Biophysics

An introduction to the physics of living organisms

The field of biophysics employs the principles of physics to study biological systems, and introduces the concept of the living state. It is a multidisciplinary approach to the study of the living state combining physics, biochemistry, molecular and cell biology, medicine and engineering. The physics of macromolecules and macromolecular assemblies is a particularly important aspect of this broader field.

Biophysics: Physical Processes Underlying the living state offers an introduction to the general principles of the living state and their biological applications. Beginning with an historical overview of fundamental scientific theories and fields, the book then provides a brief introduction to cell biology and biochemistry, and then an overview of basic thermodynamics, kinetics, information theory, electrostatics in solution, fluid mechanics and macromolecular physics, and their relationship to the living state. After a presentation of physical methods, with an emphasis on light scattering, different biological macromolecules, selected aspects of their functions, and their physical properties and interactions are surveyed. A brief introduction to vision, biomotion, and theoretical biology is also provided. Exploration of some frontier issues in prebiotic origins of life, consciousness, and astrobiology round out the book. The result is a multifaceted window into the broad and evolving field of biophysics.

Biophysics readers will also find:

• Problems at the conclusion of each chapter to reinforce and focus student knowledge
• A gathering of topics in basic physics and physical chemistry which are seldom found in a single source

This textbook is suitable for physics and engineering students studying biophysics, macromolecular science, and biophysical chemistry, as well as for polymer scientists, chemists, biochemists, cell and molecular biologists, bioengineers, and others.

Preface xvi

Acknowledgments xx

About the Companion Website xxi

Part I Scientific Overview, Biological and Biochemical Surveys 1

1 Background Notions, Histories, and Fundamental Issues in Physics and Biophysics 3

1.1 The Evolution of Scientific Thought 3

1.2 Historical Sketch of Atomic Theory and Evolutionary and Genetic Thought 7

1.3 Historical Developments in Biophysics 15

1.4 Subfields in Biophysics 19

1.5 Interdisciplinarity 20

1.6 Disciplinary Physics 23

1.7 Are Currently Known Physical Laws Adequate for Understanding Living State Phenomena? 28

1.8 Unifying Characteristics of the Living State 29

1.9 Summary 30

2 Overview of Biological Cell Structure 34

2.1 The Prokaryotic Cell 34

2.2 The Eukaryotic Cell 36

2.3 Plant Cell 37

2.4 Where Do Viruses Fit in? 37

2.5 Overview of Cell Functions 39

2.6 Specialized Cell Types and Structures 44

2.7 Molecular Biology Methods 50

2.8 Summary 52

3 Biochemistry Survey 53

3.1 Amino Acids and Proteins 53

3.2 Nucleic Acids 58

3.3 Carbohydrates 62

3.4 Lipids 64

3.5 Metabolism 67

3.6 Summary 73

Part II Physical Processes Underlying the Living State 75

4 Thermodynamics, Reaction Kinetics, and Information Theory 77

4.1 Thermodynamically Based Forces 77

4.2 Thermodynamic Laws 78

4.3 Thermodynamic Processes Involving Ideal Gases 82

4.4 Connection Between Ideal Gas Law and Molecular Kinetic Energy 84

4.5 The Boltzmann Distribution 86

4.6 The Partition Function 91

4.7 Statistical Interpretation of Entropy 93

4.8 Ideal Osmotic Solutions 94

4.9 Working Substances and Bioenergetics Cycles 99

4.10 The Hydrophobic Effect 99

4.11 Surface Tension 99

4.12 Thermodynamics of Multicomponent Solutions 102

4.13 Chemical Potential for Nonideal Solutions 107

4.14 Excluded Volume Approach to Nonideal Solutions 112

4.15 Chemical Equilibrium 117

4.16 Reaction Kinetics 122

4.17 Phase Transitions 125

4.18 Nonequilibrium Thermodynamics 126

4.19 Information Theory 126

4.20 Summary 132

5 Electrostatics in Solution 137

5.1 Review of Electrostatics (in MKSA Units) 137

5.2 Covalent Bonds in the Living State are Stable Against Thermal Energy 144

5.3 “Weak Electrostatic Forces” Allow for Self-organization and Rapid Dynamic Processes 144

