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Full Description
Rapid developments in experimental techniques continue to push back the limits in the resolution, size, and complexity of the chemical and biological systems that can be investigated. This challenges the theoretical community to develop innovative methods for better interpreting experimental results. Normal Mode Analysis (NMA) is one such technique. Capable of providing unique insights into the structural and dynamical properties of complex systems, it is now finding a wide range of applications in chemical and biological problems.
From the fundamental physical ideas to cutting-edge applications and beyond, this book presents a broad overview of normal mode analysis and its value in state-of-the-art research. The first section introduces NMA, examines NMA algorithm development at different resolutions, and explores the application of those techniques in the study of biological systems. Later chapters cover method developments based on or inspired by NMA but going beyond the harmonic approximation inherent in standard NMA techniques.
Normal mode analysis complements traditional approaches with computational efficiency and applicability to large systems that are beyond the reach of older methods. This book offers a unique opportunity to learn from the experiences of an international, interdisciplinary panel of top researchers and explore the latest developments and applications of NMA to biophysical and chemical problems.
Contents
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.
