Introduction to Biopolymer Physics Book

Preface     vii
Biopolymers     1
Introduction     1
Primary structures     4
Nucleic acid primary structure     4
Protein primary structure     6
Polysaccharide primary structures     9
Secondary structures     11
Secondary structures of nucleic acids     11
Secondary structures of proteins     14
Secondary structures of polysaccharides     17
Tertiary structure and stabilizing interactions     17
Questions     20
Polymer conformation     23
The ideal chain     23
The Kuhn chain     26
The worm-like chain     27
Excluded volume interactions     32
Confinement in a tube; introduction to scaling     34
Deflection in a narrow tube     36
Stars and radial brushes     38
Chains under traction     39
An ideal chain under small tension     40
Worm-like chain     40
Swollen chain     42
From the dilute to the semi-dilute regime     45
Chain statistics in the semi-dilute regime     49
Questions     51
Polyelectrolytes     55
Counterion condensation     55
The electrostatic potential     61
Non-linear Poisson-Boltzmann theory     66
Polyelectrolytes in excess salt     66
Charge distribution in the cell model     69
The electrostatic persistence length     76
Electrostatic excluded volume     80
Flexible chains and electrostatic blobs     87
Spherical polyelectrolyte brushes     89
Spherical polyelectrolyte brush without salt     90
Salted spherical polyelectrolyte brush     94
Polyelectrolytes in the semi-dilute regime     99
Salt-free polyelectrolytes; a hierarchy of blobs     99
Salted polyelectrolytes     101
Questions     103
Polymer dynamics     105
Single chain dynamics     105
Pulling a chain into a hole     111
Dynamics of non-entangled chains in the semi-dilute regime     114
Entangled polymer dynamics; reptation     117
Dynamic scaling of polyelectrolytes     121
Polyelectrolytes without salt     121
Salted polyelectrolytes     124
Comparison with experimental results     126
Gel electrophoresis      131
Questions     134
Higher order structures and their transitions     137
Supercoiled DNA     137
Topology     138
Molecular free energy     142
Long-range structure and branching     151
Alternate secondary DNA structures     155
B-Z transition     155
Cruciforms     159
Helix-coil transition     161
Protein folding     167
Questions     171
Mesoscopic structures     175
Lyotropic liquid crystals     175
Virial theory     177
Liquid crystalline orientation order     182
Isotropic-anisotropic phase coexistence     185
Hexagonal packing of DNA     190
Undulation enhanced electrostatic interaction     192
Melting of the hexagonal phase     196
DNA equation of state     198
Bacteriophage DNA packaging     201
Crowding and entropy driven interactions (depletion)     208
Entropic colloidal interactions in solutions of macromolecules     210
Phase separation of small particles in a polymer solution     215
Questions     220
Poisson-Boltzmann theory for a monovalent salt      223
Summary of scaling laws     227
List of important symbols     229
Recommended reading     233
References     235
Index     243