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Biophysics Searching for Principles
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CONTENTS Introduction 1 A. About our subject 1 Looking back 3 Looking forward 4 B. About this book 6 C. About this draft 8 Acknowledgments 8 I. Photon counting in vision 11 A. Posing the problem 11 B. Single molecule dynamics 29 C. Dynamics of biochemical networks 38 D. The first synapse, and beyond 49 E. Perspectives 59 II. Noise isn’t negligible 63 A. Molecular fluctuations and chemical reactions 63 B. Molecule counting 79 C. More about noise in perception 101 D. Proofreading and active noise reduction 118 E. Perspectives 134 III. No fine tuning 135 A. Sequence ensembles 136 B. Ion channels and neuronal dynamics 153 C. The states of cells 166 D. Long time scales in neural networks 182 E. Perspectives 191 IV. Efficient representation 195 A. Entropy and information 195 B. Does biology care about bits? 218 C. Optimizing information flow 233 D. Gathering information and making models 247 E. Perspectives 258 V. Outlook 261 A. Appendix 263 1. Poisson processes 263 2. Correlations, power spectra and all that 270 3. Electronic transition in large molecules 276 4. Cooperativity 281 5. X–ray diffraction and biomolecular structure 286 6. Berg and Purcell, revisited 290 7. Dimensionality reduction 298 !William Bialek is the John Archibald Wheeler/Battelle Professor in Physics, and a member of the multidisciplinary Lewis–Sigler Institute for Integrative Genomics, at Princeton University. He also serves as Visiting Presidential Professor of Physics at the Graduate Center of the City University of New York. 8. Maximum entropy 298 9. Measuring information transmission 304 |
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2015-03-03 11:50:08, 32.24 M
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