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Normal Mode Analysis


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Normal mode theory and harmonic potential approximations. All-atom normal mode calculations of large molecular systems using iterative methods. The Gaussian Network Model: Theory and Applications. Normal mode analysis of macromolecules: from enzyme activity site to molecular machines. Functional information from slow mode shapes. Unveiling Molecular Mechanisms of Biological Functions in Large Macromolecular Assemblies using Elastic Network Normal Mode Analysis. Applications of Normal Mode Analysis in Structural Refinement of Supramolecular Complexes. Normal Mode Analysis in Studying Protein Motions with X-ray Crystallography. Optimizing the Parameters of the Gaussian Network Model for ATP-Binding Proteins. Effects of Sequence, Cyclization, and Superhelical Stress on the Internet Motions of DNA. Symmetry in Normal Mode Analysis of Icosahedral Viruses. Extension of the normal mode concept: Principal component analysis, jumping-among-minimum model and their applications to experimental data analysis. Imaginary-Frequency, Unstable Instantaneous Normal Modes, the Potential Energy Landscape, and Diffusion in Liquids. Driven Molecular Dynamics for Normal Modes of Biomolecules without the Hessian, and Beyond. Probing vibrational energy relaxation in proteins using normal modes. Anharminic decay of vibrational state in proteins. Collective coordinate aproaches to extended conformational sampling. Using Collective coordinates to guide conformational sampling in atomic simulations.

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Qiang Cui, Ivet Bahar

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