Acknowledgments |
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xiii | |
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1 | (10) |
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1 | (2) |
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1.2 If we had only a single lecture in statistical thermodynamics |
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3 | (8) |
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2 Elements of probability and combinatorial theory |
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11 | (21) |
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11 | (6) |
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12 | (1) |
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2.1.2 Probability distributions |
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13 | (2) |
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2.1.3 Mathematical expectation |
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15 | (1) |
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2.1.4 Moments of probability distributions |
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15 | (1) |
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2.1.5 Gaussian probability distribution |
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16 | (1) |
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2.2 Elements of combinatorial analysis |
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17 | (2) |
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17 | (1) |
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18 | (1) |
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18 | (1) |
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2.3 Distinguishable and indistinguishable particles |
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19 | (1) |
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2.4 Stirling's approximation |
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20 | (1) |
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2.5 Binomial distribution |
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21 | (2) |
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2.6 Multinomial distribution |
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23 | (1) |
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2.7 Exponential and Poisson distributions |
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23 | (1) |
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2.8 One-dimensional random walk |
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24 | (2) |
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26 | (2) |
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2.10 Central limit theorem |
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28 | (1) |
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29 | (1) |
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29 | (3) |
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3 Phase spaces, from classical to quantum mechanics, and back |
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32 | (34) |
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32 | (11) |
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3.1.1 Newtonian mechanics |
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32 | (3) |
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3.1.2 Generalized coordinates |
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35 | (2) |
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3.1.3 Lagrangian mechanics |
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37 | (3) |
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3.1.4 Hamiltonian mechanics |
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40 | (3) |
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43 | (4) |
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3.2.1 Conservative systems |
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46 | (1) |
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47 | (13) |
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3.3.1 Particle-wave duality |
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49 | (9) |
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3.3.2 Heisenberg's uncertainty principle |
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58 | (2) |
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3.4 From quantum mechanical to classical mechanical phase spaces |
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60 | (2) |
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3.4.1 Born-Oppenheimer approximation |
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62 | (1) |
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62 | (1) |
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63 | (3) |
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66 | (25) |
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4.1 Distribution function and probability density in phase space |
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66 | (3) |
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4.2 Ensemble average of thermodynamic properties |
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69 | (1) |
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70 | (1) |
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71 | (1) |
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4.5 Microcanonical ensemble |
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71 | (2) |
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4.6 Thermodynamics from ensembles |
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73 | (2) |
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4.7 S = kB In Ω, or entropy understood |
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75 | (4) |
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79 | (4) |
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4.9 Ω with quantum uncertainty |
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83 | (3) |
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4.10 Liouville's equation |
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86 | (3) |
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89 | (1) |
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89 | (2) |
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91 | (19) |
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5.1 Probability density in phase space |
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91 | (4) |
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5.2 NVT ensemble thermodynamics |
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95 | (2) |
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5.3 Entropy of an NVT system |
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97 | (2) |
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5.4 Thermodynamics of NVT ideal gases |
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99 | (4) |
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5.5 Calculation of absolute partition functions is impossible and unnecessary |
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103 | (1) |
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5.6 Maxwell-Boltzmann velocity distribution |
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104 | (3) |
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107 | (1) |
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107 | (3) |
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6 Fluctuations and other ensembles |
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110 | (14) |
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6.1 Fluctuations and equivalence of different ensembles |
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110 | (3) |
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6.2 Statistical derivation of the NVT partition function |
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113 | (2) |
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6.3 Grand-canonical and isothermal-isobaric ensembles |
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115 | (2) |
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6.4 Maxima and minima at equilibrium |
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117 | (3) |
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6.5 Reversibility and the second law of thermodynamics |
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120 | (2) |
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122 | (1) |
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122 | (2) |
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124 | (15) |
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7.1 Molecular degrees of freedom |
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124 | (1) |
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125 | (10) |
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130 | (2) |
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7.2.2 Vibrations included |
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132 | (3) |
