130 resultados para Molecular Dynamics, Simulation, Modeling, Protein, Coarse Graining


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We report a previously unknown body-centered-tetragonal structure for ZnO. This structure results from a phase transformation from wurtzite in [0001]-oriented nanorods during uniaxial tensile loading and is the most stable phase for ZnO when stress is above 7 GPa. The stress-induced phase transformation has important implications for the electronic, piezoelectric, mechanical, and thermal responses of ZnO. The discovery of this polymorph brings about a more complete understanding of the extent and nature of polymorphism in ZnO. A crystalline structure-load triaxiality map is developed to summarize the relationship between structure and loading.

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Deformation twins have been observed in nanocrystalline (nc) fcc metals with medium-to-high stacking fault energies such as aluminum, copper, and nickel. These metals in their coarse-grained states rarely deform by twining at room temperature and low strain rates. Several twinning mechanisms have been reported that are unique to nc metals. This paper reviews experimental evidences on deformation twinning and partial dislocation. emissions from grain boundaries, twinning mechanisms, and twins with zero-macro-strain. Factors that affect the twinning propensity and recent analytical models on the critical grain sizes for twinning are also discussed. The current issues on deformation twinning in nanocrystalline metals are listed.

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Metallic nanowires have many attractive properties such as ultra-high yield strength and large tensile elongation. However, recent experiments show that metallic nanowires often contain grain boundaries, which are expected to significantly affect mechanical properties. By using molecular dynamics simulations, here, we demonstrate that polycrystalline Cu nanowires exhibit tensile deformation behavior distinctly different from their single-crystal counterparts. A significantly lowered yield strength was observed as a result of dislocation emission from grain boundaries rather than from free surfaces, despite of the very high surface to volume ratio. Necking starts from the grain boundary followed by fracture, resulting in reduced tensile ductility. The high stresses found in the grain boundary region clearly play a dominant role in controlling both inelastic deformation and fracture processes in nanoscale objects. These findings have implications for designing stronger and more ductile structures and devices on nanoscale.

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Macroscopic strain was hitherto considered a necessary corollary of deformation twinning in coarse-grained metals. Recently, twinning has been found to be a preeminent deformation mechanism in nanocrystalline face-centered-cubic (fcc) metals with medium-to-high stacking fault energies. Here we report a surprising discovery that the vast majority of deformation twins in nanocrystalline Al, Ni, and Cu, contrary to popular belief, yield zero net macroscopic strain. We propose a new twinning mechanism, random activation of partials, to explain this unusual phenomenon. The random activation of partials mechanism appears to be the most plausible mechanism and may be unique to nanocrystalline fcc metals with implications for their deformation behavior and mechanical properties.

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Molecular dynamics simulations have been carried our to study the atomic structure of the crystalline component of nanocrystalline alpha-iron. A two-dimensional computational block is used to simulate the consolidation process. It is found that dislocations are generated in the crystallites during consolidation when the grain size is large enough. The critical value of the grain size for dislocation generation appears to be about 9 nm. This result agrees with experiment qualitatively. AN dislocations that are preset in the original grains glide out during consolidation. It shows that dislocations in the crystallites we generated in consolidation process, but not in the original grains. Higher consolidation pressure results in more dislocations. Furthermore, new interfaces are found within crystallites. These interfaces might result from the special environment of nanomaterial. (C) 1998 Acta Metallurgica Inc.

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Previous experiments on nanocrystalline Ni were conducted under quasistatic strain rates (similar to 3x10(-3)/s), which are much lower than that used in typical molecular dynamics simulations (>3x10(7)/s), thus making direct comparison of modeling and experiments very difficult. In this study, the split Hopkinson bar tests revealed that nanocrystalline Ni prefers twinning to extended partials, especially under higher strain rates (10(3)/s). These observations contradict some reported molecular dynamics simulation results, where only extended partials, but no twins, were observed. The accuracy of the generalized planar fault energies is only partially responsible, but cannot fully account for such a difference. (C) 2007 American Institute of Physics.

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Molecular dynamics simulations are carried out in order to study the atomic structure of crystalline component, of nanocrystalline alpha-Fe when it is consolidated from small grains. A two-dimensional computational block is used to simulate the consolidation process. All the preset dislocations in the original grains glide out of them in the consolidation process, but new dislocations can generate when the grain size is large enough. It shows that dislocations exist in the consolidated material rather than in the original grains. Whether dislocations exist in the crystalline component of the resultant model nana-material depends upon grain size. The critical value of grain size for dislocation generation appears to be about 9 nm. This result agrees with experiments qualitatively.

