Oscillations of a coronal plasma slab excited by an external source

2020 ◽  
Vol 496 (3) ◽  
pp. 3035-3042 ◽  
Author(s):  
I Lopin ◽  
I Nagorny
Keyword(s):  
Normal Mode Analysis ◽  
Normal Modes ◽  
External Source ◽  
Coronal Plasma ◽  
Mode Analysis ◽  
Rigid Boundary ◽  
Trapped Mode ◽  
Kink Mode ◽  
Damping Rate ◽  
Plasma Slab

ABSTRACT The dispersive properties of fast oscillations in a coronal plasma slab are studied. These oscillations are assumed to be generated by an external source, located at a finite distance from the slab. It is shown that the problem reduces to examination of the normal modes of a system, consisting of a slab cavity and a finitely distant rigid boundary. The relation that governs the eigenfrequencies of the system is derived. Both the kink and the sausage modes are excited. The main finding indicates that the principal kink mode is trapped not for all axial wavenumbers. It has a non-zero cut-off wavenumber and can exist either as a trapped mode or as a leaky mode. This cut-off tends to zero for infinitely distant sources, in accordance with the well-known result from the normal mode analysis. The expressions for the frequency and damping rate of the leaky principal kink mode are derived. The effect of a finitely distant rigid boundary on the higher transverse-order kink modes and all the sausage modes is found to be only minor, when the distance between the source and the slab is much more than the transverse size of the slab. The applications of the obtained results in coronal seismology are discussed.

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.

Excitation and damping of disturbances in cylindrical coronal loops

2005 ◽  
Vol 364 (1839) ◽  
pp. 547-550 ◽  
Author(s):  
Jaume Terradas ◽  
Ramón Oliver ◽  
José Luis Ballester
Keyword(s):  
Boundary Layer ◽  
Coronal Loop ◽  
Normal Mode Analysis ◽  
Resonant Absorption ◽  
Time Dependent ◽  
Mode Analysis ◽  
Coronal Loops ◽  
Two Dimensional ◽  
Magnetohydrodynamic Equations ◽  
Kink Mode

The excitation and damping of transversal coronal loop oscillations is studied using one-and two-dimensional models of line-tied cylindrical loops. By solving the time-dependent magnetohydrodynamic equations it is shown how an initial disturbance generated in the solar corona induces kink mode oscillations. We investigate the effect of the disturbance on a loop with a non-uniform boundary layer. In particular, a strong damping of transversal oscillations due to resonant absorption is found, such as predicted by previous works based on normal mode analysis.

scholarly journals ProMode-Oligomer: Database of Normal Mode Analysis in Dihedral Angle Space for a Full-Atom System of Oligomeric Proteins

2012 ◽  
Vol 6 (1) ◽  
pp. 9-19 ◽  
Author(s):  
Hiroshi Wako ◽  
Shigeru Endo
Keyword(s):  
Normal Mode ◽  
Protein Complexes ◽  
Normal Mode Analysis ◽  
Normal Modes ◽  
Point Of View ◽  
Mode Analysis ◽  
Dihedral Angles ◽  
Oligomeric Proteins ◽  
Displacement Vectors ◽  
Atom System

The database ProMode-Oligomer (http://promode.socs.waseda.ac.jp/promode_oligomer) was constructed by collecting normal-mode-analysis (NMA) results for oligomeric proteins including protein-protein complexes. As in the ProMode database developed earlier for monomers and individual subunits of oligomers (Bioinformatics vol. 20, pp. 2035–2043, 2004), NMA was performed for a full-atom system using dihedral angles as independent variables, and we released the results (fluctuations of atoms, fluctuations of dihedral angles, correlations between atomic fluctuations, etc.). The vibrating oligomer is visualized by animation in an interactive molecular viewer for each of the 20 lowest-frequency normal modes. In addition, displacement vectors of constituent atoms for each normal mode were decomposed into two characteristic motions in individual subunits, i.e., internal and external (deformation and rigid-body movements of the individual subunits, respectively), and then the mutual movements of the subunits and the movement of atoms around the interface regions were investigated. These results released in ProMode-Oligomer are useful for characterizing oligomeric proteins from a dynamic point of view. The analyses are illustrated with immunoglobulin light- and heavy-chain variable domains bound to lysozyme and to a 12-residue peptide.

