Soft condensed matter physics in molecular and cell biology

Contents
......Page 9
1 Introduction......Page 13
2 The atomistic description of globular proteins: the tertiary structure......Page 14
3 Coarse-graining level 1: Secondary structure......Page 16
4 Coarse-graining level 2: Domains......Page 19
5.1 Dilute protein solutions......Page 20
5.2 Concentrated protein solutions......Page 21
6 Further coarse-graining......Page 23
7 Conclusion......Page 24
References......Page 26
Part I Soft Matter Background......Page 29
1 Introduction......Page 31
1.1 Forces between colloids......Page 33
1.1.1 Hard-core repulsion......Page 35
1.1.3 Dispersion forces......Page 36
1.1.4 DLVO Potential......Page 37
1.1.5 Depletion interaction......Page 38
1.1.6 Depletion Flocculation......Page 40
2 Colloidal phase behaviour......Page 43
2.1 Entropic Phase transitions......Page 44
2.1.1 Computer simulation of (liquid) crystals......Page 45
2.1.2 To boil or not to boil.........Page 46
3.1 Hydrodynamic effects in colloidal suspensions......Page 48
3.2 Homogeneous nucleation in colloidal suspensions......Page 51
3.2.1 Coil-globule transition in the condensation of dipolar colloids?......Page 52
3.2.2 Crystallisation near a critical point......Page 55
References......Page 58
1 Introduction......Page 61
2 Statistical physics of single chains......Page 62
3 Statistical physics of many chains......Page 66
4 Polymer dynamics......Page 70
References......Page 74
1 Introduction......Page 75
2 The constituents of lipid bilayer membranes......Page 76
3.1 Aggregation......Page 78
3.2 Molecular considerations and packing......Page 80
4 Bilayer membrane phases......Page 81
5.1 Surface tension, frame tension......Page 83
5.3 Bending elasticity......Page 84
6 Fluctuations......Page 85
7 Domains, shapes and other current issues......Page 86
References......Page 87
1.1 Physical origin and spontaneous shapes of lipid monolayers......Page 91
1.2 Amphiphile monolayers in water and oil system......Page 92
1.3 Amphiphile monolayers in pure water......Page 93
1.4 Experimental studies of elasticities of strongly curved membranes......Page 94
2.1 Dividing surface......Page 95
2.2 Gibbs' energy of interface......Page 96
2.3.1 Stretching modulus......Page 99
2.3.2 Bending modulus......Page 100
2.4 Further developments......Page 101
3 Description in terms of microscopic properties......Page 103
4 Equations of equilibrium and shape of interfaces......Page 105
References......Page 107
1 Introduction......Page 109
2 The Poisson-Boltzmann theory......Page 110
3.1.1 Counter-ion only......Page 113
3.1.2 Added electrolyte......Page 115
3.2 Modified Poisson-Boltzmann equation......Page 116
3.3 Two planar surfaces......Page 118
3.3.1 Counter-ions only......Page 119
3.3.2 Added electrolyte......Page 121
4 Poisson-Boltzmann equation in cylindrical coordinates......Page 124
4.2 The non-linear PB solution: Counter-ion only and Manning condensation......Page 125
5 Poisson-Boltzmann equation in spherical coordinates: Charged colloids......Page 128
6 Beyond the PB treatment......Page 129
7 Concluding remarks......Page 130
References......Page 132
1 Introduction......Page 135
2 A preliminary: Diffusion on a flat landscape......Page 138
3 First passage times: an exact result......Page 140
4 Landscapes and intermediate states......Page 143
5 Higher-dimensional barrier crossing......Page 145
References......Page 147
Part II Biological Applications......Page 149
1 Introduction......Page 151
2 Single-filament properties......Page 152
2.1 Worm-like chain......Page 153
2.2 Force extension......Page 155
2.3 Dynamics......Page 159
3 Solutions of semi-flexible polymer......Page 161
4 Network elasticity......Page 162
5 Nonlinear response......Page 164
References......Page 166
1 Introduction......Page 169
1.1.2 Secondary structure......Page 170
1.1.3 Tertiary structure......Page 172
1.2 DNA editing......Page 173
2 Micromanipulation techniques......Page 174
2.1 Orders of magnitude......Page 175
2.2.1 Microfibres......Page 176