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7.2.3 Subatomic degrees of freedom |
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135 | (1) |
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7.3 Equipartition theorem |
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135 | (2) |
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137 | (1) |
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137 | (2) |
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139 | (16) |
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140 | (4) |
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8.1.1 Application of the virial theorem: equation of state for non-ideal systems |
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142 | (2) |
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8.2 Pairwise interaction potentials |
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144 | (5) |
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8.2.1 Lennard-Jones potential |
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146 | (2) |
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8.2.2 Electrostatic interactions |
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148 | (1) |
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8.2.3 Total intermolecular potential energy |
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149 | (1) |
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8.3 Virial equation of state |
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149 | (1) |
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8.4 van der Waals equation of state |
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150 | (3) |
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153 | (1) |
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153 | (2) |
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155 | (18) |
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155 | (1) |
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9.2 Molecular distributions |
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155 | (3) |
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9.3 Physical interpretation of pair distribution functions |
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158 | (4) |
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9.4 Thermodynamic properties from pair distribution functions |
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162 | (2) |
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164 | (6) |
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9.5.1 Heat capacity of monoatomic crystals |
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164 | (3) |
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9.5.2 The Einstein model of the specific heat of crystals |
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167 | (2) |
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9.5.3 The Debye model of the specific heat of crystals |
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169 | (1) |
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170 | (1) |
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171 | (2) |
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10 Beyond pure, single-component systems |
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173 | (17) |
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173 | (4) |
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10.1.1 Properties of mixing for ideal mixtures |
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176 | (1) |
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177 | (5) |
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10.2.1 The law of corresponding states |
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181 | (1) |
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10.3 Regular solution theory |
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182 | (4) |
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10.3.1 Binary vapor-liquid equilibria |
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185 | (1) |
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10.4 Chemical reaction equilibria |
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186 | (2) |
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188 | (1) |
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188 | (2) |
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11 Polymers - Brownian dynamics |
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190 | (12) |
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190 | (8) |
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11.1.1 Macromolecular dimensions |
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190 | (4) |
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194 | (2) |
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11.1.3 Dynamic models of macromolecules |
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196 | (2) |
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198 | (3) |
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201 | (1) |
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201 | (1) |
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12 Non-equilibrium thermodynamics |
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202 | (13) |
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12.1 Linear response theory |
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202 | (2) |
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12.2 Time correlation functions |
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204 | (4) |
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12.3 Fluctuation-dissipation theorem |
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208 | (2) |
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12.4 Dielectric relaxation of polymer chains |
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210 | (3) |
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213 | (1) |
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214 | (1) |
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215 | (17) |
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13.1 Continuous-deterministic reaction kinetics |
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216 | (2) |
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13.2 Away from the thermodynamic limit - chemical master equation |
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218 | (7) |
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13.2.1 Analytic solution of the chemical master equation |
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221 | (4) |
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13.3 Derivation of the master equation for any stochastic process |
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225 | (6) |
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13.3.1 Chapman-Kolmogorov equation |
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226 | (1) |
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227 | (1) |
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13.3.3 Fokker-Planck equation |
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228 | (1) |
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229 | (1) |
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13.3.5 Chemical Langevin equations |
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230 | (1) |
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231 | (1) |
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231 | (1) |
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232 | (23) |
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14.1 Tractable exploration of phase space |
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232 | (2) |
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14.2 Computer simulations are tractable mathematics |
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234 | (1) |
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14.3 Introduction to molecular simulation techniques |
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235 | (15) |
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14.3.1 Construction of the molecular model |
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235 | (4) |
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14.3.2 Semi-empirical force field potential |
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239 | (3) |
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14.3.3 System size and geometry |
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242 | (1) |
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14.3.4 Periodic boundary conditions |
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243 | (1) |
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14.3.5 Fortran code for periodic boundary conditions |
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244 | (1) |
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14.3.6 Minimum image convection |
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245 | (5) |
