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1 An Overview: The Challenge of Complex Systems |
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1 | (6) |
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1 | (6) |
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1.1.1 Data Assimilation as a Communications Problem |
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3 | (2) |
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1.1.2 Outline of this Book |
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5 | (2) |
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2 Examples as a Guide to the Issues |
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7 | (44) |
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2.1 The Malkus Waterwheel |
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8 | (9) |
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2.1.1 A Physics Question About the Waterwheel |
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10 | (7) |
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2.2 The Colpitts Oscillator |
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17 | (19) |
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2.2.1 Colpitts Circuit Equations |
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19 | (1) |
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2.2.2 Estimation with Chaotic Signals |
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20 | (5) |
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2.2.3 Instability of the Synchronization Manifold |
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25 | (2) |
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2.2.4 Regularized Cost Function |
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27 | (1) |
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2.2.5 Experimental Colpitts Oscillator Redux |
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28 | (5) |
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2.2.6 Numerical Optimization Methods |
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33 | (3) |
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2.3 A Hodgkin-Huxley Neuron Model |
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36 | (10) |
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2.3.1 Biophysics of the Hodgkin-Huxley Model |
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36 | (4) |
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2.3.2 Estimating Parameters and Unobserved States of the HH Model |
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40 | (2) |
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2.3.3 Predicting the Response of the HH Model |
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42 | (3) |
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2.3.4 Consequences of the Wrong Model |
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45 | (1) |
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2.4 Synopsis and Perspectives: "Slightly Complex" Examples |
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46 | (5) |
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3 General Formulation of Statistical Data Assimilation |
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51 | (34) |
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3.1 Data Assimilation Without Data |
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52 | (6) |
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3.1.1 Deterministic Dynamics: Path Integral |
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52 | (4) |
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3.1.2 Relation to the Quantum Mechanical Path Integral |
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56 | (1) |
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57 | (1) |
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3.2 Data Assimilation with a Little Bit of Data |
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58 | (9) |
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58 | (3) |
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61 | (3) |
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64 | (3) |
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3.3 The General Data Assimilation Problem |
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67 | (8) |
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3.3.1 Differential Equations to Discrete Time Maps |
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67 | (2) |
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3.3.2 Errors and Noise: Stochastic Data Assimilation |
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69 | (6) |
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3.4 Approximating the Action |
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75 | (2) |
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3.5 The Value of a Measurement |
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77 | (1) |
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78 | (1) |
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3.7 The Scientific Value of the Path Integral |
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79 | (1) |
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3.8 Data Assimilation Path Integrals in Continuous Time |
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80 | (3) |
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3.9 Earlier Work on Path Integrals in Statistical Data Assimilation |
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83 | (1) |
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3.10 Synopsis and Perspectives: Statistical Data Assimilation |
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84 | (1) |
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4 Evaluating the Path Integral |
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85 | (40) |
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4.1 Guide to Methods for Estimating the Path Integral |
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85 | (2) |
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4.2 Stationary Path Methods |
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87 | (5) |
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89 | (2) |
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91 | (1) |
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4.3 Beyond the Stationary Path: Loop Expansions |
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92 | (9) |
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4.3.1 The Effective Action: Numerical Optimization Reappears |
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92 | (1) |
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4.3.2 The Effective Action |
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93 | (1) |
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4.3.3 Dyson-Schwinger Equations for Statistical Data Assimilation |
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94 | (4) |
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4.3.4 The Effective Action: Loop Expansion |
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98 | (3) |
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4.4 Estimating the Path Distribution exp[ -A0(X)] |
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101 | (2) |
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4.4.1 Langevin Equations: Fokker-Planck |
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101 | (2) |
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103 | (9) |
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4.5.1 Metropolis-Hastings (Rosenbluth) Methods |
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103 | (1) |
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4.5.2 Using GPU Parallel Processing |
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104 | (2) |
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4.5.3 Example Monte Carlo Problem: NaKL Neuron Model |
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106 | (6) |
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4.6 Consistency of Model Errors |
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112 | (11) |
