Molecular Dynamics Simulation to Study the Effect of Empirical Potential Functions on Modeling of Diamond-Like Carbon

2013 ◽  
Author(s):  
Longqiu Li ◽  
Ming Xu ◽  
Wenping Song ◽  
Guangyu Zhang ◽  
Andrey Ovcharenko
Keyword(s):  
Molecular Dynamics ◽  
Amorphous Carbon ◽  
Md Simulations ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Empirical Potential ◽  
Mechanical And Tribological Properties ◽  
Empirical Potentials ◽  
Rebo Potential ◽  
Quenching Method

Molecular dynamics (MD) simulations is an effective method to investigate the mechanical and tribological properties of amorphous carbon since the coordinates of all atoms can be calculated as a function of time. Several empirical potentials can be used to model the interatomic interactions of carbon atoms, including the Tersoff potential, the Reactive Bond Order (REBO) potential and its revised versions, and the Reactive Force Field (ReaxFF) potential. The choice of empirical potential is one of the fundamental and important assumptions in the MD approach since it can affect the properties of amorphous carbon during the MD simulations. In this study, liquid quenching method is used to model amorphous carbon for computational efficiency. We will study the influence of the three types of potentials, specifically the Tersoff potential, the 2nd REBO potential and the ReaxFF potential on DLC parameters. These parameters include the sp3 content as a function of density, the arrangement of the amorphous carbon atoms, hybridization and the radial distribution functions G(r).

Molecular Dynamics Simulation for Temperature and Graphite-Like Structure Effects on Amorphous Carbon Graphitization

2019 ◽  
Vol 956 ◽  
pp. 78-86
Author(s):  
Jia Wang ◽  
Cheng Lin Liu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Amorphous Carbon ◽  
Initial Density ◽  
Annealing Treatment ◽  
Rapid Quenching ◽  
Dynamics Simulation ◽  
Graphitization Degree ◽  
Effects Of Temperature ◽  
Quenching Method

The effects of temperature and graphite-like structure additive on the graphitization process of amorphous carbon were investigated through molecular dynamics simulation. The molecular models of amorphous carbon and graphite-like structure-amorphous carbon were constructed with the initial density of 1.62 g/cm3 and carbon atoms number of 4096 by rapid quenching method. After annealing treatment at 3200 K, 3600 K and 4000 K respectively, the evolution rules of sp2 C atoms and the instantaneous conformations of the graphite-like structure-amorphous carbon system were analyzed to investigate the effects of temperature and graphite-like structure on the graphitization process. It could be found that increasing graphitization temperature properly could improve graphitization degree of amorphous carbon. Addition of graphite-like structure could promote recrystallization of the irregular carbon atoms in amorphous carbon materials, thus accelerating graphitization process and promoting graphitization of the system.

Choosing Appropriate Interatomic Potentials for Nanometric Molecular Dynamics (MD) Simulations

2016 ◽  
Vol 686 ◽  
pp. 194-199
Author(s):  
Akinjide O. Oluwajobi ◽  
Xun Chen
Keyword(s):  
Molecular Dynamics ◽  
Diamond Tool ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Interatomic Potentials ◽  
Embedded Atom ◽  
Pair Potentials ◽  
Empirical Potentials ◽  
Nanometric Machining ◽  
Cutting Processes

There is a need to choose appropriate interatomic empirical potentials for the molecular dynamics (MD) simulation of nanomachining, so as to represent chip formation and other cutting processes reliably. Popularly applied potentials namely; Lennard-Jones (LJ), Morse, Embedded Atom Method (EAM) and Tersoff were employed in the molecular dynamics simulation of nanometric machining of copper workpiece with diamond tool. The EAM potentials were used for the modelling of the copper-copper atom interactions. The pairs of EAM-Morse and EAM-LJ were used for the workpiece-tool (copper-diamond) atomic interface. The Tersoff potential was used for the carbon-carbon interactions in the diamond tool. Multi-pass simulations were carried out and it was observed that the EAM-LJ and the EAM-Morse pair potentials with the tool modelled as deformable with Tersoff potential were best suitable for the simulation. The former exhibit the lowest cutting forces and the latter has the lowest potential energy.

scholarly journals Dynamic and Static Properties of Aqueous NaCl Solutions at 25°C as a Function of NaCl Concentration: A Molecular Dynamics Simulation Study

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Song Hi Lee
Keyword(s):  
Molecular Dynamics ◽  
Radial Distribution ◽  
Dynamic Properties ◽  
Md Simulations ◽  
Distribution Functions ◽  
Molar Conductivity ◽  
Dynamics Simulation ◽  
Radial Distribution Functions ◽  
Deep Minimum ◽  
Nacl Concentration