Perturbed normal-mode analysis of induction times, relaxation times, and reaction rates in unimolecular reactions

1979 ◽  
Vol 57 (13) ◽  
pp. 1723-1730 ◽  
Author(s):  
Andrew W. Yau ◽  
Huw O. Pritchard
Keyword(s):  
Normal Mode ◽  
Transition Probabilities ◽  
Normal Mode Analysis ◽  
Relaxation Times ◽  
Normal Modes ◽  
Reaction Rates ◽  
Mode Analysis ◽  
Decomposition Reactions ◽  
Induction Times ◽  
Network Relationship

A perturbed normal-mode analysis is presented of the induction (or incubation) time, the relaxation rate, and the reaction rate of a diluted unimolecular system. At high temperature, the unimolecular rate approaches the Lindemann behaviour and the low-pressure rate is related to the normal modes of relaxation of the reactive states in a simple manner. In a step-ladder model system, the network relationship between the normal modes and the microscopic transition probabilities leads to explicit theoretical correlations between the respective experimental quantities. Illustrative calculations of such correlations are presented for the decomposition reactions of N2O and CO2 diluted in Ar at shock wave temperatures, and are compared with experiment.

scholarly journals Skeletal animation for visualizing dynamic shapes of macromolecules

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Yutaka Ueno ◽  
Shinya Muraoka ◽  
Tetsuo Sato
Keyword(s):  
Computer Graphics ◽  
Normal Mode Analysis ◽  
Normal Modes ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Mode Analysis ◽  
Protein Molecules ◽  
Skeletal Animation ◽  
Detailed Computer ◽  
Animation Software

AbstractWe apply a skeletal animation technique developed for general computer graphics animation to display the dynamic shape of protein molecules. Polygon-based models for macromolecules such as atomic representations, surface models, and protein ribbon models are deformed by the motion of skeletal bones that provide coarse-grained descriptions of detailed computer graphics models. Using the animation software Blender, we developed methods to generate the skeletal bones for molecules. Our example of the superposition of normal modes demonstrates the thermal fluctuating motion obtained from normal mode analysis. The method is also applied to display the motions of protein molecules using trajectory coordinates of a molecular dynamics simulation. We found that a standard motion capture file was practical and useful for describing the motion of the molecule using available computer graphics tools.

scholarly journals A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations

2013 ◽  
Author(s):  
Vincent Frappier ◽  
Rafael Najmanovich
Keyword(s):  
Potential Energy ◽  
Normal Mode Analysis ◽  
Protein Structures ◽  
Normal Modes ◽  
Potential Energy Function ◽  
Contact Model ◽  
Coarse Grained ◽  
Mode Analysis ◽  
Elastic Network Model ◽  
Elastic Network

Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM) methods with Cαonly representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations.

Normal-Mode Analysis of a Baroclinic Wave-Mean Oscillation

2006 ◽  
Vol 63 (11) ◽  
pp. 2795-2812 ◽  
Author(s):  
Christopher L. Wolfe ◽  
Roger M. Samelson
Keyword(s):  
Normal Mode Analysis ◽  
Normal Modes ◽  
Generalized Solution ◽  
Horizontal Resolution ◽  
Basic Flow ◽  
Mode Analysis ◽  
Baroclinic Wave ◽  
Mean Oscillation ◽  
The Stability ◽  
Time Periodic

Abstract The stability of a time-periodic baroclinic wave-mean oscillation in a high-dimensional two-layer quasigeostrophic spectral model is examined by computing a full set of time-dependent normal modes (Floquet vectors) for the oscillation. The model has 72 × 62 horizontal resolution and there are 8928 Floquet vectors in the complete set. The Floquet vectors fall into two classes that have direct physical interpretations: wave-dynamical (WD) modes and damped-advective (DA) modes. The WD modes (which include two neutral modes related to continuous symmetries of the underlying system) have large scales and can efficiently exchange energy and vorticity with the basic flow; thus, the dynamics of the WD modes reflects the dynamics of the wave-mean oscillation. These modes are analogous to the normal modes of steady parallel flow. On the other hand, the DA modes have fine scales and dynamics that reduce, to first order, to damped advection of the potential vorticity by the basic flow. While individual WD modes have immediate physical interpretations as discrete normal modes, the DA modes are best viewed, in sum, as a generalized solution to the damped advection problem. The asymptotic stability of the time-periodic basic flow is determined by a small number of discrete WD modes and, thus, the number of independent initial disturbances, which may destabilize the basic flow, is likewise small. Comparison of the Floquet exponent spectrum of the wave-mean oscillation to the Lyapunov exponent spectrum of a nearby aperiodic trajectory suggests that this result will still be obtained when the restriction to time periodicity is relaxed.

scholarly journals Structural Communication between the E. coli Chaperones DnaK and Hsp90

