scholarly journals Bridging Between Material Properties Of Proteins And The Underlying Molecular Interactions

2021 ◽  
Author(s):  
Guang Song
Keyword(s):  
Molecular Interactions ◽  
Material Properties ◽  
Elastic Moduli ◽  
Normal Mode Analysis ◽  
Physical Property ◽  
Elastic Solid ◽  
Mode Analysis ◽  
Young’S Moduli ◽  
Protein Interfaces ◽  
Charmm Force Field

AbstractIn this work, we develop a novel method that bridges between material properties of proteins, particularly the modulus of elasticity, and the underlying molecular interactions. To this end, we employ both an all-atom normal mode analysis (NMA) model with the CHARMM force field and an elastic solid model for proteins and protein interfaces. And the “bridge” between the two models is a common physical property that they both can predict: the magnitude of thermal vibrations. This connection allows one to calibrate the Young’s moduli of proteins and protein interface regions. We find that the elastic moduli of proteins are mostly in the range of a few Gpa to 10 Gpa, while the elastic moduli of the interface regions are about an order smaller. The work is significant as it represents the first attempt to systematically compute the moduli of elasticity of proteins from molecular interactions.

A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes

2019 ◽  
Vol 21 (8) ◽  
pp. 4359-4366 ◽  
Author(s):  
D. Vijay Anand ◽  
Zhenyu Meng ◽  
Kelin Xia
Keyword(s):  
Normal Mode ◽  
Network Model ◽  
Material Properties ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Particle Model ◽  
Elastic Network Model ◽  
Elastic Network ◽  
Virtual Particle ◽  
Biomolecular Complexes

The CMVP-ENM for virus normal mode analysis. With a special ratio parameter, CMVP-ENM can characterize the multi-material properties of biomolecular complexes and systematically enhance or suppress the modes for different components.

scholarly journals Harmonic waves solution in dual-phase-lag magneto-thermoelasticity

Open Physics ◽  
2019 ◽  
Vol 17 (1) ◽  
pp. 8-15 ◽  
Author(s):  
Muhammad Rafiq ◽  
Baljeet Singh ◽  
Samreen Arifa ◽  
Muhammad Nazeer ◽  
Muhammad Usman ◽  
...  
Keyword(s):  
Magnetic Field ◽  
Normal Mode Analysis ◽  
Attenuation Factor ◽  
Plane Waves ◽  
Elastic Solid ◽  
Mode Analysis ◽  
Phase Lag ◽  
Harmonic Waves ◽  
Dual Phase ◽  
Analytical Technique

Abstract The current work analyzes the transmission behavior of plane harmonic waves in an isotropic medium. The observation is made for homogeneous type solid in the context of generalized dual phase lag model of thermoelasticity. Concept micro-temperature, where the microelements have different temperatures has also been considered. The basic focus of thework is to predict the influence of initially applied magnetic field on plane waves through the elastic solid. We have made an attempt to find exact solution of the problem using an analytical technique of a normal mode analysis method. The theoretical results are obtained for a generalized solid in order to test the numerical calculation of a magnesium crystal. It is found that the magnetic field reduces the strength of the attenuation factor.

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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