The influence of quantum forces on molecular dynamics simulation results for hydrated aluminium(III)

2006 ◽  
Vol 422 (4-6) ◽  
pp. 492-495 ◽  
Author(s):  
Thomas S. Hofer ◽  
Bernhard R. Randolf ◽  
Bernd M. Rode
2014 ◽  
Vol 513-517 ◽  
pp. 113-116
Author(s):  
Jen Ching Huang ◽  
Fu Jen Cheng ◽  
Chun Song Yang

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.


2012 ◽  
Vol 500 ◽  
pp. 696-701
Author(s):  
Ying Zhu ◽  
Sen Song ◽  
Ling Ling Xie ◽  
Shun He Qi ◽  
Qian Qian Liu

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.


2012 ◽  
Vol 3 ◽  
pp. 586-588 ◽  
Author(s):  
Saurav Goel ◽  
Alexander Stukowski ◽  
Gaurav Goel ◽  
Xichun Luo ◽  
Robert L Reuben

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.


2012 ◽  
Vol 715-716 ◽  
pp. 599-604 ◽  
Author(s):  
Stephen M. Foiles

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.


Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3379 ◽  
Author(s):  
Caijing Han ◽  
Li Fang ◽  
Chunlei Liu ◽  
Yunna Gao ◽  
Weihong Min

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.


Soft Matter ◽  
2015 ◽  
Vol 11 (11) ◽  
pp. 2213-2219 ◽  
Author(s):  
Awaneesh Singh ◽  
Sanjay Puri

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.


1999 ◽  
Vol 28 (6) ◽  
pp. 447-456 ◽  
Author(s):  
Alessandro Paciaroni ◽  
Maria Elena Stroppolo ◽  
Caterina Arcangeli ◽  
Anna Rita Bizzarri ◽  
Alessandro Desideri ◽  
...  

1994 ◽  
Vol 344 (1309) ◽  
pp. 239-260 ◽  

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.


2012 ◽  
Vol 500 ◽  
pp. 702-706
Author(s):  
Ying Zhu ◽  
Ling Ling Xie ◽  
Sen Song ◽  
Shun Hen Qi ◽  
Qian Qian Liu

The work in the optimization of the simulation of nanoindentation based on the molecular dynamics was mainly introduced in this paper. One optimization method, freeze atoms method was proposed according to the characteristics of nanoindentation process itself, then did the simulation calculation through the use of freeze atoms method and the traditional calculation method, It was found that the difference between simulation results and experimental results of hardness decreased gradually with enlarge the scale of molecular dynamics simulation (with increase of the indentation depth), from 32.39% of 5nm decreased to 14.6% of 25nm. By comparison, it was found that the optimized algorithm could improve the efficiency of simulation in large-scale molecular dynamics simulation., confirmed the correctness and effectiveness of freeze atoms method.


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