Effect of the surface on the internal structure of CdSe crystal lattice based on molecular dynamics simulations

The results of molecular dynamics (MD) simulations of CdSe crystals terminated by low-index atomic planes, (100), (110) and (111), are presented. The effect of the crystal termination on the atomic arrangement (interatomic distances) at the surface and underneath the surface is examined. It is shown that the crystal lattice is distorted in lateral and normal directions to the depth of up to about 2 nm from the surface. The exact characteristic of the changes of interatomic distances is specific to the type of the atomic plane terminating the crystal lattice. At some surfaces, the very last monoatomic layer loses the long-range ordering and becomes quasi amorphous. The atoms group into randomly distributed pairs or short linear groups.

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Molecular kinetic theory of boundary slip on textured surfaces by molecular dynamics simulations

A theoretical model extended from the Frenkel-Eyring molecular kinetic theory (MKT) was applied to describe the boundary slip on textured surfaces. The concept of the equivalent depth of potential well was adopted to characterize the solid-liquid interactions on the textured surfaces. The slip behaviors on both chemically and topographically textured surfaces were investigated using molecular dynamics (MD) simulations. The extended MKT slip model is validated by our MD simulations under various situations, by constructing different complex surfaces and varying the surface wettability as well as the shear stress exerted on the liquid. This slip model can provide more comprehensive understanding of the liquid flow on atomic scale by considering the influence of the solid-liquid interactions and the applied shear stress on the nano-flow. Moreover, the slip velocity shear-rate dependence can be predicted using this slip model, since the nonlinear increase of the slip velocity under high shear stress can be approximated by a hyperbolic sine function.     

Numerical distortion and effects of thermostat in molecular dynamics simulations of single-walled carbon nanotubes

In this paper, single-walled carbon nanotubes （SWCNTs） are studied through molecular dynamics （MD） simulation. The simulations are performed at temperatures of 1 and 300K separately, with atomic interactions characterized by the second Reactive Empirical Bond Order （REBO） potential, and temperature controlled by a certain thermostat, i.e. by separately using the velocity scaling, the Berendsen scheme, the Nose-Hoover scheme, and the generalized Langevin scheme. Results for a （5,5） SWCNT with a length of 24.5 nm show apparent distortions in nanotube configuration, which can further enter into periodic vibrations, except in simulations using the generalized Langevin thermostat, which is ascribed to periodic boundary conditions used in simulation. The periodic boundary conditions may implicitly be applied in the form of an inconsistent constraint along the axis of the nanotube. The combination of the inconsistent constraint with the cumulative errors in calculation causes the distortions of nanotubes. When the generalized Langevin thermostat is applied, inconsistently distributed errors are dispersed by the random forces, and so the distortions and vibrations disappear. This speculation is confirmed by simulation in the case without periodic boundary conditions, where no apparent distortion and vibration occur. It is also revealed that numerically induced distortions and vibrations occur only in simulation of nanotubes with a small diameter and a large length-to-diameter ratio. When MD simulation is applied to a system with a particular geometry, attention should be paid to avoiding the numerical distortion and the result infidelity.     

Confirming the lattice contraction in CdSe nanocrystals grown in a glass matrix by Raman scattering

This work gives the evidence of the lattice contraction in CdSe nanocrystals (NCs) grown in a glass matrix. The CdSe NCs were investigated by atomic force microscopy (AFM), optical absorption (OA), and Raman spectroscopy. The average size of CdSe NCs can be estimated by AFM images. Using the OA spectra and the effective‐mass approximation, it was also possible to estimate the average sizes of CdSe NCs, which agree very well with the AFM data. These results showed that the CdSe NCs grow with increasing time of heat treatment. The blue shift of the longitudinal optical (LO) modes and surface optical (SO) phonon modes with an increase in the average radius of the NCs, shown in the Raman spectra, was explained by the lattice contraction in CdSe NCs caused by thermodynamic interactions at the interface with the host glass matrix. Copyright © 2010 John Wiley & Sons, Ltd.     

