Normal Mode Analysis

Author : Qiang Cui,Ivet Bahar
Publisher : CRC Press
Page : 432 pages
File Size : 45,9 Mb
Release : 2005-12-12
Category : Medical
ISBN : 9781420035070

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Normal Mode Analysis by Qiang Cui,Ivet Bahar Pdf

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.

Author : Alexander F. Vakakis
Publisher : Springer Science & Business Media
Page : 290 pages
File Size : 48,8 Mb
Release : 2013-06-29
Category : Science
ISBN : 9789401724524

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Normal Modes and Localization in Nonlinear Systems by Alexander F. Vakakis Pdf

The nonlinear normal modes of a parametrically excited cantilever beam are constructed by directly applying the method of multiple scales to the governing integral-partial differential equation and associated boundary conditions. The effect of the inertia and curvature nonlin earities and the parametric excitation on the spatial distribution of the deflection is examined. The results are compared with those obtained by using a single-mode discretization. In the absence of linear viscous and quadratic damping, it is shown that there are nonlinear normal modes, as defined by Rosenberg, even in the presence of a principal parametric excitation. Furthermore, the nonlinear mode shape obtained with the direct approach is compared with that obtained with the discretization approach for some values of the excitation frequency. In the single-mode discretization, the spatial distribution of the deflection is assumed a priori to be given by the linear mode shape ¢n, which is parametrically excited, as Equation (41). Thus, the mode shape is not influenced by the nonlinear curvature and nonlinear damping. On the other hand, in the direct approach, the mode shape is not assumed a priori; the nonlinear effects modify the linear mode shape ¢n. Therefore, in the case of large-amplitude oscillations, the single-mode discretization may yield inaccurate mode shapes. References 1. Vakakis, A. F., Manevitch, L. I., Mikhlin, Y. v., Pilipchuk, V. N., and Zevin A. A., Nonnal Modes and Localization in Nonlinear Systems, Wiley, New York, 1996.

Author : Andreas Kukol
Publisher : Humana Press
Page : 474 pages
File Size : 49,8 Mb
Release : 2017-04-30
Category : Science
ISBN : 1493954911

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Molecular Modeling of Proteins by Andreas Kukol Pdf

Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions and notes on troubleshooting and avoiding common pitfalls. Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical and biosciences interested in utilizing this powerful technology.

Author : Nedjeljka Žagar,Joseph Tribbia
Publisher : Springer
Page : 318 pages
File Size : 40,7 Mb
Release : 2020-12-06
Category : Mathematics
ISBN : 3030609626

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Modal View of Atmospheric Variability by Nedjeljka Žagar,Joseph Tribbia Pdf

This book reviews the theory and applications of the normal-mode functions in numerical weather prediction and weather and climate dynamics. The normal-mode functions, the eigensolutions of the linearized primitive equations describing the evolution of atmospheric winds and mass variables, have been used for a long time. They have played an important role in the development of data assimilation schemes and the initialization of numerical weather prediction models. Chapters also present how the normal modes can be applied to many theoretical and numerical problems in the atmospheric sciences, such as equatorial wave dynamics, baroclinic instability, energy transfers, and predictability across scales.

Author : Valerie Daggett
Publisher : Elsevier
Page : 477 pages
File Size : 40,6 Mb
Release : 2003-11-26
Category : Medical
ISBN : 9780080493787

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Protein Simulations by Valerie Daggett Pdf

Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function. * Force Fields* Ligand Binding* Protein Membrane Simulation* Enzyme Dynamics* Protein Folding and unfolding simulations

Author : Howard Georgi
Publisher : Addison Wesley Publishing Company
Page : 442 pages
File Size : 55,9 Mb
Release : 1993
Category : Science
ISBN : UOM:39015025294284

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The Physics of Waves by Howard Georgi Pdf

The first complete introduction to waves and wave phenomena by a renowned theorist. Covers damping, forced oscillations and resonance; normal modes; symmetries; traveling waves; signals and Fourier analysis; polarization; diffraction.

