| 1 | Introduction : coarse graining in biological soft matter | 1 |
| 1 | Introduction | 1 |
| 2 | The atomistic description of globular proteins : the tertiary structure | 2 |
| 3 | Coarse-graining level 1 : secondary structure | 4 |
| 4 | Coarse-graining level 2 : domains | 7 |
| 5 | Coarse-graining level 3 : proteins as colloids | 8 |
| 6 | Further coarse-graining | 11 |
| 7 | Conclusion | 12 |
| 2 | Introduction to colloidal systems | 19 |
| 1 | Introduction | 19 |
| 2 | Colloidal phase behaviour | 31 |
| 3 | Colloid dynamics | 36 |
| 3 | The physics of floppy polymers | 49 |
| 1 | Introduction | 49 |
| 2 | Statistical physics of single chains | 50 |
| 3 | Statistical physics of many chains | 54 |
| 4 | Polymer dynamics | 58 |
| 4 | Self-assembly and properties of lipid membranes | 63 |
| 1 | Introduction | 63 |
| 2 | The constituents of lipid bilayer membranes | 64 |
| 3 | Self assembly | 66 |
| 4 | Bilayer membrane phases | 69 |
| 5 | Membrane energies | 71 |
| 6 | Fluctuations | 73 |
| 7 | Domains, shapes and other current issues | 74 |
| 5 | Some aspects of membrane elasticity | 79 |
| 1 | Introduction | 79 |
| 2 | Gibbs' description | 83 |
| 3 | Description in terms of microscopic properties | 91 |
| 4 | Equations of equilibrium and shape of interfaces | 93 |
| 6 | Introduction to electrostatics in soft and biological matter | 97 |
| 1 | Introduction | 97 |
| 2 | The Poisson-Boltzmann theory | 98 |
| 3 | PB equation in planar geometry | 101 |
| 4 | Poisson-Boltzmann equation in cylindrical coordinates | 112 |
| 5 | Poisson-Boltzmann equation in spherical coordinates : charged colloids | 116 |
| 6 | Beyond the PB treatment | 117 |
| 7 | Concluding remarks | 118 |
| 7 | Thermal barrier hopping in biological physics | 123 |
| 1 | Introduction | 123 |
| 2 | A preliminary : diffusion on a flat landscape | 126 |
| 3 | First passage times : an exact result | 128 |
| 4 | Landscapes and intermediate states | 131 |
| 5 | Higher-dimensional barrier crossing | 133 |
| 8 | Elasticity and dynamics of cytoskeletal filaments and their networks | 139 |
| 1 | Introduction | 139 |
| 2 | Single-filament properties | 140 |
| 3 | Solutions of semi-flexible polymer | 149 |
| 4 | Network elasticity | 150 |
| 5 | Nonlinear response | 152 |
| 6 | Discussion | 154 |
| 9 | Twisting and stretching DNA : single-molecule studies | 157 |
| 1 | Introduction | 157 |
| 2 | Micromanipulation techniques | 162 |
| 3 | Stretching DNA | 166 |
| 4 | DNA under torsion | 168 |
| 5 | DNA-protein interactions | 177 |
| 10 | Interactions and conformational fluctuations in DNA arrays | 181 |
| 1 | Introduction | 181 |
| 2 | Electrostatic interactions | 182 |
| 3 | Equation of state : no thermal fluctuations | 188 |
| 4 | Equation of state : the effect of thermal fluctuations (1) | 189 |
| 5 | Equation of state : the effect of thermal fluctuations (2) | 194 |
| 6 | Conclusion | 198 |
| 11 | Sequence-structure relationships in proteins | 201 |
| 1 | Introduction | 201 |
| 2 | Energy functions for fold recognition | 205 |
| 3 | The evolutionary capacity of proteins | 218 |
| 12 | Physical and functional aspects of protein dynamics | 225 |
| 1 | Introduction | 225 |
| 2 | Hydration effects and the dynamical transition | 225 |
| 3 | Neutron scattering from proteins | 228 |
| 4 | Protonation reactions in proteins | 233 |
| 5 | Coupling between conformational and protonation state changes in membrane proteins | 233 |
| 6 | Analysis of conformational changes in proteins | 235 |
| 7 | Conclusions | 239 |
| 13 | Models of cell motility | 243 |
| 1 | Summary | 243 |
| 14 | Single-molecule force spectroscopy of proteins | 249 |
| 1 | Introduction | 249 |
| 2 | Pattern recognition in force-extension traces | 252 |
| 15 | A practical guide to optical tweezers | 259 |
| 1 | Introduction | 259 |
| 2 | Basic principles | 259 |
| 3 | Heating in optical tweezers | 262 |
| 4 | Resonant trapping | 263 |
| 5 | Photobleaching in optical tweezers | 265 |
| 6 | Displacement detection and detection bandwidth | 268 |
| 7 | Signal-to-noise ratio and resolution | 269 |
| 8 | Conclusions | 273 |
| 16 | Solution scattering | 275 |
| 1 | Introduction | 275 |
| 2 | Static scattering | 276 |
| 3 | Dynamic scattering | 296 |
| 4 | Examples | 302 |
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