The Physics of Living Processes: A Mesoscopic Approach

Preface xiiiAcknowledgements xviiI Building Blocks 11 Molecules 31.1 Chemical Bonds and Molecular Interactions 31.2 Chirality 71.3 Proteins 71.4 Lipids 151.5 Nucleic Acids 161.6 Carbohydrates 211.7 Water 241.8 Proteoglycans and Glycoproteins 251.9 Viruses 261.10 Other Molecules 28Suggested Reading 28Tutorial Questions 1 292 Cells 312.1 The First Cell 322.2 Metabolism 332.3 Central Dogma of Biology 342.4 Darwin's Theory of Natural Selection 382.5 Mutations and Cancer 402.6 Prokaryotic Cells 412.7 Eukaryotic Cells 412.8 Chromosomes 442.9 Cell Cycle 452.10 Genetic Code 452.11 Genetic Networks 452.12 Human Genome Project 472.13 Genetic Fingerprinting 492.14 Genetic Engineering 502.15 Tissues 512.16 Cells as Experimental Models 512.17 Stem Cells 52Suggested Reading 53Tutorial Questions 2 54II Soft Condensed-Matter Techniques in Biology 553 Introduction to Statistics in Biology 573.1 Statistics 573.2 Entropy 603.3 Information 613.4 Free Energy 623.5 Partition Function 633.6 Conditional Probability 653.7 Networks 66Suggested Reading 67Tutorial Questions 3 674 Mesoscopic Forces 694.1 Cohesive Forces 694.2 Hydrogen Bonding 714.3 Electrostatics 734.3.1 Unscreened Electrostatic Interactions 734.3.2 Screened Electrostatic Interactions 744.3.3 The Force Between Charged Aqueous Spheres 774.4 Steric and Fluctuation Forces 794.5 Depletion Forces 824.6 Hydrodynamic Interactions 844.7 Bell's Equation 844.8 Direct Experimental Measurements 86Suggested Reading 89Tutorial Questions 4 895 Phase Transitions 915.1 The Basics 915.2 Helix-Coil Transition 945.3 Globule-Coil Transition 985.4 Crystallisation 1015.5 Liquid-Liquid Demixing (Phase Separation) 104Suggested Reading 108Tutorial Questions 5 1096 Liquid Crystallinity 1116.1 The Basics 1116.2 Liquid Nematic-Smectic Transitions 1236.3 Defects 1256.4 More Exotic Possibilities for Liquid-Crystalline Phases 130Suggested Reading 132Tutorial Questions 6 1327 Motility 1357.1 Diffusion 1357.2 Low Reynolds Number Dynamics 1427.3 Motility of Cells and Micro-Organisms 1447.4 First-Passage Problem 1487.5 Rate Theories of Chemical Reactions 1527.6 Subdiffusion 153Suggested Reading 155Tutorial Questions 7 1558 Aggregating Self-Assembly 1578.1 Surface-Active Molecules (Surfactants) 1608.2 Viruses 1638.3 Self-Assembly of Proteins 1678.4 Polymerisation of Cytoskeletal Filaments (Motility) 167Suggested Reading 172Tutorial Questions 8 1729 Surface Phenomena 1739.1 Surface Tension 1739.2 Adhesion 1759.3 Wetting 1779.4 Capillarity 1809.5 Experimental Techniques 1839.6 Friction 1849.7 Adsorption Kinetics 1869.8 Other Physical Surface Phenomena 188Suggested Reading 188Tutorial Questions 9 18810 Biomacromolecules 18910.1 Flexibility of Macromolecules 18910.2 Good/Bad Solvents and the Size of Flexible Polymers 19810.3 Elasticity 20310.4 Damped Motion of Soft Molecules 20610.5 Dynamics of Polymer Chains 20910.6 Topology of Polymer Chains - Supercoiling 214Suggested Reading 216Tutorial Questions 10 21711 Charged Ions and Polymers 21911.1 Electrostatics 22211.2 Deybe-Huckel Theory 22611.3 Ionic Radius 22911.4 The Behaviour of Polyelectrolytes 23211.5 Donnan Equilibria 23411.6 Titration Curves 23611.7 Poisson-Boltzmann Theory for Cylindrical Charge Distributions 23811.8 Charge Condensation 23911.9 Other Polyelectrolyte Phenomena 243Suggested Reading 244Tutorial Questions 11 24512 Membranes 24712.1 Undulations 24812.2 Bending Resistance 25012.3 Elasticity 25312.4 Intermembrane Forces 25812.5 Passive/Active Transport 26012.6 Vesicles 267Suggested Reading 268Tutorial Questions 12 26813 Continuum Mechanics 26913.1 Structural Mechanics 27013.2 Composites 27313.3 Foams 27513.4 Fracture 27713.5 Morphology 278Suggested Reading 278Tutorial Questions 13 27914 Fluid Mechanics 28114.1 Newton's Law of Viscosity 28214.2 Navier-Stokes Equations 28214.3 Pipe Flow 28314.4 Vascular Networks 28514.5 Haemodynamics 28514.6 Circulatory Systems 28914.7 Lungs 289Suggested Reading 291Tutorial Questions 14 29115 Rheology 29315.1 Storage and Loss Moduli 29515.2 Rheological Functions 29815.3 Examples from Biology: Neutral Polymer Solutions, Polyelectrolytes, Gels, Colloids, Liquid Crystalline Polymers, Glasses, Microfluidics 29915.3.1 Neutral Polymer Solutions 29915.3.2 Polyelectrolytes 30315.3.3 Gels 30515.3.4 Colloids 30915.3.5 Liquid-Crystalline Polymers 31015.3.6 Glassy Materials 31015.3.7 Microfluidics in Channels 31215.4 Viscoelasticity of