Author : Mathias Harrer,Pim Cuijpers,Toshi A. Furukawa,David D. Ebert
Publisher : CRC Press
Page : 500 pages
File Size : 51,9 Mb
Release : 2021-09-15
Category : Mathematics
ISBN : 9781000435634

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Doing Meta-Analysis with R by Mathias Harrer,Pim Cuijpers,Toshi A. Furukawa,David D. Ebert Pdf

Doing Meta-Analysis with R: A Hands-On Guide serves as an accessible introduction on how meta-analyses can be conducted in R. Essential steps for meta-analysis are covered, including calculation and pooling of outcome measures, forest plots, heterogeneity diagnostics, subgroup analyses, meta-regression, methods to control for publication bias, risk of bias assessments and plotting tools. Advanced but highly relevant topics such as network meta-analysis, multi-three-level meta-analyses, Bayesian meta-analysis approaches and SEM meta-analysis are also covered. A companion R package, dmetar, is introduced at the beginning of the guide. It contains data sets and several helper functions for the meta and metafor package used in the guide. The programming and statistical background covered in the book are kept at a non-expert level, making the book widely accessible. Features • Contains two introductory chapters on how to set up an R environment and do basic imports/manipulations of meta-analysis data, including exercises • Describes statistical concepts clearly and concisely before applying them in R • Includes step-by-step guidance through the coding required to perform meta-analyses, and a companion R package for the book

Author : R. Sabadini,Bert Vermeersen
Publisher : Springer
Page : 329 pages
File Size : 53,9 Mb
Release : 2014-11-14
Category : Science
ISBN : 9789401717090

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Global Dynamics of the Earth by R. Sabadini,Bert Vermeersen Pdf

This volume opens up new perspectives on the physics of the Earth's interior for graduate students and researchers working in the fields of geophysics and geodesy. It looks at our planet in an integrated fashion, linking the physics of its interior to the geophysical and geodetic techniques that record, over a broad spectrum of spatial wavelengths, the ongoing modifications in the shape and gravity field of the planet. Basic issues related to the rheological properties of the Earth's mantle and to its slow deformation will be understood, in both mathematical and physical terms, within the framework of an analytical normal mode relaxation theory. Fundamentals of this theory are developed in the first, tutorial part. The second part deals with a wide range of applications, ranging from changes in the Earth's rotation to post-seismic deformation and sea-level variations induced by post-glacial rebound. In the study of the physics of the Earth's interior, the book bridges the gap between seismology and geodynamics.

Author : Markus Reiher
Publisher : Springer Science & Business Media
Page : 368 pages
File Size : 50,9 Mb
Release : 2007-01-08
Category : Science
ISBN : 9783540380825

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Atomistic Approaches in Modern Biology by Markus Reiher Pdf

With contributions by numerous experts

Author : Roy Leon Courtney
Publisher : Unknown
Page : 60 pages
File Size : 43,7 Mb
Release : 1971
Category : Finite element method
ISBN : UIUC:30112106747717

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Finite-element Modeling Studies in the Normal-mode Method and Normal-mode Synthesis by Roy Leon Courtney Pdf

Author : Oren M. Becker,Alexander D. MacKerell Jr.,Benoit Roux,Masakatsu Watanabe
Publisher : CRC Press
Page : 534 pages
File Size : 47,7 Mb
Release : 2001-02-09
Category : Medical
ISBN : 020390382X

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Computational Biochemistry and Biophysics by Oren M. Becker,Alexander D. MacKerell Jr.,Benoit Roux,Masakatsu Watanabe Pdf

Covering theoretical methods and computational techniques in biomolecular research, this book focuses on approaches for the treatment of macromolecules, including proteins, nucleic acids, and bilayer membranes. It uses concepts in free energy calculations, conformational analysis, reaction rates, and transition pathways to calculate and interpret b

Author : Dewey H. Hodges,G. Alvin Pierce
Publisher : Cambridge University Press
Page : 0 pages
File Size : 55,7 Mb
Release : 2014-01-02
Category : Technology & Engineering
ISBN : 110761709X

