) |
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175 | (1) |
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175 | (1) |
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11.3 Basic facts about gravity |
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175 | (1) |
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11.4 Newton's theory of universal gravitation |
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176 | (3) |
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11.4.1 The fatal grip of gravity |
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176 | (2) |
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178 | (1) |
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11.4.3 Gravity is long-ranged |
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178 | (1) |
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11.5 Gravitational thermodynamics |
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179 | (1) |
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11.6 Gravitational balloons |
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180 | (2) |
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11.6.1 Entropy and gravity |
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181 | (1) |
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11.7 Cosmological thermodynamics |
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182 | (1) |
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11.8 Einstein's theory of general gravitation |
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182 | (2) |
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11.8.1 Entry general relativity |
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183 | (1) |
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11.9 Cosmological chronicles |
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184 | (3) |
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185 | (2) |
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11.10 Pause of reflection |
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187 | (1) |
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11.10.1 Dancing in the dark |
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187 | (1) |
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187 | (1) |
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11.11 Black hole thermodynamics |
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188 | (1) |
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11.12 Black holes get grey (not much though ...) |
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189 | (4) |
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11.12.1 Bekenstein--Hawking black hole entropy |
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191 | (2) |
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11.13 The thermal history of the Universe |
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193 | (1) |
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193 | (2) |
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195 | (16) |
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195 | (1) |
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12.2 Nature's spending review |
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195 | (3) |
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196 | (2) |
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198 | (1) |
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199 | (2) |
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201 | (2) |
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12.6 Stopovers in the landscape |
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203 | (1) |
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12.7 The duel and the duet |
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204 | (3) |
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12.8 In the biological world |
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207 | (1) |
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207 | (1) |
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12.10 Appendix 12.1: Arrhenius law |
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208 | (3) |
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Part III The Physics-Biology Interface |
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13 Survival in Molecular Hyperland, the Ozland Valleys |
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211 | (25) |
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13.1 A tour to molecular hyperland |
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211 | (1) |
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211 | (3) |
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13.2.1 Surviving in hyperland |
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212 | (1) |
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13.2.2 Weeding out wasteland |
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213 | (1) |
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13.3 The art of coarse graining |
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214 | (1) |
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215 | (1) |
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13.5 Modelling DNA translocation |
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216 | (2) |
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216 | (2) |
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218 | (2) |
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13.7 Coarse-grained molecular dynamics |
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220 | (2) |
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13.7.1 Molecular trains and their delays |
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220 | (2) |
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13.8 Extreme coarse-graining: Lineland |
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222 | (1) |
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13.9 The Langevin approach |
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223 | (4) |
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13.10 Biological ballerinas: Protein folding |
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227 | (2) |
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13.11 Coarse-graining proteins |
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229 | (1) |
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13.12 Of proteins and monkeys: The Levinthal's paradox |
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230 | (2) |
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13.13 Why does it work (when it does ...)? |
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232 | (1) |
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13.13.1 The closure problem |
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232 | (1) |
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233 | (1) |
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13.15 Appendix 13.1: Order parameter for translocation |
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234 | (2) |
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236 | (26) |
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14.1 Navigating the free-energy landscape, on time |
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236 | (1) |
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236 | (1) |
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14.3 Rare events are rare, not impossible |
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237 | (3) |
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237 | (2) |
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14.3.2 Biological blue moon time |
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239 | (1) |
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14.4 Deep corrugations: The funnel |
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240 | (2) |
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241 | (1) |
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14.5 Picasso and the proteins |
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242 | (2) |
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14.6 The principle of minimal frustration |
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244 | (3) |
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14.6.1 Stravinski's constrained freedom |
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246 | (1) |
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247 | (3) |
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14.8 The good and the bad funnels |
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250 | (1) |
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14.8.1 Beacons in The Ocean of Complexity |
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250 | (1) |
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14.9 Navigation routes in the landscape |
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251 | (2) |
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14.9.1 Down the steepest slope |
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251 | (1) |
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14.9.2 With a little help from our molecular chaos friend |
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251 | (2) |
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14.10 Protein folding revisited |
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253 | (2) |
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14.10.1 Multiple-Order parameters |
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254 | (1) |
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14.11 The gifts of non-equilibrium |
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255 | (2) |
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14.11.1 From mountains to quicksand |
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255 | (1) |
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14.11.2 Burnt bridges and cryptic pockets |
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256 | (1) |
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14.11.3 Trains that don't pass twice |
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256 | (1) |
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14.12 The quark, the jaguar, and the free-energy principle |
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257 | (1) |
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258 | (1) |
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14.14 Appendix 14.1 Funnel acceleration |
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258 | (1) |
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14.15 Appendix 14.2 Mistaking rare events for impossible ones |
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259 | (3) |
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15 Soft Matter, the Stuff that Dreams are Made of |
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262 | (25) |
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262 | (1) |
