normal mode analysis
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2022 ◽  
Vol 17 ◽  
pp. 10-18
Author(s):  
Pardeep Kumar

The thermal convection of a plasma in porous medium is investigated in the presence of finite Larmor radius (FLR) and Hall effects. Following linear stability theory and normal mode analysis method, the dispersion relation is obtained. It is found that the presence of a magnetic field (and hence the presence of FLR and Hall effects) introduces oscillatory modes in the system which were, otherwise, non-existent in their absence. When the instability sets in as stationary convection, the FLR may have a stabilizing or destabilizing effect, but a completely stabilizing one for a certain wave-number range. Similarly, the Hall currents may have a stabilizing or destabilizing effect but a completely stabilizing one for the same wave-number range under certain condition, whereas the medium permeability always has a destabilizing effect for stationary convection. Also it is found that the system is stable for 𝑔𝛼𝜅 𝜈𝛽 ≤ 27𝜋 4 4 and under the condition 𝑔𝛼𝜅 𝜈𝛽 > 27𝜋 4 4 , the system becomes unstable.


Author(s):  
Tim Gebler ◽  
Dominik Plümacher ◽  
Judith Kahle ◽  
Martin Oberlack

Abstract We investigate the two-dimensional (2D) stability of rotational shear flows in an unbounded domain. The eigenvalue problem is formulated by using a novel algebraic mode decomposition distinct from the normal modes with temporal evolution $\exp(\omega t)$. Based on the work of \citeasnoun{NoldOberlack2013}, we show how these new modes can be constructed from the symmetries of the linearized stability equation. For the azimuthal base flow velocity $V(r)=r^{-1}$ an additional symmetry exists, such that a mode with algebraic temporal evolution $t^s$ is found. $s$ refers to an eigenvalue for the algebraic growth or decay of the kinetic energy of the perturbations. An eigenvalue problem for the viscous and inviscid stability using algebraic modes is formulated on an infinite domain with $r \to \infty$. An asymptotic analysis of the eigenfunctions shows that the flow is linearly stable under 2D perturbations. We find stable modes with the algebraic mode ansatz, which can not be obtained by a normal mode analysis. The stability results are in line with Rayleigh's inflection point theorem.


Author(s):  
Xing Nie ◽  
Yong Yang ◽  
Tianlv Xu ◽  
Malgorzata Biczysko ◽  
Steven Kirk ◽  
...  

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.


Author(s):  
Yanxing Zhang ◽  
Wei Wang ◽  
Yudong Wang ◽  
Nengneng Xu ◽  
guang tian ◽  
...  

Abstract Praseodymium nickelate, Pr2NiO4 (PNO), is a promising electrode to promote oxygen reduction reaction (ORR) in a solid oxide fuel cell, but it exhibits phase transformation during electrochemical operation. The origins of the simultaneous phase transformation and high electrochemical performance still remain obscure. We carried out a systematic density functional theory study to elucidate the mechanism for this conjugated phenomenon. Both electronic structure/charge and normal-mode analysis suggest the presence of peroxide. Our study shows that the formation of peroxide (O22-) is attributed to both oxygen interstitials and Pr vacancies. The peroxide species limits the oxygen ion migration due to the additional energy required to break its O-O bond, which leads to a decrease in ORR activity. Subsequently, we investigate the diffusion paths of Pr-ions while comparing them with those of other Ln3+ ions (La, Nd, Pm, Sm, Gd, Tb, Dy, and Ho) in PNO. The formation energies for various Ln3+ cation occupancies are calculated, as well as segregation energies in CeO2(111) surfaces. Finally, criteria for effective Ln3+ dopants are developed. La, Nd, and Pm are proposed as potential substituents in PNO to obtain a stable structure.


2021 ◽  
Vol 5 (4) ◽  
pp. 250
Author(s):  
Ali Mubaraki ◽  
Saad Althobaiti ◽  
Rahmatullah Ibrahim Nuruddeen

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.


Open Biology ◽  
2021 ◽  
Vol 11 (12) ◽  
Author(s):  
Nehad Noby ◽  
Husam Sabah Auhim ◽  
Samuel Winter ◽  
Harley L. Worthy ◽  
Amira M. Embaby ◽  
...  

Here we determined the structure of a cold active family IV esterase (EstN7) cloned from Bacillus cohnii strain N1. EstN7 is a dimer with a classical α/β hydrolase fold. It has an acidic surface that is thought to play a role in cold-adaption by retaining solvation under changed water solvent entropy at lower temperatures. The conformation of the functionally important cap region is significantly different to EstN7's closest relatives, forming a bridge-like structure with reduced helical content providing greater access to the active site through more than one substrate access tunnel. However, dynamics do not appear to play a major role in cold adaption. Molecular dynamics at different temperatures, rigidity analysis, normal mode analysis and geometric simulations of motion confirm the flexibility of the cap region but suggest that the rest of the protein is largely rigid. Rigidity analysis indicates the distribution of hydrophobic tethers is appropriate to colder conditions, where the hydrophobic effect is weaker than in mesophilic conditions due to reduced water entropy. Thus, it is likely that increased substrate accessibility and tolerance to changes in water entropy are important for of EstN7's cold adaptation rather than changes in dynamics.


