Atomistic Explorations of Mechanisms Dictating the Shear Thinning Behavior and 3D Printability of Graphene Flake Infused Epoxy Inks

2021 ◽  
Author(s):  
Bhargav Chava ◽  
Eva K Thorn ◽  
Siddhartha Das
Keyword(s):  
Molecular Dynamic ◽  
Md Simulation ◽  
Shear Thinning ◽  
Graphene Flake ◽  
Marine Systems ◽  
3D Printed

Nanofiller-based epoxy inks have found extensive use in fabricating 3D printed nanocomposites for applications in aerospace, automobile, and marine systems. Here we employ an all-atom molecular dynamic (MD) simulation to...

Structure prediction of SPAK C-terminal domain and analysis of its binding to RFXV/I motifs by homology modelling, docking, and molecular dynamics simulation studies

2020 ◽  
Vol 16 ◽  
Author(s):  
Mubarak A. Alamri ◽  
Ahmed D. Alafnan ◽  
Obaid Afzal ◽  
Alhumaidi B. Alabbas ◽  
Safar M. Alqahtani
Keyword(s):  
Molecular Dynamic ◽  
Dynamic Stability ◽  
Md Simulation ◽  
Homology Modelling ◽  
Antihypertensive Agents ◽  
Structure And Function ◽  
Dynamics Simulation ◽  
Dimensional Structure ◽  
Terminal Domain ◽  
And Function

Background: The STE20/SPS1-related proline/alanine-rich kinase (SPAK) is a component of WNKSPAK/OSR1 signaling pathway that plays an essential role in blood pressure regulation. The function of SPAK is mediated by its highly conserved C-terminal domain (CTD) that interacts with RFXV/I motifs of upstream activators, WNK kinases, and downstream substrate, cation-chloride cotransporters. Objective: To determine and validate the three-dimensional structure of the CTD of SPAK and to study and analyze its interaction with the RFXV/I motifs. Methods: A homology model of SPAK CTD was generated and validated through multiple approaches. The model was based on utilizing the OSR1 protein kinase as a template. This model was subjected to 100 ns molecular dynamic (MD) simulation to evaluate its dynamic stability. The final equilibrated model was used to dock the RFQV-peptide derived from WNK4 into the primary pocket that was determined based on the homology sequence between human SPAK and OSR1 CTDs. The mechanism of interaction, conformational rearrangement and dynamic stability of the binding of RFQV-peptide to SPAK CTD were characterized by molecular docking and molecular dynamic simulation. Results: The MD simulation suggested that the binding of RFQV induces a large conformational change due to the distribution of salt bridge within the loop regions. These results may help in understanding the relation between the structure and function of SPAK CTD and to support drug design of potential SPAK kinase inhibitors as antihypertensive agents. Conclusion: This study provides deep insight into SPAK CTD structure and function relationship.

scholarly journals An Overview of Molecular Dynamic Simulation for Corrosion Inhibition of Ferrous Metals

Metals ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 46
Author(s):  
Nur Izzah Nabilah Haris ◽  
Shafreeza Sobri ◽  
Yus Aniza Yusof ◽  
Nur Kartinee Kassim
Keyword(s):  
Molecular Dynamic ◽  
Corrosion Inhibition ◽  
High Performance ◽  
Md Simulation ◽  
Ferrous Metal ◽  
Working Mechanism ◽  
Inhibitor Molecule ◽  
As Adsorption ◽  
Inhibition Studies ◽  
Selection Of

Molecular dynamics (MD) simulation is a powerful tool to study the molecular level working mechanism of corrosion inhibitors in mitigating corrosion. In the past decades, MD simulation has emerged as an instrument to investigate the interactions at the interface between the inhibitor molecule and the metal surface. Combined with experimental measurement, theoretical examination from MD simulation delivers useful information on the adsorption ability and orientation of the molecule on the surface. It relates the microscopic characteristics to the macroscopic properties which enables researchers to develop high performance inhibitors. Although there has been vast growth in the number of studies that use molecular dynamic evaluation, there is still lack of comprehensive review specifically for corrosion inhibition of organic inhibitors on ferrous metal in acidic solution. Much uncertainty still exists on the approaches and steps in performing MD simulation for corrosion system. This paper reviews the basic principle of MD simulation along with methods, selection of parameters, expected result such as adsorption energy, binding energy and inhibitor orientation, and recent publications in corrosion inhibition studies.

