Molecular dynamics simulation studies on the plastic behaviors of an iron nanowire under torsion

RSC Advances ◽  
2016 ◽  
Vol 6 (34) ◽  
pp. 28792-28800 ◽  
Author(s):  
Chong Qiao ◽  
Yanli Zhou ◽  
Xiaolin Cai ◽  
Weiyang Yu ◽  
Bingjie Du ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Plastic Deformation ◽  
Molecular Dynamics Simulation ◽  
Deformation Mechanism ◽  
Driving Force ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Plastic Deformation Mechanism ◽  
Constant Torsion ◽  
External Driving

The plastic deformation mechanism of iron (Fe) nanowires under torsion is studied using the molecular dynamics (MD) method by applying an external driving force at a constant torsion speed.

scholarly journals Reveal the Deformation Mechanism of (110) Silicon from Cryogenic Temperature to Elevated Temperature by Molecular Dynamics Simulation

Nanomaterials ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 1632
Author(s):  
Jing Han ◽  
Yuanming Song ◽  
Wei Tang ◽  
Cong Wang ◽  
Liang Fang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Plastic Deformation ◽  
Elevated Temperature ◽  
Deformation Mechanism ◽  
Cryogenic Temperature ◽  
Dynamics Simulation ◽  
Structure Evolution ◽  
Load Pressure ◽  
Plastic Deformation Mechanism ◽  
Indentation Strain

Silicon undergoes a brittle-to-ductile transition as its characteristic dimension reduces from macroscale to nanoscale. The thorough understanding of the plastic deformation mechanism of silicon at the nanoscale is still challenging, although it is essential for developing Si-based micro/nanoelectromechanical systems (MEMS/NEMS). Given the wide application of silicon in extreme conditions, it is, therefore, highly desirable to reveal the nanomechanical behavior of silicon from cryogenic temperature to elevated temperature. In this paper, large-scale molecular dynamics (MD) simulations were performed to reveal the spherical nanoindentation response and plastic deformation mechanism of (110)Si at the temperature range of 0.5 K to 573 K. Special attention was paid to the effect of temperature. Multiple pop-ins detected in load/pressure-indentation strain curves are impacted by temperature. Four featured structures induced by nanoindentation, including high-pressure phases, extrusion of α-Si, dislocations, and crack, are observed at all temperatures, consistent with experiment results. The detailed structure evolution of silicon was revealed at the atomic scale and its dependence on temperature was analyzed. Furthermore, structure changes were correlated with pop-ins in load/pressure-indentation strain curves. These results may advance our understanding of the mechanical properties of silicon.

scholarly journals Computational Investigations on the Binding Mode of Ligands for the Cannabinoid-Activated G Protein-Coupled Receptor GPR18

Biomolecules ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 686 ◽  
Author(s):  
Alexander Neumann ◽  
Viktor Engel ◽  
Andhika B. Mahardhika ◽  
Clara T. Schoeder ◽  
Vigneshwaran Namasivayam ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
G Protein ◽  
Phenyl Ring ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Binding Modes ◽  
G Protein Coupled Receptor ◽  
G Protein Coupled

GPR18 is an orphan G protein-coupled receptor (GPCR) expressed in cells of the immune system. It is activated by the cannabinoid receptor (CB) agonist ∆9-tetrahydrocannabinol (THC). Several further lipids have been proposed to act as GPR18 agonists, but these results still require unambiguous confirmation. In the present study, we constructed a homology model of the human GPR18 based on an ensemble of three GPCR crystal structures to investigate the binding modes of the agonist THC and the recently reported antagonists which feature an imidazothiazinone core to which a (substituted) phenyl ring is connected via a lipophilic linker. Docking and molecular dynamics simulation studies were performed. As a result, a hydrophobic binding pocket is predicted to accommodate the imidazothiazinone core, while the terminal phenyl ring projects towards an aromatic pocket. Hydrophobic interaction of Cys251 with substituents on the phenyl ring could explain the high potency of the most potent derivatives. Molecular dynamics simulation studies suggest that the binding of imidazothiazinone antagonists stabilizes transmembrane regions TM1, TM6 and TM7 of the receptor through a salt bridge between Asp118 and Lys133. The agonist THC is presumed to bind differently to GPR18 than to the distantly related CB receptors. This study provides insights into the binding mode of GPR18 agonists and antagonists which will facilitate future drug design for this promising potential drug target.

scholarly journals Molecular Docking and Molecular Dynamics Simulation Studies of Triterpenes from Vernonia patula with the Cannabinoid Type 1 Receptor

2021 ◽  
Vol 22 (7) ◽  
pp. 3595
Author(s):  
Md Afjalus Afjalus Siraj ◽  
Md. Sajjadur Rahman ◽  
Ghee T. Tan ◽  
Veronique Seidel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Cannabinoid Type 1 Receptor ◽  
Docking Approach

A molecular docking approach was employed to evaluate the binding affinity of six triterpenes, namely epifriedelanol, friedelin, α-amyrin, α-amyrin acetate, β-amyrin acetate, and bauerenyl acetate, towards the cannabinoid type 1 receptor (CB1). Molecular docking studies showed that friedelin, α-amyrin, and epifriedelanol had the strongest binding affinity towards CB1. Molecular dynamics simulation studies revealed that friedelin and α-amyrin engaged in stable non-bonding interactions by binding to a pocket close to the active site on the surface of the CB1 target protein. The studied triterpenes showed a good capacity to penetrate the blood–brain barrier. These results help to provide some evidence to justify, at least in part, the previously reported antinociceptive and sedative properties of Vernonia patula.

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