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 H This full-colour undergraduate textbook, based on a two semester course, presents the Y fundamentals of biological physics, introducing essential modern topics that include cells, S polymers, polyelectrolytes, membranes, liquid crystals, phase transitions, self-assembly, photonics, fluid mechanics, motility, chemical kinetics, enzyme kinetics, systems biology, I C nerves, physiology, the senses, and the brain. The comprehensive coverage, featuring in-depth S explanations of recent rapid developments, demonstrates this to be one of the most diverse of modern scientific disciplines. O F The Physics of Living Processes: A Mesoscopic Approach is comprised of five principal sections: L • Building Blocks I V • Soft Condensed Matter Techniques in Biology • Experimental Techniques I N • Systems Biology G • Spikes, Brains and the Senses P The unique focus is predominantly on the mesoscale — structures on length scales between R those of atoms and the macroscopic behaviour of whole organisms. The connections between O molecules and their emergent biological phenomena provide a novel integrated perspective C on biological physics, making this an important text across a variety of scientific disciplines including biophysics, physics, physical chemistry, chemical engineering and bioengineering. E S 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 ©2014JohnWiley&Sons,Ltd. RegisteredOffice JohnWiley&Sons,Ltd,TheAtrium,SouthernGate,Chichester,WestSussex,PO198SQ,UnitedKingdom Fordetailsofourglobaleditorialoffices,forcustomerservicesandforinformationabouthowtoapplyforpermissiontoreusethecopyrightmaterial inthisbookpleaseseeourwebsiteatwww.wiley.com. TherightoftheauthortobeidentifiedastheauthorofthisworkhasbeenassertedinaccordancewiththeCopyright,DesignsandPatentsAct1988. Allrightsreserved.Nopartofthispublicationmaybereproduced,storedinaretrievalsystem,ortransmitted,inanyformorbyanymeans,electronic, mechanical,photocopying,recordingorotherwise,exceptaspermittedbytheUKCopyright,DesignsandPatentsAct1988,withoutthepriorpermissionof thepublisher. 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ISBN:9781118449943 Setin10/12ptTimesbySPiPublisherServices,Pondicherry,India PrintedandboundinSingaporebyC.O.S. 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