Computational Simulations of Li Ion Conduction in (Li,La)TiO3

2006 ◽  
Vol 320 ◽  
pp. 275-278 ◽  
Author(s):  
Toyoki Okumura ◽  
Ayumi Dodomi ◽  
Morihiro Saito ◽  
Jun Kuwano
Keyword(s):  
Molecular Dynamics ◽  
Neutron Diffraction ◽  
First Principles ◽  
Pair Correlation ◽  
Md Simulations ◽  
Computational Simulations ◽  
Nmr Studies ◽  
Local Environments ◽  
Li Ion ◽  
A Site

The locations and local environments of the Li ions in La0.56Li0.33TiO3 have been investigated by classical molecular dynamics (MD) simulations and first-principles (FP) calculations. The pair correlation functions of Li-O and Li-Ti indicate that the Li ions are located somewhat broadly mainly in the vicinity of the midpoint between the center of the A-site and the center of the bottleneck formed by four O2-. This is consistent well with that suggested from previous neutron diffraction and 6Li-NMR studies. The FP calculations suggest a different location of the Li ion in the vicinity of the midpoint between the centers of two adjcent bottlenecks; however it coincides with one of the locations shown by the trajectories simulated with the MD calculations.

Na ion dynamics in P2-Nax[Ni1/3Ti2/3]O2: a combination of quasi-elastic neutron scattering and first-principles molecular dynamics study

2020 ◽  
Vol 8 (47) ◽  
pp. 25290-25297
Author(s):  
Qian Chen ◽  
Niina H. Jalarvo ◽  
Wei Lai
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
First Principles ◽  
Md Simulations ◽  
First Principle ◽  
Ion Dynamics ◽  
Elastic Neutron ◽  
Elastic Neutron Scattering ◽  
First Principles Molecular Dynamics

The Na dynamics in P2-Nax[Ni1/3Ti2/3]O2 were investigated through a combination of QENS experiments and first-principle MD simulations.

A-Site Distribution in La1−xSrxMnO3: a Computational Study

2008 ◽  
Vol 1074 ◽  
Author(s):  
Yun Hee Jang ◽  
François Gervais ◽  
Yves Lansac
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Colossal Magnetoresistance ◽  
Computational Study ◽  
Mixed Valence ◽  
Magnetic Tunnel Junction ◽  
Md Simulations ◽  
Site Distribution ◽  
Mixed Valence Manganites ◽  
A Site

ABSTRACTThe possibility of an A-site (La3+/Sr2+) ordering in a colossal magnetoresistance manganite (CMR) La3/4Sr1/4MnO3 was explored using molecular dynamics (MD) simulations with a newly developed force field (FF) and quantum mechanics (QM) calculations on the structures obtained from MD. The calculated degrees of stabilization (enthalpy gain) of various patterns of A-site ordering are not significant enough to overcome the accompanying entropy loss, supporting the random A-site distribution in La3/4Sr1/4MnO3. This approach combining MD and QM as well as the versatile FF developed in this study should be useful to investigate the structures and functions of magnetic tunnel junction devices involving mixed-valence manganites.

scholarly journals Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations

2018 ◽  
Author(s):  
Michael Wall ◽  
Gaetano Calabró ◽  
Christopher I. Bayly ◽  
David Mobley ◽  
Gregory Warren
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Neutron Diffraction ◽  
Water Structure ◽  
Md Simulations ◽  
Neutron Density ◽  
Macromolecular Crystallography ◽  
Field Development ◽  
Biomolecular Solvation ◽  
Dynamics Simulations

In order to compare ordered water positions from experiment with those from molecular dynamics (MD) simulations, a number of MD models of water structure in crystalline endoglucanase were calculated. The starting MD model was derived from a joint X-ray and neutron diffraction crystal structure, enabling the use of experimentally assigned protonation states. Simulations were performed in the crystalline state, using a periodic 2x2x2 supercell with explicit solvent. Water electron and neutron density maps were computed from MD trajectories using standard macromolecular crystallography methods. In one set of simulations, harmonic restraints were applied to bias the protein structure toward the crystal structure. For these simulations, the recall of crystallographic waters using strong peaks in the MD water electron density was excellent, and there also was substantial visual agreement between the boomerang-like wings of the neutron density and the crystalline water hydrogen positions. An unrestrained simulation also was performed. For this simulation, the recall of crystallographic waters was much lower. The results demonstrate that it is now possible to recover crystallographic water structure using restrained MD simulations, but that it is not yet reasonable to expect unrestrained MD simulations to do the same. Further development and generalization of MD water models for force field development, macromolecular crystallography, and medicinal chemistry applications is now warranted. In particular, the combination of room-temperature crystallography, neutron diffraction, and crystalline MD simulations promises to substantially advance modeling of biomolecular solvation.

C2N: an excellent two-dimensional monolayer membrane for He separation

2015 ◽  
Vol 3 (42) ◽  
pp. 21351-21356 ◽  
Author(s):  
Lei Zhu ◽  
Qingzhong Xue ◽  
Xiaofang Li ◽  
Tiantian Wu ◽  
Yakang Jin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
First Principles ◽  
Density Functional ◽  
Md Simulations ◽  
Separation Performance ◽  
Two Dimensional ◽  
Functional Theory

Using the first-principles density functional theory (DFT) and molecular dynamics (MD) simulations, we investigate the He separation performance of a porous C2N monolayer synthesized recently.

