Soft Condensed Matter Physics in Molecular And Cell Biology

by Poon; W.C.K.

• ISBN13: 9780750310239
• ISBN10: 0750310235
• Edition: 1st
• Format: Hardcover
• Copyright: 2006-01-13
• Publisher: CRC Press

Summary

The focus of this volume is based on the poignant realization that biology is soft matter come alive. The chapters in this volume originated as lectures in the NATO Advanced Science Institute and Scottish Universities Summer Schools in Physics. The book provides a thorough grounding in the fundamental nature and properties of soft matter, and then explores its application in biology, especially with regard to DNA investigations, and the study of protein behavior. The final section of the book considers experimental techniques, covering single molecule force spectroscopy of proteins, the use of optical tweezers, and solution scattering.

Table of Contents

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