A molecular dynamics model of melting and glass transition in an idealized two-dimensional material I

In a preparatory study of structural relaxations and plastic flow in a two-dimensional idealized atomic glass, the process of melting and quenching through a glass transition has been studied by computer simulation using a molecular dynamics model. In this model, the transition from a solid to a melt was observed to take place when liquid-like structural elements composed of dipoles of five- and seven-sided Voronoi polygons percolate through the two-dimensional structure of distorted hexagons in the form of strings. Such dipoles constitute discrete elements of excess free volume within which liquid like behaviour is established in the sense of reduced cohesion or local elastic moduli. Upon quenching the melt, the percolation condition of liquid-like regions is retained for under-cooled melts between the melting point and a glass transition temperature below which the percolation condition is broken and the thermal expansion is sharply reduced. The simulation that has used empirical pair potentials characteristic of Cu and Zr has substantially underpredicted the melting and glass transition temperatures and overpredicted the thermal expansion of C u x Zr 1-x type glasses. These defects of the model can be partly attributed to the two-dimensional nature of the material, which stores larger concentrations of free volume than a corresponding three-dimensional material. In spite of these quantitative shortcomings, the model gives valuable insight into the topological features of the local atomic configurations at melting and upon vitrification.

2018 ◽  
Vol 60 (5) ◽  
pp. 846
Author(s):  
Г.М. Полетаев ◽  
Д.В. Новоселова ◽  
И.В. Зоря ◽  
М.Д. Старостенков

AbstractThe formation of an excess free volume in triple junctions during crystallization has been studied by the molecular dynamics model using nickel as an example. It is shown that an excess free volume that forms during nickel crystallization in triple junctions predominantly forms as a result of the fixation of the liquid phase volume when contacting three crystallization fronts that contains, after crystallization, a high fraction of the free volume. In some cases, as the free volume is concentrated in triple junctions, a comparatively small crystalline subgrain (from one to several nanometers in diameter) forms, and the subgrain has the orientation different from those of contacting grains and exists in the extended state.


1990 ◽  
Vol 202 ◽  
Author(s):  
M. Karimi ◽  
P. Tibbits ◽  
D. Ila ◽  
I. Dalins ◽  
G. Vidali

ABSTRACTIsothermal-isobaric Molecular Dynamics (MD) simulation of a submonolayer Pb film in c(2×2) ordered structure adsorbed on a Cu(100) substrate showed retention of order to high T. The Embedded Atom Method (EAM) calculated the energy of atoms of overlayer and substrate. The time-averaged squared modulus of the two dimensional structure factor for the Pb overlayer measured the order of the overlayer. The results are for increasing T only, and require verification by simulated cooling.


The kinetics of structural relaxation in a two-dimensional model atomic glass quenched infinitely rapidly from the melt to 0.55 of the glass transition tem perature was simulated by the molecular dynamics methods to study the chronological ordering of the atomic kinematics associated with such relaxations. Over the very short periods of ageing ( ca .200 atomic fluctuations) accessible to the molecular dynamics (MD) method, a Williams-Watts form of relaxation with a fractional exponent of 0.5 was found to hold for excess enthalpy, free volume and site distortion parameter. The distribution of free energy barriers associated with the relaxation that resulted from the analysis could be scaled up to describe processes occurring on macroscopic timescales, and agrees well with experimental results in Cu x Zr 1-x glasses. Results on the clustering of relaxations and other topological features of the relaxation process are also reported.


1998 ◽  
Vol 12 (29n31) ◽  
pp. 3091-3094
Author(s):  
Taner Edis ◽  
J. D. Fan ◽  
D. Bagayoko ◽  
J. T. Wang

The anisotropic radial distribution function and two-dimensional (2D) structure factor was calculated for the Cu-1 plane in YBa2Cu3O 6+x when x ≈ 0, based on data generated by a molecular dynamics simulation. The results indicate a stable square lattice and support the validity of layered two-dimensional screened Coulomb potential used in the simulation.


Crystals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 238 ◽  
Author(s):  
Lu Xie ◽  
Tingwei Sun ◽  
Chenwei He ◽  
Haojie An ◽  
Qin Qin ◽  
...  

The PSI-graphene, a two-dimensional structure, was a novel carbon allotrope. In this paper, based on molecular dynamics simulation, the effects of stretching direction, temperature and vacancy defects on the mechanical properties of PSI-graphene were studied. We found that when PSI-graphene was stretched along 0° and 90° at 300 K, the ultimate strength reached a maximum of about 65 GPa. And when stretched along 54.2° and 155.2° at 300 K, the Young’s modulus had peaks, which were 1105 GPa and 2082 GPa, respectively. In addition, when the temperature was raised from 300 K to 900 K, the ultimate strength in all directions was reduced. The fracture morphology of PSI-graphene stretched at different angles was also shown in the text. In addition, the number of points removed from PSI-graphene sheet also seriously affected the tensile properties of the material. It was found that, compared with graphene, PSI-graphene didn’t have the negative Poisson’s ratio phenomenon when it was stretched along the direction of 0°, 11.2°, 24.8° and 34.7°. Our results provided a reference for studying the multi-angle stretching of other carbon structures at various temperatures.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11951
Author(s):  
Suparna Ghosh ◽  
Seketoulie Keretsu ◽  
Seung Joo Cho

Rho-associated kinase-1 (ROCK1) has been recognized for its pivotal role in heart diseases, different types of malignancy, and many neurological disorders. Hyperactivity of ROCK phosphorylates the protein kinase-C (PKC), which ultimately induces smooth muscle cell contraction in the vascular system. Inhibition of ROCK1 has been shown to be a promising therapy for patients with cardiovascular disease. In this study, we have conducted molecular modeling techniques such as docking, molecular dynamics (MD), and 3-Dimensional structure-activity relationship (3D-QSAR) on a series of N-ethyl-4-(pyridin-4-yl)benzamide-based compounds. Docking and MD showed critical interactions and binding affinities between ROCK1 and its inhibitors. To establish the structure-activity relationship (SAR) of the compounds, 3D-QSAR techniques such as Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) were used. The CoMFA (q2 = 0.774, r2 = 0.965, ONC = 6, and ${r}_{pred}^{2}$ = 0.703) and CoMSIA (q2 = 0.676, r2 = 0.949, ONC = 6, and ${r}_{pred}^{2}$ = 0.548) both models have shown reasonable external predictive activity, and contour maps revealed favorable and unfavorable substitutions for chemical group modifications. Based on the contour maps, we have designed forty new compounds, among which, seven compounds exhibited higher predictive activity (pIC50). Further, we conducted the MD study, ADME/Tox, and SA score prediction using the seven newly designed compounds. The combination of docking, MD, and 3D-QSAR studies helps to understand the coherence modification of existing molecules. Our study may provide valuable insight into the development of more potent ROCK1 inhibitors.


The topological features of atom motions in a high-temperature melt, a sub-cooled melt above T g , and a glass below T g , were analysed in detail by means of a two-dimensional molecular dynamics simulation. A striking analogy was observed between the structure and properties of the liquid-like material separating quasi-ordered domains of atom clusters, and high-angle grain boundaries. The main feature of the structural relaxation below the melting point, both above and below T g was the gradual dissolution and disappearance of the liquid-like material, permitting increasing order in the previously quasi-ordered domains and a growth in their sizes. In these processes, many sequences reminiscent of cancellation of dislocation pairs, or mutual reactions to give more stable sets, were observed.


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