Molecular dynamics simulations of nanoscale and sub-nanoscale friction behavior between graphene and a silicon tip: analysis of tip apex motion

Nanoscale ◽  
2015 ◽  
Vol 7 (14) ◽  
pp. 6295-6303 ◽  
Author(s):  
Hong Min Yoon ◽  
Youngmo Jung ◽  
Seong Chan Jun ◽  
Sasidhar Kondaraju ◽  
Joon Sang Lee
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Md Simulation ◽  
Simulation System ◽  
Friction Behavior ◽  
Simulation Process ◽  
Nanoscale Friction ◽  
Detailed Simulation ◽  
Dynamics Simulations

Schematic of (a) MD simulation system, (b) detailed simulation process, and (c) FFM experiment setup.

MDBenchmark: A Toolkit to Optimize the Performance of Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Michael Gecht ◽  
Marc Siggel ◽  
Max Linke ◽  
Gerhard Hummer ◽  
Juergen Koefinger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Open Source ◽  
Material Properties ◽  
Computation Time ◽  
Simulation System ◽  
Software Environment ◽  
Novice Users ◽  
Hardware Configuration ◽  
Dynamics Simulations

Molecular dynamics simulations resolve biomolecular processes and material properties with incomparable detail. As a result, they consume a significant fraction of worldwide supercomputing resources. With our open source benchmarking software MDBenchmark, expert and novice users alike can easily determine the optimal settings for their specific simulation system, MD engine, software environment, and hardware configuration. Ultimately, saving computation time, energy, and money at essentially no additional cost will produce better science.<br>

Investigation of friction behavior between tire and pavement by molecular dynamics simulations

2021 ◽  
Vol 300 ◽  
pp. 124037
Author(s):  
Fucheng Guo ◽  
Jiupeng Zhang ◽  
Zixuan Chen ◽  
Mingliang Zhang ◽  
Jianzhong Pei ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Friction Behavior ◽  
Dynamics Simulations

The folding mechanism and key metastable state identification of the PrP127–147 monomer studied by molecular dynamics simulations and Markov state model analysis

2017 ◽  
Vol 19 (18) ◽  
pp. 11249-11259 ◽  
Author(s):  
Shuangyan Zhou ◽  
Qianqian Wang ◽  
Yuwei Wang ◽  
Xiaojun Yao ◽  
Wei Han ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Prion Protein ◽  
Structural Dynamics ◽  
Md Simulation ◽  
Markov State Model ◽  
Markov State ◽  
Folding Mechanism ◽  
State Identification ◽  
Dynamics Simulations

MD simulation combined with MSM analysis was employed to investigate the structural dynamics and the folding mechanism of the key fragment 127–147 monomer of prion protein.

MDBenchmark: A Toolkit to Optimize the Performance of Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Michael Gecht ◽  
Marc Siggel ◽  
Max Linke ◽  
Gerhard Hummer ◽  
Juergen Koefinger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Open Source ◽  
Material Properties ◽  
Computation Time ◽  
Simulation System ◽  
Software Environment ◽  
Novice Users ◽  
Hardware Configuration ◽  
Dynamics Simulations

Molecular dynamics simulations resolve biomolecular processes and material properties with incomparable detail. As a result, they consume a significant fraction of worldwide supercomputing resources. With our open source benchmarking software MDBenchmark, expert and novice users alike can easily determine the optimal settings for their specific simulation system, MD engine, software environment, and hardware configuration. Ultimately, saving computation time, energy, and money at essentially no additional cost will produce better science.<br>

Dipropargyl ether bisphenol A based boron-containing polymer: synthesis, characterization and molecular dynamics simulations of the resulting pyrolysis and carbonization

RSC Advances ◽  
2015 ◽  
Vol 5 (5) ◽  
pp. 3390-3398 ◽  
Author(s):  
N. Gao ◽  
X. Jiang ◽  
Y. H. Liu
Keyword(s):  
Molecular Dynamics ◽  
Bisphenol A ◽  
Molecular Dynamics Simulations ◽  
Time Evolution ◽  
Small Molecule ◽  
Md Simulation ◽  
Polymer Synthesis ◽  
Color Code ◽  
Pyrolysis Products ◽  
Dynamics Simulations

The time evolution of major pyrolysis products including small-molecule species of a dipropargyl ether bisphenol A based novel boron-containing polymer was examined via ReaxFF-MD simulation (Color code: C, grey; O, red; H, white; B, yellow).

Molecular dynamics simulations of the isotopic effect on nanoscale friction

2021 ◽  
Vol 127 (9) ◽  
Author(s):  
D. Matté ◽  
G. L. Rech ◽  
L. M. Leidens ◽  
J. E. Zorzi ◽  
A. F. Michels ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Isotopic Effect ◽  
Nanoscale Friction ◽  
Dynamics Simulations

Mechanical Properties of Vacancy-containing Graphene and Graphite Estimated by Molecular Dynamics Simulations

2011 ◽  
Vol 1362 ◽  
Author(s):  
Akihiko Ito ◽  
Shingo Okamoto
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Tensile Strength ◽  
Molecular Dynamics Simulations ◽  
Young’S Modulus ◽  
Md Simulation ◽  
Pristine Graphene ◽  
Cluster Type ◽  
Slip Deformation ◽  
Dynamics Simulations

ABSTRACTUsing molecular dynamics (MD) simulation, we investigated the mechanical properties of graphene and graphite, which contain cluster-type vacancies. We found that as the vacancy size increases, the tensile strength drastically decreases to at least 56% of that of pristine graphene, whereas Young’s modulus hardly changes. In vacancy-containing graphene, we also found that slip deformation followed by fracture occurs under zigzag tension. In general, tensile strength decreases as the size of cluster-type vacancies increases. However, the tensile strength of graphene with a clustered sextuple vacancy increases as the vacancy disappears because slip deformation proceeds. Furthermore, we found that slip deformation by vacancies in graphite occurs less easily than in graphene.Our results suggest that the shape of vacancies affects the strengths of graphene and graphite.

scholarly journals Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Wolfgang Schreiner ◽  
Rudolf Karch ◽  
Bernhard Knapp ◽  
Nevena Ilieva
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Md Simulation ◽  
Time Intervals ◽  
Variable Time ◽  
Dynamics Simulations ◽  
Stationary Shape

Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of “lagged RMSD-analysis” as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δt) has reached a stationary shape, the simulation has not yet converged.

Seawater desalination using pillared graphene as a novel nano-membrane in reverse osmosis process: nonequilibrium MD simulation study

2018 ◽  
Vol 20 (34) ◽  
pp. 22241-22248 ◽  
Author(s):  
Sayyed Jalil Mahdizadeh ◽  
Elaheh K. Goharshadi ◽  
Golnoosh Akhlamadi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Reverse Osmosis ◽  
Simulation Study ◽  
Md Simulation ◽  
Nonequilibrium Molecular Dynamics ◽  
Seawater Desalination ◽  
Dynamics Simulations ◽  
Graphene Nanostructures

Herein, the applicability and efficiency of two types of pillared graphene nanostructures, namely, (6,6)@G and (7,7)@G, were investigated as membranes in reverse osmosis seawater desalination using extensive nonequilibrium molecular dynamics simulations.

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