scholarly journals Three-dimensional Brownian diffusion of rod-like macromolecules in the presence of randomly distributed spherical obstacles: Molecular dynamics simulation

2010 ◽  
Vol 133 (23) ◽  
pp. 234904 ◽  
Author(s):  
Farzaneh Sakha ◽  
Hossein Fazli
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Brownian Diffusion

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.

AFM-Based Nanoscratching: A 3D Molecular Dynamics Simulation With Experimental Verification

2014 ◽  
Author(s):  
Rapeepan Promyoo ◽  
Hazim El-Mounayri ◽  
Kody Varahramyan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Md Simulation ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Dimensional Model ◽  
Gold Substrate ◽  
Three Dimensional Model ◽  
Friction Forces ◽  
Defect Mechanism

In this paper, a developed three-dimensional model for AFM-based nanomachining is applied to study mechanical scratching at the nanoscale. The correlation between the scratching conditions, including applied force, scratching depth, and distant between any two scratched grooves, and the defect mechanism in the substrate/workpiece is investigated. The simulations of nanoscratching process are performed on different crystal orientations of single-crystal gold substrate, Au(100), Au(110), and Au(111). The material deformation and groove geometry are extracted from the final locations of atoms, which are displaced by the rigid indenter. The simulation also allows for the prediction of normal and friction forces at the interface between the indenter and substrate. An AFM is used to conduct actual scratching at the nanoscale, and provide measurements to which the MD simulation predictions are compared. The predicted forces obtained from MD simulation compares qualitatively with the experimental results.

Thermal conductance bottleneck of a three dimensional graphene–CNT hybrid structure: a molecular dynamics simulation

2020 ◽  
Vol 22 (1) ◽  
pp. 337-343 ◽  
Author(s):  
Zepei Yu ◽  
Yanhui Feng ◽  
Daili Feng ◽  
Xinxin Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Thermal Transport ◽  
Three Dimensional ◽  
Thermal Conductance ◽  
Hybrid Structure ◽  
Dynamics Simulation ◽  
Atomistic Structure

We observed the atomistic structure of the junction to study mechanism governing the thermal transport across GCNT.

Dynamic Three-Dimensional Nanowetting Behavior of Imidazolium-Based Ionic Liquids Probed by Molecular Dynamics Simulation

2017 ◽  
Vol 121 (42) ◽  
pp. 23716-23726 ◽  
Author(s):  
Yongji Guan ◽  
Qunfeng Shao ◽  
Wenqiong Chen ◽  
Shimin Liu ◽  
Xiaoping Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulation ◽  
Three Dimensional ◽  
Dynamics Simulation
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