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14.4 How to start a simulation |
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250 | (2) |
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14.5 Non-dimensional simulation parameters |
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252 | (1) |
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14.6 Neighbor lists: a time-saving trick |
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252 | (1) |
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253 | (1) |
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254 | (1) |
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15 Monte Carlo simulations |
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255 | (18) |
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15.1 Sampling of probability distribution functions |
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256 | (1) |
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15.2 Uniformly random sampling of phase space |
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257 | (2) |
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15.3 Markov chains in Monte Carlo |
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259 | (3) |
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262 | (6) |
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15.4.1 How to generate states |
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263 | (1) |
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15.4.2 How to accept states |
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264 | (2) |
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15.4.3 Metropolis Monte Carlo pseudo-code |
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266 | (1) |
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15.4.4 Importance sampling with a coin and a die |
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267 | (1) |
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15.4.5 Biased Monte Carlo |
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268 | (1) |
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15.5 Grand canonical Monte Carlo |
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268 | (1) |
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15.6 Gibbs ensemble Monte Carlo for phase equilibria |
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269 | (2) |
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271 | (1) |
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272 | (1) |
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16 Molecular dynamics simulations |
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273 | (14) |
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16.1 Molecular dynamics simulation of simple fluids |
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274 | (1) |
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16.2 Numerical integration algorithms |
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274 | (5) |
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16.2.1 Predictor-corrector algorithms |
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276 | (1) |
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277 | (2) |
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16.3 Selecting the size of the time step |
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279 | (1) |
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16.4 How long to run the simulation? |
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280 | (1) |
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16.5 Molecular dynamics in other ensembles |
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280 | (4) |
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16.5.1 Canonical ensemble molecular dynamics simulations |
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282 | (2) |
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16.6 Constrained and multiple time step dynamics |
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284 | (1) |
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285 | (1) |
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286 | (1) |
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17 Properties of matter from simulation results |
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287 | (8) |
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17.1 Structural properties |
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287 | (2) |
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17.2 Dynamical information |
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289 | (3) |
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17.2.1 Diffusion coefficient |
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289 | (1) |
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17.2.2 Correlation functions |
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290 | (1) |
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17.2.3 Time correlation functions |
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291 | (1) |
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17.3 Free energy calculations |
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292 | (2) |
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17.3.1 Free energy perturbation methods |
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292 | (1) |
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293 | (1) |
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17.3.3 Thermodynamic integration methods |
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293 | (1) |
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294 | (1) |
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294 | (1) |
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18 Stochastic simulations of chemical reaction kinetics |
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295 | (13) |
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18.1 Stochastic simulation algorithm |
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296 | (1) |
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18.2 Multiscale algorithms for chemical kinetics |
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297 | (3) |
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18.2.1 Slow-discrete region (I) |
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299 | (1) |
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18.2.2 Slow-continuous region (II) |
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299 | (1) |
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18.2.3 Fast-discrete region (III) |
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299 | (1) |
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18.2.4 Fast-continuous stochastic region (IV) |
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300 | (1) |
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18.2.5 Fast-continuous deterministic region (V) |
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300 | (1) |
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300 | (2) |
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18.4 Hybrid stochastic algorithm |
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302 | (2) |
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18.4.1 System partitioning |
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302 | (1) |
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18.4.2 Propagation of the fast subsystem - chemical Langevin equations |
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303 | (1) |
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18.4.3 Propagation of the slow subsystem - jump equations |
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303 | (1) |
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18.5 Hy3S - Hybrid stochastic simulations for supercomputers |
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304 | (1) |
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18.6 Multikin - Multiscale kinetics |
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305 | (1) |
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305 | (1) |
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306 | (2) |
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A Physical constants and conversion factors |
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308 | (1) |
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308 | (1) |
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308 | (1) |
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B Elements of classical thermodynamics |
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309 | (3) |
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B.1 Systems, properties, and states in thermodynamics |
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309 | (1) |
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B.2 Fundamental thermodynamic relations |
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310 | (2) |
Index |
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312 | |