2021 ◽  
pp. 4039-4055
Author(s):  
N. Manjunatha ◽  
R. Sumithra

The problem of non-Darcian-Bènard double diffusive magneto-Marangoni convection   is considered in a horizontal infinite two layer system. The system consists of a two-component fluid layer placed above a porous layer, saturated with the same fluid with a constant heat sources/sink in both the layers, in the presence of a vertical magnetic field.   The lower porous layer is bounded by rigid boundary, while the upper boundary of the fluid region is free with the presence of Marangoni effects.  The system of ordinary differential equations obtained after normal mode analysis is solved in a closed form for the eigenvalue and the Thermal Marangoni Number (TMN) for two cases of Thermal Boundary Combinations (TBC); these are type (i) Adiabatic-Adiabatic and type (ii) Adiabatic-Isothermal.  The corresponding two TMNs   are obtained and the impacts of the porous parameter, solute Marangoni number, modified internal Rayleigh numbers, viscosity ratio, and the diffusivity ratios on the non-Darcian-Bènard double diffusive magneto - Marangoni convection are studied in detail.


Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1761
Author(s):  
Vladimir Camel ◽  
Gaston Zolla

RuBisCO is the most abundant enzyme on earth; it regulates the organic carbon cycle in the biosphere. Studying its structural evolution will help to develop new strategies of genetic improvement in order to increase food production and mitigate CO2 emissions. In the present work, we evaluate how the evolution of sequence and structure among isoforms I, II and III of RuBisCO defines their intrinsic flexibility and residue-residue interactions. To do this, we used a multilevel approach based on phylogenetic inferences, multiple sequence alignment, normal mode analysis, and molecular dynamics. Our results show that the three isoforms exhibit greater fluctuation in the loop between αB and βC, and also present a positive correlation with loop 6, an important region for enzymatic activity because it regulates RuBisCO conformational states. Likewise, an increase in the flexibility of the loop structure between αB and βC, as well as Lys330 (form II) and Lys322 (form III) of loop 6, is important to increase photosynthetic efficiency. Thus, the cross-correlation dynamics analysis showed changes in the direction of movement of the secondary structures in the three isoforms. Finally, key amino acid residues related to the flexibility of the RuBisCO structure were indicated, providing important information for its enzymatic engineering.


PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0258818
Author(s):  
Byung Ho Lee ◽  
Soon Woo Park ◽  
Soojin Jo ◽  
Moon Ki Kim

Large-scale conformational changes are essential for proteins to function properly. Given that these transition events rarely occur, however, it is challenging to comprehend their underlying mechanisms through experimental and theoretical approaches. In this study, we propose a new computational methodology called internal coordinate normal mode-guided elastic network interpolation (ICONGENI) to predict conformational transition pathways in proteins. Its basic approach is to sample intermediate conformations by interpolating the interatomic distance between two end-point conformations with the degrees of freedom constrained by the low-frequency dynamics afforded by normal mode analysis in internal coordinates. For validation of ICONGENI, it is applied to proteins that undergo open-closed transitions, and the simulation results (i.e., simulated transition pathways) are compared with those of another technique, to demonstrate that ICONGENI can explore highly reliable pathways in terms of thermal and chemical stability. Furthermore, we generate an ensemble of transition pathways through ICONGENI and investigate the possibility of using this method to reveal the transition mechanisms even when there are unknown metastable states on rough energy landscapes.


2021 ◽  
Vol 55 (6) ◽  
pp. 927-940
Author(s):  
V. M. Golyshev ◽  
D. V. Pyshnyi ◽  
A. A. Lomzov

Abstract The development of approaches for predictive calculation of hybridization properties of various nucleic acid (NA) derivatives is the basis for the rational design of the NA-based constructs. Modern advances in computer modeling methods provide the feasibility of these calculations. We have analyzed the possibility of calculating the energy of DNA/RNA and RNA/RNA duplex formation using representative sets of complexes (65 and 75 complexes, respectively). We used the classical molecular dynamics (MD) method, the MMPBSA or MMGBSA approaches to calculate the enthalpy (ΔH°) component, and the quasi-harmonic approximation (Q-Harm) or the normal mode analysis (NMA) methods to calculate the entropy (ΔS°) contribution to the Gibbs energy ($$\Delta G_{{37}}^{^\circ }$$ ) of the NA complex formation. We have found that the MMGBSA method in the analysis of the MD trajectory of only the NA duplex and the empirical linear approximation allow calculation of the enthalpy of formation of the DNA, RNA, and hybrid duplexes of various lengths and GC content with an accuracy of 8.6%. Within each type of complex, the combination of rather efficient MMGBSA and Q-Harm approaches being applied to the trajectory of only the bimolecular complex makes it possible to calculate the $$\Delta G_{{37}}^{^\circ }$$ of the duplex formation with an error value of 10%. The high accuracy of predictive calculation for different types of natural complexes (DNA/RNA, DNA/RNA, and RNA/RNA) indicates the possibility of extending the considered approach to analogs and derivatives of nucleic acids, which gives a fundamental opportunity in the future to perform rational design of new types of NA-targeted sequence-specific compounds.


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