Print version record.

Molecular Machines presents a dynamic new approach to the physics of enzymes and DNA from the perspective of materials science. Unified around the concept of molecular deformability--how proteins and DNA stretch, fold, and change shape--this book describes the complex molecules of life from the innovative perspective of materials properties and dynamics, in contrast to structural or purely chemical approaches. It covers a wealth of topics, including nonlinear deformability of enzymes and DNA; the chemo-dynamic cycle of enzymes; supra-molecular constructions with internal stress; nano-rheology and viscoelasticity; and chemical kinetics, Brownian motion, and barrier crossing. Essential reading for researchers in materials science, engineering, and nanotechnology, the book also describes the landmark experiments that have established the materials properties and energy landscape of large biological molecules. Molecular Machines is also ideal for the classroom. It gives graduate students a working knowledge of model building in statistical mechanics, making it an essential resource for tomorrow's experimentalists in this cutting-edge field. In addition, mathematical methods are introduced in the bio-molecular context--for example, DNA conformational transitions are used to illustrate the transfer matrix formalism. The result is a generalized approach to mathematical problem solving that enables students to apply their findings more broadly. Molecular Machines represents the next leap forward in nanoscience, as researchers strive to harness proteins, enzymes, and DNA as veritable machines in medicine, technology, and beyond.

Includes bibliographical references (pages 165-172) and index.

Cover; Title; Copyright; CONTENTS; Preface; Acknowledgments; Dedication; 1 Brownian Motion; 1.1 Random Walk; 1.2 Polymer as a Simple Random Walk; 1.3 Direct Calculation of p(R); 1.4 The Langevin Approach; 1.5 Correlation Functions; 1.6 Barrier Crossing; 1.7 What is Equilibrium?; 2 Statics of DNA Deformations; 2.1 Introduction; 2.2 DNA Melting; 2.3 Zipper Model; 2.4 Experimental Melting Curves; 2.5 Base Pairing and Base Stacking as Separate Degrees of Freedom; 2.6 Hamiltonian Formulation of the Zipper Model; 2.7 2 × 2Model: Cooperativity from Local Rules; 2.8 Nearest Neighbor Model.

2.9 Connection to Nonlinear Dynamics2.10 Linear and Nonlinear Elasticity of DNA; 2.11 Bending Modulus and Persistence Length; 2.12 Measurements of DNA Elasticity: Long Molecules; 2.13 Measurements of DNA Elasticity: Short Molecules; 2.14 The Euler Instability; 2.15 The DNA Yield Transition; 3 Kinematics of Enzyme Action; 3.1 Introduction; 3.2 Michaelis-Menten Kinetics; 3.3 The Method of the DNA Springs; 3.4 Force and Elastic Energy in the Enzyme-DNA Chimeras; 3.5 Injection of Elastic Energy vs. Activity Modulation; 3.6 Connection to Nonlinear Dynamics: Two Coupled Nonlinear Springs.

4 Dynamics of Enzyme Action4.1 Introduction; 4.2 Enzymes are Viscoelastic; 4.3 Nonlinearity of the Enzyme's Mechanics; 4.4 Timescales; 4.5 Enzymatic Cycle and Viscoelasticity: Motors; 4.6 Internal Dissipation; 4.7 Origin of the Restoring Force g; 4.8 Models Based on Chemical Kinetics (Fisher and Kolomeisky, 1999); 4.9 Different Levels of Microscopic Description; 4.10 Connection to Information Flow; 4.11 Normal Mode Analysis; 4.12 Many States of the Folded Protein: Spectroscopy; 4.13 Interesting Topics in Nonequilibrium Thermodynamics Relating to Enzyme Dynamics; Bibliography.

Chapter 1: Brownian MotionChapter 2: Statics of DNA Deformations; Chapter 3: Kinematics of Enzyme Action; Chapter 4: Dynamics of Enzyme Action; Index.

IEEE IEEE Xplore Princeton University Press eBooks Library