Prediction of molecular-dynamics simulation results using feedforward neural networks: Reaction of a C2 dimer with an activated diamond (100) surface

2005 ◽  
Vol 123 (22) ◽  
pp. 224711 ◽  
Author(s):  
Paras M. Agrawal ◽  
Abdul N. A. Samadh ◽  
Lionel M. Raff ◽  
Martin T. Hagan ◽  
Satish T. Bukkapatnam ◽  
...  
Keyword(s):  
Neural Networks ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Feedforward Neural Networks ◽  
Dynamics Simulation ◽  
Simulation Results

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.

Nano-Indentation Simulation Study Based on Parallel Computing

2012 ◽  
Vol 500 ◽  
pp. 696-701
Author(s):  
Ying Zhu ◽  
Sen Song ◽  
Ling Ling Xie ◽  
Shun He Qi ◽  
Qian Qian Liu
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computing ◽  
Molecular Dynamics Simulation ◽  
Large Scale ◽  
Dynamics Simulation ◽  
Parallel Computer ◽  
Nano Indentation ◽  
Simulation Results ◽  
The Impact ◽  
Simulation Time

This method of parallel computing into nanoindentation molecular dynamics simulation (MDS), the author uses a nine-node parallel computer and takes the single crystal aluminum as the experimental example, to implement the large-scale process simulation of nanoindentation. Compared the simulation results with experimental results is to verify the reliability of the simulation. The method improves the computational efficiency and shortens the simulation time and the expansion of scale simulation can significantly reduce the impact of boundary conditions, effectively improve the accuracy of the molecular dynamics simulation of nanoindentation.

scholarly journals Nanotribology at high temperatures

2012 ◽  
Vol 3 ◽  
pp. 586-588 ◽  
Author(s):  
Saurav Goel ◽  
Alexander Stukowski ◽  
Gaurav Goel ◽  
Xichun Luo ◽  
Robert L Reuben
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Melting Point ◽  
High Temperatures ◽  
Conceptual Understanding ◽  
Experimental Verification ◽  
Elevated Temperatures ◽  
Dynamics Simulation ◽  
Major Constraint ◽  
Simulation Results

Recent molecular dynamics simulation results have increased conceptual understanding of the grazing and the ploughing friction at elevated temperatures, particularly near the substrate’s melting point. In this commentary we address a major constraint concerning its experimental verification.

scholarly journals Molecular Dynamics Simulation of Grain Growth in Nanocrystalline Ni

2012 ◽  
Vol 715-716 ◽  
pp. 599-604 ◽  
Author(s):  
Stephen M. Foiles
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Grain Growth ◽  
High Density ◽  
Dynamics Simulation ◽  
Square Root ◽  
Twin Boundaries ◽  
Parabolic Kinetics ◽  
Simulation Results ◽  
The Creation

Grain growth in nanocrystalline Ni has been simulated by molecular dynamics. The simulations show the creation of a high density of twin boundaries during the growth as well as the formation of vacancies consistent with recent experimental observations. The growth follows parabolic kinetics with the diameter increasing with the square root of time consistent with behavior of conventional scale metals but in disagreement with prior simulation results.

scholarly journals Construction of Novel Aspartokinase Mutant A380I and Its Characterization by Molecular Dynamics Simulation

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3379 ◽  
Author(s):  
Caijing Han ◽  
Li Fang ◽  
Chunlei Liu ◽  
Yunna Gao ◽  
Weihong Min
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
High Throughput Screening ◽  
Model Comparison ◽  
Site Directed Mutagenesis ◽  
Dynamics Simulation ◽  
Wild Type ◽  
Open Conformation ◽  
Simulation Results ◽  
Optimal Ph

In this study, a novel monomer aspartokinase (AK) from Corynebacterium pekinense was identified, and its monomer model was constructed. Site 380 was identified by homologous sequencing and monomer model comparison as the key site which was conserved and located around the binding site of the inhibitor Lys. Furthermore, the mutant A380I with enzyme activity 11.32-fold higher than wild type AK (WT-AK), was obtained by site-directed mutagenesis and high throughput screening. In the mutant A380I, the optimal temperature was raised from 26 °C (WT-AK) to 28 °C, the optimal pH remained unchanged at 8.0, and the half-life was prolonged from 4.5 h (WT-AK) to 6.0 h, indicating enhanced thermal stability. The inhibition of A380I was weakened at various inhibitor concentrations and even activated at certain inhibitor concentrations (10 mM of Lys, 5 mM or 10 mM of Lys + Thr, 10 mM of Lys + Met, 5 mM of Lys + Thr + Met). Molecular dynamics simulation results indicated that the occupancy rate of hydrogen bond between A380I and ATP was enhanced, the effect of Lys (inhibitor) on the protein was weakened, and the angle between Ser281-Tyre358 and Asp359-Gly427 was increased after mutation, leading to an open conformation (R-state) that favored the binding of substrate.

Phase separation in ternary fluid mixtures: a molecular dynamics study

Soft Matter ◽  
2015 ◽  
Vol 11 (11) ◽  
pp. 2213-2219 ◽  
Author(s):  
Awaneesh Singh ◽  
Sanjay Puri
Keyword(s):  
Molecular Dynamics ◽  
Phase Separation ◽  
Molecular Dynamics Simulation ◽  
Separation Process ◽  
Hydrodynamic Flow ◽  
Dynamics Simulation ◽  
Fluid Mixtures ◽  
Phase Separation Process ◽  
Simulation Results ◽  
Late Stages

Our molecular dynamics simulation results strongly support the contention that the hydrodynamic flow should control the phase-separation process in ternary fluid (ABC) mixtures at late stages.

Incoherent neutron scattering of copper azurin: a comparison with molecular dynamics simulation results

1999 ◽  
Vol 28 (6) ◽  
pp. 447-456 ◽  
Author(s):  
Alessandro Paciaroni ◽  
Maria Elena Stroppolo ◽  
Caterina Arcangeli ◽  
Anna Rita Bizzarri ◽  
Alessandro Desideri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Neutron Scattering ◽  
Dynamics Simulation ◽  
Incoherent Neutron Scattering ◽  
Simulation Results ◽  
Incoherent Neutron

Molecular dynamics simulation of a hydrated phospholipid bilayer

1994 ◽  
Vol 344 (1309) ◽  
pp. 239-260 ◽  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Complex Systems ◽  
Phospholipid Bilayer ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Hydrocarbon Chains ◽  
Membrane Bound ◽  
Simulation Results ◽  
Well Data

A hydrated bilayer of the phospholipid 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) has been studied in the course of a molecular dynamics simulation. Comparison of the simulation results with experiment indicates that generally the two agree well. Data are presented concerning all the major system regions, including the hydrocarbon chains, the glycerol region, the lipid headgroups and the hydrating water molecules. The simulations suggest that this model can be extended to the study of more complex systems of greater biochemical interest, such as membrane bound proteins.

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