Molecular Dynamics Simulation of Vibrational Friction Force Due to Molecular Deformation in Confined Lubricant Film

2003 ◽  
Vol 125 (3) ◽  
pp. 587-591 ◽  
Author(s):  
Kentaro Tanaka ◽  
Takahisa Kato ◽  
Yoichiro Matsumoto
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Friction Force ◽  
Lubricant Film ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Magnetic Storage ◽  
Stick Slip ◽  
Molecular Deformation ◽  
Load Conditions

The lubrication by thin film has become a very important role in micro machine, magnetic storage device and so on. As the thickness of lubricant film becomes thinner to several nanometers, the conventional law of lubrication becomes unable to use. Nonequilibrium molecular dynamics simulation (NEMD) was carried out to investigate the dynamic behavior of thin lubricant film confined between walls. The model used in these simulations is composed of two solid walls and fluorocarbon polymer lubricant. One of the walls is supporting a load and at the same time moving at constant velocity. Results indicate that the frictional behavior of confined lubricant varied with load; velocity field in the film retain liquid like structure under low load conditions, on the other hand, under high load conditions lubricant film becomes solidified and periodical stick and slip motion is observed at the layer near the wall. At the same time periodically vibrating friction force is observed. In this case, radius of gyration of lubricant molecules also changes periodically. It is concluded that the periodical vibration of friction force is caused by stick-slip with molecular deformation.

scholarly journals Influence of Nanoscale Textured Surfaces and Subsurface Defects on Friction Behaviors by Molecular Dynamics Simulation

Nanomaterials ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 1617 ◽  
Author(s):  
Ruiting Tong ◽  
Zefen Quan ◽  
Yangdong Zhao ◽  
Bin Han ◽  
Geng Liu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Friction Force ◽  
Copper Substrate ◽  
Dynamics Simulation ◽  
Textured Surfaces ◽  
Friction Forces ◽  
Subsurface Structures ◽  
Texture Orientation ◽  
Subsurface Defects

In nanomaterials, the surface or the subsurface structures influence the friction behaviors greatly. In this work, nanoscale friction behaviors between a rigid cylinder tip and a single crystal copper substrate are studied by molecular dynamics simulation. Nanoscale textured surfaces are modeled on the surface of the substrate to represent the surface structures, and the spacings between textures are seen as defects on the surface. Nano-defects are prepared at the subsurface of the substrate. The effects of depth, orientation, width and shape of textured surfaces on the average friction forces are investigated, and the influence of subsurface defects in the substrate is also studied. Compared with the smooth surface, textured surfaces can improve friction behaviors effectively. The textured surfaces with a greater depth or smaller width lead to lower friction forces. The surface with 45° texture orientation produces the lowest average friction force among all the orientations. The influence of the shape is slight, and the v-shape shows a lower average friction force. Besides, the subsurface defects in the substrate make the sliding process unstable and the influence of subsurface defects on friction forces is sensitive to their positions.

Binding of biguanides to β-lactoglobulin: molecular-docking and molecular dynamics simulation studies

2014 ◽  
Vol 68 (11) ◽  
Author(s):  
Mehdi Sahihi ◽  
Yousef Ghayeb
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Hydrophobic Interactions ◽  
Mean Value ◽  
Transport Protein ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Accessible Surface ◽  
Β Lactoglobulin

AbstractBiguanides are a class of drugs derived from biguanide and they are the most widely used drugs for diabetes mellitus or pre-diabetes treatment. An investigation of their interaction and a transport protein such as β-lactoglobulin (BLG) at atomic level could be a valuable factor in controlling their transport to biological sites. Molecular-docking and molecular dynamics simulation methods were used to study the interaction of metformin, phenformin and buformin as biguanides and BLG as transport protein. The molecular-docking results revealed that these biguanides bind to BLG and that the BLG affinity for binding the biguanides decreases in the following order: phenformin — buformin — metformin. The docking results also show the hydrophobic interactions to have a significant role in the BLG-biguanides complex stability. Analysis of molecular dynamic simulation trajectories shows that the root mean square deviation of various systems attained equilibrium and fluctuated around the mean value at various times. The time evolution of the radius of gyration and the total solvent-accessible surface of the protein showed that BLG and BLG-biguanide complexes became stable at approximately 2500 ps and that there was not any conformational change in the BLG-biguanide complexes. In addition, the profiles of atomic fluctuations show the rigidity of the ligand-binding site during the simulation.

scholarly journals Phytochemicals from Leucas zeylanica Targeting Main Protease of SARS-CoV-2: Chemical Profiles, Molecular Docking, and Molecular Dynamics Simulations

Biology ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 789
Author(s):  
Mycal Dutta ◽  
Abu Montakim Tareq ◽  
Ahmed Rakib ◽  
Shafi Mahmud ◽  
Saad Ahmed Sami ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Surface Area ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Gas Chromatography Mass Spectrometry ◽  
Radius Of Gyration ◽  
Hydrogen Bond Formation ◽  
Main Protease