scholarly journals in Silico Docking and Molecular Dynamic Simulation of 3-Dehydroquinate Dehydratase from Mycobacterium Tuberculosis Through Virtual Screening and Pharmacokinetics Studies

2020 ◽  
Author(s):  
Mustafa Alhaji Isa ◽  
Muhammad M Ibrahim
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Virtual Screening ◽  
Molecular Dynamic ◽  
In Silico ◽  
Md Simulation ◽  
Binding Energies ◽  
In Silico Docking ◽  
Pharmacokinetic Properties

The 3-hydroquinate synthase (DHQase) is an enzyme that catalyzes the third step of the shikimate pathway in <i>Mycobacterium tuberculosis</i> (MTB), by converting 3-dehydroquinate into 3-dehydroshikimate. In this study, the novel inhibitors of DHQase from MTB was identified using in silico approach. The crystal structure of DHQase bound to 1,3,4-trihydroxy-5-(3-phenoxypropyl)-cyclohexane-1-carboxylic acid (CA) obtained from the Protein Data Bank (PDB ID: 3N76). The structure prepared through energy minimization and structure optimization. A total of 9699 compounds obtained from Zinc and PubChem databases capable of binding to DHQase and subjected to virtual screening through Lipinski’s rule of five and molecular docking analysis. Eight (8) compounds with good binding energies, ranged between ─8.99 to ─8.39kcal/mol were selected, better than the binding energy of ─4.93kcal/mol for CA and further filtered for pharmacokinetic properties (Absorption, Distribution, Metabolism, Excretion, and Toxicity or ADMET). Five compounds (ZINC14981770, ZINC14741224, ZINC14743698, ZINC13165465, and ZINC8442077) which had desirable pharmacokinetic properties selected for molecular dynamic (MD) simulation and molecular generalized born surface area (MM-GBSA) analyses. The results of the analyses showed that all the compounds formed stable and rigid complexes after the 50ns MD simulation and also had a lower binding as compared to CA. Therefore, these compounds considered as good inhibitors of MTB after in vitro and in vivo validation.”

Study of the Formation and Break of Lubricant Bridge in the Head Disk Interface Using Molecular Dynamic Method

2016 ◽  
Author(s):  
Xiangyu Dai ◽  
Xiao Lei ◽  
Hui Li
Keyword(s):  
Molecular Dynamic ◽  
Md Simulation ◽  
Molecular Dynamic Method ◽  
Dynamic Method ◽  
Rapid Heating ◽  
Three Dimensional ◽  
Simulation Method ◽  
Disk Interface ◽  
Helium Atoms ◽  
Heating And Cooling

Nowadays, heat assisted magnetic recording (HAMR) technology has been proposed to reach higher storage density. In this paper, the molecular dynamic (MD) simulation method is used to investigate the damage and recovery of the lubricant perfluoropolyethers (PFPE) layer under rapid heating and cooling in HAMR. Full-atom model for three-dimensional slider-lubricants-disk substrate system are built. The lubricant adheres to the diamond like carbon (DLC) substrate, and the space between slider and lubricant is filled with helium atoms. The results show that with higher heating speed, the PFPE will be easier to evaporate and form lubricant bridge. In addition, the thickness and stability of the lubricant bridge are significantly affected by the heating speed and the rotation speed of disk.

scholarly journals Development of palladium nanoparticles deposition on a copper substrate using a molecular dynamic (MD) simulation: a cold gas dynamic spray process

