Books  Animal & General Biology  Animal & General Biology 

The Physics of Living Processes: A Mesoscopic Approach

Textbook

By: Thomas Andrew Waigh (Author)

John Wiley & Sons

Paperback | Oct 2014 | #219077 | ISBN-13: 9781118449943
Availability: Usually dispatched within 5 days Details
NHBS Price: £49.99 $63/€59 approx

About this book

This full-colour undergraduate textbook, based on a two semester course, presents the fundamentals of biological physics, introducing essential modern topics that include cells, polymers, polyelectrolytes, membranes, liquid crystals, phase transitions, self-assembly, photonics, fluid mechanics, motility, chemical kinetics, enzyme kinetics, systems biology, nerves, physiology, the senses, and the brain. The comprehensive coverage, featuring in-depth explanations of recent rapid developments, demonstrates this to be one of the most diverse of modern scientific disciplines.

The Physics of Living Processes: A Mesoscopic Approach is comprised of five principal sections:
- Building Blocks
- Soft Condensed Matter Techniques in Biology
- Experimental Techniques
- Systems Biology
- Spikes, Brains and the Senses

The unique focus is predominantly on the mesoscale – structures on length scales between those of atoms and the macroscopic behaviour of whole organisms. The connections between molecules and their emergent biological phenomena provide a novel integrated perspective on biological physics, making this an important text across a variety of scientific disciplines including biophysics, physics, physical chemistry, chemical engineering and bioengineering. An extensive set of worked tutorial questions are included, which will equip the reader with a range of new physical tools to approach problems in the life sciences from medicine, pharmaceutical science and agriculture.


Contents

Concise table of contents:

Preface xiii
Acknowledgements xvii

I Building Blocks 1
1 Molecules 3
2 Cells 31

II Soft Condensed-Matter Techniques in Biology 55
3 Introduction to Statistics in Biology 57
4 Mesoscopic Forces 69
5 Phase Transitions 91
6 Liquid Crystallinity 111
7 Motility 135
8 Aggregating Self-Assembly 157
9 Surface Phenomena 173
10 Biomacromolecules 189
11 Charged Ions and Polymers 219
12 Membranes 247
13 Continuum Mechanics 269
14 Fluid Mechanics 281
15 Rheology 293
16 Motors 315
17 Structural Biomaterials 331
18 Phase Behaviour of DNA 347

III Experimental Techniques 355
19 Experimental Techniques 357

IV Systems Biology 437
20 Chemical Kinetics 439
21 Enzyme Kinetics 461
22 Introduction to Systems Biology 473

V Spikes, Brains and the Senses 501
23 Spikes 503
24 Physiology of Cells and Organisms 527
25 The Senses 541
26 Brains 555

Suggested Reading 567
Tutorial Questions 26 568
Appendix A: Physical Constants 569
Appendix B: Answers to Tutorial Questions 571
Index 593


Detailed table of contents:

Preface xiii
Acknowledgements xvii

I Building Blocks 1
1 Molecules 3
1.1 Chemical Bonds and Molecular Interactions 3
1.2 Chirality 7
1.3 Proteins 7
1.4 Lipids 15
1.5 Nucleic Acids 16
1.6 Carbohydrates 21
1.7 Water 24
1.8 Proteoglycans and Glycoproteins 25
1.9 Viruses 26
1.10 Other Molecules 28
Suggested Reading 28
Tutorial Questions 1 29

2 Cells 31
2.1 The First Cell 32
2.2 Metabolism 33
2.3 Central Dogma of Biology 34
2.4 Darwin's Theory of Natural Selection 38
2.5 Mutations and Cancer 40
2.6 Prokaryotic Cells 41
2.7 Eukaryotic Cells 41
2.8 Chromosomes 44
2.9 Cell Cycle 45
2.10 Genetic Code 45
2.11 Genetic Networks 45
2.12 Human Genome Project 47
2.13 Genetic Fingerprinting 49
2.14 Genetic Engineering 50
2.15 Tissues 51
2.16 Cells as Experimental Models 51
2.17 Stem Cells 52
Suggested Reading 53
Tutorial Questions 2 54

II Soft Condensed-Matter Techniques in Biology 55
3 Introduction to Statistics in Biology 57
3.1 Statistics 57
3.2 Entropy 60
3.3 Information 61
3.4 Free Energy 62
3.5 Partition Function 63
3.6 Conditional Probability 65
3.7 Networks 66
Suggested Reading 67
Tutorial Questions 3 67

4 Mesoscopic Forces 69
4.1 Cohesive Forces 69
4.2 Hydrogen Bonding 71
4.3 Electrostatics 73
4.3.1 Unscreened Electrostatic Interactions 73
4.3.2 Screened Electrostatic Interactions 74
4.3.3 The Force Between Charged Aqueous Spheres 77
4.4 Steric and Fluctuation Forces 79
4.5 Depletion Forces 82
4.6 Hydrodynamic Interactions 84
4.7 Bell's Equation 84
4.8 Direct Experimental Measurements 86
Suggested Reading 89
Tutorial Questions 4 89

