scholarly journals A kinetic theory of the pulsational mode of gravitational collapse in star-forming molecular clouds

2021 ◽  
Author(s):  
Dawroichuh Challam ◽  
Pralay Kumar Karmakar
Keyword(s):  
Kinetic Theory ◽  
Gravitational Collapse ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Collapse Mechanism ◽  
Linear Dispersion ◽  
Ion Density ◽  
Star Forming ◽  
Dust Charge ◽  
Dense Molecular Cloud

Abstract A kinetic theory formulation of the pulsational mode of gravitational collapse (PMGC) in a complex unmagnetized self-gravitating partially ionized dense molecular cloud (DMC) is proposed. Applying a linear normal mode analysis, a quintic linear dispersion relation with a unique set of multi-parametric plasma-dependent coefficients is obtained. The reliability of the calculation scheme is validated in light of the various predictions available in the literature. It is then numerically analyzed in the parametric windows of judicious realistic input values. Our results indicate that the dust mass, equilibrium electron density, and equilibrium ion density act as destabilizing agencies to the PMGC evolution. In contrast, the dust charge number, equilibrium dust density, and dust temperature act as stabilizing agencies. The oscillatory and propagatory features of the PMGC are illustratively explained and comparatively validated in accordance with the observed astrophysical scenarios. This paper ends up with a brief highlight of the non-trivial implications and applications of the results actualizable in the self-gravitational collapse mechanism leading to varied structure formation processes in the mysterious astrocosmic universe.

Kinetic theory of the evolution of collective plasma excitations in an external electric field

1976 ◽  
Vol 16 (2) ◽  
pp. 129-148 ◽  
Author(s):  
R. Balescu ◽  
I. Paiva-Veretennicoff
Keyword(s):  
External Field ◽  
Kinetic Theory ◽  
Electric Field ◽  
Normal Mode Analysis ◽  
Kinetic Equations ◽  
Mode Analysis ◽  
Parametric Effects ◽  
Collective Plasma ◽  
External Time ◽  
System Approaches

The kinetic theory of a plasma is developed on the basis of a normal mode analysis-In the absence of any external field, the system approaches a ‘plasmadynamical (PD) state’, described by fourteen amplitudes of the PD modes. The corresponding eigenvalues and eigenvectors are constructed explicitly. When an external time-dependent electric field is switched on, transitions between these modes determine the evolution of the plasma. Assuming that a PD regime is valid, the kinetic equations reduce to a set of equations describing parametric effects and nonlinear mode-mode couplings. A new source term, arising from the interference between collisions and external field, also appears. Some qualitative implications are discussed.

A new electrostatic mode in a dusty plasma due to dust charge fluctuation

2009 ◽  
Vol 75 (3) ◽  
pp. 389-393 ◽  
Author(s):  
A. A. MAMUN
Keyword(s):  
Dusty Plasma ◽  
Acoustic Waves ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Charge Fluctuation ◽  
Dust Charge ◽  
Perturbation Mode ◽  
Basic Features ◽  
Electron Acoustic ◽  
Electrostatic Perturbation

AbstractA dusty plasma consisting of cold and hot electrons, cold ions, and charge fluctuating isolated cold dust has been considered. It has been shown by a normal mode analysis that in such a dusty plasma there exists a new type of electrostatic perturbation mode due to the charge fluctuation of the isolated dust. The basic features of this new electrostatic perturbation mode, which are different from those of the electron-acoustic waves, have also been analytically identified. The implications of these results in both the space and laboratory dusty plasma conditions are briefly discussed.

Application of the ESMACS Binding Free Energy Protocol to a Highly Varied Ligand Dataset: Lactate Dehydogenase A

2019 ◽  
Author(s):  
David Wright ◽  
Fouad Husseini ◽  
Shunzhou Wan ◽  
Christophe Meyer ◽  
Herman Van Vlijmen ◽  
...  
Keyword(s):  
Free Energy ◽  
Surface Area ◽  
Binding Free Energy ◽  
Normal Mode Analysis ◽  
Binding Mode ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
Mode Analysis ◽  
Energy Calculation ◽  
Accessible Surface

<div>Here, we evaluate the performance of our range of ensemble simulation based binding free energy calculation protocols, called ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) for use in fragment based drug design scenarios. ESMACS is designed to generate reproducible binding affinity predictions from the widely used molecular mechanics Poisson-Boltzmann surface area (MMPBSA) approach. We study ligands designed to target two binding pockets in the lactate dehydogenase A target protein, which vary in size, charge and binding mode. When comparing to experimental results, we obtain excellent statistical rankings across this highly diverse set of ligands. In addition, we investigate three approaches to account for entropic contributions not captured by standard MMPBSA calculations: (1) normal mode analysis, (2) weighted solvent accessible surface area (WSAS) and (3) variational entropy. </div>

