COMPUTER SIMULATION OF EPITAXIAL GROWTH OF SILICON ON Si (001) SURFACE

2002 ◽  
Vol 16 (01n02) ◽  
pp. 227-232 ◽  
Author(s):  
M. H. LIANG ◽  
X. XIE ◽  
S. LI
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Epitaxial Growth ◽  
Interatomic Potential ◽  
Simulation Method ◽  
Growth Direction ◽  
Dynamics Simulation ◽  
Interatomic Potentials ◽  
Weber Potential ◽  
Deposition Conditions

Epitaxial growth of silicon on Si (001) surface has been studied with interatomic potential based molecular dynamics simulation method. Three silicon interatomic potentials developed separately by Stillinger-Weber, Tersoff, and Bazant-Kaxiras were used. Energetic beam of 8 eV, substrate temperature of 500K and deposition rate of 1.15 ps/atom were used as the deposition conditions. Morphologies of the growth were obtained and densities in the growth direction analyzed. Epitaxial growth under the deposition conditions imposed was found possible only using the Stillinger-Weber potential. Disordered growths of differing degree were obtained using the Bazant-Kaxiras and Tersoff potentials. The disordered growth may be attributed to the existence of an epitaxial transition temperature higher than 500K that these potentials might have.

scholarly journals Computer simulation of complex of lysine dendrigraft with molecules of therapeutic KED peptide

2019 ◽  
Vol 24 ◽  
pp. 02008
Author(s):  
Igor Neelov ◽  
Valerii Bezrodnyi ◽  
Anna Marchenko ◽  
Emil Fatullaev ◽  
Sofia Miktaniuk
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Molecular Dynamics Simulation ◽  
Complex Formation ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Stable Complex ◽  
Target Organs ◽  
Therapeutic Peptides ◽  
Drug And Gene Delivery

Lysine dendrimers and dendrigrafts are often used in biomedicine for drug and gene delivery to different target organs or cells. In present paper the possibility of complex formation by lysine dendrigraft and 16 molecules of therapeutic KED peptide was investigated using molecular dynamics simulation method. A system containing of one dendrigraftt and 16 KED peptides in water were studied. It was shown that stable complex consisting of the dendrigraft and the peptide molecules formed and structure of this complex was studied. Similar complexes could be used in future for delivery of other therapeutic peptides to target organs.

Molecular Dynamics Simulation of Thermal Conductivity of Silicon Films Using Environment-Dependent Interatomic Potential

Volume 4 ◽  
2004 ◽  
Author(s):  
Xinwei Wang ◽  
Cecil Lawrence
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Film Thickness ◽  
Lattice Boltzmann ◽  
Interatomic Potential ◽  
Silicon Films ◽  
Dynamics Simulation ◽  
Nonequilibrium Molecular Dynamics ◽  
Boltzmann Method ◽  
Weber Potential

In this work, nonequilibrium molecular dynamics is used to predict the thermal conductivity of nanoscale thin silicon films in the thickness direction. Recently developed environment-dependent interatomic potential for silicon, which offers considerable improvement over the more common Stillinger-Weber potential, is used. Silicon films of various thicknesses are modeled to establish the variation of thermal conductivity with the film thickness. The obtained relationship between the thermal conductivity and the film thickness is compared with the results of the Lattice Boltzmann method, and sound agreement is observed.

Molecular Dynamics Simulation With Interval-Valued Interatomic Potentials

2016 ◽  
Author(s):  
Anh Tran ◽  
Yan Wang
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Interatomic Potential ◽  
Thermal Fluctuation ◽  
Potential Functions ◽  
Dynamics Simulation ◽  
Computational Time ◽  
System Control ◽  
Interatomic Potentials ◽  
Time Step

In molecular dynamics (MD) simulation, the two main sources of uncertainty are the interatomic potential functions and thermal fluctuation. The accuracy of the interatomic potential functions plays a vital role toward the reliability of MD simulation prediction. Reliable molecular dynamics (R-MD) is an interval-based MD simulation platform, where atomistic positions and velocities are represented as Kaucher (or generalized) intervals to capture the uncertainty associated with the inter-atomic potentials. The advantage of this uncertainty quantification (UQ) approach is that the uncertainty effect can be assessed on-the-fly with only one run of simulation, and thus the computational time for UQ is significantly reduced. In this paper, an extended interval statistical ensemble is introduced to quantify the uncertainty associated with the system control variables, such as temperature and pressure at each time-step. This method allows for quantifying and propagating the uncertainty in the system as MD simulation advances. An example of interval isothermal-isobaric (NPT) ensemble is implemented to demonstrate the feasibility of applying the intrusive UQ technique toward MD simulation.