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4.6.1 An Example from the Lorenz96 Model with D = 100 |
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115 | (3) |
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4.6.2 An Example from the Lorenz96 Model with D = 20 |
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118 | (4) |
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4.6.3 Comments on Consistent Model Errors |
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122 | (1) |
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4.7 Synopsis and Perspectives: Evaluating the Path Integral |
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123 | (2) |
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125 | (74) |
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5.1 The Roles of Twin Experiments |
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126 | (1) |
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126 | (19) |
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5.2.1 NaKL Hodgkin-Huxley Model |
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127 | (2) |
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5.2.2 The Importance of the Regularizing Variable u(t) |
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129 | (2) |
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5.2.3 Frequency Content of the Stimulus Iapp(t) |
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131 | (1) |
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5.2.4 Additive Noise in the Observations |
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132 | (2) |
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5.2.5 An Additional Current: Ih |
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134 | (1) |
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5.2.6 NaKLh Twin Experiments |
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135 | (3) |
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5.2.7 Model Testing Through Prediction |
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138 | (1) |
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5.2.8 Robustness to Model Errors; NaKL Model ↔ NaKLh Model |
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139 | (1) |
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5.2.9 NaKLh Data Presented to an NaKL Model |
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140 | (3) |
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5.2.10 NaKL Data Driving an NaKLh Model; Pruning a Big Model |
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143 | (2) |
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145 | (14) |
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146 | (3) |
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149 | (5) |
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5.3.3 CLEs for Lorenz96 Models |
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154 | (3) |
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5.3.4 Lorenz96 Model: Variational Principle; No Model Errors |
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157 | (2) |
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5.4 Monte Carlo Estimation of the Path Integral for the Lorenz96 Model |
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159 | (15) |
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5.4.1 How Many Observations Are Required? |
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162 | (4) |
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5.4.2 Results of Monte Carlo Estimation of the Path Integral for Moments of X and Model Parameters |
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166 | (1) |
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5.4.3 Prediction by Model Equations for t > tm |
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167 | (5) |
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5.4.4 Non-Gaussian Measurement Error |
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172 | (1) |
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5.4.5 How Often Should One Make Measurements? |
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172 | (2) |
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5.5 Shallow Water Equations |
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174 | (18) |
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5.5.1 One-Layer Shallow Water Flow |
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175 | (3) |
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5.5.2 Statistical Data Analysis for the Shallow Water Equations |
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178 | (2) |
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5.5.3 Generating the Data |
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180 | (2) |
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5.5.4 Synchronization of the Data with the Model Output |
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182 | (5) |
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5.5.5 Results for the Shallow Water Equations: Synchronization Implies Predictability |
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187 | (5) |
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5.6 Synopsis and Perspectives: Twin Experiments |
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192 | (7) |
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6 Analysis of Experimental Data |
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199 | (22) |
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6.1 The Avian Song System: Individual Neurons |
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200 | (2) |
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6.2 Experimental Procedures for HVC Neurons |
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202 | (1) |
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6.2.1 HVC Slice Preparation: Experimental Procedure |
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202 | (1) |
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6.3 Experimental Results and Analysis |
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203 | (1) |
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203 | (4) |
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6.5 Details of the Numerical Evaluation |
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207 | (1) |
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6.5.1 Estimation and Prediction of HVC Neuron Responses to Injected Current |
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208 | (1) |
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6.6 Results from Data Acquisition and Analysis |
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208 | (11) |
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6.6.1 Neuron 20110413_4_1 Epoch 22 |
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208 | (2) |
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6.6.2 Neuron 20120517_1_1 Epochs 11 and 12 |
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210 | (4) |
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6.6.3 Neuron 20120406_1_3 Epochs 19 and 15 |
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214 | (2) |
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6.6.4 Estimated Currents and Channel Kinetics |
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216 | (3) |
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6.7 Comments on the Analysis of These Data |
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219 | (1) |
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6.8 Synopsis and Perspectives: Analysis of Experimental Data |
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219 | (2) |
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221 | (6) |
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7.1 "More Measurements": The Use of Time Delay Phase Space Reconstruction |
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223 | (4) |
Bibliography |
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227 | (6) |
Index |
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233 | |