scholarly journals The Chirality of Isotopomers of Glycine Compared using Next-Generation QTAIM

2021 ◽  
Author(s):  
Xing Nie ◽  
Yong Yang ◽  
Tianlv Xu ◽  
Malgorzata Biczysko ◽  
Steven Kirk ◽  
...  
Keyword(s):  
Stress Tensor ◽  
Electric Fields ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Electronic Charge ◽  
Next Generation ◽  
Promising Tool ◽  
External Forces ◽  
Mass Dependent ◽  
Alpha Carbon

The effect of the presence of a deuterium (D) or tritium (T) isotope bonded to the alpha carbon of glycine is determined without the need to apply external forces e.g. electric fields or using normal mode analysis. Isotopic effects were accounted for using the mass-dependent diagonal Born-Oppenheimer energy correction (DBOC) at the CCSD level of theory. We calculated the stress tensor trajectories of the dominant C-N bond within next generation quantum theory of atoms in molecules (NG-QTAIM). S-character chirality was discovered using the stress tensor trajectories, instead of the Cahn–Ingold–Prelog (CIP) rules, for ordinary glycine. The S-character chirality was preserved after the substitution of the H on the alpha carbon for a D isotope but transformed to R-character chirality after replacement with the T isotope. This reversal of the chirality depending on the presence of a single D or T isotope bound to the alpha carbon adds to the debate on the nature of the extraterrestrial origins of chirality in simple amino acids. We demonstrate that NG-QTAIM is a promising tool for understanding isotopic induced electronic charge density changes, useful in analysis of infrared (IR) or circular dichroism (CD) spectra explaining changes in mode couplings and bands intensities or sign.

scholarly journals A multiscale model of mechanotransduction by the ankyrin chains of the NOMPC channel

2019 ◽  
Vol 151 (3) ◽  
pp. 316-327 ◽  
Author(s):  
David Argudo ◽  
Sara Capponi ◽  
Neville P. Bethel ◽  
Michael Grabe
Keyword(s):  
Normal Mode Analysis ◽  
Multiscale Model ◽  
Force Balance ◽  
Mode Analysis ◽  
Sensory Cells ◽  
Force Transmission ◽  
Balance Analysis ◽  
Dynamics Simulations ◽  
External Forces ◽  
Electrical Impulses

Our senses of touch and hearing are dependent on the conversion of external mechanical forces into electrical impulses by the opening of mechanosensitive channels in sensory cells. This remarkable feat involves the conversion of a macroscopic mechanical displacement into a subnanoscopic conformational change within the ion channel. The mechanosensitive channel NOMPC, responsible for hearing and touch in flies, is a homotetramer composed of four pore-forming transmembrane domains and four helical chains of 29 ankyrin repeats that extend 150 Å into the cytoplasm. Previous work has shown that the ankyrin chains behave as biological springs under extension and that tethering them to microtubules could be involved in the transmission of external forces to the NOMPC gate. Here we combine normal mode analysis (NMA), full-atom molecular dynamics simulations, and continuum mechanics to characterize the material properties of the chains under extreme compression and extension. NMA reveals that the lowest-frequency modes of motion correspond to fourfold symmetric compression/extension along the channel, and the lowest-frequency symmetric mode for the isolated channel domain involves rotations of the TRP domain, a putative gating element. Finite element modeling reveals that the ankyrin chains behave as a soft spring with a linear, effective spring constantof 22 pN/nm for deflections ≤15 Å. Force–balance analysis shows that the entire channel undergoes rigid body rotation during compression, and more importantly, each chain exerts a positive twisting moment on its respective linker helices and TRP domain. This torque is a model-independent consequence of the bundle geometry and would cause a clockwise rotation of the TRP domain when viewed from the cytoplasm. Force transmission to the channel for compressions >15 Å depends on the nature of helix–helix contact. Our work reveals that compression of the ankyrin chains imparts a rotational torque on the TRP domain, which potentially results in channel opening.

scholarly journals Propagation of Surface Waves in a Rotating Coated Viscoelastic Half-Space under the Influence of Magnetic Field and Gravitational Forces

2021 ◽  
Vol 5 (4) ◽  
pp. 250
Author(s):  
Ali Mubaraki ◽  
Saad Althobaiti ◽  
Rahmatullah Ibrahim Nuruddeen
Keyword(s):  
Magnetic Field ◽  
Surface Waves ◽  
Half Space ◽  
Normal Mode Analysis ◽  
Frequency Equation ◽  
Mode Analysis ◽  
Gravitational Forces ◽  
External Forces ◽  
High Level ◽  
The Magnetic Field

The present manuscript focuses on the study of surface wave propagation in a rotating coated viscoelastic half-space and its response to external forces comprised of the magnetic field and gravitational forces. A celebrated normal mode analysis procedure is adopted as the methodology of interest for its high level of efficiency in the literature. The analytically obtained frequency equation is analyzed for certain scenarios of curiosity, in addition to the determination of the resulting displacements and stresses. Moreover, certain physical data of relevance with the viscoelasticity index of unity are considered for the numerical simulations. As for the findings, the presented graphical illustrations showed that both the magnetic field and rotation positively accelerated the dispersion of surface waves in the coated half-space, while the obtained approximate fields in the half-space are found to be oscillatory as they steadily move towards the limiting point.

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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