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Biophysics:
Searching for Principles
William Bialek

Book Description | Endorsements
Introduction [in PDF format]

TABLE OF CONTENTS:

Acknowledgments ix

PART I EXPLORING THE PHENOMENA

1. Introduction 3

  • 1.1 About Our Subject 3
  • 1.2 About This Book 11

2. Photon Counting in Vision 17

  • 2.1 A First Look 17
  • 2.2 Dynamics of Single Molecules 51
  • 2.3 Biochemical Amplification 68
  • 2.4 The First Synapse and Beyond 97
  • 2.5 Coda 115

3. Lessons, Problems, Principles 117

PART II CANDIDATE PRINCIPLES

4. Noise Is Not Negligible 127

  • 4.1 Fluctuations and Chemical Reactions 127
  • 4.2 Motility and Chemotaxis in Bacteria 149
  • 4.3 Molecule Counting, More Generally 172
  • 4.4 More about Noise in Perception 192
  • 4.5 Proofreading and Active Noise Reduction 218
  • 4.6 Perspectives 245

5. No Fine Tuning 247

  • 5.1 Sequence Ensembles 248
  • 5.2 Ion Channels and Neuronal Dynamics 279
  • 5.3 The States of Cells 299
  • 5.4 Long Time Scales in Neural Networks 329
  • 5.5 Perspectives 349

6. Efficient Representation 353

  • 6.1 Entropy and Information 354
  • 6.2 Noise and Information Flow 369
  • 6.3 Does Biology Care about Bits? 395
  • 6.4 Optimizing Information Flow 421
  • 6.5 Gathering Information and Making Models 449
  • 6.6 Perspectives 467

7. Outlook 469

Appendix Some Further Topics 473

  • A.1 Poisson Processes 473
  • A.2 Correlations, Power Spectra, and All That 484
  • A.3 Diffraction and Biomolecular Structure 495
  • A.4 Electronic Transitions in Large Molecules 503
  • A.5 The Kramers Problem 512
  • A.6 Berg and Purcell, Revisited 521
  • A.7 Maximum Entropy 533
  • A.8 Measuring Information Transmission 545

Annotated Bibliography 557
Index 625

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File created: 10/23/2013

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