Structural features and rare earth ion clustering behavior in lanthanum phosphate and aluminophosphate glasses from molecular dynamics simulations

Molecular dynamics simulations are used to examine the molecular microstructures and the “clustering” behavior of supercritical water at 400 °C and different densities.

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Cluster, Surface and Bulk Properties of ZnCd Binary Alloys: Molecular-Dynamics Simulations

Materials Science Forum ◽

10.4028/www.scientific.net/msf.502.51 ◽

2005 ◽

Vol 502 ◽

pp. 51-56 ◽

Cited By ~ 1

Author(s):

Sakir Erkoc

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Density Functional ◽

Structural Features ◽

Bulk Materials ◽

Bulk Properties ◽

Atom Clusters ◽

Dynamics Simulations ◽

Mixed Clusters ◽

Stable Structures

The structural and electronic properties of isolated neutral ZnmCdn clusters for m+n £ 3 have been investigated by performing density functional theory calculations at B3LYP level. The optimum geometries, vibrational frequencies, electronic structures, and the possible dissosiation channels of the clusters considered have been obtained. An empirical many-body potential energy function (PEF), which comprices two- and three-body atomic interactions, has been developed to investigate the structural features and energetics of ZnmCdn (m+n=3,4) microclusters. The most stable structures were found to be triangular for the three-atom clusters and tetrahedral for the four-atom clusters. On the other hand, the structural features and energetics of Znn-mCdm (n=7,8) microclusters, and Zn50, Cd50, Zn25Cd25, Zn12Cd38, and Zn38Cd12 nanoparticles have been investigated by performing molecular-dynamics computer simulations using the developed PEF. The most stable structures were found to be compact and three-dimensional for all elemental and mixed clusters. An interesting structural feature of the mixed clusters is that Zn and Cd atoms do not mix in mixed clusters, they come together almost without mixing. Surface and bulk properties of Zn, Cd, and ZnCd systems have been investigated too by performing molecular-dynamics simulations using the developed PEF. Surface reconstruction and multilayer relaxation on clean surfaces, adatom on surface, substitutional atom on surface and bulk materials, and vacancy on surface and bulk materials have been studied extensively.

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Mechanistic and Structural Insights on the IL-15 System through Molecular Dynamics Simulations

Molecules ◽

10.3390/molecules24183261 ◽

2019 ◽

Vol 24 (18) ◽

pp. 3261

Author(s):

Sousa ◽

Laurent ◽

Quéméner ◽

Mortier ◽

Questel

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Structural Features ◽

Cellular Functions ◽

Α Subunit ◽

X Ray Crystallography ◽

Receptor Complexes ◽

Protein Interfaces ◽

Dynamics Simulations ◽

Comparison Of The Results

Interleukin 15 (IL-15), a four-helix bundle cytokine, is involved in a plethora of different cellular functions and, particularly, plays a key role in the development and activation of immune responses. IL-15 forms receptor complexes by binding with IL-2Rβ- and common γ(γc)-signaling subunits, which are shared with other members of the cytokines family (IL-2 for IL-2Rβ- and all other γc- cytokines for γc). The specificity of IL-15 is brought by the non-signaling α-subunit, IL-15Rα. Here we present the results of molecular dynamics simulations carried out on four relevant forms of IL-15: its monomer, IL-15 interacting individually with IL-15Rα (IL-15/IL-15Rα), with IL-2Rβ/γc subunits (IL-15/IL-2Rβ/γc) or with its three receptors simultaneously (IL-15/IL-15Rα/IL-2Rβ/γc). Through the analyses of the various trajectories, new insights on the structural features of the interfaces are highlighted, according to the considered form. The comparison of the results with the experimental data, available from X-ray crystallography, allows, in particular, the rationalization of the importance of IL-15 key residues (e.g. Asp8, Lys10, Glu64). Furthermore, the pivotal role of water molecules in the stabilization of the various protein-protein interfaces and their H-bonds networks are underlined for each of the considered complexes.

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The Bearings from Rare-Earth (RE = La, Lu, Sc, Y) Cations on the Oxygen Environments in Aluminosilicate Glasses: A Study by Solid-State 17O NMR, Molecular Dynamics Simulations, and DFT Calculations

The Journal of Physical Chemistry C ◽

10.1021/acs.jpcc.6b02032 ◽

2016 ◽

Vol 120 (24) ◽

pp. 13181-13198 ◽

Cited By ~ 18

Author(s):

Aleksander Jaworski ◽

Baltzar Stevensson ◽

Mattias Edén

Keyword(s):

Molecular Dynamics ◽

Rare Earth ◽

Solid State ◽

Dft Calculations ◽

Molecular Dynamics Simulations ◽

17O Nmr ◽

Aluminosilicate Glasses ◽

Dynamics Simulations

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Insight into the Structure and Dynamics of Polymers by Neutron Scattering Combined with Atomistic Molecular Dynamics Simulations

Polymers ◽

10.3390/polym12123067 ◽

2020 ◽

Vol 12 (12) ◽

pp. 3067

Author(s):

Arantxa Arbe ◽

Fernando Alvarez ◽

Juan Colmenero

Keyword(s):

Molecular Dynamics ◽

Neutron Scattering ◽

Molecular Dynamics Simulations ◽

Structural Features ◽

Length Scales ◽

Polymeric Systems ◽

Structure And Dynamics ◽

Dynamical Features ◽

Dynamics Simulations ◽

Insight Into

Combining neutron scattering and fully atomistic molecular dynamics simulations allows unraveling structural and dynamical features of polymer melts at different length scales, mainly in the intermolecular and monomeric range. Here we present the methodology developed by us and the results of its application during the last years in a variety of polymers. This methodology is based on two pillars: (i) both techniques cover approximately the same length and time scales and (ii) the classical van Hove formalism allows easily calculating the magnitudes measured by neutron scattering from the simulated atomic trajectories. By direct comparison with experimental results, the simulated cell is validated. Thereafter, the information of the simulations can be exploited, calculating magnitudes that are experimentally inaccessible or extending the parameters range beyond the experimental capabilities. We show how detailed microscopic insight on structural features and dynamical processes of various kinds has been gained in polymeric systems with different degrees of complexity, and how intriguing questions as the collective behavior at intermediate length scales have been faced.

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