Molecular Dynamics Simulation of Nanoscale Contact Process of Plane on Plane

Considering the process of the plane of rectangular indenter contacting on the plane of rectangular basal body in nanoscale as research object, molecular dynamics method is used for modeling, solving and simulation analysis. The change of atomic state and acting force in the contact process of nanoscale plane and plane is analysis from atomic aspect. The result showed that: when the plane of the rectangular indenter is from the surface of the base body a certain distance, due to attractive force, produced by inter-atomic force, the surface of the substrate produces atoms projection phenomenon; As the indenter continue to move down,the inter-atomic force becomes repulsive force, generates the contact pressure which gradually increases as the contact depth increases; The lattice under the indenter is deformed with pressure action. When indenter is in disengagement stage, the contact pressure decreases rapidly, and appears to reverse tensile stress. With action of the reverse tensile stress, dislocation configuration gradually change and restructuring. At same time, due to the surface effect, a number of substrate atoms are adsorbed in the surface of indenter, which caused by adhesion,and pulled out of the base body with the indenter.

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Faculty Opinions recommendation of Molecular dynamics simulation analysis of membrane defects and pore propensity of hemifusion diaphragms.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.717988413.793473345 ◽

2013 ◽

Author(s):

Jan Hoh

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Analysis ◽

Dynamics Simulation ◽

Membrane Defects

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Identification of Anti-SARS-CoV-2 Compounds from Food Using QSAR-Based Virtual Screening, Molecular Docking, and Molecular Dynamics Simulation Analysis

Pharmaceuticals ◽

10.3390/ph14040357 ◽

2021 ◽

Vol 14 (4) ◽

pp. 357

Author(s):

Magdi E. A. Zaki ◽

Sami A. Al-Hussain ◽

Vijay H. Masand ◽

Siddhartha Akasapu ◽

Sumit O. Bajaj ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Docking ◽

Virtual Screening ◽

Simulation Analysis ◽

Qsar Model ◽

Quantitative Structure Activity Relationship ◽

Dynamics Simulation ◽

Multilinear Regression ◽

Qsar Analysis ◽

Main Protease

Due to the genetic similarity between SARS-CoV-2 and SARS-CoV, the present work endeavored to derive a balanced Quantitative Structure−Activity Relationship (QSAR) model, molecular docking, and molecular dynamics (MD) simulation studies to identify novel molecules having inhibitory potential against the main protease (Mpro) of SARS-CoV-2. The QSAR analysis developed on multivariate GA–MLR (Genetic Algorithm–Multilinear Regression) model with acceptable statistical performance (R2 = 0.898, Q2loo = 0.859, etc.). QSAR analysis attributed the good correlation with different types of atoms like non-ring Carbons and Nitrogens, amide Nitrogen, sp2-hybridized Carbons, etc. Thus, the QSAR model has a good balance of qualitative and quantitative requirements (balanced QSAR model) and satisfies the Organisation for Economic Co-operation and Development (OECD) guidelines. After that, a QSAR-based virtual screening of 26,467 food compounds and 360 heterocyclic variants of molecule 1 (benzotriazole–indole hybrid molecule) helped to identify promising hits. Furthermore, the molecular docking and molecular dynamics (MD) simulations of Mpro with molecule 1 recognized the structural motifs with significant stability. Molecular docking and QSAR provided consensus and complementary results. The validated analyses are capable of optimizing a drug/lead candidate for better inhibitory activity against the main protease of SARS-CoV-2.

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Molecular Dynamics Simulation Study of Lecithin Inhibiting Hydrate-Dissociation

Materials Science Forum ◽

10.4028/www.scientific.net/msf.890.252 ◽

2017 ◽

Vol 890 ◽

pp. 252-259

Author(s):

Le Wang ◽

Guan Cheng Jiang ◽

Xin Lin ◽

Xian Min Zhang ◽

Qi Hui Jiang

Keyword(s):

Molecular Dynamics ◽

Water Movement ◽

Simulation Analysis ◽

Mass Density ◽

Dynamics Simulation ◽

Dissociation Process ◽

Hydrate Dissociation ◽

Hydrocarbon Chains ◽

Dynamics Simulations ◽

Mass Density Profile

Molecular dynamics simulations are used to study the dissociation inhibiting mechanism of lecithin for structure I hydrates. Adsorption characteristics of lecithin and PVP (poly (N-vinylpyrrolidine)) on the hydrate surfaces were performed in the NVT ensemble at temperatures of 277K and the hydrate dissociation process were simulated in the NPT ensemble at same temperature. The results show that hydrate surfaces with lecithin is more stable than the ones with PVP for the lower potential energy. The conformation of lecithin changes constantly after the balanced state is reached while the PVP molecular dose not. Lecithin molecule has interaction with lecithin nearby and hydrocarbon-chains of lecithin molecules will form a network to prevent the diffusion of water and methane molecules, which will narrow the available space for hydrate methane and water movement. Compared with PVP-hydrate simulation, analysis results (snapshots and mass density profile) of the dissociation simulations show that lecithin-hydrate dissociates more slowly.

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Molecular Dynamics Simulation of AFM-Based Nanomachining Processes

ASME 2011 International Manufacturing Science and Engineering Conference, Volume 2 ◽

10.1115/msec2011-50270 ◽

2011 ◽

Author(s):

Rapeepan Promyoo ◽

Hazim El-Mounayri ◽

Kody Varahramyan ◽

Ashlie Martini

Keyword(s):

Molecular Dynamics ◽

Friction Coefficient ◽

Md Simulation ◽

Computational Models ◽

Dynamics Simulation ◽

Radius Of Curvature ◽

Force Microscopy ◽

Indentation Force ◽

Atomic Force ◽

Development And Validation

Recently, atomic force microscopy (AFM) has been widely used for nanomachining and fabrication of micro/ nanodevices. This paper describes the development and validation of computational models for AFM-based nanomachining (nanoindentation and nanoscratching). The Molecular Dynamics (MD) technique is used to model and simulate mechanical indentation and scratching at the nanoscale in the case of gold and silicon. The simulation allows for the prediction of indentation forces and the friction force at the interface between an indenter and a substrate. The effects of tip curvature and speed on indentation force and friction coefficient are investigated. The material deformation and indentation geometry are extracted based on the final locations of atoms, which are displaced by the rigid tool. In addition to modeling, an AFM was used to conduct actual indentation at the nanoscale, and provide measurements to validate the predictions from the MD simulation. The AFM provides resolution on nanometer (lateral) and angstrom (vertical) scales. A three-sided pyramid indenter (with a radius of curvature ∼ 50 nm) is raster scanned on top of the surface and in contact with it. It can be observed from the MD simulation results that the indentation force increases as the depth of indentation increases, but decreases as the scratching speed increases. On the other hand, the friction coefficient is found to be independent of scratching speed.

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