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

Electrostatic oscillations in cold inhomogeneous plasma I. Differential equation approach

1971 ◽  
Vol 5 (2) ◽  
pp. 239-263 ◽  
Author(s):  
Z. Sedláček
Keyword(s):  
Differential Equation ◽  
Green Function ◽  
Normal Mode Analysis ◽  
Inhomogeneous Plasma ◽  
Mode Analysis ◽  
Complex Frequency ◽  
Plasma Oscillations ◽  
The Laplace Transform ◽  
Collective Oscillations ◽  
The Green Function

Small amplitude electrostatic oscillations in a cold plasma with continuously varying density have been investigated. The problem is the same as that treated by Barston (1964) but instead of his normal-mode analysis we employ the Laplace transform approach to solve the corresponding initial-value problem. We construct the Green function of the differential equation of the problem to show that there are branch-point singularities on the real axis of the complex frequency-plane, which correspond to the singularities of the Barston eigenmodes and which, asymptotically, give rise to non-collective oscillations with position-dependent frequency and damping proportional to negative powers of time. In addition we find an infinity of new singularities (simple poles) of the analytic continuation of the Green function into the lower half of the complex frequency-plane whose position is independent of the spatial co-ordinate so that they represent collective, exponentially damped modes of plasma oscillations. Thus, although there may be no discrete spectrum, in a more general sense a dispersion relation does exist but must be interpreted in the same way as in the case of Landau damping of hot plasma oscillations.

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

Linear and nonlinear behaviour of two-stream instabilities in collisionless plasmas

2015 ◽  
Vol 81 (6) ◽  
Author(s):  
Y. W. Hou ◽  
M. X. Chen ◽  
M. Y. Yu ◽  
B. Wu
Keyword(s):  
Normal Mode Analysis ◽  
System Size ◽  
Point Of View ◽  
Mode Analysis ◽  
Nonlinear Behaviour ◽  
Initial Growth ◽  
Small Magnitude ◽  
Plasma Oscillations ◽  
Numerical Noise ◽  
Growth Properties

The transient, growth and nonlinear saturation stages in the evolution of the electrostatic two-stream instabilities as described by the Vlasov–Poisson system are reconsidered by numerically following the evolution of the total wave energy of the plasma oscillations excited from (numerical) noise. Except for peculiarities related to the necessarily finite (even though very small) magnitude of the perturbations in the numerical simulation, the existence and initial growth properties of the instabilities from the numerical results are found to be consistent with those from linear normal mode analysis and the Penrose criteria. However, contradictory to the traditional point of view, the growth of instability before saturation is not always linear. The initial stage of the growth can exhibit fine structures that can be attributed to the harmonics of the excited plasma oscillations, whose wavelengths are determined by the system size and the numerical noise. As expected, saturation of the unstable oscillations is due to electron trapping when they reach sufficiently large amplitudes.

THEORETICAL INVESTIGATIONS ON ELUCIDATING FUNDAMENTAL MECHANISMS OF CATALYSIS AND DYNAMICS INVOLVED IN TRANSCRIPTION BY RNA POLYMERASE

2013 ◽  
Vol 12 (08) ◽  
pp. 1341005 ◽  
Author(s):  
FÁTIMA PARDO-AVILA ◽  
LIN-TAI DA ◽  
YING WANG ◽  
XUHUI HUANG
Keyword(s):  
Rna Polymerase ◽  
Conformational Changes ◽  
Normal Mode Analysis ◽  
Md Simulations ◽  
Mode Analysis ◽  
Transcription Process ◽  
Nucleotide Addition ◽  
Theoretical Investigations ◽  
State Models ◽  
Elongation Process

RNA polymerase is the enzyme that synthesizes RNA during the transcription process. To understand its mechanism, structural studies have provided us pictures of the series of steps necessary to add a new nucleotide to the nascent RNA chain, the steps altogether known as the nucleotide addition cycle (NAC). However, these static snapshots do not provide dynamic information of these processes involved in NAC, such as the conformational changes of the protein and the atomistic details of the catalysis. Computational studies have made efforts to fill these knowledge gaps. In this review, we provide examples of different computational approaches that have improved our understanding of the transcription elongation process for RNA polymerase, such as normal mode analysis, molecular dynamic (MD) simulations, Markov state models (MSMs). We also point out some unsolved questions that could be addressed using computational tools in the future.

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