The Physics of Living Processes: A Mesoscopic Approach

619 Pages·2014·5.377 MB·English

by  Thomas Andrew Waigh

28mm
THE PHYSICS OF Waigh
THE PHYSICS OF
LIVING PROCESSES
LIVING PROCESSES
A Mesoscopic Approach
T A Mesoscopic Approach
Thomas Andrew Waigh H
School of Physics and Astronomy, Photon Science Institute, University of Manchester, UK E

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

modern scientific disciplines. O
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The Physics of Living Processes: A Mesoscopic Approach is comprised of five principal sections:
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• Building Blocks I
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• Soft Condensed Matter Techniques in Biology
• Experimental Techniques I
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• Systems Biology
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• Spikes, Brains and the Senses

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

The Physics of Living Processes

The Physics of Living Processes
A Mesoscopic Approach
THOMAS ANDREW WAIGH
School of Physics and Astronomy and Photon Science Institute,
University of Manchester, UK
Thiseditionfirstpublished2014
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1 2014
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 CentralDogma of Biology 34
2.4 Darwin’s Theoryof Natural Selection 38
2.5 Mutationsand 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 HumanGenome 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
vi Contents
II Soft Condensed-Matter Techniquesin 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 ChargedAqueous Spheres 77
4.4 Steric and Fluctuation Forces 79
4.5 Depletion Forces 82
4.6 Hydrodynamic Interactions 84
4.7 Bell’sEquation 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
Contents vii
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 CytoskeletalFilaments (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 AdsorptionKinetics 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/BadSolvents 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 Topologyof 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
viii Contents
11.3 Ionic Radius 229
11.4 The Behaviour of Polyelectrolytes 232
11.5 Donnan Equilibria 234
11.6 TitrationCurves 236
11.7 Poisson–Boltzmann Theoryfor 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 BendingResistance 250
12.3 Elasticity 253
12.4 IntermembraneForces 258
12.5 Passive/ActiveTransport 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 Lawof 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 andLoss Moduli 295
15.2 Rheological Functions 298
15.3 Examples from Biology:Neutral Polymer Solutions, Polyelectrolytes, Gels,
Colloids, Liquid Crystalline Polymers, Glasses, Microfluidics 299