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Introduction to Structural Dynamics and Aeroelasticity by Dewey H. Hodges,G. Alvin Pierce Pdf

This text provides an introduction to structural dynamics and aeroelasticity, with an emphasis on conventional aircraft. The primary areas considered are structural dynamics, static aeroelasticity, and dynamic aeroelasticity. The structural dynamics material emphasizes vibration, the modal representation, and dynamic response. Aeroelastic phenomena discussed include divergence, aileron reversal, airload redistribution, unsteady aerodynamics, flutter, and elastic tailoring. More than one hundred illustrations and tables help clarify the text, and more than fifty problems enhance student learning. This text meets the need for an up-to-date treatment of structural dynamics and aeroelasticity for advanced undergraduate or beginning graduate aerospace engineering students. Praise from the First Edition "Wonderfully written and full of vital information by two unequalled experts on the subject, this text meets the need for an up-to-date treatment of structural dynamics and aeroelasticity for advanced undergraduate or beginning graduate aerospace engineering students." - Current Engineering Practice "Hodges and Pierce have written this significant publication to fill an important gap in aeronautical engineering education. Highly recommended." - Choice ". . . a welcome addition to the textbooks available to those with interest in aeroelasticity. . . . As a textbook, it serves as an excellent resource for advanced undergraduate and entry-level graduate courses in aeroelasticity. . . . Furthermore, practicing engineers interested in a background in aeroelasticity will find the text to be a friendly primer." - AIAA Bulletin

Author : Peter Larkin
Publisher : Elsevier
Page : 286 pages
File Size : 43,9 Mb
Release : 2017-11-13
Category : Science
ISBN : 9780128042090

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Infrared and Raman Spectroscopy by Peter Larkin Pdf

Infrared and Raman Spectroscopy, Principles and Spectral Interpretation, Second Edition provides a solid introduction to vibrational spectroscopy with an emphasis on developing critical interpretation skills. This book fully integrates the use of both IR and Raman spectroscopy as spectral interpretation tools, enabling the user to utilize the strength of both techniques while also recognizing their weaknesses. This second edition more than doubles the amount of interpreted IR and Raman spectra standards and spectral unknowns. The chapter on characteristic group frequencies is expanded to include increased discussions of sulphur and phosphorus organics, aromatic and heteroaromatics as well as inorganic compounds. New topics include a discussion of crystal lattice vibrations (low frequency/THz), confocal Raman microscopy, spatial resolution in IR and Raman microscopy, as well as criteria for selecting Raman excitation wavelengths. These additions accommodate the growing use of vibrational spectroscopy for process analytical monitoring, nanomaterial investigations, and structural and identity determinations to an increasing user base in both industry and academia. Integrates discussion of IR and Raman spectra Pairs generalized IR and Raman spectra of functional groups with tables and text Includes over 150 fully interpreted, high quality IR and Raman reference spectra Contains fifty-four unknown IR and Raman spectra, with a corresponding answer key

Author : Dominik Marx,Jürg Hutter
Publisher : Cambridge University Press
Page : 503 pages
File Size : 43,8 Mb
Release : 2009-04-30
Category : Science
ISBN : 9781139477192

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Ab Initio Molecular Dynamics by Dominik Marx,Jürg Hutter Pdf

Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car–Parrinello approach, correcting various misconceptions currently found in research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages and enabling developers to improve and add new features in their code.

Author : Ron Milo,Rob Phillips
Publisher : Garland Science
Page : 400 pages
File Size : 46,7 Mb
Release : 2015-12-07
Category : Science
ISBN : 9781317230694

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Cell Biology by the Numbers by Ron Milo,Rob Phillips Pdf

A Top 25 CHOICE 2016 Title, and recipient of the CHOICE Outstanding Academic Title (OAT) Award. How much energy is released in ATP hydrolysis? How many mRNAs are in a cell? How genetically similar are two random people? What is faster, transcription or translation?Cell Biology by the Numbers explores these questions and dozens of others provid