scholarly journals The speed-locking effect of particles on a graphene layer with travelling surface wave

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Dan Wang ◽  
Lifeng Wang ◽  
Zhili Hu
Keyword(s):  
Surface Wave ◽  
Graphene Layer ◽  
Pair Potential ◽  
Thermal Fluctuation ◽  
Initial Position ◽  
Dynamics Simulation ◽  
Initial Kinetic Energy ◽  
Fast Diffusion ◽  
Diffusion Phenomena ◽  
Locking Effect

Abstract Fast diffusion induced by thermal fluctuation and vibration has been detected at nanoscales. In this paper, the movement of particle on a graphene layer with travelling surface wave is studied by molecular dynamics simulation and theoretical model. It is proved that the particle will keep moving at the wave speed with certain prerequisite conditions, namely speed-locking effect. By expressing van der Waals (vdW) potential between particle and wavy surface as a function of curvatures, the mechanism is clarified based on the puddle of potential in a relative wave-frame coordinate. Two prerequisite conditions are proposed: the initial position of particle should locate in the potential puddle, and the initial kinetic energy cannot drive particle to jump out of the potential puddle. The parametric analysis indicates that the speed-locking region will be affected by wavelength, amplitude and pair potential between particle and wave. With smaller wavelength, larger amplitude and stronger vdW potential, the speed-locking region is larger. This work reveals a new kind of coherent movement for particles on layered material based on the puddle potential theory, which can be an explanation for fast diffusion phenomena at nano scales.

Molecular Dynamics Simulation of the Buckling Behavior of Boron Nitride Nanotubes under Uniaxial Compressive Loading

2010 ◽  
Vol 297-301 ◽  
pp. 984-989 ◽  
Author(s):  
S. Ebrahimi-Nejad ◽  
Ali Shokuhfar ◽  
A. Zare-Shahabadi
Keyword(s):  
Boron Nitride ◽  
Compressive Loading ◽  
Pair Potential ◽  
Md Simulations ◽  
Boron Nitride Nanotubes ◽  
Dynamics Simulation ◽  
Buckling Loads ◽  
Buckling Behavior ◽  
Bond Stretching ◽  
Different Diameters

Boron Nitride nanotubes (BNNTs) together with carbon nanotubes (CNTs) have attracted the wide attention of the scientific community and have been considered as promising materials due to their unique structural and physical properties. In this paper, the behavior of BNNTs of different diameters under compressive loading has been studied through molecular dynamic (MD) simulations. We have used a Lennard-Jones pair potential to characterize the interactions between non-bonded atoms and harmonic potentials for bond stretching and bond angle vibrations. Results of the MD simulations determine the critical buckling loads of the BNNTs of various diameters under uniaxial compression, and indicate that for the simulated BNNTs of length L = 6 nm, the critical buckling loads increase by increasing the nanotube diameters.

Multiscale Analysis of Silicon LPCVD Reactor

2005 ◽  
Author(s):  
Yukinori Sakiyama ◽  
Shu Takagi ◽  
Yoichiro Matsumoto
Keyword(s):  
Potential Energy ◽  
Ab Initio ◽  
Multiscale Analysis ◽  
Potential Model ◽  
Research Work ◽  
Pair Potential ◽  
Dynamics Simulation ◽  
Molecular Orbital Calculations ◽  
Ongoing Research ◽  
Trajectory Calculations

We demonstrate the multiscale analysis of the transport phenomena in a low pressure reactor. In this method, the macroscopic phenomena such as the temperature and the density distribution are related to the microscopic electronic structure of atom/molecule. By connecting the different scales with physical models, the macroscopic properties are obtained starting from the first principle calculation without any empirical parameters. Here, we take the silicon epitaxial growth from a gas mixture of silane and hydrogen as an example. As the first step of this method, we calculated the intermolecular potential energy of SiH4/H2 using the ab initio molecular orbital calculations. Then, an analytical pair potential model was constructed to reproduce the potential energy surface obtained from the ab initio calculation. We have confirmed the validation of the potential model by comparing the experimental data of the transport properties with the molecular dynamics simulation using the potential model. Subsequently, the binary molecular collision models were constructed by the classical trajectory calculation using the potential model as the second step of the multiscale analysis. The trajectory calculations were conducted for the various combinations of the initial translational and the rotational energy. Through the statistical analysis of the trajectory calculations, the elastic/inelastic collision cross section and the scattering angle model were constructed. Finally, the direct simulation Monte Carlo simulation of flow field in a low parssure reactor was executed. The thin film thickness distribution was also investigated and discussed. This method was extended to analyze the surface reaction, which is an ongoing research work and only the current progress is reported here.