the Cell 312Suggested Reading 314Tutorial Questions 15 31416 Motors 31516.1 Self-Assembling Motility - Polymerisation of Actin and Tubulin 31716.2 Parallelised Linear Stepper Motors - Striated Muscle 32016.3 Rotatory Motors 32516.4 Ratchet Models 32716.5 Other Systems 329Suggested Reading 329Tutorial Questions 16 33017 Structural Biomaterials 33117.1 Cartilage - Tough Shock Absorbers in Human Joints 33117.2 Spider Silk 34117.3 Elastin and Resilin 34217.4 Bone 34317.5 Adhesive Proteins 34317.6 Nacre and Mineral Composites 345Suggested Reading 346Tutorial Questions 17 34618 Phase Behaviour of DNA 34718.1 Chromatin - Naturally Packaged DNA Chains 34718.2 DNA Compaction - An Example of Polyelectrolyte Complexation 35018.3 Facilitated Diffusion 351Suggested Reading 354III Experimental Techniques 35519 Experimental Techniques 35719.1 Mass Spectroscopy 35719.2 Thermodynamics 35919.2.1 Differential Scanning Calorimetry 36019.2.2 Isothermal Titration Calorimetry 36019.2.3 Surface Plasmon Resonance and Interferometry-Based Biosensors 36019.3 Hydrodynamics 36219.4 Optical Spectroscopy 36319.4.1 Rayleigh Scattering 36319.4.2 Brillouin Scattering 36419.4.3 Terahertz/Microwave Spectroscopy 36419.4.4 Infrared Spectroscopy 36519.4.5 Raman Spectroscopy 36619.4.6 Nonlinear Spectroscopy 36719.4.7 Circular Dichroism and UV Spectroscopy 36919.5 Optical Microscopy 36919.5.1 Fluorescence Microscopy 37619.5.2 Super-Resolution Microscopy 37819.5.3 Nonlinear Microscopy 38219.5.4 Polarisation Microscopy 38219.5.5 Optical Coherence Tomography 38219.5.6 Holographic Microscopy 38319.5.7 Other Microscopy Techniques 38319.6 Single-Molecule Detection 38419.7 Single-Molecule Mechanics and Force Measurements 38419.8 Electron Microscopy 39519.9 Nuclear Magnetic Resonance Spectroscopy 39619.10 Static Scattering Techniques 39719.11 Dynamic Scattering Techniques 40819.12 Osmotic Pressure 41219.13 Chromatography 41519.14 Electrophoresis 41519.15 Sedimentation 42019.16 Rheology 42419.17 Tribology 43119.18 Solid Mechanical Properties 432Suggested Reading 432Tutorial Questions 19 433IV Systems Biology 43720 Chemical Kinetics 43920.1 Conservation Laws 44020.2 Free Energy 44020.3 Reaction Rates 44120.4 Consecutive Reactions 44920.5 Case I and II Reactions 45020.6 Parallel Reactions 45220.7 Approach to Chemical Equilibrium 45320.8 Quasi-Steady-State Approximation 45620.9 General Kinetic Equation Analysis 459Suggested Reading 459Tutorial Questions 20 46021 Enzyme Kinetics 46121.1 Michaelis-Menten Kinetics 46121.2 Lineweaver-Burke Plot 46521.3 Enzyme Inhibition 46621.4 Competitive Inhibition 46621.5 Allosteric Inhibition 46721.6 Cooperativity 46821.7 Hill Plot 47021.8 Single Enzyme Molecules 470Suggested Reading 472Tutorial Questions 21 47222 Introduction to Systems Biology 47322.1 Integrative Model of the Cell 47322.2 Transcription Networks 47422.3 Gene Regulation 47422.4 Lac Operon 47722.5 Repressilator 47922.6 Autoregulation 48122.7 Network Motifs 48322.8 Robustness 48922.9 Morphogenesis 49022.10 Kinetic Proofreading 49222.11 Temporal Programs 49322.12 Nonlinear Models 49422.13 Population Dynamics 497Suggested Reading 498Tutorial Questions 22 499V Spikes, Brains and the Senses 50123 Spikes 50323.1 Structure and Function of a Neuron 50323.2 Membrane Potential 50323.3 Ion Channels 50623.4 Voltage Clamps and Patch Clamps 50823.5 Nernst Equation 50923.6 Electrical Circuit Model of a Cell Membrane 51123.7 Cable Equation 51323.8 Hodgkin-Huxley Model 51523.9 Action Potential 51823.10 Spikes - Travelling Electrical Waves 52023.11 Cell Signalling 523Suggested Reading 524Tutorial Questions 23 52524 Physiology of Cells and Organisms 52724.1 Feedback Loops 52824.2 Nonlinear Behaviour 53324.3 Potential Outside an Axon 53324.4 Electromechanical Properties of the Heart 53524.5 Electrocardiogram 53624.6 Electroencephalography 537Suggested Reading 539Tutorial Questions 24 54025 The Senses 54125.1 Biological Senses 54125.2 Weber's Law 54225.3 Information Processing and Hyperacuity 54325.4 Mechanoreceptors 54325.5 Chemoreceptors 54525.6 Photoreceptors 54925.7 Thermoreceptors 55125.8 Electroreceptors 55225.9 Magnetoreceptors 552Suggested Reading 553Tutorial Questions 25 55426 Brains 55526.1 Neural Encoding Inverse Problem 55826.2 Memory 56026.3 Motor Processes 56426.4 Connectome 56526.5 Cohesive Properties 566Suggested Reading 567Tutorial Questions 26 568Appendix A: Physical Constants 569Appendix B: Answers to Tutorial Questions 571Index 593