Stability of the Fullerenes Thin Film Deposited on the SI(100) Surface

1993 ◽  
Vol 308 ◽  
Author(s):  
H. Rafii-Tabar ◽  
Y. Kawazoe ◽  
H. Kamiyama
Keyword(s):  
Thin Film ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Theoretical Basis ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Many Body ◽  
Si Substrate ◽  
Monolayer Film ◽  
Simulation Based

ABSTRACTWe have performed a constant temperature classical molecular dynamics simulation of the epitaxial growth of a C60 monolayer film deposited on the dimerized Si(100) surface. Our simulation, based on non-central many-body inter-atomic potentials, is capable of predicting the structural stability of the C60 film and the Si substrate and provides a theoretical basis for the results of a recently-performed STM- based experiment for this system.Three-dimensional geometries have been generated on computer and used for the animation of the simulation runs.

Improved Sampling Strategies for Protein Model Refinement based on Molecular Dynamics Simulation

2020 ◽  
Author(s):  
Lim Heo ◽  
Collin Arbour ◽  
Michael Feig
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structure Prediction ◽  
Protein Structures ◽  
Conformational Space ◽  
Dynamics Simulation ◽  
Model Refinement ◽  
Protein Model ◽  
Lower Accuracy ◽  
Simulation Based

Protein structures provide valuable information for understanding biological processes. Protein structures can be determined by experimental methods such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, or cryogenic electron microscopy. As an alternative, in silico methods can be used to predict protein structures. Those methods utilize protein structure databases for structure prediction via template-based modeling or for training machine-learning models to generate predictions. Structure prediction for proteins distant from proteins with known structures often results in lower accuracy with respect to the true physiological structures. Physics-based protein model refinement methods can be applied to improve model accuracy in the predicted models. Refinement methods rely on conformational sampling around the predicted structures, and if structures closer to the native states are sampled, improvements in the model quality become possible. Molecular dynamics simulations have been especially successful for improving model qualities but although consistent refinement can be achieved, the improvements in model qualities are still moderate. To extend the refinement performance of a simulation-based protocol, we explored new schemes that focus on an optimized use of biasing functions and the application of increased simulation temperatures. In addition, we tested the use of alternative initial models so that the simulations can explore conformational space more broadly. Based on the insight of this analysis we are proposing a new refinement protocol that significantly outperformed previous state-of-the-art molecular dynamics simulation-based protocols in the benchmark tests described here. <br>

The Study on Young's Modulus of Multilayered Cu/Ni Multilayered Nano Thin Films by Molecular Dynamics Simulation

2014 ◽  
Vol 513-517 ◽  
pp. 113-116
Author(s):  
Jen Ching Huang ◽  
Fu Jen Cheng ◽  
Chun Song Yang
Keyword(s):  
Thin Film ◽  
Thin Films ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Strain Rate ◽  
Young’S Modulus ◽  
Potential Function ◽  
Dynamics Simulation ◽  
System Temperature ◽  
Simulation Results

The Youngs modulus of multilayered nanothin films is an important property. This paper focused to investigate the Youngs Modulus of Multilayered Ni/Cu Multilayered nanoThin Films under different condition by Molecular Dynamics Simulation. The NVT ensemble and COMPASS potential function were employed in the simulation. The multilayered nanothin film contained the Ni and Cu thin films in sequence. From simulation results, it is found that the Youngs modulus of Cu/Ni multilayered nanothin film is different at different lattice orientations, temperatures and strain rate. After experiments, it can be found that the Youngs modulus of multilayered nanothin film in the plane (100) is highest. As thickness of the thin film and system temperature rises, Youngs modulus of multilayered nanothin film is reduced instead. And, the strain rate increases, the Youngs modulus of Cu/Ni multilayered nanothin film will also increase.

Molecular Dynamics Simulation of Sputtering with Mmany-Body Interactions

1988 ◽  
Vol 100 ◽  
Author(s):  
Davy Y. Lo ◽  
Tom A. Tombrello ◽  
Mark H. Shapiro ◽  
Don E. Harrison
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Single Crystal ◽  
Low Energy ◽  
Dynamics Simulation ◽  
Embedded Atom Method ◽  
Many Body ◽  
Embedded Atom ◽  
Dynamics Simulations ◽  
Small Single Crystal

ABSTRACTMany-body forces obtained by the Embedded-Atom Method (EAM) [41 are incorporated into the description of low energy collisions and surface ejection processes in molecular dynamics simulations of sputtering from metal targets. Bombardments of small, single crystal Cu targets (400–500 atoms) in three different orientations ({100}, {110}, {111}) by 5 keV Ar+ ions have been simulated. The results are compared to simulations using purely pair-wise additive interactions. Significant differences in the spectra of ejected atoms are found.

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