ABEEM/MM-BASED PAIR POTENTIAL FOR MOLECULAR DYNAMICS SIMULATION OF Fe2+(aq) AND Fe3+(aq)

2006 ◽  
Vol 05 (spec01) ◽  
pp. 341-353 ◽  
Author(s):  
XIN LI ◽  
ZHONG-ZHI YANG
Keyword(s):  
Pair Potential ◽  
High Spin State ◽  
Binding Energies ◽  
Dynamics Simulation ◽  
Water Model ◽  
Ionic Clusters ◽  
Dynamic Simulations ◽  
Electronegativity Equalization Method ◽  
Hydration Shells ◽  
Dynamical Properties

On the basis of atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), we have constructed the effective Fe 2+ and Fe 3+ ion-water potential by fitting to ab initio structures and binding energies for ionic clusters, where Fe 2+ and Fe 3+ ions are in their high spin state. We then apply the ion-water interaction potential in combination with the ABEEM-7P water model to molecular dynamic simulations of single-ion Fe 2+( aq ) and Fe 3+( aq ) solutions, managing to reproduce many experimental, structural and dynamical properties of the solutions. The effects of ionic charges on structural and dynamical properties of water molecules in the hydration shells are discussed.

scholarly journals Molecular Dynamics Simulation and Measurement of Contact Angle of Water Droplet on a Platinum Surface

2001 ◽  
Author(s):  
Satish G. Kandlikar ◽  
Shigeo Maruyama ◽  
Mark E. Steinke ◽  
Tatsuto Kimura
Keyword(s):  
Molecular Dynamics ◽  
Liquid Droplet ◽  
Contact Region ◽  
Pair Potential ◽  
Heat Bath ◽  
Spreading Rate ◽  
Contact Angles ◽  
Dynamics Simulation ◽  
Platinum Surface ◽  
Receding Contact

Abstract A water liquid droplet in contact with a platinum surface was simulated by the molecular dynamics method. Water molecules were modeled by SPC/E and one layer of harmonic molecules represented the platinum surface with the constant temperature heat bath model using the phantom molecules. Here, the water-platinum pair potential developed by Spohr (1989) based on extended Hückel calculations was employed. In the spreading process of the liquid droplet on the platinum surface, the area of contact region between water and platinum expanded just in proportional to the one-third power of time. This spreading rate was clearly in contrast to the case of Lennard-Jones droplet. The contact angles of water on a platinum surface under saturated conditions are measured. The measurements are made in a vacuum container using de-ionized and degassed water on a clean platinum surface. The equilibrium static, advancing and receding contact angles are measured by changing the orientation of the platinum surface. The droplets of different masses are placed on the horizontal platinum surface. The surface is the inclined to 20, 30 and 40 degrees. The advancing and receding contact angles under these conditions are measured.

scholarly journals Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps

2021 ◽  
Vol 478 (5) ◽  
pp. 1023-1042
Author(s):  
Hideaki Sato ◽  
Masakazu Sugishima ◽  
Mai Tsukaguchi ◽  
Takahiro Masuko ◽  
Mikuru Iijima ◽  
...  
Keyword(s):  
Binding Site ◽  
Substrate Binding ◽  
Thermal Fluctuation ◽  
Crystal Structure Analysis ◽  
Dynamics Simulation ◽  
Side Chains ◽  
Amino Acid Residues ◽  
Substrate Binding Site ◽  
Cofactor Binding ◽  
Single Substrate

Hydroxymethylbilane synthase (HMBS), which is involved in the heme biosynthesis pathway, has a dipyrromethane cofactor and combines four porphobilinogen (PBG) molecules to form a linear tetrapyrrole, hydroxymethylbilane. Enzyme kinetic study of human HMBS using a PBG-derivative, 2-iodoporphobilinogen (2-I-PBG), exhibited noncompetitive inhibition with the inhibition constant being 5.4 ± 0.3 µM. To elucidate the reaction mechanism of HMBS in detail, crystal structure analysis of 2-I-PBG-bound holo-HMBS and its reaction intermediate possessing two PBG molecules (ES2), and inhibitor-free ES2 was performed at 2.40, 2.31, and 1.79 Å resolution, respectively. Their overall structures are similar to that of inhibitor-free holo-HMBS, and the differences are limited near the active site. In both 2-I-PBG-bound structures, 2-I-PBG is located near the terminus of the cofactor or the tetrapyrrole chain. The propionate group of 2-I-PBG interacts with the side chain of Arg173, and its acetate group is associated with the side chains of Arg26 and Ser28. Furthermore, the aminomethyl group and pyrrole nitrogen of 2-I-PBG form hydrogen bonds with the side chains of Gln34 and Asp99, respectively. These amino acid residues form a single substrate-binding site, where each of the four PBG molecules covalently binds to the cofactor (or oligopyrrole chain) consecutively, ultimately forming a hexapyrrole chain. Molecular dynamics simulation of the ES2 intermediate suggested that the thermal fluctuation of the lid and cofactor-binding loops causes substrate recruitment and oligopyrrole chain shift needed for consecutive condensation. Finally, the hexapyrrole chain is hydrolyzed self-catalytically to produce hydroxymethylbilane.