We present the result of molecular dynamics (MD) simulations to calculate the molar conductivity Λ m =   λ N a + +   λ C l − of NaCl in SPC/E water at 25°C as a function of NaCl concentration (c) using Ewald sums employing a velocity Verlet algorithm. It is found that the MD result for Λm with Ewald sum parameter κ = 0.10 Å−1 gives the closest one to the experimental data and that the obtained radial distribution functions g i i (r) with κ = 0.10 Å−1 show a dramatic change with a very deep minimum of g NaCl (r) and, as a result, sharp maxima of g NaNa (r) and g ClCl (r) at the distance 9.95 Å, which indicates a characteristic of ionic atmosphere, the basis of the Debye–Hückel theory of ionic solutions. The static and dynamic properties of NaCl (aq) solutions are analyzed in terms of radial distribution functions, hydration numbers, coordination numbers around Na+ and Cl−, residence times of water around Na+ and Cl−, water diffusion, and ion-ion electrostatic energies to explain the behavior of the molar conductivity Λm of NaCl obtained from our MD simulations.

On the Use of the Reverse Monte Carlo Technique to Generate Amorphous Carbon Structures

1998 ◽  
Vol 09 (07) ◽  
pp. 917-926 ◽  
Author(s):  
Vittorio Rosato ◽  
Juan C. Lascovich ◽  
Antonino Santoni ◽  
Luciano Colombo
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Amorphous Carbon ◽  
Radial Distribution ◽  
Tight Binding ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Reverse Monte Carlo ◽  
Atomic Structures ◽  
Dynamics Simulations

The reverse Monte Carlo (RMC) technique has been used to generate atomic structures of amorphous carbon based on the radial distribution functions and the fraction of differently coordinated sites measured on experimental samples. The resulting structures have been subsequently relaxed via a Tight Binding Molecular Dynamics simulation (TBMD). The radial distribution function, the energy and the fraction of 2-, 3- and 4-fold coordinated sites, evaluated on the relaxed structures, have been compared to those calculated for atomic systems generated on the basis of the "conventional" numerical melt-quench technique. We thus suggest the possibility of using RMC modeling as a useful and convenient tool for generating amorphous structures to be used as initial configurations in Molecular Dynamics simulations.

scholarly journals Understanding Covalent Grafting of Nanotubes onto Polymer Nanocomposites: Molecular Dynamics Simulation Study

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2621
Author(s):  
Seunghwa Yang
Keyword(s):  
Molecular Dynamics ◽  
Load Transfer ◽  
Cell Model ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Covalent Grafting ◽  
Modelling Strategies ◽  
Multi Walled Carbon Nanotubes ◽  
Walled Carbon Nanotubes ◽  
External Loads

Here, we systematically interrogate the effects of grafting single-walled (SWNT) and multi-walled carbon nanotubes (MWNT) to polymer matrices by using molecular dynamics (MD) simulations. We specifically investigate key material properties that include interfacial load transfer, alteration of nanotube properties, and dispersion of nanotubes in the polymer matrix. Simulations are conducted on a periodic unit cell model of the nanocomposite with a straight carbon nanotube and an amorphous polyethylene terephthalate (PET) matrix. For each type of nanotube, either 0%, 1.55%, or 3.1% of the carbon atoms in the outermost nanotubes are covalently grafted onto the carbon atoms of the PET matrix. Stress-strain curves and the elastic moduli of nanotubes and nanocomposites are determined based on the density of covalent grafting. Covalent grafting promotes two rivalling effects with respect to altering nanotube properties, and improvements in interfacial load transfer in the nanocomposites are clearly observed. The enhanced interface enables external loads applied to the nanocomposites to be efficiently transferred to the grafted nanotubes. Covalent functionalization of the nanotube surface with PET molecules can alter the solubility of nanotubes and improve dispersibility. Finally, we discuss the current limitations and challenges in using molecular modelling strategies to accurately predict properties on the nanotube and polymers systems studied here.

A Study on the Uniaxial Tension of FCC Metals at Nano Level Using MD

2008 ◽  
Vol 32 ◽  
pp. 255-258
Author(s):  
Bohayra Mortazavi ◽  
Akbar Afaghi Khatibi
Keyword(s):  
Molecular Dynamics ◽  
Uniaxial Tension ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Face Centered Cubic ◽  
Engineering Strain ◽  
Fcc Metals ◽  
Engineering Stress ◽  
Nano Science ◽  
Face Centered

Molecular Dynamics (MD) are now having orthodox means for simulation of matter in nano-scale. It can be regarded as an accurate alternative for experimental work in nano-science. In this paper, Molecular Dynamics simulation of uniaxial tension of some face centered cubic (FCC) metals (namely Au, Ag, Cu and Ni) at nano-level have been carried out. Sutton-Chen potential functions and velocity Verlet formulation of Noise-Hoover dynamic as well as periodic boundary conditions were applied. MD simulations at different loading rates and temperatures were conducted, and it was concluded that by increasing the temperature, maximum engineering stress decreases while engineering strain at failure is increasing. On the other hand, by increasing the loading rate both maximum engineering stress and strain at failure are increasing.