5 Phase Transitions 91
5.1 The Basics 91
5.2 Helix–Coil Transition 94
5.3 Globule–Coil Transition 98
5.4 Crystallisation 101
5.5 Liquid–Liquid Demixing (Phase Separation) 104
Suggested Reading 108
Tutorial Questions 5 109

6 Liquid Crystallinity 111
6.1 The Basics 111
6.2 Liquid Nematic–Smectic Transitions 123
6.3 Defects 125
6.4 More Exotic Possibilities for Liquid-Crystalline Phases 130
Suggested Reading 132
Tutorial Questions 6 132

7 Motility 135
7.1 Diffusion 135
7.2 Low Reynolds Number Dynamics 142
7.3 Motility of Cells and Micro-Organisms 144
7.4 First-Passage Problem 148
7.5 Rate Theories of Chemical Reactions 152
7.6 Subdiffusion 153
Suggested Reading 155
Tutorial Questions 7 155

8 Aggregating Self-Assembly 157
8.1 Surface-Active Molecules (Surfactants) 160
8.2 Viruses 163
8.3 Self-Assembly of Proteins 167
8.4 Polymerisation of Cytoskeletal Filaments (Motility) 167
Suggested Reading 172
Tutorial Questions 8 172

9 Surface Phenomena 173
9.1 Surface Tension 173
9.2 Adhesion 175
9.3 Wetting 177
9.4 Capillarity 180
9.5 Experimental Techniques 183
9.6 Friction 184
9.7 Adsorption Kinetics 186
9.8 Other Physical Surface Phenomena 188
Suggested Reading 188
Tutorial Questions 9 188

10 Biomacromolecules 189
10.1 Flexibility of Macromolecules 189
10.2 Good/Bad Solvents and the Size of Flexible Polymers 198
10.3 Elasticity 203
10.4 Damped Motion of Soft Molecules 206
10.5 Dynamics of Polymer Chains 209
10.6 Topology of Polymer Chains – Supercoiling 214
Suggested Reading 216
Tutorial Questions 10 217

11 Charged Ions and Polymers 219
11.1 Electrostatics 222
11.2 Deybe–Huckel Theory 226
11.3 Ionic Radius 229
11.4 The Behaviour of Polyelectrolytes 232
11.5 Donnan Equilibria 234
11.6 Titration Curves 236
11.7 Poisson–Boltzmann Theory for Cylindrical Charge Distributions 238
11.8 Charge Condensation 239
11.9 Other Polyelectrolyte Phenomena 243
Suggested Reading 244
Tutorial Questions 11 245

12 Membranes 247
12.1 Undulations 248
12.2 Bending Resistance 250
12.3 Elasticity 253
12.4 Intermembrane Forces 258
12.5 Passive/Active Transport 260
12.6 Vesicles 267
Suggested Reading 268
Tutorial Questions 12 268

13 Continuum Mechanics 269
13.1 Structural Mechanics 270
13.2 Composites 273
13.3 Foams 275
13.4 Fracture 277
13.5 Morphology 278
Suggested Reading 278
Tutorial Questions 13 279

14 Fluid Mechanics 281
14.1 Newton's Law of Viscosity 282
14.2 Navier–Stokes Equations 282
14.3 Pipe Flow 283
14.4 Vascular Networks 285
14.5 Haemodynamics 285
14.6 Circulatory Systems 289
14.7 Lungs 289
Suggested Reading 291
Tutorial Questions 14 291

15 Rheology 293
15.1 Storage and Loss Moduli 295
15.2 Rheological Functions 298
15.3 Examples from Biology: Neutral Polymer Solutions, Polyelectrolytes, Gels, Colloids, Liquid Crystalline Polymers, Glasses, Microfluidics 299
15.3.1 Neutral Polymer Solutions 299
15.3.2 Polyelectrolytes 303
15.3.3 Gels 305
15.3.4 Colloids 309
15.3.5 Liquid-Crystalline Polymers 310
15.3.6 Glassy Materials 310
15.3.7 Microfluidics in Channels 312
15.4 Viscoelasticity of the Cell 312
Suggested Reading 314
Tutorial Questions 15 314

16 Motors 315
16.1 Self-Assembling Motility – Polymerisation of Actin and Tubulin 317
16.2 Parallelised Linear Stepper Motors – Striated Muscle 320
16.3 Rotatory Motors 325
16.4 Ratchet Models 327
16.5 Other Systems 329
Suggested Reading 329
Tutorial Questions 16 330

17 Structural Biomaterials 331
17.1 Cartilage – Tough Shock Absorbers in Human Joints 331
17.2 Spider Silk 341
17.3 Elastin and Resilin 342
17.4 Bone 343
17.5 Adhesive Proteins 343
17.6 Nacre and Mineral Composites 345
Suggested Reading 346
Tutorial Questions 17 346

18 Phase Behaviour of DNA 347
18.1 Chromatin – Naturally Packaged DNA Chains 347
18.2 DNA Compaction – An Example of Polyelectrolyte Complexation 350
18.3 Facilitated Diffusion 351
Suggested Reading 354

