scholarly journals An Extended van der Waals Equation of State Based on Molecular Dynamics Simulation

2009 ◽  
Vol 8 (3) ◽  
pp. 97-104 ◽  
Author(s):  
Yosuke KATAOKA ◽  
Yuri YAMADA
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Equation Of State ◽  
Van Der Waals ◽  
Dynamics Simulation ◽  
Van Der Waals Equation

scholarly journals The Potential role of Procyanidin as a Therapeutic Agent against SARS-CoV-2: A Text Mining, Molecular Docking and Molecular Dynamics Simulation Approach

2020 ◽  
Author(s):  
Nikhil Maroli ◽  
Balu Bhasuran ◽  
Jeyakumar Natarajan ◽  
Ponmalai Kolandaivel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Text Mining ◽  
Van Der Waals ◽  
Interaction Network ◽  
Van Der Waals Interactions ◽  
Entity Recognition ◽  
Dynamics Simulation ◽  
Inhibition Mechanism

<p></p><p></p><p>A novel coronavirus (SARS-CoV-2) has caused a major outbreak in human all over the world. There are several proteins interplay during the entry and replication of this virus in human. Here, we have used text mining and named entity recognition method to identify co-occurrence of the important COVID 19 genes/proteins in the interaction network based on the frequency of the interaction. Network analysis revealed a set of genes/proteins, highly dense genes/protein clusters and sub-networks of Angiotensin-converting enzyme 2 (ACE2), Helicase, spike (S) protein (trimeric), membrane (M) protein, envelop (E) protein, and the nucleocapsid (N) protein. The isolated proteins are screened against procyanidin-a flavonoid from plants using molecular docking. Further, molecular dynamics simulation of critical proteins such as ACE2, Mpro and spike proteins are performed to elucidate the inhibition mechanism. The strong network of hydrogen bonds and hydrophobic interactions along with van der Waals interactions inhibit receptors, which are essential to the entry and replication of the SARS-CoV-2. The binding energy which largely arises from van der Waals interactions is calculated (ACE2=-50.21 ± 6.3, Mpro=-89.50 ± 6.32 and spike=-23.06 ± 4.39) through molecular mechanics Poisson-Boltzmann surface area also confirm the affinity of procyanidin towards the critical receptors.</p><p></p><p></p>

INVESTIGATION FOR MOLECULAR ATTRACTION IMPACT BETWEEN CONTACTING SURFACES IN MICRO-GEARS

2013 ◽  
Vol 27 (27) ◽  
pp. 1350150
Author(s):  
PING YANG ◽  
XIALONG LI ◽  
YANFANG ZHAO ◽  
HAIYING YANG ◽  
SHUTING WANG ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Van Der Waals ◽  
Research Work ◽  
Van Der Waals Force ◽  
Computational Method ◽  
Gear Train ◽  
Dynamics Simulation ◽  
Geometrical Properties ◽  
Molecular Attraction

The aim of this research work is to provide a systematic method to perform molecular attraction impact between contacting surfaces in micro-gear train. This method is established by integrating involute profile analysis and molecular dynamics simulation. A mathematical computation of micro-gear involute is presented based on geometrical properties, Taylor expression and Hamaker assumption. In the meantime, Morse potential function and the cut-off radius are introduced with a molecular dynamics simulation. So a hybrid computational method for the Van Der Waals force between the contacting faces in micro-gear train is developed. An example is illustrated to show the performance of this method. The results show that the change of Van Der Waals force in micro-gear train has a nonlinear characteristic with parameters change such as the modulus of the gear and the tooth number of gear etc. The procedure implies a potential feasibility that we can control the Van Der Waals force by adjusting the manufacturing parameters for gear train design.

scholarly journals Does the single-walled carbon nanotube affect the rate constant of binding of biotin to streptavidin? Molecular dynamics simulation perspective

2019 ◽  
Vol 44 (3) ◽  
pp. 234-243
Author(s):  
Orkide Soltani ◽  
Mohammad Reza Bozorgmehr ◽  
Mohammad Momen-Heravi
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Carbon Nanotube ◽  
Molecular Dynamics Simulation ◽  
Complex Formation ◽  
Van Der Waals ◽  
Dynamics Simulation ◽  
Electrostatic Forces ◽  
Single Walled Carbon Nanotube ◽  
Arrhenius Dependence

The interaction of biotin and streptavidin in the presence and absence of a carbon nanotube was studied by molecular dynamics simulation. With respect to the Arrhenius dependence of the rate constants with temperature, those of streptavidin–biotin complex formation ([Formula: see text]) and streptavidin–biotin complex dissociation ([Formula: see text]) were calculated from molecular dynamics simulation trajectories. Nanotube has reduced the amount of and k1and k1. However, the biotin position in streptavidin does not change much. The results obtained from MMPBSA calculations show that the contribution of the van der Waals forces to both systems (in the absence and presence of the nanotube) was greater than that of electrostatic forces. The presence of the nanotube also led to the reduction of van der Waals and electrostatic forces in the interaction of biotin with streptavidin. However, this reduction was greater for electrostatic forces. In the absence of a nanotube, there are four hydrogen bonds between streptavidin and biotin, which are related to the residues Ser27, Tyr43, Ser45 and Ser88. In the presence of the nanotube, the hydrogen bonding of biotin with Ser45 is removed.

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