Shear strain-induced structure relaxation of Ni Σ17 [110](223) grain boundary: A molecular dynamics simulation

2022 ◽  
Author(s):  
Hongtao Xue ◽  
Xudong Yu ◽  
Xin Zhou ◽  
Fuling Tang ◽  
Xiuyan Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Relaxation ◽  
Energy State ◽  
Strain Range ◽  
High Energy ◽  
Inhibitory Effect ◽  
Dynamics Simulation ◽  
State Transformation ◽  
Structure Relaxation ◽  
Entry Points

The stabilization of grain boundaries (GBs) is beneficial for improving the stability and mechanical properties of nanocrystalline (NC) metals. Molecular dynamics (MD) calculations were performed to investigate the shear response of Ni [Formula: see text]17 [110](223) symmetrical tilt GB. It was found that under the action of shear, the nucleation and evolution of the GB source Shockley partial dislocations ultimately result in the low-energy-state transformation of the GB structure units (SUs). However, the Ag atom contained in the GB increases the shear stress and strain required for the GB relaxation, and the strain range for the GB relaxation is expanded, indicating the inhibitory effect of the Ag atom on the structural relaxation of Ni [Formula: see text]17 [110](223) GB. As the temperature increases from 10 K to 250 K, the structural relaxation of Ni [Formula: see text]17 [110](223) GB becomes easier to proceed. In addition to segregation-induced GB stabilization, strain-induced GB relaxation and the roles of foreign atom and temperature clarified in this work could provide several new entry points for stabilizing high-energy GBs.

Molecular Dynamics Simulations of High Energy Cascades in Iron

1994 ◽  
Vol 373 ◽  
Author(s):  
Roger E. Stoller
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
High Energy ◽  
Dynamics Simulation ◽  
Method Of Molecular Dynamics ◽  
Energy Cascades ◽  
Iron Based ◽  
The Many ◽  
Property Changes ◽  
Dynamics Simulations

AbstractA series of high-energy, up to 20 keV, displacement cascades in iron have been investigated for times up to 200 ps at 100 K using the method of molecular dynamics simulation. Thesimulations were carried out using the MOLDY code and a modified version of the many-bodyinteratomic potential developed by Finnis and Sinclair. The paper focuses on those results obtained at the highest energies, 10 and 20 keV. The results indicate that the fraction of the Frenkel pairs surviving in-cascade recombination remains fairly high in iron and that the fraction of the surviving point defects that cluster is lower than in materials such as copper. In particular, vacancy clustering appears to be inhibited in iron. Some of the interstitial clusters were observed to exhibit an unexpectedly complex, three-dimensional morphology. The observations are discussed in terms of their relevance to microstructural evolution and mechanical property changes in irradiated iron-based alloys.

scholarly journals An Analysis Based on Molecular Docking and Molecular Dynamics Simulation Study of Bromelain as Anti-SARS-CoV-2 Variants

2021 ◽  
Vol 12 ◽  
Author(s):  
Trina Ekawati Tallei ◽  
Fatimawali ◽  
Afriza Yelnetty ◽  
Rinaldi Idroes ◽  
Diah Kusumawaty ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Three Dimensional ◽  
Md Simulations ◽  
Inhibitory Effect ◽  
Dynamics Simulation ◽  
Novel Coronavirus

The rapid spread of a novel coronavirus known as SARS-CoV-2 has compelled the entire world to seek ways to weaken this virus, prevent its spread and also eliminate it. However, no drug has been approved to treat COVID-19. Furthermore, the receptor-binding domain (RBD) on this viral spike protein, as well as several other important parts of this virus, have recently undergone mutations, resulting in new virus variants. While no treatment is currently available, a naturally derived molecule with known antiviral properties could be used as a potential treatment. Bromelain is an enzyme found in the fruit and stem of pineapples. This substance has been shown to have a broad antiviral activity. In this article, we analyse the ability of bromelain to counteract various variants of the SARS-CoV-2 by targeting bromelain binding on the side of this viral interaction with human angiotensin-converting enzyme 2 (hACE2) using molecular docking and molecular dynamics simulation approaches. We have succeeded in making three-dimensional configurations of various RBD variants using protein modelling. Bromelain exhibited good binding affinity toward various variants of RBDs and binds right at the binding site between RBDs and hACE2. This result is also presented in the modelling between Bromelain, RBD, and hACE2. The molecular dynamics (MD) simulations study revealed significant stability of the bromelain and RBD proteins separately up to 100 ns with an RMSD value of 2 Å. Furthermore, despite increases in RMSD and changes in Rog values of complexes, which are likely due to some destabilized interactions between bromelain and RBD proteins, two proteins in each complex remained bonded, and the site where the two proteins bind remained unchanged. This finding indicated that bromelain could have an inhibitory effect on different SARS-CoV-2 variants, paving the way for a new SARS-CoV-2 inhibitor drug. However, more in vitro and in vivo research on this potential mechanism of action is required.