5.4 Hydrogen Bonds 147

5.5 Electrically Charged Macromolecules and Colloids in Solution 148

5.6 Poisson–Boltzmann Equation 148

5.7 Osmotic Pressure of an Ideal Polyelectrolyte Solution with a Semi-Permeable Membrane: Donnan Equilibrium 158

5.8 Self-energy of a Hydrated Ion 161

5.9 Force on an Ion near an Interface of Two Media with Different Dielectric Constants 162

5.10 Bjerrum Length and Counterion Condensation 163

5.11 Summary 163

6 Fluid Mechanics and Transport Processes 167

6.1 Conceptual Approach to Viscosity 168

6.2 The Stress Tensor 170

6.3 Navier–Stokes Equation of Motion for Incompressible, Viscous Fluids 170

6.4 Applications of Navier–Stokes for Steady Flow 173

6.5 Hemodynamics 177

6.6 The Intrinsic Viscosity [η] of Particles in a Fluid 177

6.7 Force–Flux Relations 180

6.8 Diffusion 184

6.9 The Nernst–Planck Equation 189

6.10 Fluctuation–Dissipation and a Qualitative Overview of Its Consequences 191

6.11 Coupled Forces and Flows: Onsager’s Reciprocal Relationships 195

6.12 Fluid Transport in Plants 196

6.13 Diffusional Versus Directed Motion 197

6.14 Time Reversal Symmetry and Its Breaking 198

6.15 Techniques for Determining Transport Properties 198

6.16 Summary 199

Part III Polymer Science 205

7 Overview of Polymer Science 207

7.1 Biological and Synthetic Polymers 207

7.2 Brief Overview of Classes of Organic Molecules 208

7.3 Synthetic Polymers 215

7.4 Polymerization Reactions 221

7.5 Free Radicals and Chain Reactions 224

7.6 Free Radical Polymerization Kinetics 225

7.7 Ideal Living Polymerization 232

7.8 Chain Growth Copolymerization Kinetics 234

7.9 Cumulative and Instantaneous Polymer Characteristics During Free Radical Reactions 238

7.10 Fully Automatic Feedback Control of Molar Mass and Conversion During Chain Growth Polymerization 239

7.11 Linear Step Growth Reactions 243

7.12 Molar Mass Distributions (MMD) and Averages 244

7.13 Experimental Methods for Determining Molar Mass Distributions 251

7.14 Summary 256

8 Polymer Physics 260

8.1 Polymer Conformations and Dimensions 260

8.2 Polymer Excluded Volume (EV) 276

8.3 Hydrodynamic Characteristics of Polymers in Solution 278

8.4 Electrically Charged Polymers: Polyelectrolytes 281

8.5 Case Study of Polystyrene Characteristics in Tetrahydrofuran 285

8.6 Thermodynamics of Polymer Solutions 285

8.7 Rheology 288

8.8 Solid-state Properties 290

8.9 Summary 290

9 Light Scattering and Cognate Methods 295

9.1 Overview of Light Scattering 295

9.2 The Maxwell Electromagnetic Equations and the Prediction of Electromagnetic Waves and Their Properties, in Gaussian (CGS) Units 297

9.3 Radiation Emitted by an Accelerated Charge 304

9.4 Basic Scattering Theory: Light Emitted from an Oscillating Electric Dipole 305

9.5 Relation of Light Scattering by Pure Liquids to Thermodynamic Fluctuations 311

9.6 The Angular Dependence of Scattered Light: Intramolecular Interference Effects on Scattering 315

9.7 The Angular Dependence of Scattered Light: Intermolecular Interference Effects on Scattering: The structure factor S(q,c) 326

