Foreword |
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xi | |
Preface |
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xiii | |
Acknowledgments |
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xv | |
Notation |
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xvii | |
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1 | (5) |
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1.1 What is stochastic thermodynamics? |
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1 | (2) |
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1.2 Why does it work and why is it useful? |
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3 | (1) |
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3 | (3) |
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6 | (32) |
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6 | (5) |
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2.2 Thermodynamic efficiency |
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11 | (1) |
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2.3 Free energy and nonequilibrium free energy |
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12 | (3) |
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2.4 Statistical mechanics |
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15 | (4) |
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19 | (2) |
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21 | (3) |
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2.7 Trajectories of master equations |
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24 | (2) |
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2.8 Fokker-Planck equation (*) |
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26 | (3) |
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2.9 Langevin equation (*) |
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29 | (3) |
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32 | (3) |
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35 | (1) |
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36 | (2) |
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Chapter 3 Stochastic Thermodynamics |
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38 | (29) |
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38 | (2) |
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3.2 Work and heat in stochastic thermodynamics |
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40 | (2) |
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3.3 Mesoscopic and calorimetric heat (*) |
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42 | (2) |
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3.4 ATP hydrolysis by myosin |
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44 | (2) |
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46 | (1) |
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47 | (1) |
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3.7 Stochastic entropy and entropy production in a manipulated two-level system |
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48 | (2) |
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3.8 Average entropy production rate |
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50 | (1) |
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3.9 Network theory of nonequilibrium steady states (*) |
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51 | (2) |
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3.10 Stochastic chemical reactions |
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53 | (2) |
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3.11 Linear response theory (*) |
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55 | (3) |
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3.12 More on coarse graining (*) |
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58 | (4) |
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3.13 Continuous systems (*) |
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62 | (2) |
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64 | (1) |
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65 | (2) |
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Chapter 4 Fluctuation Relations |
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67 | (37) |
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4.1 Irreversibility and entropy production |
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67 | (2) |
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4.2 Integral fluctuation relation |
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69 | (1) |
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4.3 Dragged particle on a ring |
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70 | (3) |
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4.4 Back to linear response theory (*) |
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73 | (3) |
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4.5 Detailed fluctuation relation |
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76 | (2) |
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4.6 The Jarzynski and Crooks relations |
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78 | (2) |
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80 | (1) |
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4.8 Fluctuation relations in practice |
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81 | (1) |
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4.9 Adiabatic and nonadiabatic entropy production and the Hatano-Sasa relation |
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82 | (2) |
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4.10 Systems with odd-parity variables |
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84 | (2) |
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4.11 Trajectory probability for Langevin equations (*) |
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86 | (1) |
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4.12 Fluctuation relation for the Langevin equation (*) |
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87 | (2) |
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4.13 Brownian particle in a time-dependent harmonic potential (*) |
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89 | (3) |
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4.14 Brownian motion with inertia (*) |
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92 | (2) |
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4.15 Hamiltonian systems (*) |
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94 | (6) |
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100 | (1) |
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101 | (3) |
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Chapter 5 Thermodynamics of Information |
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104 | (26) |
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104 | (2) |
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5.2 Back to nonequilibrium free energy |
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106 | (1) |
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5.3 Information in stochastic thermodynamics |
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107 | (2) |
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5.4 The Sagawa-Ueda relation |
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109 | (1) |
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5.5 The Mandal-Jarzynski machine |
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110 | (2) |
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112 | (3) |
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5.7 Information cost in sensing |
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115 | (7) |
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5.8 Information reservoirs |
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122 | (3) |
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5.9 Fluctuation relations with information reservoirs (*) |
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125 | (2) |
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127 | (1) |
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128 | (2) |
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Chapter 6 Large Deviations: Theory and Practice |
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130 | (30) |
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6.1 Large deviations in a nutshell |
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130 | (4) |
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6.2 Currents, traffic, and other observables |
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134 | (3) |
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6.3 Large deviations and fluctuation relations |
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137 | (1) |
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6.4 Fluctuation theorem for currents (*) |
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138 | (2) |
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140 | (2) |
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6.6 Michaelis-Menten reaction scheme |
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142 | (4) |
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6.7 Fluctuation relations in a model of kinesin (*) |
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146 | (5) |
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151 | (3) |
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6.9 Levels of large deviations (*) |
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154 | (4) |
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158 | (1) |
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158 | (2) |
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Chapter 7 Experimental Applications |
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160 | (1) |
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71 The hairpin as a paradigm |
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160 | (12) |
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161 | (1) |
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7.3 Equilibrium free energies from nonequilibrium manipulations |
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162 | (5) |
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167 | (1) |
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167 | (4) |
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171 | (1) |
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172 | (32) |
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8.1 Stochastic efficiency |
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172 | (4) |
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8.2 Uncertainty relations |
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176 | (4) |
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8.3 Applications of uncertainty relations |
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180 | (1) |
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181 | (4) |
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8.5 Fully irreversible processes |
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185 | (2) |
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187 | (4) |
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191 | (4) |
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195 | (2) |
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197 | (5) |
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202 | (1) |
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203 | (1) |
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204 | (3) |
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207 | (26) |
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A.1 Convex functions and the Jensen inequality |
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207 | (4) |
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A.2 Legendre transformation |
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211 | (2) |
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A.3 Probabilities and probability distributions |
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213 | (1) |
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A.4 Generating functions and cumulant generating functions |
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214 | (3) |
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A.5 Ergodic properties of Markov processes |
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217 | (2) |
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219 | (1) |
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A.7 Derivation of the Fokker-Planck equation |
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220 | (2) |
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A.8 Ito formula and Stratonovich-Ito mapping |
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222 | (2) |
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A.9 Basis of the cycle space |
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224 | (1) |
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A.10 Actions and trajectory probabilities for Langevin equations |
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225 | (1) |
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A.11 The Bennett-Crooks estimator for the free-energy difference |
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226 | (2) |
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A.12 Cauchy-Schwarz inequality |
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228 | (1) |
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A.13 Bound for the current rate function |
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229 | (4) |
Bibliography |
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233 | (8) |
Author Index |
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241 | (4) |
Index |
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245 | |