Site Balance Models in Plasma Processing: A Comparison to Molecular Dynamics Simulations

1995 ◽  
Vol 389 ◽  
Author(s):  
M.E. Barone ◽  
D.B. Graves
Keyword(s):  
Molecular Dynamics ◽  
Steady State ◽  
Molecular Dynamics Simulations ◽  
Phenomenological Models ◽  
Silicon Surface ◽  
Plasma Processing ◽  
Md Simulations ◽  
Balance Model ◽  
Dynamics Simulations ◽  
A Site

ABSTRACTMolecular dynamics (MD) simulations were conducted of Cl+ impact (at 10, 25 and 50 eV) of an initially bare silicon surface, leading to steady state coverage of Cl in a mixed chlorosilyl layer. Our main goal in this study was to compare the MD predictions to models of ion-assisted etching involving the concept of a site balance. For the case of 50 eV Cl+ etching silicon, the coverage vs. exposure results in the simulation could be reasonably well reproduced in a site balance model, but only if the correct parameters in the model were taken from the simulation. The results of the comparison suggest that MD simulations can be helpful in the development of physically sound phenomenological models of ion-assisted etching.

Molecular dynamics simulations for CL-20/TNT co-crystal based polymer-bonded explosives

2017 ◽  
Vol 16 (08) ◽  
pp. 1750072
Author(s):  
Qiang Cao ◽  
Ji Jun Xiao ◽  
Pei Gao ◽  
Shen Shen Li ◽  
Feng Zhao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Pair Correlation ◽  
Md Simulations ◽  
High Energy ◽  
Binding Energies ◽  
Polymer Binders ◽  
Polymer Bonded Explosives ◽  
Dynamics Simulations ◽  
Theoretical Results ◽  
Crystal Compound

Molecular dynamics (MD) simulations were carried out to study the polymer-bonded explosives (PBXs) where the explosive base was the well-known high energy co-crystal compound, 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexazaisowurtzitane/2,4,6-trinitrotoluene (CL-20/TNT), and the polymer binders were fluorine rubber (F[Formula: see text], fluorine resin (F[Formula: see text], polyvinyl acetate (PVAc) and polystyrene (PS), respectively. The binding energies, pair correlation functions (PCFs) and mechanical properties of the PBXs were reported. According to our theoretical results of binding energies, the compatibility of the PBXs is predicted to be in the following order: CL-20/TNT/PVAc[Formula: see text] CL-20/TNT/F[Formula: see text] [Formula: see text] CL-20/TNT/PS [Formula: see text] CL-20/TNT/F[Formula: see text]. The binding energies of the PBXs on three crystalline surfaces, (100), (001), (010), of the CL-20/TNT co-crystal were also compared: CL-20/TNT(100)[Formula: see text]CL-20/TNT(001)[Formula: see text]CL-20/TNT(010) for F[Formula: see text], F[Formula: see text], and PS; CL-20/TNT(001)[Formula: see text]CL-20/TNT(100)[Formula: see text]CL-20/TNT(010) for PVAc. The PCF analysis reveals that there exist H-bonds between H and O, F, and N atoms on all three interfaces and among all H-bonds, N H-bond has the fewest number. For the CL-20/TNT co-crystal, the moduli can be reduced by adding a small amount of the polymer binders but the ductility can be prolonged only by F[Formula: see text] and F[Formula: see text].

scholarly journals Aβ Fibrils Can Act as Aqueous Pores: a Molecular Dynamics Study

2018 ◽  
Author(s):  
S. Natesh ◽  
J. R. Sachleben ◽  
T. R Sosnick ◽  
K. F. Freed ◽  
S. C. Meredith ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Rotational Symmetry ◽  
Md Simulations ◽  
Salt Bridges ◽  
Nmr Studies ◽  
Explicit Solvent ◽  
Hydrogen Deuterium ◽  
A Cell ◽  
Aβ Fibrils ◽  
Bidirectional Flow

AbstractAggregation of Aβ peptides is important in the etiology of Alzheimer’s Disease (AD), an increasingly prevalent neurodegenerative disease. We ran multiple ∼ 300 ns all-atom explicit solvent molecular dynamics (MD) simulations starting from three NMR-based structural models of Aβ(1-40 residues) fibrils having 2-fold (pdb code 2LMN) or 3-fold rotational symmetry (2LMP, and 2M4J). The 2M4J structure is based on an AD brain-seeded fibril whereas 2LMP and 2LMN represent two all-synthetic fibrils. Fibrils are constructed to contain either 6 or an infinite number of layers made using periodic images. The 6 layer fibrils partially unravel over the simulation time, mainly at their ends, while infinitely long fibrils do not. Once formed, the D23-K28 salt bridges are very stable and form within and between chains. Fibrils tend to retain (2LMN and 2LMP) or develop (2M4J) a “stagger” or register shift of β-strands along the fibril axis. The brain-seeded fibril rapidly develops gaps at the sides of the fibril, which allows bidirectional flow of water and ions from the bulk phase in and out the central longitudinal core of the fibril. Similar but less marked changes were also observed for the 2LMP fibrils. The residues defining the gaps largely coincide with those demonstrated to have relatively rapid Hydrogen-Deuterium exchange in solid state NMR studies. These observations suggest that Aβ(1-40 residues) fibrils may act as aqueous pores that might disrupt water and ion fluxes if inserted into a cell membrane.

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