Papers by Keyword: Molecular Dynamic Simulation

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Authors: Mian Wang, Jian Yi Wang
Abstract: Conformational changes of wild-type (WT) hIAPP and the S20P mutant in explicit water are investigated using molecular dynamics. In the whole simulation, WT shows compacter structure and has more hydrogen-bond networks than S20P. The residues 14-18 in WT is always maintained as a helical structure which is stabilized by the hydrogen bond between Ser20 and NH group of His18, and the other regions in WT partially loosen from α-helix structures into the coil structures. The S20P mutant in a shortage of hydrogen-bond interaction unfolds faster than WT. This work provides insight into the specific conformation of IAPP which is associated with the generation of amyloid fibrils.
Authors: Shinji Ando, Katsuhiro Oyabu, Kousei Hirayama, Masayuki Tsushida, Hideki Tonda
Abstract: A crack propagation behavior of hcp crystal has been simulated by molecular dynamics method using Lennard-Jones type potential. A notch was introduced to model crystals with free surfaces. The size of the model was 13nm×24nm×4.6nm and about 80000 atoms were included in the model. A crack propagated by applying tensile strain on top and bottom layer of the model crystal. A definite dependence of crystallographic orientation on crack propagation behavior was obtained. In a model crystal with initial notch plane and direction were (101 0), [1 210], the crack propagated parallel to notch plane and two sets of prismatic slips were occurred at the crack. Therefore, the crack in this crystal is deduced to extend by alternating shear on two intersecting {101 0}, <1 210> prismatic slip systems. In a model crystal with (0001), [101 0] initial crack, {101 1} first order pyramidal slip occurred at crack tip and following {101 2} twin was also observed. In a model crystal with (10 1 0), [0001] initial crack, the crack propagates parallel to initial crack plane. Crack propagation rate of the crack near surface is faster than the crack in interior of the model. In this case, two prismatic slips were occurred in front of the crack. This result explains a mechanism of forming ‘Herring-born pattern’ which was observed in the titanium single crystal. Results obtained by these three models are well described the fatigue crack propagation behavior in hcp titanium crystals.
Authors: Fei Gao, Eric J. Bylaska, William J. Weber
Abstract: The defect properties and atomic configurations in GaN have been comparatively investigated using density functional theory (DFT) and molecular dynamics method with two representative potentials. The DFT calculations show that the relaxation of vacancies is generally small, but the relaxation around antisite defects is large. The N interstitials, starting from any possible configurations, eventually relax into a N+-N< 0 2 11 > split interstitial. In the case of Ga interstitials, the most stable configuration is a Ga octahedral interstitial, but the Ga+-Ga< 0 2 11 > split interstitial can bridge the gap between non-bounded Ga atoms. The formation energies of vacancies and antisite defects obtained using the Stillinger-Weber potential (SW) are in reasonable agreement with those obtained by DFT calculations, whereas the Tersoff-Brenner (TB) potential better describes the behavior of N interstitials.
Authors: Wen Xu, Qing Hua Zeng, Ai Bing Yu, Donald R. Paul
Abstract: The properties of interphase in polymer composites are often different from those of bulk polymer matrix, which may include chemical, physical, microstructural, and mechanical properties. The nature of interphase is critical to the overall properties and performance of polymer materials, in particular in nanofiller reinforced composites. Experimental efforts have been made to determine the effective interphase thickness and its properties, for example, by nanoindentation and nanoscratch techniques. Yet, it is very difficult to quantify the interphase and its properties because of its nanoscale nature and the unclear boundary. In this regard, computer simulation, e.g., molecular dynamics, provides an effective tool to characterize such interphase and the properties. In this work, molecular dynamics simulations are applied to quantify the interphase thickness in clay-based polymer nanocomposites. Then, the mechanical properties of the so-called effective nanofiller (i.e., the physical size of nanofiller plus the thickness of interphase) will be determined by a series of simulations.
Authors: Xiao Gang Jian, Yun Hua Zhang
Abstract: This paper briefly reviews the overseas and domestic research status of the mechanics of hetero film-substrate interface based on molecular dynamics simulation, on this basis building the accurate model of diamond coatings/WC interface and executing the molecular dynamic simulation, exactly measuring the adhesive strength of the diamond coatings/WC interface, finally exploring the influence of interface scales on the adhesive strength of the diamond coatings/WC interface and verifying the feasibility of studying the microscopic structure by molecular dynamics simulation to characterize the mechanical properties of macrostructure, which has important significance for optimizing deposition process of diamond coatings to improve the adhesive strength of the interface.
Authors: Wei Yang, Xinling Ma, Hong Tao Wang, Wei Hong
Authors: Jin Qiu Zhang, Jian Zhang, Ya Nan Kong, Hong Liang Cuan
Abstract: The aim of this research is to improve characteristic of magnetorheological fluid, and to supply theoretic basis for preparing MRF and applying MRF. By molecular dynamical simulation in MATLAB, microstructure of MRF, mechanism of MRF, and factors of affecting MRF characteristic were investigated. Based on theory of magnetic dipoles and microstructure characteristic of MRF, various factors affecting magnetic chain structure were considered, microcosmic model of MRF was established, factors affecting velocity of MRF forming chains were analyzed.
Authors: Dao Yuan Yang, Hui Yu Yuan, Fen Ling Qian, Juan Wu, Kai Zhu, Rui Zhang
Abstract: After preparing samples (3mm long×4mm wide×36mm high) of Al2O3-MgAlON composites and sintered at 1500°C for 2 h in N2 atmosphere, samples’ cracks were carved by a Vickers hardometer’s pressing head on the center of the sample surface (4 mm×36 mm). Subsequently, the cracks were healed at 1000°C-1550°C for 6 h respectively. Effects of healing temperature on sample’s strength, crack healing dynamics and its molecular dynamics simulation were investigated. The results suggested that: the optimum range of cracks healing temperature was 1300°C-1550°C, and the healing process accelerated at 1300°C, meanwhile, the strength of samples increased significantly. Cracks completely healing finished at 1550°C. The dynamics equation of crack healing was lnν = -Q/kT+lnC. Through characterizing the crack healing rate with the recovering rate of sample’s strength, the diffusion activation energy Q = 4.264 × 10-30 J•K-1 and diffusion constant C=7.359 were claimed. The result of the molecular dynamics simulation suggested that cracks healing process was caused by diffusion could be divided into five stages: passivation of crack tips, formation of salient island, crack shrinkage, generation of secondary crack, and complete healing.
Authors: Fang Li Duan, He Bing Qiu, Ji Ming Yang, Cong Ying Wu
Abstract: Large-scale molecular dynamics simulations are performed to study the effect of atomic-scale surface roughness on nano-contact. The modeling system consists of rigid spherical tips with different surface roughness and elastic flat substrate. Our results show that atomic-scale multi-asperity can change the contact behavior from consistent with the Hertz model to the Persson model. However, adhesion will reduce the influence of surface roughness, to the extent that the two tips with different roughness show similar variations of real contact area with applied load. The maximum compression and tensile stress of the rough tip is about 2 times and 1.5 times that of the smooth one, respectively. Moreover, the rough tip exhibits larger repulsive force and attractive force in the entire range of simulated load. Our simulations suggest that pull-off force cannot characterize the extent of the influence of adhesion on contact behavior at the nanoscale.
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