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a contemporary coronavirus, has impacted global economic activity and has a high transmission rate. As a result of the virus’s severe medical effects, developing effective vaccinations is vital. Plant-derived metabolites have been discovered as potential SARS-CoV-2 inhibitors. The SARS-CoV-2 main protease (Mpro) is a target for therapeutic research because of its highly conserved protein sequence. Gas chromatography–mass spectrometry (GC-MS) and molecular docking were used to screen 34 compounds identified from Leucas zeylanica for potential inhibitory activity against the SARS-CoV-2 Mpro. In addition, prime molecular mechanics–generalized Born surface area (MM-GBSA) was used to screen the compound dataset using a molecular dynamics simulation. From molecular docking analysis, 26 compounds were capable of interaction with the SARS-CoV-2 Mpro, while three compounds, namely 11-oxa-dispiro[4.0.4.1]undecan-1-ol (−5.755 kcal/mol), azetidin-2-one 3,3-dimethyl-4-(1-aminoethyl) (−5.39 kcal/mol), and lorazepam, 2TMS derivative (−5.246 kcal/mol), exhibited the highest docking scores. These three ligands were assessed by MM-GBSA, which revealed that they bind with the necessary Mpro amino acids in the catalytic groove to cause protein inhibition, including Ser144, Cys145, and His41. The molecular dynamics simulation confirmed the complex rigidity and stability of the docked ligand–Mpro complexes based on the analysis of mean radical variations, root-mean-square fluctuations, solvent-accessible surface area, radius of gyration, and hydrogen bond formation. The study of the postmolecular dynamics confirmation also confirmed that lorazepam, 11-oxa-dispiro[4.0.4.1]undecan-1-ol, and azetidin-2-one-3, 3-dimethyl-4-(1-aminoethyl) interact with similar Mpro binding pockets. The results of our computerized drug design approach may assist in the fight against SARS-CoV-2.

scholarly journals In silico identification of novel chemical compounds with anti-TB potential for the inhibition of InhA and EthR from Mycobacterium tuberculosis

2020 ◽  
Author(s):  
Sajal Kumar Halder ◽  
Fatiha Elma
Keyword(s):  
Molecular Dynamics ◽  
Mycobacterium Tuberculosis ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Chemical Compounds ◽  
Dynamics Simulation ◽  
Health Concern ◽  
Radius Of Gyration

ABSTRACTTuberculosis (TB) continuously pose a major public health concern around the globe, with a mounting death toll of approximately 1.4 million in 2019. The reduced bioavailability, increased toxicity and resistance of several first-line and second-line anti-TB drugs such as isoniazid, ethionamide have necessitated the search for new medications. In this research, we have identified several novel chemical compounds with anti-TB properties using various computational tools like molecular docking analysis, drug-likeness evaluation, ADMET profiling, P450 site of metabolism prediction and molecular dynamics simulation study. This study involves fifty drug-like compounds with antibacterial activity that inhibit InhA and EthR involved in the synthesis of one of the major lipid components, mycolic acid, which is crucial for the viability of Mycobacterium tuberculosis. Among these fifty compounds, 3-[3-(4-Fluorophenyl)-1,2,4-oxadiazol-5-yl]-N-(2-methylphenyl) piperidine-1-carboxamide (C22) and 5-(4-Ethyl-phenyl)-2-(1H-tetrazol-5-ylmethyl)-2H-tetrazole (C29) were found to pass the two-step molecular docking, P450 site of metabolism prediction and pharmacokinetics filtering analysis successfully. Their binding stability for target proteins have been evaluated through RMSD, RMSF, Radius of gyration analysis from 10 ns Molecular Dynamics Simulation (MDS) run. Our identified drugs could be a capable therapeutic for Tuberculosis drug discovery, having said that more in vitro and in vivo testing is required to justify their potential as novel drug and mode of action.

scholarly journals Mechanical and Tribological Properties of Nitrile Rubber Reinforced by SiO2: Molecular Dynamics Simulation  Mechanical and Tribological Properties of Nitrile Rubber Reinforced by SiO2: Molecular Dynamics Simulation

2021 ◽  
Author(s):  
Xueshen Liu ◽  
Xincong Zhou ◽  
Fuming Kuang ◽  
Houxiu Zuo ◽  
Jian Huang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Tribological Properties ◽  
Friction Stress ◽  
Nitrile Rubber ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Fractional Free Volume ◽  
Mechanical And Tribological Properties ◽  
Molecular Scale

Abstract This paper investigated the mechanism of enhancing the mechanical and tribological properties of nitrile rubber (NBR) with SiO 2 on the molecular scale. Molecular dynamics (MD) simulations were performed on molecular structure models of pure NBR, NBR/SiO 2 and three-layer friction pairs. The results showed that the hydrogen bonds and interfacial interaction between SiO 2 and NBR molecular chains decreased the fractional free volume of NBR nanocomposites, and increased the shear modulus of NBR by 25% compared with that of pure NBR. During the friction process, SiO 2 decreased the radius of gyration of NBR molecular chains and effectively lowered the peak atomic velocity, the peak temperature and the peak friction stress at the interface between NBR and copper atoms. The average friction stress on NBR/SiO 2 was 34% lower than that on NBR, which meant the tribological properties of NBR were significantly improved by SiO 2 . The mechanism of SiO 2 reinforcing NBR on a molecular scale can lay a theoretical foundation for the design of water-lubricated rubber bearings.

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