chapter 1 Normal Mode Theory and Harmonic Potential Approximations / chapter 2 All-Atom Normal Mode Calculations of Large Molecular Systems Using Iterative Methods / chapter 3 The Gaussian Network Model: Theory and Applications / chapter 4 Normal Mode Analysis of Macromolecules: From Enzyme Active Sites to Molecular Machines / chapter 5 Functional Information from Slow Mode Shapes / chapter 6 Unveiling Molecular Mechanisms of Biological Functions in Large Macromolecular Assemblies Using Elastic Network Normal Mode Analysis / chapter 7 Applications of Normal Mode Analysis in Structural Refinement of Supramolecular Complexes / chapter 8 Normal Mode Analysis in Studying Protein Motions with X-Ray Crystallography / chapter 9 Optimizing the Parameters of the Gaussian Network Model for ATP-Binding Proteins / chapter 10 Effects of Sequence, Cyclization, and Superhelical Stress on the Internal Motions of DNA / chapter 11 Symmetry in Normal Mode Analysis of Icosahedral Viruses / chapter 12 Extension of the Normal Mode Concept: Principal Component Analysis, Jumping-Among-Minima Model, and Their Applications to Experimental Data Analysis / chapter 13 Imaginary-Frequency, Unstable Instantaneous Normal Modes, the Potential Energy Landscape, and Diffusion in Liquids / chapter 14 Driven Molecular Dynamics for Normal Modes of Biomolecules without the Hessian, and Beyond / chapter 15 Probing Vibrational Energy Relaxation in Proteins Using Normal / chapter 16 Anharmonic Decay of Vibrational States in Proteins / chapter 17 Collective Coordinate Approaches to Extended Conformational Sampling / chapter 18 Using Collective Coordinates to Guide Conformational Sampling in Atomic Simulations