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CONTENTS
4 Metastable intermediates in DNA unzipping 4.1 Detection of intermediate states . . . . . . . . . . . . 4.1.1 Bayesian analysis of FDCs . . . . . . . . . . . 4.1.2 Statistical inference of intermediate states . . 4.1.3 CUR size distribution . . . . . . . . . . . . . 4.1.4 Results . . . . . . . . . . . . . . . . . . . . . . 4.2 Toy model . . . . . . . . . . . . . . . . . . . . . . . . 4.2.1 Approximate solution . . . . . . . . . . . . . . 4.2.2 Height of the force rips . . . . . . . . . . . . . 4.2.3 CUR size distribution . . . . . . . . . . . . . 4.2.4 Fit of CUR size distributions . . . . . . . . . 4.2.5 Variability of CUR size distributions . . . . . 4.3 Comparison of CUR size distributions and discussion 4.4 Conclusions . . . . . . . . . . . . . . . . . . . . . . .
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143 . 145 . 145 . 148 . 149 . 150 . 150 . 153 . 154 . 154 . 156 . 157 . 158 . 162
5 Salt dependence of nearest-neighbor base-pair free energies 165 5.1 Discrepancies between melting and unzipping experiments . . 167 5.2 Parameters defining the theoretical FDC . . . . . . . . . . . . 169 5.2.1 Elastic response of the ssDNA . . . . . . . . . . . . . . 170 5.2.2 Drift and shift function . . . . . . . . . . . . . . . . . . 174 5.2.3 Free energy of the end loop . . . . . . . . . . . . . . . 176 5.3 Fit of FDCs . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177 5.3.1 Monte Carlo optimization . . . . . . . . . . . . . . . . 179 5.3.2 Independence of initial conditions . . . . . . . . . . . . 181 5.4 Salt dependence and thermodynamic properties of NNBP interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183 5.4.1 Inference of NNBP enthalpies and entropies . . . . . . 187 5.4.2 Prediction of melting temperatures . . . . . . . . . . . 188 5.5 Discussion of results . . . . . . . . . . . . . . . . . . . . . . . 190 5.5.1 Regarding the heterogeneous salt correction . . . . . . 190 5.5.2 About the prediction of melting temperatures . . . . . 192 5.6 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193 6 Unzipping of DNA at controlled force 6.1 Controlled force experiments in optical tweezers 6.1.1 Force feedback . . . . . . . . . . . . . . 6.1.2 Unzipping/Rezipping cycles at controlled 6.1.3 Hysteresis . . . . . . . . . . . . . . . . . 6.2 Detection of metastable intermediate states . . . 6.2.1 Free energy landscape . . . . . . . . . . 6.3 Scaling properties of unzipping . . . . . . . . .
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195 . 196 . 197 . 197 . 200 . 202 . 202 . 203