III Experimental Techniques 355
19 Experimental Techniques 357
19.1 Mass Spectroscopy 357
19.2 Thermodynamics 359
19.2.1 Differential Scanning Calorimetry 360
19.2.2 Isothermal Titration Calorimetry 360
19.2.3 Surface Plasmon Resonance and Interferometry-Based Biosensors 360
19.3 Hydrodynamics 362
19.4 Optical Spectroscopy 363
19.4.1 Rayleigh Scattering 363
19.4.2 Brillouin Scattering 364
19.4.3 Terahertz/Microwave Spectroscopy 364
19.4.4 Infrared Spectroscopy 365
19.4.5 Raman Spectroscopy 366
19.4.6 Nonlinear Spectroscopy 367
19.4.7 Circular Dichroism and UV Spectroscopy 369
19.5 Optical Microscopy 369
19.5.1 Fluorescence Microscopy 376
19.5.2 Super-Resolution Microscopy 378
19.5.3 Nonlinear Microscopy 382
19.5.4 Polarisation Microscopy 382
19.5.5 Optical Coherence Tomography 382
19.5.6 Holographic Microscopy 383
19.5.7 Other Microscopy Techniques 383
19.6 Single-Molecule Detection 384
19.7 Single-Molecule Mechanics and Force Measurements 384
19.8 Electron Microscopy 395
19.9 Nuclear Magnetic Resonance Spectroscopy 396
19.10 Static Scattering Techniques 397
19.11 Dynamic Scattering Techniques 408
19.12 Osmotic Pressure 412
19.13 Chromatography 415
19.14 Electrophoresis 415
19.15 Sedimentation 420
19.16 Rheology 424
19.17 Tribology 431
19.18 Solid Mechanical Properties 432
Suggested Reading 432
Tutorial Questions 19 433

IV Systems Biology 437
20 Chemical Kinetics 439
20.1 Conservation Laws 440
20.2 Free Energy 440
20.3 Reaction Rates 441
20.4 Consecutive Reactions 449
20.5 Case I and II Reactions 450
20.6 Parallel Reactions 452
20.7 Approach to Chemical Equilibrium 453
20.8 Quasi-Steady-State Approximation 456
20.9 General Kinetic Equation Analysis 459
Suggested Reading 459
Tutorial Questions 20 460

21 Enzyme Kinetics 461
21.1 Michaelis–Menten Kinetics 461
21.2 Lineweaver–Burke Plot 465
21.3 Enzyme Inhibition 466
21.4 Competitive Inhibition 466
21.5 Allosteric Inhibition 467
21.6 Cooperativity 468
21.7 Hill Plot 470
21.8 Single Enzyme Molecules 470
Suggested Reading 472
Tutorial Questions 21 472

22 Introduction to Systems Biology 473
22.1 Integrative Model of the Cell 473
22.2 Transcription Networks 474
22.3 Gene Regulation 474
22.4 Lac Operon 477
22.5 Repressilator 479
22.6 Autoregulation 481
22.7 Network Motifs 483
22.8 Robustness 489
22.9 Morphogenesis 490
22.10 Kinetic Proofreading 492
22.11 Temporal Programs 493
22.12 Nonlinear Models 494
22.13 Population Dynamics 497
Suggested Reading 498
Tutorial Questions 22 499

V Spikes, Brains and the Senses 501
23 Spikes 503
23.1 Structure and Function of a Neuron 503
23.2 Membrane Potential 503
23.3 Ion Channels 506
23.4 Voltage Clamps and Patch Clamps 508
23.5 Nernst Equation 509
23.6 Electrical Circuit Model of a Cell Membrane 511
23.7 Cable Equation 513
23.8 Hodgkin–Huxley Model 515
23.9 Action Potential 518
23.10 Spikes – Travelling Electrical Waves 520
23.11 Cell Signalling 523
Suggested Reading 524
Tutorial Questions 23 525

24 Physiology of Cells and Organisms 527
24.1 Feedback Loops 528
24.2 Nonlinear Behaviour 533
24.3 Potential Outside an Axon 533
24.4 Electromechanical Properties of the Heart 535
24.5 Electrocardiogram 536
24.6 Electroencephalography 537
Suggested Reading 539
Tutorial Questions 24 540

25 The Senses 541
25.1 Biological Senses 541
25.2 Weber's Law 542
25.3 Information Processing and Hyperacuity 543
25.4 Mechanoreceptors 543
25.5 Chemoreceptors 545
25.6 Photoreceptors 549
25.7 Thermoreceptors 551
25.8 Electroreceptors 552
25.9 Magnetoreceptors 552
Suggested Reading 553
Tutorial Questions 25 554

26 Brains 555
26.1 Neural Encoding Inverse Problem 558
26.2 Memory 560
26.3 Motor Processes 564
26.4 Connectome 565
26.5 Cohesive Properties 566
Suggested Reading 567
Tutorial Questions 26 568

Appendix A: Physical Constants 569
Appendix B: Answers to Tutorial Questions 571
Index 593


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