Molecular dynamics studies of brittle fracture of SiO2

By applying for molecular dynamics (MD) simulation and Griffith fracture criterion, the brittle behavior of crack extension of mode I type is investigated. The critical stress intensity factor (SIF)K-Ic(MD) of crack extension is calculated, and the evolution of atoms near crack tip is observed. It is found that K-Ic(MD) is in good agreement with the Griffith ftacture criterion K-Ic(Griffith).

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.

Effect Of Water On Brittle Fracture Of Sio2 By Molecular Dynamics Study

The influence of water on the brittle behavior of beta-cristobalite is studied by means of molecular dynamics (MD) simulation With the TTAM potential. Crack extension of mode 1 type is observed as the crack opening is filled LIP With water. The critical stress intensity factor K-lc(MD) is used to characterize the crack extension of MD simulation. The surface energy of SiO2 covered with layers of water is calculated at temperature of 300 K. Based oil the Griffith fracture criterion, the critical stress intensity factor K-lc(Griffith) is calculated, and it is in good agreement with that of MD simulation. (C) 2008 Elsevier B.V. All rights reserved.

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.

An Atomistic-Continuum Hybrid Simulation Of Fluid Flows Over Superhydrophobic Surfaces

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.

An atomistic-continuum hybrid simulation of fluid flows over superhydrophobic surfaces

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.

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.

Controlling electronic structures by irradiation in single-walled SiC nanotubes: a first-principles molecular dynamics study

Using first-principles molecular dynamics simulations, the displacement threshold energy and defect configurations are determined in SiC nanotubes. The simulation results reveal that a rich variety of defect structures (vacancies, Stone-Wales defects and antisite defects) are formed with threshold energies from 11 to 64 eV. The threshold energy shows an anisotropic behavior and exhibits a dramatic decrease with decreasing tube diameter. The electronic structure can be altered by the defects formed by irradiation, which suggests that the electron irradiation may be a way to use defect engineering to tailor electronic properties of SiC nanotubes.

Self-organized superlattices along the [001] growth direction in In0.52Al0.48As layers grown on nominally (001) InP substrates by molecular beam epitaxy

Horizontal self-organized superlattice structures consisting of alternating In-rich and Al-rich layers formed naturally during solid-source molecular beam epitaxy (MBE) growth of In0.52Al0.48As on exactly (001) InP substrates, with In and At fluxes unchanged. The growth temperatures were changed from 490 to 510 degrees C, the most commonly used growth temperature for In0.52Al0.48As alloy. No self-organized superlattices (SLs) were observed at the growth temperature 490 degrees C, and self-organized SLs were observed in InAlAs layers at growth temperatures ranging from 498 to 510 degrees C. The results show that the period of the SLs is very highly regular, with the value of similar to 6 nm, and the composition of In or Al varies approximately sinusoidally along the [001] growth direction. The theoretical simulation results confirm that the In composition modulation amplitude is less than 0.02 relative the In composition of the In0.52Al0.48As lattice matched with the InP substrate. The influence of InAs self-organized quantum wires on the spontaneously formed InxAl1-xAs/InyAl1-yAs SLs was also studied and the formation of self-organized InxAl1-xAs/InyAl1-yAs SLs was attributed to the strain-mediated surface segregation process during MBE growth of In0.52Al0.48As alloy. (C) 2005 Published by Elsevier Ltd.

Monte Carlo simulation of the modulated effect induced by the dislocation to the quantum dot growth

Performing an event-based continuous kinetic Monte Carlo simulation, we investigate the modulated effect induced by the dislocation on the substrate to the growth of semiconductor quantum dots (QDs). The relative positions between the QDs and the dislocations are studied. The stress effects to the growth of the QDs are considered in simulation. The simulation results are compared with the experiment and the agreement between them indicates that this simulation is useful to study the growth mode and the atomic kinetics during the growth of the semiconductor QDs. (c) 2006 Elsevier Ltd. All rights reserved.

Kinetic Monte Carlo simulation of spatially ordered growth of quantum dots on patterned substrate

We report the growth of well-ordered InAs QD chains by molecular beam epitaxy system. In order to analyze and extend the results of our experiment, a detailed kinetic Monte Carlo simulation is developed to investigate the effects of different growth conditions to the selective growth of InAs quantum dots (QDs). We find that growth temperature plays a more important role than growth rate in the spatial ordering of the QDs. We also investigate the effect of periodic stress on the shape of QDs in simulation. The simulation results are in good qualitative agreement with our experiment. (c) 2006 Elsevier Ltd. All rights reserved.

Investigation of periodicity fluctuations in strained (GaNAs)(1)(GaAs)(m) superlattices by the kinematical simulation of x-ray diffraction

Periodicity fluctuations of layer thickness and composition in a superlattice not only decrease the intensity, they also broaden the width of the satellite peaks in the x-ray diffraction pattern. In this letter, we develop a method that is dependent on the width of satellite peaks to assess periodicity fluctuations of a superlattice quickly. A linear relation of the magnitude of fluctuations, peak width and peak order has been derived from x-ray diffraction kinematical theory. By means of this method, periodicity fluctuations in strained (GaNAs)(1)(GaAs)(m) superlattices grown on GaAs substrates by molecular beam epitaxy have been studied. Distinct satellite peaks indicate that the superlattices are of high quality. The N composition of 0.25 and its fluctuation of 20% in a strained GaNxAs1-x monolayer are obtained from simulations of the measured diffraction pattern. The x-ray simulations and in situ observation results of reflection high-energy electron diffraction are in good agreement. (C) 1999 American Institute of Physics. [S0003-6951(99)00828-1].

Structural characterization of SiGe/Si single wells grown by disilane and solid-Ge molecular beam epitaxy with varied disilane cracking temperature

Structural properties of SiGe/Si single wells are studied by double-crystal X-ray diffraction. Four SiGe/Si single wells have been grown on Si (0 0 1) at 750 degrees C by disilane and solid-Ge molecular beam epitaxy with varied disilane cracking temperature. Using dynamic theory, together with kinematic theory and the specific growth procedure adopted, structural parameters in the multilayer structure are determined precisely. The results are compared with those obtained from PL and XTEM as well as AES measurements. It is found that disilane adsorption is dependent on cracking temperature as well as Ge incorporation. Disilane adsorption is increased by cracking disilane while it decreased with Ge incorporation (C) 1998 Elsevier Science B.V. All rights reserved.

Kinetic Monte Carlo simulation of semiconductor quantum dot growth

Performing an event-based continuous kinetic Monte Carlo (KMC) simulation, We investigate the growth conditions which are important to form semiconductor quantum dot (QD) in molecular beam epitaxy (MBE) system. The simulation results provide a detailed characterization of the atomic kinetic effects. The KMC simulation is also used to explore the effects of periodic strain to the epitaxy growth of QD. The simulation results are in well qualitative agreement with experiments.