Normal Mode Analysis

Normal Mode Analysis : Theory and Applications to Biological and Chemical Systems

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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 more

Product details

  • Hardback | 432 pages
  • 165 x 240 x 30mm | 748.44g
  • Taylor & Francis Inc
  • Chapman & Hall/CRC
  • Boca Raton, FL, United States
  • English
  • 124 black & white illustrations, 32 colour illustrations, 17 black & white tables
  • 158488472X
  • 9781584884729

Table of contents

Normal mode theory and harmonic potential approximations Konrad Hinsen All-atom normal mode calculations of large molecular systems using iterative methods Liliane Mouawad and David Perahia The Gaussian network model: Theory and applications A.J. Radar, Chakra Chennubhotla, Lee-Wei Yang, Ivet Bahar Normal mode analysis of macromolecules: from enzyme activity site to molecular machines Guohui Li, Adam Van Wynsbergh, Omar N.A. Demerdash, Qiang Cui Functional information from slow mode shapes Yves-Henri Sanejouand Unveiling molecular mechanisms of biological functions in large macromolecular assemblies using elastic network normal mode analysis Florence Tama, Charles L. Brooks III Applications of normal mode analysis in structural refinement of supramolecular complexes Jianpeng Ma Normal mode analysis in studying protein motions with x-ray crystallography George N. Phillips, Jr. Optimizing the parameters of the Gaussian network model for ATP-binding proteins Taner Z. Sen, Robert L. Jernigan Effects of sequence, cyclization, and superhelical stress on the internet motions of DNA Atsushi Matsumoto, Wilma K. Olson Symmetry in normal mode analysis of icosahedral viruses Herman W.T. van Vlijmen Extension of the normal mode concept: Principal component analysis, jumping-among-minima model, and their applications to experimental data analysis Akio Kitao Imaginary-frequency, unstable instantaneous normal modes, the potential energy landscape, and diffusion in liquids T.Keyes Driven molecular dynamics for normal modes of biomolecules without the Hessian, and beyond Martina Kaledin, Alexey L. Kaledin, Alex Brown, and Joel Bowman Probing vibrational energy relaxation in proteins using normal modes Hiroshi Fujisaki, Lintao Bu, and John E. Straub Anharmonic decay of vibrational state in proteins Xin Yu, David M. Leitner Collective coordinate approaches to extended conformational sampling Michael Nilges, Rogher Abseher Using collective coordinates to guide conformational sampling in atomic simulations Haiyan Liu, Zhiyong Zhang, Jianbin He, Yunyu Shishow more