Molecular Dynamics Simulation of Molten Alkali Nitrates

2001 ◽  
Vol 56 (5) ◽  
pp. 337-341 ◽  
Author(s):  
G. Vöhringer ◽  
J. Richter
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Short Range ◽  
Spin Echo ◽  
Isotope Effects ◽  
Pair Potential ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Self Diffusion ◽  
Transport Effects

Abstract Molecular dynamics (MD) simulations have been performed for several pure alkali nitrate melts. Special attention was paid to the examination of the interaction potential: macroscopic quantities like pressure were calculated and compared with real values. To improve the results the commonly used potential for alkali nitrates (Coulomb pair potential and Born-type repulsion) has been extended by a short-range-attraction term to meet the real behaviour of the liquid. With these improved potentials, simulations of pure LiNO3, NaNO3, KNO3, and RbNO3 have been performed with special regard to the influence of size and mass of the cations on the transport effects to show analogies to isotope effects. The calculated self diffusion coefficients (SDC) have been compared to results obtained with the NMR spin echo method.

Molecular dynamics simulation of interhalogen compounds. 1. Liquid chlorine trifluoride (ClF3): structure and thermodynamics

1992 ◽  
Vol 70 (1) ◽  
pp. 34-38 ◽  
Author(s):  
Ramesh K. Wadi ◽  
Vivek Saxena
Keyword(s):  
Molecular Dynamics ◽  
Thermodynamic Properties ◽  
Md Simulation ◽  
Pair Potential ◽  
Liquid Structure ◽  
Spectroscopic Studies ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Self Diffusion ◽  
Laser Raman

The results of a molecular dynamics (MD) simulation study of liquid chlorine trifluoride (ClF3) at 217, 260, and 287 K are reported. The cubic simulation cell consists of 108 ClF3 molecules assumed to be interacting via site–site Lennard–Jones 12–6 pair potential. The parameters for F–F and Cl–Cl interaction are the same as used for the simulation of F2, and Cl2, respectively, and those for the Cl–F cross interaction are calculated using Lorentz–Berthelot rules. These results are then used to calculate various radial distribution functions characteristic of the liquid structure. Thermodynamic properties, namely, configurational energy, constant volume specific heat, and internal pressure are also reported. The time-dependent properties, mean square force and torque, self diffusion coefficient, and the quantum corrections to the free energy, were also obtained. The dimer configuration drawn based on the observed contact distances was found to be in good agreement with the results of matrix isolation infrared and laser Raman spectroscopic studies. Keywords: MD simulation, interhalogens, liquid structure, thermodynamic properties.

The Basic Theories of Molecular Dynamics Simulation

2013 ◽  
Vol 444-445 ◽  
pp. 1483-1488
Author(s):  
Wen Hai Gai ◽  
Ran Guo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Equations Of Motion ◽  
Time Integration ◽  
Pair Potential ◽  
Dynamics Simulation ◽  
Integration Algorithm ◽  
Quantum Mechanical Method ◽  
Multi Body ◽  
System 1

Molecular dynamics simulation Refers to multi-body system consisting of atomicnucleusand electrons, solving Newton's equations of motion. Each nucleus is seen as a movement under the combined action of all other nucleus and electrons. By analyzing the force of every particle in the system, classical or quantum mechanical method is used to solve the position and velocity of individual particles in the system for a certain time, and to determine the state of motion of the particle, then to calculate the structure and properties of the system [1]. This paper describes the basic concepts and methods of molecular dynamics which are comprised of inter-atomic potential function like pair potential and multi-body potentials, time integration algorithm and so and.

The self-similar character of the microscopic thermal fluctuation inside an argon–copper nanofluid

2016 ◽  
Vol 18 (31) ◽  
pp. 21930-21936 ◽  
Author(s):  
T. Jia ◽  
D. Gao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Thermal Behavior ◽  
Thermal Fluctuation ◽  
The Self ◽  
Dynamics Simulation ◽  
Similar Character ◽  
Self Similar

The microscopic thermal behavior inside an argon–copper nanofluid is investigated based on equilibrium molecular dynamics simulation.

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