First-Principles-Based Machine-Learning Molecular Dynamics for Crystalline Polymers with van der Waals Interactions

2021 ◽  
pp. 6000-6006
Author(s):  
Sung Jun Hong ◽  
Hoje Chun ◽  
Jehyun Lee ◽  
Byung-Hyun Kim ◽  
Min Ho Seo ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
First Principles ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Crystalline Polymers

scholarly journals First-principles calculations and experimental studies of XYZ2 thermoelectric compounds: detailed analysis of van der Waals interactions

2018 ◽  
Vol 6 (40) ◽  
pp. 19502-19519 ◽  
Author(s):  
Jan-Hendrik Pöhls ◽  
Zhe Luo ◽  
Umut Aydemir ◽  
Jon-Paul Sun ◽  
Shiqiang Hao ◽  
...  
Keyword(s):  
Detailed Analysis ◽  
First Principles ◽  
Van Der Waals ◽  
Experimental Studies ◽  
Van Der Waals Interactions ◽  
First Principles Calculations ◽  
Prediction Of Properties

van der Waals interactions enhanced the prediction of properties in layered thermoelectrics.

scholarly journals Machine Learning Classical Interatomic Potentials for Molecular Dynamics from First-Principles Training Data

2019 ◽  
Vol 123 (12) ◽  
pp. 6941-6957 ◽  
Author(s):  
Henry Chan ◽  
Badri Narayanan ◽  
Mathew J. Cherukara ◽  
Fatih G. Sen ◽  
Kiran Sasikumar ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
First Principles ◽  
Training Data ◽  
Interatomic Potentials

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>

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