On the lattice dynamics of disordered surfaces

The local frequency distribution functions of the surface layers of a semi-infinite simple cubic crystal with randomly adsorbed impurities have been calculated for the (001) surface. A method based on the coherent potential approximation was used. The results are displayed for various concentrations and masses of adsorbed impurities.The author wishes to thank M.Ovold, I.Karasová and J.Kudrnovský for useful discussions and stimulating suggestions.     

Modification of carrier dynamics in CdSe nanocrystals by excess Cd in deposition bath

Photoexcited carrier dynamics in thin CdSe nanocrystalline films prepared by chemical bath deposition are strongly dependent on the deposition parameters. In this paper, we show how an increase in concentration of CdSO₄ in deposition bath affects the photoexcited carrier dynamics in nanocrystals. We used ultrafast absorption and photoluminescence laser spectroscopy to compare the carrier dynamics in samples prepared with and without increased CdSO₄ concentration. We have found that in the Cd-rich samples the spectral dependences of both photoluminescence and absorption dynamics are considerably less pronounced and the dynamics are slower. The observed effects were explained by the suppression of surface mediated carrier relaxation due to the passivation of individual nanocrystals by cadmium hydroxide and/or by sulphatocomplexes of Cd²⁺.     

Interpretation of NMR data on proteins by molecular dynamics simulations

The stability and the internal mobility of the recently determined solution structure of the activation domain of porcine procarboxypeptidase B (ADB; Vendrell J., Billeter M., Wider G., Avilés F.X., Wüthrich K.: EMBO J.10, 11–15 (1991)) was studied by unrestrained molecular dynamics. A 66 residue long polypeptide corresponding to the structurally well-defined fragment of ADB was immersed in a water bath and carefully equilibrated. A trajectory of 90 ps was then recorded at room temperature, using no constraints deduced from NMR distance measurements. The averages of the inverse third power of the proton-proton distances, for which NMR distance measurements are available, were calculated and converted to time averages of the distances. Comparison of these time averaged distances with the corresponding distance constraints used in the determination of the solution structure show that the dynamic structure described by the molecular dynamics trajectory is consistent with the NMR data for the polypeptide backbone and for most side chains. In the course of the 90 ps trajectory, the ß-sheet of ADB remains intact and well-defined. The last helix of the protein domain is also stable, but moves with respect to the rest of the protein, while the first helix shows increased instability. The structural fluctuations of the side chain do in general not exceed those observed among the 20 conformers describing the solution structure.     

Molecular dynamics simulations of the nano-droplet impact process on hydrophobic surfaces

Large-scale molecular dynamics simulations are used to study the dynamic processes of a nano-droplet impacting on hydrophobic surfaces at a microscopic level. Both the impact phenomena and the velocity distributions are recorded and analyzed. According to the simulation results, similar phenomena are obtained to those in macro-experiments. Impact velocity affects the spread process to a greater degree than at a level of contact angle when the velocity is relatively high. The velocity distribution along the X axis during spread is wave-like, either W- or M-shaped, and the velocity at each point is oscillatory; while the edges have the highest spread velocity and there are crests in the distribution curve which shift toward the edges over time. The distribution along the Y axis is 〈- or 〉-shaped, and the segments above the middle have the lowest decrease rate in the spreading process and the highest increase rate in the retraction process.     

Breaking the symmetry between interaction and replacement in evolutionary dynamics on graphs

We study the evolution of cooperation modeled as symmetric 2x2 games in a population whose structure is split into an interaction graph defining who plays with whom and a replacement graph specifying evolutionary competition. We find it is always harder for cooperators to evolve whenever the two graphs do not coincide. In the thermodynamic limit, the dynamics on both graphs is given by a replicator equation with a rescaled payoff matrix in a rescaled time. Analytical results are obtained in the pair approximation and for weak selection. Their validity is confirmed by computer simulations.     