2.2.3 Magnetic trap......Page 177
3 Stretching DNA......Page 178
4 DNA under torsion......Page 180
4.1 Topological formalism......Page 181
4.2 Biological motivations......Page 182
4.3.1 Buckling instability of DNA......Page 184
4.3.2 Torque-induced transitions......Page 187
4.3.3 The rod-like chain (RLC)......Page 188
5 DNA-protein interactions......Page 189
Acknowledgements......Page 190
References......Page 191
1 Introduction......Page 193
2 Electrostatic interactions......Page 194
2.1 Poisson-Boltzmann theory......Page 195
2.2 The cell model......Page 196
2.3 Osmotic pressure......Page 198
2.4 Interaction between cylindrical macromolecules......Page 199
3 Equation of state: No thermal fluctuations......Page 200
4 Equation of state: The effect of thermal fluctuations ( 1)......Page 201
4.1 A macroscopic theory of the equation of state in an ordered macromolecular array......Page 202
5.1 Variational calculation of the osmotic pressure in a hexagonal array......Page 206
References......Page 210
1 Introduction......Page 213
2 Energy functions for fold recognition......Page 217
2.1 Statistical potentials......Page 218
2.2 Potentials from mathematical programming......Page 223
3 The evolutionary capacity of proteins......Page 230
3.1 The counting algorithm......Page 231
3.2 Computing temperatures for all protein folds......Page 232
References......Page 235
2.1 The dynamical transition in proteins......Page 237
2.2 The role of solvent in the dynamical transition......Page 238
2.4 Dynamical transition and protein function......Page 239
3 Neutron scattering from proteins......Page 240
3.1 Analysing elastic scattering at low Q......Page 241
3.2 Measured mean square displacement......Page 242
3.3 Temperature-dependent......Page 243
3.5 Dynamical transition and neutron frequency windows......Page 244
5 Coupling between conformational and protonation state changes in membrane proteins......Page 245
6 Analysis of conformational changes in proteins......Page 247
6.1 Penalty function methods......Page 248
6.2 Heuristic methods......Page 249
6.4 Multiple pathways......Page 250
References......Page 251
1 Summary......Page 255
References......Page 257
Part III Experimental Techniques......Page 259
1 Introduction......Page 261
2.1 Subjective vs. objective......Page 264
2.2 Pattern recognition in force-extension traces......Page 265
2.3 Degree of coincidence......Page 266
2.4 Application of the recognition method to GFP unfolding......Page 267
2.5 Statistical analysis of datasets......Page 269
References......Page 270
2 Basic principles......Page 271
3 Heating in optical tweezers......Page 274
4 Resonant trapping......Page 275
5 Photobleaching in optical tweezers......Page 277
6 Displacement detection and detection bandwidth......Page 280
7 Signal-to-noise ratio and resolution......Page 281
7.1 Position-clamp experiments......Page 283
7.2 Force-clamp experiments......Page 284
References......Page 285
1 Introduction......Page 287
2 Static scattering......Page 288
2.1 Scattering by a small volume element......Page 289
2.2 Scattering by an extended particle......Page 291
2.4 Average scattered intensity......Page 293
2.5.2 Homogeneous sphere......Page 295
2.5.3 Polymer......Page 297
2.6 Structure factor......Page 300
2.7 Absolute scattered intensity......Page 301
2.7.1 Neutron scattering......Page 303
2.7.2 X-ray scattering......Page 304
2.7.4 Contrast variation......Page 305
2.8 Data analysis......Page 307
3 Dynamic scattering......Page 308
3.1 Correlation functions......Page 309
3.2 Correlation function of Brownian particles......Page 311
3.3 Data analysis......Page 313
4.1 Gluten - data analysis (model fitting)......Page 314
4.2 PCNA - data analysis (indirect Fourier transform)......Page 316
4.3 Structure of a virus- contrast variation......Page 317
4.4 Concentrated DNA solutions-structure factor as a measure of particle arrangement......Page 318
4.5 Solution structure of ocr - shape determination using dynamic light scattering......Page 320
References......Page 322
Participants......Page 323