9.8 Mie Scattering 328

9.9 Scattering Model for Index of Refraction 330

9.10 Scattering at Interfaces 331

9.11 Single Photon Scattering 337

9.12 Dynamic Light Scattering 338

9.13 X-ray Diffraction and Crystallography 342

9.14 Raman Scattering 342

9.15 Optical Activity 343

9.16 Superconducting Quantum Interference Devices (SQUIDs) 344

9.17 Antimatter and PET Imaging 345

9.18 Electron Microscopy 346

9.19 Summary 347

Part IV Examples of Specific Living State Phenomena 353

10 Proteins: Structure, Folding, Enzyme Kinetics, and Cooperativity 355

10.1 The Protein Folding Problem 355

10.2 Protein Aggregation 360

10.3 Enzyme Kinetics 370

10.4 Cooperative Binding in Proteins 377

10.5 Cooperativity in the Helix–Coil Transition 381

10.6 Histones and Other Chromosomal Proteins 383

10.7 The Action of Proteins Often Depends on Correlated Internal Motions 383

10.8 Directed Protein Motion and Protein Motors 384

10.9 Allostery and Feedback Regulation 385

10.10 Energetics of Iscosahedral Viral Self-assembly 385

10.11 Summary 387

11 DNA and RNA Properties and Structures: The Genetic Code 391

11.1 Structure and Macromolecular Properties of RNA and DNA 391

11.2 The Genetic Code 393

11.3 Brief Description of Gene Expression with a Focus on Protein Synthesis 395

11.4 Chromatin and DNA Mechanics 397

11.5 Summary 399

12 Some Polysaccharide Phenomena 403

12.1 Polymer and Polyelectrolyte Properties of Polysaccharides 403

12.2 Proteoglycans and Extracellular Matrix Functions 404

12.3 Proteoglycan Degradation Mechanisms Found by Light Scattering 408

12.4 Summary 411

13 Phospholipids Membranes: Channels and Nerve Impulses 413

13.1 General Properties of Membranes 413

13.2 Membrane Potentials 413

13.3 The Voltage Clamp and Patch Clamp 418

13.4 Membrane Current–Voltage Curves 419

13.5 Membrane Channel Proteins 420

13.6 Passive Propagation of Potentials Along an Axon 421

13.7 Action Potentials and Nerve Impulse Propagation 423

13.8 Summary 428

14 Integrated Biological Systems 430

14.1 Light and Life 430

14.2 Vision 432

14.3 Cilial and Flagellar Biomotion 439

14.4 Theoretical Biology: Cycles, Instabilities, and Attractors 439

14.5 Dissipative, Far from Equilibrium Spatially Self-organizing Systems 444

14.6 Summary 448

15 On the Frontier 450

15.1 Prebiotic Origins of Life 450

15.2 Quantum Biology 454

15.3 Neuroscience and the Question of Consciousness 456

15.4 Artificial Intelligence 460

15.5 Astrobiology and Exoplanets 463

15.6 Summary 467

Afterword 472

Appendix I: Probability Distributions and Their Averages 473

Appendix II: Review of Vector Calculus and Notation Used 479

Index 483

Wayne F. Reed is professor of physics with an interdisciplinary appointment in chemical and biomolecular engineering at Tulane University, New Orleans, USA. He has published extensively in the area of polymer reactions, biomacromolecules, new macromolecular characterization instrumentation, and related subjects, and has a long history of fruitful industrial collaboration.

An introduction to the physics of living organisms

The field of biophysics employs the principles of physics to study biological systems, and introduces the concept of the living state. It is a multidisciplinary approach to the study of the living state combining physics, biochemistry, molecular and cell biology, medicine and engineering. The physics of macromolecules and macromolecular assemblies is a particularly important aspect of this broader field.

Biophysics: Physical Processes Underlying the living state offers an introduction to the general principles of the living state and their biological applications. Beginning with an historical overview of fundamental scientific theories and fields, the book then provides a brief introduction to cell biology and biochemistry, and then an overview of basic thermodynamics, kinetics, information theory, electrostatics in solution, fluid mechanics and macromolecular physics, and their relationship to the living state. After a presentation of physical methods, with an emphasis on light scattering, different biological macromolecules, selected aspects of their functions, and their physical properties and interactions are surveyed. A brief introduction to vision, biomotion, and theoretical biology is also provided. Exploration of some frontier issues in prebiotic origins of life, consciousness, and astrobiology round out the book. The result is a multifaceted window into the broad and evolving field of biophysics.

Biophysics readers will also find:

• Problems at the conclusion of each chapter to reinforce and focus student knowledge
• A gathering of topics in basic physics and physical chemistry which are seldom found in a single source

This textbook is suitable for physics and engineering students studying biophysics, macromolecular science, and biophysical chemistry, as well as for polymer scientists, chemists, biochemists, cell and molecular biologists, bioengineers, and others.