2020 ◽  
Vol 7 ◽  
pp. 29 ◽  
Author(s):  
Sunday Temitope Oyinbo ◽  
Tien-Chien Jen ◽  
Samson A. Aasa ◽  
Olayinka Oluwatosin Abegunde ◽  
Yudan Zhu
Keyword(s):  
Molecular Dynamic ◽  
Md Simulation ◽  
Low Cost ◽  
Substrate Surface ◽  
Copper Substrate ◽  
Pd Nanoparticle ◽  
Gas Dynamic ◽  
Cold Gas Dynamic Spray ◽  
Gas Dynamic Spray ◽  
Cold Gas

The objective of this study is to create an ultra-thin palladium foil with a molecular dynamic (MD) simulation technique on a copper substrate surface. The layer formed onto the surface consists of a singular 3D palladium (Pd) nanoparticle structure which, by the cold gas dynamic spray (CGDS) technique, is especially incorporated into the low-cost copper substrate. Pd and Cu have been chosen for their possible hydrogen separation technology applications. The nanoparticles were deposited to the substrate surface with an initial velocity ranging from 500 to 1500 m/s. The particle radius was 1 to 4 nm and an angle of impact of 90° at room temperature of 300 K, in order to evaluate changes in the conduct of deformation caused by effects of size. The deformation mechanisms study revealed that the particle and substrate interface is subject to the interfacial jet formation and adiabatic softening resulting in a uniform layering. However, shear instabilities at high impact speeds were confirmed by the evolution of von Mises shear strain, temperature evolution and plastic strain. The results of this study can be used to further our existing knowledge in the complex spraying processes of cold gas dynamic spray technology.

scholarly journals A study on the surface quality and brittle–ductile transition during the elliptical vibration-assisted nanocutting process on monocrystalline silicon via molecular dynamic simulations

RSC Advances ◽  
2017 ◽  
Vol 7 (7) ◽  
pp. 4179-4189 ◽  
Author(s):  
Bo Zhu ◽  
Dan Zhao ◽  
Hongwei Zhao ◽  
Jian Guan ◽  
Pengliang Hou ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Surface Quality ◽  
Md Simulation ◽  
Diamond Tool ◽  
Monocrystalline Silicon ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Elliptical Vibration ◽  
Brittle Ductile Transition

Molecular dynamic (MD) simulation was applied to investigate surface quality and brittle–ductile transition of monocrystalline silicon with a diamond tool during elliptical vibration-assisted nanocutting (EVANC) and traditional nanocutting process.

scholarly journals Pharmacoinformatics and Molecular Dynamic Simulation Studies Reveal Potential Inhibitors of SARS-CoV-2 Main Protease 3CLpro

2020 ◽  
Author(s):  
Mubarak A. Alamri ◽  
Muhammad Tahir ul Qamar ◽  
Safar M. Alqahtani
Keyword(s):  
Molecular Dynamic ◽  
Protease Inhibitors ◽  
Md Simulation ◽  
Simulation Studies ◽  
Simulation Approach ◽  
Main Protease ◽  
Essential Enzyme ◽  
Potential Inhibitors ◽  
Further Development ◽  
Catalytic Dyad

The SARS-CoV-2 was confirmed to cause the regional outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, China. The 3C-like protease (3CLpro), an essential enzyme for viral replication, is a valid target to compacts SARS-CoV and MERS-CoV. In this research, an integrated library consisting of 1000 compounds from Asinex Focused Covalent (AFCL) library and 16 FDA-approved protease inhibitors were screened against SARS-CoV-2 3CLpro. Top compounds with significant docking scores and making stable interactions with catalytic dyad residues were obtained. The screening results in identification of compound 621 from AFCL library as well as Paritaprevir and Simeprevir from FDA-approved protease inhibitors as potential inhibitors of SARS-CoV-2 3CLpro. The mechanism and dynamic stability of binding between the identified compounds and SARS-CoV-2 3CLpro were characterized using 50 nanoseconds (ns) molecular dynamic (MD) simulation approach. The identified compounds are potential inhibitors worthy of further development as SARS-CoV-2 3CLpro inhibitors/drugs. Importantly, the identified FDA-approved therapeutics could be ready for clinical trials to treat infected patients and help to curb the COVID-19.

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