Evaluation of Static Differential Capacitance at the [C4mim+][TFSA−]/Electrode Interface Using Molecular Dynamics Simulation Combined with Electrochemical Surface Plasmon Resonance Measurements

2021 ◽  
Author(s):  
Shiwei Zhang ◽  
Naoya Nishi ◽  
Seiji Katakura ◽  
Tetsuo Sakka
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Surface Plasmon Resonance ◽  
Quantitative Analysis ◽  
Molecular Dynamics Simulation ◽  
Surface Plasmon ◽  
Md Simulations ◽  
Differential Capacitance ◽  
Dynamics Simulation ◽  
Electrode Interface

Molecular dynamic (MD) simulations have been performed for 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide ([C4mim+][TFSA−]), an ionic liquid (IL), on a charged graphene electrode to achieve the quantitative analysis of the static differential capacitance...

scholarly journals An electric double layer structure and differential capacitance at the electrode interface of tributylmethylammonium bis(trifluoromethanesulfonyl)amide studied using a molecular dynamics simulation

2020 ◽  
Vol 22 (9) ◽  
pp. 5198-5210 ◽  
Author(s):  
Seiji Katakura ◽  
Naoya Nishi ◽  
Kazuya Kobayashi ◽  
Ken-ichi Amano ◽  
Tetsuo Sakka
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Molecular Dynamics Simulation ◽  
Quaternary Ammonium ◽  
Electric Double Layer ◽  
Layer Structure ◽  
Differential Capacitance ◽  
Dynamics Simulation ◽  
Double Layer Structure ◽  
Electrode Interface

A molecular dynamics simulation at the electrode interface of a quaternary ammonium ionic liquid, tributylmethylammonium bis(trifluoromethanesulfonyl)amide ([N1444+][TFSA−]), has been performed.

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.

Molecular Dynamics Simulation of Neutron Damage in β-SIC

1998 ◽  
Vol 540 ◽  
Author(s):  
J.M. Perlado ◽  
L. Malerba ◽  
T. Diaz De La Rubia
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Point Defects ◽  
Damage Accumulation ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Temperature Sensitive ◽  
Neutron Damage ◽  
Preliminary Study ◽  
Threshold Displacement

AbstractMolecular Dynamics (MD) simulations of neutron damage in β-SiC have been performed using a modified version of the Tersoff potential. The Threshold Displacement Energy (TDE) for Si and C atoms at 300 K has been determined along directions [001], [110], [111] and [ 1 1 1 ]. The existence of recombination barriers, which allow the formation of metastable, temperature-sensitive defects even below the threshold, has been observed. Displacement cascades produced by both C- and Si-recoils of energies spanning from 0.5 keV up to, respectively, 5 keV and 8 keV have also been simulated at 300 K and 1300 K. Their analysis, together with the analysis of damage accumulation (∼3.4×10-3 DPA) at 1300 K, reveals that the two sub-lattices exhibit opposite responses to irradiation: whereas only a little damage is produced on the “ductile” Si sub-lattice, many point-defects accumulate on the much more “fragile” C sub-lattice. A preliminary study of the nature and clustering tendency of these defects is performed. The possibility of disorder-induced amorphization is considered and the preliminary result is that no amorphization takes place at the dose and temperature simulated.

Molecular Dynamics Simulation of Thermodynamic Properties for CO2/Ionic Liquid Systems

2009 ◽  
Vol 25 (11) ◽  
pp. 2291-2295
Author(s):  
WANG Wei-Bin ◽  
◽  
◽  
YIN Jian-Zhong ◽  
SUN Li-Hua ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Molecular Dynamics Simulation ◽  
Thermodynamic Properties ◽  
Dynamics Simulation ◽  
Liquid Systems
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