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The gliding behavior of edge dislocation near a grain boundary(QB) in copper under pure shear stresses is simulated by using molecular dynamics(MD) method. Many-body potential incorporating the embedded atom method (EAM) is used. The critical shear stresses for a single disocation to pass across GB surface are obtained at values of sigma(c)=23MPa similar to 68 MPa and 137 MPa similar to 274 MPa for Sigma=165 small angle tilt GB at 300 K and 20 K, respectively. The first result agrees with the experimental yield stress sigma(y)(=42 MPa) quite well. It suggests that there might be one of the reasons of initial plastic yielding caused by single dislocation gliding across GB. In addition, there might be possibility to obtain yield strength from microscopic analysis. Moreover, the experimental value of sigma(y) at low temperature is generally higher than that at room temperature. So, these results are in conformity qualitatively with experimental fact. On the other hand, the Sigma=25 GB is too strong an obstacle to the dislocation. In this case, a dislocation is able to pass across GB under relatively low stress only when it is driven by other dislocations. This is taken to mean that dislocation pile-up must be built up in front of this kind of GB, if this GB may take effect on the process of plastic deformation.

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A simple derivation based on continuum mechanics is given, which shows the surface stress is critical for yield strength at ultra-small scales. Molecular dynamics (MD) simulations with modified embedded atom method (MEAM) are employed to investigate the mechanical behaviors of single-crystalline metal nanowires under tensile loading. The calculated yield strengths increasing with the decrease of the cross-sectional area of the nanowires are in accordance with the theoretical prediction. Reorientation induced by stacking faults is observed at the nanowire edge. In addition. the mechanism of yielding is discussed in details based on the snapshots of defects evolution. The nanowires in different crystallographic orientations behave differently in stretching deformation. This study on the plastic properties of metal nanowires will be helpful to further understanding of the mechanical properties of nanomaterials. (C) 2009 Elsevier B.V. All rights reserved.

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Recent experiments have found that slip length could be as large as on the order of 1 mu m for fluid flows over superhydrophobic surfaces. Superhydrophobic surfaces can be achieved by patterning roughness on hydrophobic surfaces. In the present paper, an atomistic-continuum hybrid approach is developed to simulate the Couette flows over superhydrophobic surfaces, in which a molecular dynamics simulation is used in a small region near the superhydrophobic surface where the continuum assumption is not valid and the Navier-Stokes equations are used in a large region for bulk flows where the continuum assumption does hold. These two descriptions are coupled using the dynamic coupling model in the overlap region to ensure momentum continuity. The hybrid simulation predicts a superhydrophobic state with large slip lengths, which cannot be obtained by molecular dynamics simulation alone.

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Recent experiments have found that slip length could be as large as on the order of 1 mu m for fluid flows over superhydrophobic surfaces. Superhydrophobic surfaces can be achieved by patterning roughness on hydrophobic surfaces. In the present paper an atomistic-continuum hybrid approach is developed to simulate the Couette flows over superhydrophobic surfaces in which a molecular dynamics simulation is used in a small region near the superhydrophobic surface where the continuum assumption is not valid and the Navier-Stokes equations are used in a large region for bulk flows where the continuum assumption does hold. These two descriptions are coupled using the dynamic coupling model in the overlap region to ensure momentum continuity. The hybrid simulation predicts a superhydrophobic state with large slip lengths which cannot be obtained by molecular dynamics simulation alone.

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Wettability alternation phenomena is considered one of the most important enhanced oil recovery (EOR) mechanisms in the chemical flooding process and induced by the adsorption of surfactant on the rock surface. These phenomena are studied by a mesoscopic method named as dissipative particle dynamics (DPD). Both the alteration phenomena of water-wet to oil-wet and that of oil-wet to water-wet are simulated based on reasonable definition of interaction parameters between beads. The wetting hysteresis phenomenon and the process of oil-drops detachment from rock surfaces with different wettability are simulated by adding long-range external forces on the fluid particles. The simulation results show that, the oil drop is liable to spread on the oil-wetting surface and move in the form of liquid film flow, whereas it is likely to move as a whole on the water-wetting surface. There are the same phenomena occuring in wettability-alternated cases. The results also show that DPD method provides a feasible approach to the problems of seepage flow with physicochemical phenomena and can be used to study the mechanism of EOR of chemical flooding.

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本文选用经过实验验证的碱基序列 ,用简化的方式 ,构建了被水分子和镁离子修饰的核酸序列的分子模型 ,应用分子力学模拟方法对序列进行能量优化 ,对优化后序列的构象参数、成键状况和能量数据等进行了分析。对tRNAHHis GUG的识别特性作了初步的探索 ,得到了和实验结果相近的结论。此外 ,还从能力学的角度讨论了溶剂 -溶质 -溶剂相互作用形成的网状氢键网络对核酸结构稳定性的影响 ,探讨了非Crick_WatsonGU、UU配对的能力学特征并存在于被水分子和镁离子修饰的核酸序列中的GU、UU配对情况。