Qiang Cui, Ivet Bahar's Normal Mode Analysis: Theory and Applications to Biological PDF

By Qiang Cui, Ivet Bahar

ISBN-10: 142003507X

ISBN-13: 9781420035070

ISBN-10: 158488472X

ISBN-13: 9781584884729

Fast advancements in experimental options proceed to ward off the bounds within the answer, dimension, and complexity of the chemical and organic structures that may be investigated. This demanding situations the theoretical group to boost cutting edge tools for higher reading experimental effects. common Mode research (NMA) is one such approach. in a position to offering specified insights into the structural and dynamical houses of advanced structures, it truly is now discovering a variety of functions in chemical and organic difficulties. From the basic actual rules to state of the art functions and past, this booklet offers a wide review of ordinary mode research and its price in state of the art learn. the 1st part introduces NMA, examines NMA set of rules improvement at varied resolutions, and explores the applying of these suggestions within the learn of organic platforms. Later chapters disguise procedure advancements in keeping with or encouraged by means of NMA yet going past the harmonic approximation inherent in common NMA concepts. common mode research enhances conventional techniques with computational potency and applicability to giant structures which are past the succeed in of older tools. This e-book deals a different chance to benefit from the stories of a world, interdisciplinary panel of most sensible researchers and discover the newest advancements and functions of NMA to biophysical and chemical difficulties.

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Additional info for Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems (Chapman & Hall/CRC Mathematical & Computational Biology)

Example text

Appendix A Detailed Description of the DIMB Method . . . . . . . . . . 1 Initial Guess Vectors . . . . . . . . . . . . . . . . . . . . . . . . . 2 Iterative Procedure for Obtaining the NMs . . . . . . . . . . . . References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ; characterizing these conformational changes is of general concern [1–4].

All the 3N vectors {qk } are orthonormal thus linearly independent; they form a new basis set defining the NM reference frame for the molecule. In this frame, each of the molecule’s structures corresponds to a point whose coordinate along a given direction qk is the NM coordinate uk . This is analogous to what is observed for one atom in the three-dimensional Cartesian space, where the atom is a point and its position is determined by its coordinates (x, y, z) along the three vectors of the basis set {e1 , e2 , e3 }, which are the unit vectors along X, Y, and Z directions.

1 Methods Based on the Rayleigh Quotient. . . . . . . . . . . . 2 Perturbation Method . . . . . . . . . . . . . . . . . . . . . . . . 3 Mixed Basis Method . . . . . . . . . . . . . . . . . . . . . . . . . 4 The DIMB Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Initial Guess Vectors . . . . . . . . . . . . . . . . . . . . . . . . .

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Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems (Chapman & Hall/CRC Mathematical & Computational Biology) by Qiang Cui, Ivet Bahar


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