scholarly journals Normal Mode Analysis as a Routine Part of a Structural Investigation

2020 ◽  
Author(s):  
Jacob A Bauer ◽  
Jelena Pavlović ◽  
Vladena Bauerová-Hlinková
Keyword(s):  
Normal Mode ◽  
Structural Investigation ◽  
Normal Mode Analysis ◽  
Mode Analysis

scholarly journals Normal Mode Analysis as a Routine Part of a Structural Investigation

Molecules ◽  
2019 ◽  
Vol 24 (18) ◽  
pp. 3293 ◽  
Author(s):  
Jacob A. Bauer ◽  
Jelena Pavlović ◽  
Vladena Bauerová-Hlinková
Keyword(s):  
Normal Mode ◽  
Structural Study ◽  
Computer Technology ◽  
Structural Investigation ◽  
Normal Mode Analysis ◽  
Computational Cost ◽  
Normal Modes ◽  
Mode Analysis ◽  
Computationally Expensive ◽  
The Web

Normal mode analysis (NMA) is a technique that can be used to describe the flexible states accessible to a protein about an equilibrium position. These states have been shown repeatedly to have functional significance. NMA is probably the least computationally expensive method for studying the dynamics of macromolecules, and advances in computer technology and algorithms for calculating normal modes over the last 20 years have made it nearly trivial for all but the largest systems. Despite this, it is still uncommon for NMA to be used as a component of the analysis of a structural study. In this review, we will describe NMA, outline its advantages and limitations, explain what can and cannot be learned from it, and address some criticisms and concerns that have been voiced about it. We will then review the most commonly used techniques for reducing the computational cost of this method and identify the web services making use of these methods. We will illustrate several of their possible uses with recent examples from the literature. We conclude by recommending that NMA become one of the standard tools employed in any structural study.

RAMAN SPECTRA OF TITANIUM DI-, TRI-, AND TETRA-CHLORIDES

2001 ◽  
Vol 15 (28n30) ◽  
pp. 3865-3868 ◽  
Author(s):  
H. MIYAOKA ◽  
T. KUZE ◽  
H. SANO ◽  
H. MORI ◽  
G. MIZUTANI ◽  
...  
Keyword(s):  
Force Constant ◽  
Raman Spectra ◽  
Normal Mode ◽  
Raman Band ◽  
Normal Mode Analysis ◽  
Force Constants ◽  
Mode Analysis ◽  
Oxidation Number

We have obtained the Raman spectra of TiCl n (n= 2, 3, and 4). Assignments of the observed Raman bands were made by a normal mode analysis. The force constants were determined from the observed Raman band frequencies. We have found that the Ti-Cl stretching force constant increases as the oxidation number of the Ti species increases.

scholarly journals Normal mode analysis of spectral density of FMO trimers: Intra- and intermonomer energy transfer

2020 ◽  
Vol 153 (21) ◽  
pp. 215103
Author(s):  
Alexander Klinger ◽  
Dominik Lindorfer ◽  
Frank Müh ◽  
Thomas Renger
Keyword(s):  
Energy Transfer ◽  
Spectral Density ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis

scholarly journals Normal-mode analysis for scalar fields in BTZ black-hole background

2009 ◽  
Vol 60 (2) ◽  
pp. 169-173 ◽  
Author(s):  
Sayan K. Chakrabarti ◽  
Pulak Ranjan Giri ◽  
Kumar S. Gupta
Keyword(s):  
Black Hole ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Scalar Fields ◽  
Mode Analysis ◽  
Btz Black Hole ◽  
Black Hole Background

scholarly journals Rapid Characterization of Allosteric Networks with Ensemble Normal Mode Analysis

2016 ◽  
Vol 120 (33) ◽  
pp. 8276-8288 ◽  
Author(s):  
Xin-Qiu Yao ◽  
Lars Skjærven ◽  
Barry J. Grant
Keyword(s):  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Rapid Characterization

Normal Mode Analysis of Trp RNA Binding Attenuation Protein: Structure and Collective Motions

2011 ◽  
Vol 51 (9) ◽  
pp. 2361-2371 ◽  
Author(s):  
Guang Hu ◽  
Servaas Michielssens ◽  
Samuel L. C. Moors ◽  
Arnout Ceulemans
Keyword(s):  
Protein Structure ◽  
Normal Mode ◽  
Rna Binding ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Collective Motions

Large-Debye-distance effects in a homogeneous plasma

1989 ◽  
Vol 41 (3) ◽  
pp. 493-516 ◽  
Author(s):  
Jan Scheffel ◽  
Bo Lehnert
Keyword(s):  
Normal Mode ◽  
Numerical Solutions ◽  
Normal Mode Analysis ◽  
Distribution Functions ◽  
Mode Analysis ◽  
Larmor Radius ◽  
Order Unity ◽  
Phase Velocities ◽  
Standard Normal ◽  
Velocity Distribution Functions

The classical phenomenon of electron plasma oscillations has been investigated from new aspects. The applicability of standard normal-mode analysis of plasma perturbations has been judged from comparisons with exact numerical solutions to the linearized initial-value problem. We consider both Maxwellian and non-Maxwellian velocity distributions. Emphasis is on perturbations for which αλD is of order unity, where α is the wavenumber and λD the Debye distance. The corresponding large-Debye-distance (LDD) damping is found to substantially dominate over Landau damping. This limits the applicability of normal-mode analysis of non-Maxwellian distributions. The physics of LDD damping and its close connection to large-Larmor-radius (LLR) damping is discussed. A major discovery concerns perturbations of plasmas with non-Maxwellian, bump-in-tail, velocity distribution functions f0(ω). For sufficiently large αλD (of order unity) the plasma responds by damping perturbations that are initially unstable in the Landau sense, i.e. with phase velocities initially in the interval where df0/dw > 0. It is found that the plasma responds through shifting the phase velocity above the upper velocity limit of this interval. This is shown to be due to a resonance with the drifting electrons of the bump, and explains the Penrose criterion.

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