A Lennard-Jones Embedded-Atom Potential and Its Application to the Study of Melting

The nearest-neighbour Lennard-Jones potential from the embedded-atom method is extended to a form that includes more than nearest neighbours. The model has been applied to study melting with molecular dynamics. The calculated melting point, fractional volume change on melting, heat of fusion and linear coefficients of thermal expansion are in good agreement with experimental data. We have found that the second and third neighbours influence the melting point distinctly.

Tolman Effect On Fluid Dynamics In Carbon Nanotubes

The numerical solutions of or(R) given by two different methods (Samsonov et al., 2003; and Lu et al., 2005) are compared with the result that they are coincident closely (the difference is within 4%). We conclude that it is necessary to consider the Tolman correction in the calculation of fluid dynamics in carbon nanotubes. Although our conclusion is the same as that of Prylutskyy et al. (2005), the sign of our Tolman correction is opposite to theirs, and the difference can be attributed to the errors appeared in the paper of Prylutskyy et al.

Strengthening Mechanisms And Dislocation Dynamics In Twinned Metal Nanowires

Microtwins are frequently observed in face-centered-cubic (fcc) metal nanowires with low stacking fault energy. The authors have previously reported that the tensile Yield strength of copper nanowires can be increased by, the presence of twin boundaries. lit this work, simulations are carried out under both uniaxial tension and compression loading, to demonstrate that the strengthening effects are inherent to these nanowires, independent of the loading condition (tensile/compressive). It appears that the strengthening mechanism of the twinned nanowires can be attributed to stress redistribution due to the change of crystallographic orientations across twin boundaries, which requires larger external stress to make them Yield as compared to the twin-free wire.

MD simulation of the effect of contact area and tip radius on nanoindentation

Molecular dynamics simulations of nanoindentation are performed on monocrystal copper. A new "contact atoms" method is presented for calculating the contact area. Compared with conventional methods, this method can provide the contact area more accurately not only for sink-in but also for pile-up situation. The effect of tip radius on indentation is investigated too. The results indicate that the measured hardness of the material will become higher as the tip radius increases.

A dynamic coupling model for hybrid atomistic-continuum computations

A dynamic coupling model is developed for a hybrid atomistic-continuum computation in micro- and nano-fluidics. In the hybrid atomistic-continuum computation, a molecular dynamics (MD) simulation is utilized in one region where the continuum assumption breaks down and the Navier-Stokes (NS) equations are used in another region where the continuum assumption holds. In the overlapping part of these two regions, a constrained particle dynamics is needed to couple the MD simulation and the NS equations. The currently existing coupling models for the constrained particle dynamics have a coupling parameter, which has to be empirically determined. In the present work, a novel dynamic coupling model is introduced where the coupling parameter can be calculated as the computation progresses rather than inputing a priori. The dynamic coupling model is based on the momentum constraint and exhibits a correct relaxation rate. The results from the hybrid simulation on the Couette flow and the Stokes flow are in good agreement with the data from the full MD simulation and the solutions of the NS equations, respectively. (c) 2007 Elsevier Ltd. All rights reserved.

Atomistic investigation of the effects of temperature and surface roughness on diffusion bonding between Cu and Al

Molecular dynamics (MD) simulations are carried out to analyze the diffusion bonding at Cu/Al interfaces. The results indicate that the thickness of the interfacial layer is temperature-dependent, with higher temperatures yielding larger thicknesses. At temperatures below 750 K, the interface thickness is found to increase in a stepwise manner as a function of time. At temperatures above 750 K, the thickness increases rapidly and smoothly. When surface roughness is present, the bonding process consists of three stages. In the first stage, surfaces deform under stress, resulting in increased contact areas. The second stage involves significant plastic deformation at the interface as temperature increases, resulting in the disappearance of interstices and full contact of the surface pair. The last stage entails the diffusion of atoms under constant temperature. The bonded specimens show tensile strengths reaching 88% of the ideal Cu/Al contact strength. (c) 2007 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

A unified model for dislocation nucleation, dislocation emission and dislocation free zone

