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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
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.
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.
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.
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
The aim this volume is to present the methods, challenges, software, and applications of this widespread and yet still evolving and maturing field. Computational Protein Design, the first book with this title, guides readers through computational protein design approaches, software and tailored solutions to specific case-study targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Protein Design aims to ensure successful results in the further study of this vital field.
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.
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
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
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
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.
Instability in Geophysical Flows by William D. Smyth,Jeffrey R. Carpenter Pdf
Instabilities are present in all natural fluids from rivers to atmospheres. This book considers the physical processes that generate instability. Part I describes the normal mode instabilities most important in geophysical applications, including convection, shear instability and baroclinic instability. Classical analytical approaches are covered, while also emphasising numerical methods, mechanisms such as internal wave resonance, and simple `rules of thumb' that permit assessment of instability quickly and intuitively. Part II introduces the cutting edge: nonmodal instabilities, the relationship between instability and turbulence, self-organised criticality, and advanced numerical techniques. Featuring numerous exercises and projects, the book is ideal for advanced students and researchers wishing to understand flow instability and apply it to their own research. It can be used to teach courses in oceanography, atmospheric science, coastal engineering, applied mathematics and environmental science. Exercise solutions and MATLAB® examples are provided online. Also available as Open Access on Cambridge Core.
ARPACK Users' Guide by Richard B. Lehoucq,Danny C. Sorensen,Chao Yang Pdf
This book is a guide to understanding and using the software package ARPACK to solve large algebraic eigenvalue problems. The software described is based on the implicitly restarted Arnoldi method, which has been heralded as one of the three most important advances in large scale eigenanalysis in the past ten years. The book explains the acquisition, installation, capabilities, and detailed use of the software for computing a desired subset of the eigenvalues and eigenvectors of large (sparse) standard or generalized eigenproblems. It also discusses the underlying theory and algorithmic background at a level that is accessible to the general practitioner.
Nonlinear Structures and Systems, Volume 1 by Gaetan Kerschen,M. R. W. Brake,Ludovic Renson Pdf
Nonlinear Structures & Systems, Volume 1: Proceedings of the 37th IMAC, A Conference and Exposition on Structural Dynamics, 2019, the first volume of eight from the Conference brings together contributions to this important area of research and engineering. The collection presents early findings and case studies on fundamental and applied aspects of Nonlinear Dynamics, including papers on: Nonlinear Reduced-order Modeling Jointed Structures: Identification, Mechanics, Dynamics Experimental Nonlinear Dynamics Nonlinear Model & Modal Interactions Nonlinear Damping Nonlinear Modeling & Simulation Nonlinearity & System Identification
