Table of Contents
Preface vii
1 Brownian Motion 1
1.1 Random Walk 1
1.2 Polymer as a Simple Random Walk 4
1.3 Direct Calculation of p(R) 5
1.4 The Langevin Approach 8
1.5 Correlation Functions 12
1.6 Barrier Crossing 16
1.7 What is Equilibrium? 22
2 Statics of DNA Deformations 25
2.1 Introduction 25
2.2 DNA Melting 29
2.3 Zipper Model 34
2.4 Experimental Melting Curves 36
2.5 Base Pairing and Base Stacking as Separate Degrees of Freedom 42
2.6 Hamiltonian Formulation of the Zipper Model 46
2.7 2x2 Model: Cooperativity from Local Rules 47
2.8 Nearest Neighbor Model 52
2.9 Connection to Nonlinear Dynamics 55
2.10 Linear and Nonlinear Elasticity of DNA 56
2.11 Bending Modulus and Persistence Length 56
2.12 Measurements of DNA Elasticity: Long Molecules 60
2.13 Measurements of DNA Elasticity: Short Molecules 65
2.14 The Euler Instability 68
2.15 The DNA Yield Transition 72
3 Kinematics of Enzyme Action 81
3.1 Introduction 81
3.2 Michaelis-Menten Kinetics 82
3.3 The Method of the DNA Springs 89
3.4 Force and Elastic Energy in the Enzyme-DNA Chimeras 97
3.5 Injection of Elastic Energy vs. Activity Modulation 106
3.6 Connection to Nonlinear Dynamics: Two Coupled Nonlinear Springs 116
4 Dynamics of Enzyme Action 122
4.1 Introduction 122
4.2 Enzymes are Viscoelastic 125
4.3 Nonlinearity of the Enzyme's Mechanics 125
4.4 Timescales 128
4.5 Enzymatic Cycle and Viscoelasticiiy: Motors 129
4.6 Internal Dissipation 137
4.7 Origin of the Restoring Force g 138
4.8 Models Based on Chemical Kinetics (Fisher and Kolomeisky, 1999) 139
4.9 Different Levels of Microscopic Description 143
4.10 Connection to Information Flow 147
4.11 Normal Mode Analysis 149
4.12 Many States of the Folded Protein: Spectroscopy 153
4.13 Interesting Topics in Nonequilibrium Thermodynamics Relating to Enzyme Dynamics 158
Bibliography 165
Chapter 1 Brownian Motion 165
Chapter 2 Statics of DNA Deformations 165
Chapter 3 Kinematics of Enzyme Action 167
Chapter 4 Dynamics of Enzyme Action 169
Index 173
