Biophysics: Searching for Principles

Offers important lessons about the opportunities for quantitative, physics-style experiments on diverse biological phenomena. This title emphasizes the unifying power of abstract physical principles to motivate advanced experiments on biological systems. It covers a range of biological phenomena from the physicist's perspective.

Full Details

Interactions between the fields of physics and biology reach back over a century, and some of the most significant developments in biology - from the discovery of DNA's structure to imaging of the human brain - have involved collaboration across this disciplinary boundary. For a new generation of physicists, the phenomena of life pose exciting challenges to physics itself, and biophysics has emerged as an important subfield of this discipline. Here, William Bialek provides the first graduate-level introduction to biophysics aimed at physics students. Bialek begins by exploring how photon counting in vision offers important lessons about the opportunities for quantitative, physics-style experiments on diverse biological phenomena. He draws from these lessons three general physical principles - the importance of noise, the need to understand the extraordinary performance of living systems without appealing to finely tuned parameters, and the critical role of the representation and flow of information in the business of life. Bialek then applies these principles to a broad range of phenomena, including the control of gene expression, perception and memory, protein folding, the mechanics of the inner ear, the dynamics of biochemical reactions, and pattern formation in developing embryos. Featuring numerous problems and exercises throughout, "Biophysics" emphasizes the unifying power of abstract physical principles to motivate new and novel experiments on biological systems. It covers a range of biological phenomena from the physicist's perspective. It features 200 problems. It is draws on statistical mechanics, quantum mechanics, and related mathematical concepts. It includes an annotated bibliography and detailed appendixes. It is an instructor's manual (available only to teachers).

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