A computer simulation of the structure and elastic properties of MgSiO3 perovskite

1986 ◽  
Vol 50 (358) ◽  
pp. 693-707 ◽  
Author(s):  
A. Wall ◽  
G. D. Price ◽  
S. C. Parker
Keyword(s):  
Elastic Properties ◽  
Minimum Energy ◽  
Orthorhombic Phase ◽  
Cubic Phase ◽  
Energy Structure ◽  
Interatomic Potentials ◽  
Short Range Potential ◽  
Pair Potentials ◽  
Mgsio3 Perovskite ◽  
Partial Dislocations

AbstractThe structure and elastic properties of MgSiO3, a major mantle-forming phase, have been simulated using computer models which predict the minimum energy structure by using interatomic pair potentials to describe the net forces acting between the atoms. Four such interatomic potentials were developed in this study, and are compared with potential N1 of Miyamoto and Takeda (1984). The most successful potential (W3) was derived by fitting the short range potential parameters to both the experimentally obtained structural and elastic properties of MgSiO3 perovskite. The relative stabilities of some of the possible perovskite polymorphs, the orthorhombic, cubic, and tetragonal phases and hexagonal polytypes, were evaluated at 0 K and between 1 bar and 2 Mbar. The orthorhombic phase is found to be stable at all but the highest pressures, where the cubic phase may be stable. The temperature of the ortho-rhombic to cubic transition may decrease with increasing pressure. The energy of a stacking fault on (110) in the cubic phase was estimated using the ANNNI model and found to be about 1.95 J m−2 using potential W3. The distance of separation of partial dislocations of this type is predicted to increase with increasing pressure from 8.4 Å at 1 bar to 9.2 Å at 1 Mbar.

scholarly journals RNA Secondary Structures with Limited Base Pair Span: Exact Backtracking and an Application

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 14
Author(s):  
Ronny Lorenz ◽  
Peter F. Stadler
Keyword(s):  
Base Pair ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Minimum Energy ◽  
Optimal Structure ◽  
Energy Structure ◽  
C Elegans ◽  
Z Scores ◽  
Limited Base ◽  
Optimal Span

The accuracy of RNA secondary structure prediction decreases with the span of a base pair, i.e., the number of nucleotides that it encloses. The dynamic programming algorithms for RNA folding can be easily specialized in order to consider only base pairs with a limited span L, reducing the memory requirements to O(nL), and further to O(n) by interleaving backtracking. However, the latter is an approximation that precludes the retrieval of the globally optimal structure. So far, the ViennaRNA package therefore does not provide a tool for computing optimal, span-restricted minimum energy structure. Here, we report on an efficient backtracking algorithm that reconstructs the globally optimal structure from the locally optimal fragments that are produced by the interleaved backtracking implemented in RNALfold. An implementation is integrated into the ViennaRNA package. The forward and the backtracking recursions of RNALfold are both easily constrained to structural components with a sufficiently negative z-scores. This provides a convenient method in order to identify hyper-stable structural elements. A screen of the C. elegans genome shows that such features are more abundant in real genomic sequences when compared to a di-nucleotide shuffled background model.

Structure and Elastic Properties of Ni/Cu and Ni/Au Multilayers

1992 ◽  
Vol 291 ◽  
Author(s):  
Ademola Taiwo ◽  
Hong Yan ◽  
Gretchen Kalonji
Keyword(s):  
Phase Transformation ◽  
Elastic Properties ◽  
Embedded Atom Method ◽  
Interatomic Potentials ◽  
Multilayer Systems ◽  
Lattice Statics ◽  
Embedded Atom ◽  
Hcp Structure ◽  
Fcc Structure ◽  
Coherent Interfaces

ABSTRACTThe structure and elastic properties of Ni/Cu and Ni/Au multilayer systems are investigated as a function of the number of Ni monolayers built into the systems. We employed lattice statics simulations with the interatomic potentials described by the embedded-atom method. For the Ni/Cu systems, coherent interfaces and FCC structure are maintained, and no elastic anomaly is found. For the Ni/Au systems, when the Ni layers are thick enough, they undergo a strain-induced phase transformation from FCC to HCP structure. An enhancement of Young’s modulus of these systems is found to be associated with this structural change.

Phenomena of nonlinear oscillation and special resonance of a dielectric elastomer minimum energy structure rotary joint

2015 ◽  
Vol 106 (13) ◽  
pp. 133504 ◽  
Author(s):  
Jianwen Zhao ◽  
Junyang Niu ◽  
David McCoul ◽  
Zhi Ren ◽  
Qibing Pei
Keyword(s):  
Nonlinear Oscillation ◽  
Minimum Energy ◽  
Dielectric Elastomer ◽  
Energy Structure ◽  
Rotary Joint

Symmetric Electrodes for Solid Fuel Cells Based on Sr-Doped LaFe0.7Ni0.3O3-δ

2017 ◽  
Vol 887 ◽  
pp. 24-31
Author(s):  
Omar Ben Mya ◽  
Mahmoud Omari ◽  
Lucia dos Santos-Gomez ◽  
David Marerro-Lopezd
Keyword(s):  
Fuel Cells ◽  
Solid Fuel ◽  
Chemical Reactivity ◽  
Orthorhombic Phase ◽  
Rietveld Analysis ◽  
Cubic Phase ◽  
Total Conductivity ◽  
Sem Images ◽  
Low Frequencies ◽  
X Ray