Molecular Dynamics Simulation of a Pullout Test on a Carbon Nanotube in a Polymer Matrix

2014 ◽  
Vol 1700 ◽  
pp. 61-66
Author(s):  
Guttormur Arnar Ingvason ◽  
Virginie Rollin
Keyword(s):  
Molecular Dynamics ◽  
Polymer Matrix ◽  
Large Scale ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Polymer Molecules ◽  
Molecular Potential ◽  
Pull Out ◽  
Walled Carbon Nanotubes

ABSTRACTAdding single walled carbon nanotubes (SWCNT) to a polymer matrix can improve the delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics (MD) simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential. This potential includes non-bonded interactions, as well as bonds, angles and dihedrals to create a MD model for a SWCNT and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the COMPASS parameters. The first one was a tensile test on a SWCNT, leading to a Young’s modulus of 1.4 TPa at 300K. The second one was a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.

scholarly journals Investigation of Microscopic Structure and Ion Dynamics in Liquid Li(Na, K)EutecticCl Systems by Molecular Dynamics Simulation

2018 ◽  
Vol 8 (10) ◽  
pp. 1874 ◽  
Author(s):  
Jie Wu ◽  
Jia Wang ◽  
Haiou Ni ◽  
Guimin Lu ◽  
Jianguo Yu
Keyword(s):  
Molecular Dynamics ◽  
Ionic Conductivity ◽  
Shear Viscosity ◽  
Ion Pairs ◽  
Liquid Structure ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Molten Chloride ◽  
Ion Clusters ◽  
Self Diffusion

Molten chloride salts are the main components in liquid metal batteries, high-temperature heat storage materials, heat transfer mediums, and metal electrolytes. In this paper, interest is centered on the influence of the LiCl component and temperature on the local structure and transport properties of the molten LiCl-NaCl-KCl system over the temperature range of 900 K to 1200 K. The liquid structure and properties have been studied across the full composition range by molecular dynamics (MD) simulation of a sufficient length to collect reliable values, such as the partial radial distribution function, angular distribution functions, coordination numbers distribution, density, self-diffusion coefficient, ionic conductivity, and shear viscosity. Densities obtained from simulations were underestimated by an average 5.7% of the experimental values. Shear viscosities and ionic conductivity were in good agreement with the experimental data. The association of all ion pairs (except for Li-Li and Cl-Cl) was weakened by an increasing LiCl concentration. Ion clusters were formed in liquids with increasing temperatures. The self-diffusion coefficients and ionic conductivity showed positive dependences on both LiCl concentration and temperature, however, the shear viscosity was the opposite. By analyzing the hydrodynamic radii of each ion and the coordination stability of cation-anion pairs, it was speculated that ion clusters could be the cation-anion coordinated structure and affected the macro properties.

scholarly journals An Analysis Based on Molecular Docking and Molecular Dynamics Simulation Study of Bromelain as Anti-SARS-CoV-2 Variants

2021 ◽  
Vol 12 ◽  
Author(s):  
Trina Ekawati Tallei ◽  
Fatimawali ◽  
Afriza Yelnetty ◽  
Rinaldi Idroes ◽  
Diah Kusumawaty ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Three Dimensional ◽  
Md Simulations ◽  
Inhibitory Effect ◽  
Dynamics Simulation ◽  
Novel Coronavirus

The rapid spread of a novel coronavirus known as SARS-CoV-2 has compelled the entire world to seek ways to weaken this virus, prevent its spread and also eliminate it. However, no drug has been approved to treat COVID-19. Furthermore, the receptor-binding domain (RBD) on this viral spike protein, as well as several other important parts of this virus, have recently undergone mutations, resulting in new virus variants. While no treatment is currently available, a naturally derived molecule with known antiviral properties could be used as a potential treatment. Bromelain is an enzyme found in the fruit and stem of pineapples. This substance has been shown to have a broad antiviral activity. In this article, we analyse the ability of bromelain to counteract various variants of the SARS-CoV-2 by targeting bromelain binding on the side of this viral interaction with human angiotensin-converting enzyme 2 (hACE2) using molecular docking and molecular dynamics simulation approaches. We have succeeded in making three-dimensional configurations of various RBD variants using protein modelling. Bromelain exhibited good binding affinity toward various variants of RBDs and binds right at the binding site between RBDs and hACE2. This result is also presented in the modelling between Bromelain, RBD, and hACE2. The molecular dynamics (MD) simulations study revealed significant stability of the bromelain and RBD proteins separately up to 100 ns with an RMSD value of 2 Å. Furthermore, despite increases in RMSD and changes in Rog values of complexes, which are likely due to some destabilized interactions between bromelain and RBD proteins, two proteins in each complex remained bonded, and the site where the two proteins bind remained unchanged. This finding indicated that bromelain could have an inhibitory effect on different SARS-CoV-2 variants, paving the way for a new SARS-CoV-2 inhibitor drug. However, more in vitro and in vivo research on this potential mechanism of action is required.

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