Displacement cascade evolution in tungsten with pre-existing helium and hydrogen clusters: a molecular dynamics study

2020 ◽  
Vol 111 (8) ◽  
pp. 698-705
Author(s):  
Mohammad Abu-Shams ◽  
Jeffery Moran ◽  
Ishraq Shabib
Keyword(s):  
Molecular Dynamics ◽  
Point Defect ◽  
Radiation Damage ◽  
Point Defects ◽  
High Energy ◽  
Dynamics Simulation ◽  
Power Relationship ◽  
Hydrogen Clusters ◽  
Displacement Cascades ◽  
Hydrogen Defects

Abstract The effects of radiation damage on bcc tungsten with preexisting helium and hydrogen clusters have been investigated in a high-energy environment via a comprehensive molecular dynamics simulation study. This research determines the interactions of displacement cascades with helium and hydrogen clusters integrated into a tungsten crystal generating point defect statistics. Helium or hydrogen clusters of atoms~0.1% of the total number of atoms have been randomly distributed within the simulation model and primary knock-on-atom (PKA) energies of 2.5, 5, 7.5 and 10 keV have been used to generate displacement cascades. The simulations quantify the extent of radiation damage during a simulated irradiation cycle using the Wigner-Seitz point defect identification technique. The generated point defects in crystals with and without pre-existing helium/hydrogen defects exhibit a power relationship with applied PKA energy. The point defects are classified by their atom type, defect type, and distribution within the irradiated model. The presence of pre-existing helium and hydrogen clusters significantly increases the defects (5 - 15 times versus pure tungsten models). The vacancy composition is primarily tungsten (e. g., ~70% at 2.5 keV) in models with pre-existing helium, but the interstitials are primarily He (e. g., ~89% at 10 keV). On the other hand, models with pre-existing hydrogen have a vacancy composition that is primarily tungsten (more than 90% irrespective of PKA energy), and the interstitial composition is more balanced between tungsten (average 46%) and hydrogen (average 54%) interstitials across the PKA range. The distribution of the atoms reveals that the tungsten point defects prefer to reside close to the position of cascade initiation, but helium or hydrogen defects reside close to the positions where clusters are built.

Molecular Dynamics Simulations of Hot Electrons and Lattice Relaxation in Realistic Cascade Volumes

1992 ◽  
Vol 278 ◽  
Author(s):  
A.M. Mazzone
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Classical Mechanics ◽  
Lattice Relaxation ◽  
Simulation Method ◽  
High Energy ◽  
Hot Electrons ◽  
Dynamics Simulation ◽  
Dynamics Simulations

AbstractThis work presents a molecular dynamics simulation method designed to describe the processes of electron and lattice relaxation taking place in typical cascade volumes formed by high-energy implants. The simulation method is based on classical mechanics and includes the motions of electrons and nuclei. The results are in agreement with experiments.

Molecular Dynamics Simulation of Surface Effect on Tensile Deformation of Single Crystalline Copper

2014 ◽  
Vol 620 ◽  
pp. 61-66 ◽  
Author(s):  
Qiang Gao ◽  
Yong Bo Guo ◽  
Ying Chun Liang ◽  
Qing Chun Zhang
Keyword(s):  
Molecular Dynamics ◽  
Tensile Deformation ◽  
Surface Effect ◽  
High Energy ◽  
Dislocation Nucleation ◽  
Atomic Scale ◽  
Dynamics Simulation ◽  
Crystal Plane ◽  
Single Crystalline ◽  
Tensile Process

Based on molecular dynamics method, the tensile process of single crystalline Cu nanorod and single crystalline Cu bulk were simulated at atomic scale. The motion of atoms, total energy of atom-strain curves and number of dislocation atom-strain curves during the tensile process were acquired. The results shown that surface effect has a significant effect on the tensile mechanical properties of single crystalline Cu nanorod. For single crystalline Cu nanorod, the energy of atoms in the edges and surface were higher than the energy of atoms inside the nanorod. Dislocations nucleation in the edges that with high energy and extend along the {111} crystal plane. The nanorods produce plastic deformation and shows excellent ductility under the "dislocation nucleation-energy rising and dislocation layers cross-slip" mechanism of the alternating cycle. For single crystalline Cu bulk, dislocation nucleation randomly and extend to the entire simulation model along the {111} crystal plane quickly. The single crystalline bulk Cu produce fracture under the "microscopic vacancy-microscopic hole-penetration of microscopic holes-fracture" mechanism.

scholarly journals Molecular Dynamics Simulation of 2-Benzimidazolyl-Urea with DPPC Lipid Membrane and Comparison with a Copper(II) Complex Derivative

Membranes ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 743
Author(s):  
Georgios Rossos ◽  
Sotiris K. Hadjikakou ◽  
Nikolaos Kourkoumelis
Keyword(s):  
Molecular Dynamics ◽  
Lipid Membrane ◽  
Membrane Damage ◽  
Md Simulations ◽  
High Energy ◽  
Biological Properties ◽  
Complex Compounds ◽  
Phospholipid Bilayer ◽  
Dynamics Simulation ◽  
Benzimidazole Derivatives

Benzimidazole derivatives have gained attention recently due to their wide pharmacological activity acting as anti-inflammatory, hypotensive, analgesic, and anti-aggregatory agents. They are also common ligands in transition metal coordination chemistry, forming complex compounds with enhanced biological properties, especially in targeted cancer therapy. A key issue to understand anti-tumour effects is drug permeability through cellular membranes, as poor permeability outcomes can avert further futile drug development. In this work, we conducted atomistic molecular dynamics (MD) simulations and biased MD simulations to explore the interactions of 2-benzimidazolyl-urea with a phospholipid bilayer (dipalmitoylphosphatidylcholine, DPPC) together with a previously synthesized copper(II) complex compound. The aim was to study the permeability of these compounds by assessing their free energy profile along the bilayer normal. The simulations indicated that both the ligand (2-benzimidazolyl-urea, BZIMU) and the complex show a similar behaviour, yielding high energy barriers for the permeation process. However, with increasing concentration of BZIMU, the molecules tend to aggregate and form a cluster, leading to the formation of a pore. Clustering and pore formation can possibly explain the previously observed cytotoxicity of the BZIMU molecule via membrane damage.

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