In this paper, a unified model for dislocation nucleation, emission and dislocation free zone is proposed based on the Peierls framework. Three regions are identified ahead of the crack tip. The emitted dislocations, located away from the crack tip in the form of an inverse pileup, define the plastic zone. Between that zone and the cohesive zone immediately ahead of the crack tip, there is a dislocation free zone. With the stress field and the dislocation density field in the cohesive zone and plastic zone being, respectively, expressed in the first and second Chebyshev polynomial series, and the opening and slip displacements in trigonometric series, a set of nonlinear algebraic equations can be obtained and solved with the Newton-Raphson Method. The results of calculations for pure shearing and combined tension and shear loading after dislocation emission are given in detail. An approximate treatment of the dynamic effects of the dislocation emission is also developed in this paper, and the calculation results are in good agreement with those of molecular dynamics simulations.

Atomistic Simulation On Size-Dependent Yield Strength And Defects Evolution Of Metal Nanowires

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.

Hydroelectric Voltage Generation Based On Water-Filled Single-Walled Carbon Nanotubes

A DFT/MD mutual iterative method was employed to give insights into the mechanism of voltage generation based on water-fitted single-walled carbon nanotubes (SWCNTs). Our calculations showed that a constant voltage difference of several mV would generate between the two ends of a carbon nanotube, due to interactions between the water dipole chains and charge carriers in the tube. Our work validates this structure of a water-fitted SWCNT as a promising candidate for a synthetic nanoscale power cell, as well as a practical nanopower harvesting device at the atomic level. 

Hybrid Qm/Mm Simulation Of The Hydration Phenomena Of Dipalmitoylphosphatidylcholine Headgroup

The polar headgroup of dipalmitoylphosphatidylcholine (DPPC) molecule both in gas phase and aqueous Solution is investigated by the hybrid quantum mechanical/molecular mechanical (QM/MM) method, in which the polar head of DPPC molecule and the bound water molecules are treated with density functional theory (DFT), while the apolar hydrocarbon chain of DPPC molecule is treated with MM method. It is demonstrated that the hybrid QM/MM method is both accurate and efficient to describe the conformations of DPPC headgroup. Folded structures of headgroup are found in gas phase calculations. In this work, both monohydration and polyhydration phenomena are investigated. In monohydration, different water association sites are studied. Both the hydration energy and the quantum properties of DPPC and water molecules are calculated at the DFT level of theory after geometry optimization. The binding force of monohydration is estimated by using the scan method. In polyhydration, more extended conformations are found and hydration energies in different polyhydration styles are estimated. (C) 2008 Elsevier Inc. All rights reserved.

离子束溅射法薄膜生长中结瘤微缺陷的生长机理

用离子束溅射法制备了锆单层薄膜．用设计新型夹具和预置种子方法，对薄膜中结瘤微缺陷的生长过程进行了研究．在高分辨率光学显微镜和扫描电子显微镜下观察发现，结瘤在其生长初期呈现出分形的特征．用分子动力学和薄膜生长的扩散限制聚集模型，薄膜中结瘤微缺陷成核时的分形现象得到了很好的解释．

伦纳德琼斯薄膜材料导热系数的分子动力学研究

提出从微观的角度,借助计算机工具,将薄膜破坏发展的细节展现出来的分子动力学研究的思想。使得实验上难以观察的现象变得形象而便于理解。应用分子动力学理论,使用伦纳德琼斯势函数,采用预校正积分法和虚拟外力约束标定方法,模拟薄膜体系的传热系数受体系的密度、温度的影响,同时结合体系粒子的径向分布函数和长程分布函数分析了相应的系统结构特性。另外,采用不同的模拟尺寸获得了低维材料所特有的“高温尺寸效应”。结果显示,导热系数随密度的增加变大,随温度的上升而变大。这些数据现有测量手段是难以得到的,这类模拟可以为研究提供一些

Dynamics of RNA with A6 bulge loop

In order to understand the behavior of RNAs with large bulges In solution, molecular dynamics was performed on the RNA molecule in water with A6 bulge. The result of simulation showed that nonstacked conformation Is the main conformation in large bulges, and the backbone of large bulge is of great conformational flexibility, but bulges-induced bends are relatively rigid. The fluctuation in bulge has little influence on the bend angle of RNAs.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.