2021 ◽  
Vol 22 (4) ◽  
pp. 2200
Author(s):  
Matthew P. Grindle ◽  
Ben Carter ◽  
John Paul Alao ◽  
Katherine Connors ◽  
Riina Tehver ◽  
...  
Keyword(s):  
Normal Mode Analysis ◽  
Normal Modes ◽  
Direct Interaction ◽  
Network Models ◽  
Mode Analysis ◽  
Symmetric Model ◽  
Biologically Relevant ◽  
Substrate Protein ◽  
Allosteric Communication ◽  
Shock Proteins

The 70 kDa and 90 kDa heat shock proteins Hsp70 and Hsp90 are two abundant and highly conserved ATP-dependent molecular chaperones that participate in the maintenance of cellular homeostasis. In Escherichia coli, Hsp90 (Hsp90Ec) and Hsp70 (DnaK) directly interact and collaborate in protein remodeling. Previous work has produced a model of the direct interaction of both chaperones. The locations of the residues involved have been confirmed and the model has been validated. In this study, we investigate the allosteric communication between Hsp90Ec and DnaK and how the chaperones couple their conformational cycles. Using elastic network models (ENM), normal mode analysis (NMA), and a structural perturbation method (SPM) of asymmetric and symmetric DnaK-Hsp90Ec, we extract biologically relevant vibrations and identify residues involved in allosteric signaling. When one DnaK is bound, the dominant normal modes favor biological motions that orient a substrate protein bound to DnaK within the substrate/client binding site of Hsp90Ec and release the substrate from the DnaK substrate binding domain. The presence of one DnaK molecule stabilizes the entire Hsp90Ec protomer to which it is bound. Conversely, the symmetric model of DnaK binding results in steric clashes of DnaK molecules and suggests that the Hsp90Ec and DnaK chaperone cycles operate independently. Together, this data supports an asymmetric binding of DnaK to Hsp90Ec.

scholarly journals DFT Investigations of the Vibrational Spectra and Translational Modes of Ice II

Molecules ◽  
2019 ◽  
Vol 24 (17) ◽  
pp. 3135 ◽  
Author(s):  
Jing-Wen Cao ◽  
Jia-Yi Chen ◽  
Xiao-Ling Qin ◽  
Xu-Liang Zhu ◽  
Lu Jiang ◽  
...  
Keyword(s):  
Density Functional ◽  
Inelastic Neutron Scattering ◽  
Normal Mode Analysis ◽  
Normal Modes ◽  
Inelastic Neutron ◽  
Mode Analysis ◽  
Molecular Vibration ◽  
Functional Theory ◽  
Ir And Raman ◽  
Good Agreement

The vibrational spectrum of ice II was investigated using the CASTEP code based on first-principles density functional theory (DFT). Based on good agreement with inelastic neutron scattering (INS), infrared (IR), and Raman experimental data, we discuss the translation, libration, bending, and stretching band using normal modes analysis method. In the translation band, we found that the four-bond and two-bond molecular vibration modes constitute three main peaks in accordance with INS ranging from 117 to 318 cm−1. We also discovered that the lower frequencies are cluster vibrations that may overlap with acoustic phonons. Whale et al. found in ice XV that some intramolecular vibrational modes include many isolated-molecule stretches of only one O–H bond, whereas the other O–H bond does not vibrate. This phenomenon is very common in ice II, and we attribute it to local tetrahedral deformation. The pathway of combining normal mode analysis with experimental spectra leads to scientific assignments.

scholarly journals Symmetric and Anti-Symmetric Damping Modes of Trivelpiece–Gould Waves in Weakly and Completely Ionized Plasma Waveguides

Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 699
Author(s):  
Myoung-Jae Lee ◽  
Young-Dae Jung
Keyword(s):  
Normal Mode Analysis ◽  
Low Frequency ◽  
Mode Analysis ◽  
Harmonic Mode ◽  
Absolute Value ◽  
Plasma Waveguides ◽  
Damping Rate ◽  
Weakly Ionized ◽  
Weakly Ionized Plasma ◽  
Opposite Tendency

The collision effects on the low-frequency ion-acoustic Trivelpiece–Gould wave are investigated in weakly and completely ionized plasma waveguides by using the normal mode analysis. In weakly ionized plasma waveguides, it is found that the dependence of the harmonic mode on the absolute value of the scaled damping rate shows the opposite tendency for large and small radii of the cylindrical waveguide. It is also is found that the scaled damping rates for both weakly and completely ionized plasma waveguides decrease with an increase of the electron temperature. It is interesting to note that the scaled damping rate for weakly ionized plasma waveguides shows anti-symmetric behavior when the Trivelpiece–Gould wave propagates in the negative-z direction. However, it is found that the scaled damping rate for completely ionized plasma waveguides shows the symmetric behavior when the Trivelpiece–Gould wave propagates in the negative-z direction.

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