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15.2 The stuff that dreams are made of |
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262 | (1) |
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263 | (4) |
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15.3.1 The magnificent three: gas, liquid, and solid |
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264 | (1) |
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15.3.2 Hybrid states of matter |
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265 | (2) |
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15.4 The physics-chemistry-biology interface |
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267 | (1) |
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15.5 Molecular interactions |
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268 | (1) |
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269 | (1) |
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15.6 Electrostatic forces |
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269 | (4) |
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15.6.1 Electrostatic instability |
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270 | (2) |
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15.6.2 Long-range attraction and short-range repulsion |
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272 | (1) |
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273 | (2) |
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275 | (1) |
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275 | (6) |
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15.8.1 Van der Waals and Lennard--Jones |
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275 | (4) |
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279 | (1) |
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280 | (1) |
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15.9 More dispersion forces |
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281 | (2) |
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15.10 Pause of reflection: The ouroboros |
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283 | (1) |
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15.10.1 Die-hard prejudices |
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284 | (1) |
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15.11 Beyond dissipative structures? |
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284 | (1) |
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285 | (1) |
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15.13 Appendix 15.1: Surface tension and Laplace's law |
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286 | (1) |
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16 Water, the Wonderfluid |
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287 | (22) |
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287 | (1) |
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16.2 The magic fluid we call water |
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287 | (2) |
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288 | (1) |
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16.2.2 Water molecular networks |
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289 | (1) |
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289 | (1) |
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290 | (3) |
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16.4.1 Entropy is not (just) Disorder |
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292 | (1) |
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16.5 My name is Bond, H-Bond |
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293 | (1) |
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16.6 Hydropathy, the molecular builder |
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294 | (2) |
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16.7 Back to protein folding |
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296 | (1) |
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297 | (1) |
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16.8 Intra-molecular interactions |
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297 | (2) |
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299 | (2) |
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300 | (1) |
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16.10 The Theory of Something |
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301 | (1) |
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16.10.1 And The Theory of Everything Else |
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302 | (1) |
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16.11 Dispelling prejudices: Can you imitate birds? |
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302 | (2) |
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304 | (5) |
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Part IV Complexity and the Human Condition |
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17 Time, Complexity and the Human Condition |
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309 | (18) |
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309 | (2) |
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17.1.1 The transformations of time |
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309 | (2) |
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311 | (4) |
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17.2.1 Crossing the Boltzmann bridge |
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312 | (3) |
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315 | (1) |
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17.3.1 Brain and tears: The human condition |
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315 | (1) |
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316 | (4) |
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17.4.1 Le temps de philosophes |
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317 | (1) |
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17.4.2 Time travel and the fear of uncertainty |
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318 | (2) |
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17.5 Putting the times together: Time is us |
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320 | (3) |
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321 | (2) |
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17.6 Who wants to live forever? |
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323 | (3) |
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17.6.1 Are atoms immortal? |
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324 | (1) |
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17.6.2 The quest for immortality, in Silicon Valley |
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325 | (1) |
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326 | (1) |
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18 Harness the Hybris: Hallelujah! |
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327 | (12) |
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18.1 Escape from Helsinki: Eyjafjallajokull! |
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327 | (1) |
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328 | (2) |
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18.2.1 Should I be doing science? |
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329 | (1) |
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18.3 These are the two wings |
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330 | (1) |
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18.3.1 Typecast stereotypes |
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330 | (1) |
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18.4 A jump into the blue |
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331 | (1) |
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18.5 Of sparrows and lilies |
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332 | (2) |
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18.6 It's April again, COVID-19 time |
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334 | (2) |
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336 | (3) |
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337 | (1) |
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338 | (1) |
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339 | (17) |
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339 | (6) |
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19.1.1 Scientific notation |
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339 | (1) |
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19.1.2 Exponential and logarithms |
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340 | (2) |
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342 | (1) |
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19.1.4 Large numbers: Gates, Bezos, and Avogadro |
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342 | (1) |
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19.1.5 Huge numbers: Googol |
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343 | (1) |
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19.1.6 Towards monster numbers: DNA |
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343 | (1) |
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19.1.7 Monster numbers and beyond: Googolpex and Penrose |
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344 | (1) |
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19.1.8 Logarithmic survival |
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345 | (1) |
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345 | (3) |
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19.2.1 Thermodynamic variables |
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345 | (1) |
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19.2.2 The First Principle of Thermodynamics |
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346 | (1) |
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19.2.3 The Second Principle of Thermodynamics |
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347 | (1) |
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19.2.4 The Third Principle of Thermodynamics |
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347 | (1) |
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19.2.5 The Fourth Principle of Thermodynamics (in jesting mode ...) |
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348 | (1) |
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348 | (8) |
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19.3.1 Classical mechanics |
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349 | (1) |
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350 | (1) |
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350 | (6) |
References |
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356 | (6) |
Index |
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362 | |