Perovskite La1-xSrxFe0.7Ni0.3O3-δ with x = 0.0, 0.1 &0.2 denoted LSFNx has been investigated as potential symmetrical electrode in solid fuel cells (SOFCs). The crystal structure is in pure orthorhombic phase for x = 0.0, orthorhombic-cubic phase coexist for x = 0.1 and pure cubic phase for x = 0.2. Structural properties are studied by X-ray powder diffraction (XRPD), refined by Rietveld analysis. SEM images show the morphology of as prepared and calcined samples either the compatibility between those electrodes and LSGM electrolyte in presence of 50% wt of Ce0.8Gd0.2O2-δ, so that, lower chemical reactivity was found. Total conductivity, impedance in high, medium and low frequencies HF, MF and LF respectively, and resistance polarization (Rp) are determined in air. LaFe0.7Ni0.3O3-δ has a good response in all ranges of frequencies but La0.9Sr0.1Fe0.7Ni0.3O3-δ and La0.8Sr0.2Fe0.7Ni0.3O3-δ have response only in HF and MF and exhibit Rp values as low as LaFe0.7Ni0.3O3-δ .

Conformation and electronic structure of Carbidopa. A QM/MD study

2016 ◽  
Vol 15 (01) ◽  
pp. 1650002
Author(s):  
Ghader M. Sukker ◽  
Nuha Wazzan ◽  
Ashour Ahmed ◽  
Rifaat Hilal
Keyword(s):  
Density Functional ◽  
Minimum Energy ◽  
Geometry Optimization ◽  
Md Simulations ◽  
Energy Structure ◽  
Functional Theory ◽  
Conformational Preferences ◽  
The Density Functional Theory ◽  
Quantum Chemical Topology ◽  
Bonding Characteristics

Carbidopa (CD) is a drug used in combination with L-dopa (LD) in treatment of Parkinson’s disease (PD). CD is an inhibitor for enzyme decarboxylase, yet its mode of action is not entirely known although it is believed to involve enzyme shape recognition. The present work attempts to investigate the conformational preferences of CD. Tight geometry optimization at the density functional theory (DFT)/B3LYP/6-311[Formula: see text]G** level of theory has been carried out. The shallow nature of the potential energy surface (PES) and the presence of several local minima within a small energy range necessitate the launching of DFT-based molecular dynamics (MD) simulations. Two MD experiments were submitted for 35,000 points each. The complete trajectory in time domain of 10.5 ps is analyzed and discussed. The global minimum energy structure of CD is localized and identified by subsequent frequency calculations. The quantum theory of atom in molecules (QTAIMs) is used to extract and compare the quantum chemical topology features of the electron density distribution in CD and LD. Bonding characteristics are analyzed and discussed within the natural bond orbital (NBO) framework.

A Comparative Study of the BJH- and MCYL-Type Potentials Applied to the Gaseous Water Dimer

1991 ◽  
Vol 46 (5) ◽  
pp. 426-432
Author(s):  
Zdenek Slanina
Keyword(s):  
Gas Phase ◽  
Minimum Energy ◽  
Water Dimer ◽  
Energy Structure ◽  
Water Molecules ◽  
Constant Matrix ◽  
Force Constant Matrix ◽  
Molecular Force ◽  
Phase Water ◽  
Derivatives Of

AbstractVarious refined potentials describing the intra- and inter-molecular force fields of water molecules arc used to calculate the properties of the gas-phase water dimer. The intra-molecular parts have been taken from spectroscopic or quantum-chemical sources. The minimum energy structure was found iteratively using the first derivatives of the potential; the force-constant matrix was constructed by numerical difierentation. A quite close agreement between the Bopp-Jancso-Heinzinger and the Matsuoka-Clementi-Yoshimine-Lie potentials is found. The treatment is applied to seven observed water-dimer isotopomeric isomerizations

Modelling the Effect of Conformation on Hydrogen-Atom Abstraction from Peptides

2018 ◽  
Vol 71 (4) ◽  
pp. 257 ◽  
Author(s):  
Bun Chan ◽  
Leo Radom
Keyword(s):  
Hydrogen Atom ◽  
Minimum Energy ◽  
Experimental Studies ◽  
Constrained Systems ◽  
Hydrogen Atom Abstraction ◽  
Energy Structure ◽  
Peptide Chemistry ◽  
Fundamental Information ◽  
Peptide Models ◽  
Small Models

Computational quantum chemistry is used to examine the effect of conformation on the kinetics of hydrogen-atom abstraction by HO• from amides of glycine and proline as peptide models. In accord with previous findings, it is found that there are substantial variations possible in the conformations and the corresponding energies, with the captodative effect, hydrogen bonding, and solvation being some of the major features that contribute to the variations. The ‘minimum-energy-structure-pathway’ strategy that is often employed in theoretical studies of peptide chemistry with small models certainly provides valuable fundamental information. However, one may anticipate different reaction outcomes in structurally constrained systems due to modified reaction thermodynamics and kinetics, as demonstrated explicitly in the present study. Thus, using a ‘consistent-conformation-pathway’ approach may indeed be more informative in such circumstances, and in this regard theory provides information that would be difficult to obtain from experimental studies alone.

Ab initio study of the minimum-energy structure of trans-azobenzene

2002 ◽  
Vol 360 (3-4) ◽  
pp. 349-354 ◽  
Author(s):  
Noriyuki Kurita ◽  
Tsutomu Ikegami ◽  
Yasuyuki Ishikawa
Keyword(s):  
Ab Initio ◽  
Minimum Energy ◽  
Energy Structure ◽  
Ab Initio Study ◽  
Trans Azobenzene
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