Equilibrium Molecular Dynamics and the Thermal Behavior of Small Systems

2010 ◽  
Author(s):  
Alejandro Guajardo-Cue´llar ◽  
David B. Go ◽  
Mihir Sen
Keyword(s):  
Molecular Dynamics ◽  
Thermal Behavior ◽  
Interatomic Potential ◽  
Model System ◽  
Dynamics Simulation ◽  
Small Scale ◽  
Interatomic Potentials ◽  
Power Spectral ◽  
Anharmonic Potential ◽  
Dynamics Calculation

Equilibrium molecular dynamics can be used to investigate the heat transport due to conduction in small scale systems. The results from a molecular dynamics simulation can be used to extract the thermal behavior. In this study, an equilibrium molecular dynamics calculation of a model system using three interatomic potentials, a harmonic potential, an anharmonic potential, and the Tersoff interatomic potential, has been conducted. The characteristics of the transport are studied from the kinetic energies in the frequency domain. The power spectral density of the kinetic energy of the three different potentials is compared. This study helps to understand how heat is transported in a small system of atoms.

Preliminary Studies on Molecular Dynamics Simulation of Friction Stir Processing of Aluminium Alloys

2019 ◽  
Vol 796 ◽  
pp. 155-163
Author(s):  
Oyindamola Kayode ◽  
Oluwole A. Olufayo ◽  
Esther Titilayo Akinlabi
Keyword(s):  
Molecular Dynamics ◽  
Aluminium Alloy ◽  
Friction Stir Processing ◽  
Md Simulation ◽  
Equations Of Motion ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Interatomic Potentials ◽  
Friction Stir ◽  
Atoms And Molecules

Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules at nanoscale. It allows interaction between the atoms and molecules for a fixed period, giving an understanding of the system as they dynamically begin to evolve. The paths of the atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting atoms, where interatomic potentials or molecular mechanics force fields are used to calculate forces and potential energies between the atoms. In this study, the basic parameters used in MD simulations are briefly discussed. An MD simulation of the friction stir processing (FSP) of aluminium alloy 6061-T6 was carried out to explain the invisible thermodynamic microscopic details which occurred during the process. However, the aim of the MD simulation is not to predict precisely the process, but to predict the average thermodynamic behavior of the process if conducted in a practical state. This is to further enhance the understanding of the FSP process. The results obtained from the MD simulation prove that it may be possible to adequately represent the MD simulation of the FSP of an aluminium alloy.

Femtosecond photoelectron spectroscopy of the I2− anion: A semiclassical molecular dynamics simulation method

1999 ◽  
Vol 110 (8) ◽  
pp. 3736-3747 ◽  
Author(s):  
Victor S. Batista ◽  
Martin T. Zanni ◽  
B. Jefferys Greenblatt ◽  
Daniel M. Neumark ◽  
William H. Miller
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Photoelectron Spectroscopy ◽  
Simulation Method ◽  
Dynamics Simulation

Self-diffusion of lignite/water under different temperatures and pressure: A molecular dynamics study

2016 ◽  
Vol 30 (01) ◽  
pp. 1550253 ◽  
Author(s):  
Xinjian Liu ◽  
Yu Jin ◽  
Congliang Huang ◽  
Jingfeng He ◽  
Zhonghao Rao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Water System ◽  
Simulation Method ◽  
The Self ◽  
Dynamics Simulation ◽  
Low Rank ◽  
Self Diffusion ◽  
Change Mechanism ◽  
Different Temperatures ◽  
Temperature And Pressure

Temperature and pressure have direct and remarkable implications for drying and dewatering effect of low rank coals such as lignite. To understand the microenergy change mechanism of lignite, the molecular dynamics simulation method was performed to study the self-diffusion of lignite/water under different temperatures and pressure. The results showed that high temperature and high pressure can promote the diffusion of lignite/water system, which facilitates the drying and dewatering of lignite. The volume and density of lignite/water system will increase and decrease with temperature increasing, respectively. Though the pressure within simulation range can make lignite density increase, the increasing pressure showed a weak impact on variation of density.

THE "FOLDING" BEHAVIORS OF HOMOPOLYMERS WITH ONE END FIXED

2004 ◽  
Vol 18 (15) ◽  
pp. 2123-2139 ◽  
Author(s):  
BIN XUE ◽  
JUN WANG ◽  
WEI WANG
Keyword(s):  
Molecular Dynamics ◽  
Chain Length ◽  
Conformational Changes ◽  
Canonical Ensemble ◽  
Interaction Strength ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Native Conformation ◽  
Collapse Temperature

We study the "folding" behaviors of homopolymers with one end fixed. By using canonical ensemble molecular dynamics simulation method, we observe the conformational changes during folding processes. Long chains collapse to the helical nuclei, then regroup to helix from the free-end to form the compact conformations through the middle stages of helix-like coil and helix-like cone, while short chains do not apparently have the above mentioned middle stages. Through simulated annealing, the native conformation of homopolymer chain in our model is found to be helix. We show the relations between specific heat C v (T) and radius of gyration R g (T) as functions of temperature, chain length and the interaction strength, respectively. We find that these two quantities match well and can be combined to interpret the "folding" process of the homopolymer. It is found that the collapse temperature Tθ and the native-like folding temperature T f do not change with the chain length in our model, however the interaction strength affects the values of Tθ and T f .

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