scholarly journals Formation of Dislocations in the Growth of Silicon along Different Crystallographic Directions—A Molecular Dynamics Study

Crystals ◽  
2018 ◽  
Vol 8 (9) ◽  
pp. 346 ◽  
Author(s):  
Naigen Zhou ◽  
Xiuqin Wei ◽  
Lang Zhou
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Atomic Interaction ◽  
Seed Crystals ◽  
Dynamics Simulations ◽  
Dislocation Formation

Molecular dynamics simulations of the seeded solidification of silicon along <100>, <110>, <111> and <112> directions have been carried out. The Tersoff potential is adopted for computing atomic interaction. The control of uniaxial strains in the seed crystals is enabled in the simulations. The results show that the dislocation forms stochastically at the crystal/melt interface, with the highest probability of the formation in <111> growth, which agrees with the prediction from a previously proposed twinning-associated dislocation formation mechanism. Applications of the strains within a certain range are found to inhibit the {111}-twinning-associated dislocation formation, while beyond this range they are found to induce dislocation formation by different mechanisms.

scholarly journals Formation mechanism of bound rubber in elastomer nanocomposites: a molecular dynamics simulation study

RSC Advances ◽  
2018 ◽  
Vol 8 (23) ◽  
pp. 13008-13017 ◽  
Author(s):  
Jun Liu ◽  
Haixiao Wan ◽  
Huanhuan Zhou ◽  
Yancong Feng ◽  
Liqun Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Bound Rubber ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

The formation mechanism of the bound rubber in elastomer nanocomposites using the coarse-grained molecular-dynamics simulations.

Photoluminescent organic polymer nanofilms formed in water through a self-assembly formation mechanism

2019 ◽  
Vol 7 (11) ◽  
pp. 3286-3293 ◽  
Author(s):  
Baoxi Feng ◽  
Zhen Xu ◽  
Jiayu Wang ◽  
Fei Feng ◽  
Lin Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Real Time ◽  
Formation Mechanism ◽  
Self Assembly ◽  
Organic Polymer ◽  
Assembly Mechanism ◽  
Real Time Visualization ◽  
Dynamics Simulations

A self-assembly mechanism is demonstrated for the formation of polymer nanofilms based on real-time visualization and molecular dynamics simulations.

scholarly journals Self-assembly of endohedral metallofullerenes: a decisive role of cooling gas and metal–carbon bonding

Nanoscale ◽  
2016 ◽  
Vol 8 (6) ◽  
pp. 3796-3808 ◽  
Author(s):  
Qingming Deng ◽  
Thomas Heine ◽  
Stephan Irle ◽  
Alexey A. Popov
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Self Assembly ◽  
Crucial Role ◽  
Decisive Role ◽  
Endohedral Metallofullerenes ◽  
Dynamics Simulations ◽  
Carbon Bonding

Molecular dynamics simulations of the endohedral metallofullerene formation reveal a crucial role of the cooling gas (He) and the strength of metal–carbon bonding in the formation mechanism.

Improving the productivity of monodisperse polyhedral cages by the rational design of kinetic self-assembly pathways

2018 ◽  
Vol 20 (15) ◽  
pp. 10030-10037
Author(s):  
Xiangze Zeng ◽  
Zhan-Wei Li ◽  
Xiaoyan Zheng ◽  
Lizhe Zhu ◽  
Zhao-Yan Sun ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Self Assembly ◽  
Rational Design ◽  
Network Models ◽  
Coarse Grained ◽  
Patchy Particles ◽  
Dynamics Simulations ◽  
Assembly Pathways

By constructing kinetic network models from extensive coarse-grained molecular dynamics simulations, we elucidated the formation mechanism of the dodecahedral cage and further improved the productivity of the dodecahedral cage through the rational design of the patch arrangement of patchy particles.

scholarly journals Formation Mechanism of Ion Channel in Channelrhodopsin-2: Molecular Dynamics Simulation and Steering Molecular Dynamics Simulations

2019 ◽  
Vol 20 (15) ◽  
pp. 3780 ◽  
Author(s):  
Ting Yang ◽  
Wenying Zhang ◽  
Jie Cheng ◽  
Yanhong Nie ◽  
Qi Xin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ion Channel ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Binding Sites ◽  
Electrostatic Interactions ◽  
Potential Of Mean Force ◽  
Dynamics Simulation ◽  
Cationic Channel ◽  
Dynamics Simulations

Channelrhodopsin-2 (ChR2) is a light-activated and non-selective cationic channel protein that can be easily expressed in specific neurons to control neuronal activity by light. Although ChR2 has been extensively used as an optogenetic tool in neuroscience research, the molecular mechanism of cation channel formation following retinal photoisomerization in ChR2 is not well understood. In this paper, studies of the closed and opened state ChR2 structures are presented. The formation of the cationic channel is elucidated in atomic detail using molecular dynamics simulations on the all-trans-retinal (ChR2-trans) configuration of ChR2 and its isomerization products, 13-cis-retinal (ChR2-cis) configuration, respectively. Photoisomerization of the retinal-chromophore causes the destruction of interactions among the crucial residues (e.g., E90, E82, N258, and R268) around the channel and the extended H-bond network mediated by numerous water molecules, which opens the pore. Steering molecular dynamics (SMD) simulations show that the electrostatic interactions at the binding sites in intracellular gate (ICG) and central gate (CG) can influence the transmembrane transport of Na+ in ChR2-cis obviously. Potential of mean force (PMF) constructed by SMD and umbrella sampling also found the existing energy wells at these two binding sites during the transportation of Na+. These wells partly hinder the penetration of Na+ into cytoplasm through the ion channel. This investigation provides a theoretical insight on the formation mechanism of ion channels and the mechanism of ion permeation.

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