Study of nanoscratching of polymers by using molecular dynamics simulations

Molecular dynamic simulations are performed to study the nanoscratching behavior of polymers.The effects of scratching depth,scratching velocity and indenter/polymer interaction strength are investigated.It is found that polymer material in the scratching zone around the indenter can be removed in a ductile manner as the local temperature in the scratching zone exceeds glass transition temperature Tg.The recovery of polymer can be more significant when the temperature approaches or exceeds Tg.The tangential force,normal force and friction coefficient increase as the scratching depth increases.A larger scratching velocity leads to more material deformation and higher pile-up.The tangential force and normal force are larger for a larger scratching velocity whereas the friction coefficient is almost independent of the scratching velocities studied.It is also found that stronger indenter/polymer interaction strength results in a larger tangential force and friction coefficient.     

Gas adsorption and accumulation on hydrophobic surfaces:Molecular dynamics simulations

Molecular dynamics simulations show that the gas dissolved in water can be adsorbed at a hydrophobic interface and accumulates thereon. Initially, a water depletion layer appears on the hydrophobic interface. Gas molecules then enter the depletion layer and form a high-density gas-enriched layer. Finally, the gas-enriched layer accumulates to form a nanobubble. The radian of the nanobubble increases with time until equilibrium is reached. The equilibrium state arises through a Brenner–Lohse dynamic equilibrium mechanism, whereby the diffusive outflux is compensated by an influx near the contact line. Additionally, supersaturated gas also accumulates unsteadily in bulk water, since it can diffuse back into the water and is gradually adsorbed by a solid substrate.     

Study of lattice thermal conductivity of alpha-zirconium by molecular dynamics simulation

The non-equilibrium molecular dynamics method is adapted to calculate the phonon thermal conductivity of alphazirconium. By exchanging velocities of atoms in different regions, the stable heat flux and the temperature gradient are established to calculate the thermal conductivity. The phonon thermal conductivities under different conditions, such as different heat exchange frequencies, different temperatures, different crystallographic orientations, and crossing grain boundary (GB), are studied in detail with considering the finite size effect. It turns out that the phonon thermal conductivity decreases with the increase of temperature, and displays anisotropies along different crystallographic orientations. The phonon thermal conductivity in [0001] direction (close-packed plane) is largest, while the values in other two directions of [2īī0] and [01ī0] are relatively close. In the region near GB, there is a sharp temperature drop, and the phonon thermal conductivity is about one-tenth of that of the single crystal at 550 K, suggesting that the GB may act as a thermal barrier in the crystal.     

气体-表面相互作用的分子动力学模拟研究

采用分子动力学模拟方法研究了气体分子Ar在光滑和粗糙Pt表面上的散射规律.提出了一种速度抽样方法,计算了不同温度条件下气体分子对光滑和粗糙表面的切向动量适应系数和吸附概率.结果显示：光滑表面条件下,气体分子的切向动量系数和吸附概率都随着温度的升高而降低;粗糙度对气体分子切向动量与表面的适应具有极大的促进作用,当粗糙度足够大时,切向动量适应系数的大小趋近于1.0,对温度的敏感性也逐渐降低.采用粒子束方法对气体分子在光滑和粗糙表面上的散射规律进行了定量分析.总结了散射过程中气体分子的典型轨迹和动量变化规律,将气体分子在光滑表面的散射分为两种类型：单次碰撞后散射和多次碰撞后散射.单次碰撞后散射的气体分子平均切向动量有所减小,而经过多次碰撞后散射的气体分子则倾向于保持原有的平均切向动量.对于粗糙表面,粗糙度的存在使气体分子与表面间的动量和能量适应更加充分,导致气体分子在较粗糙表面上散射后的平均切向动量大幅减小并接近于0,且气体分子在表面上经历的碰撞次数越多,其散射后的能量损失越严重.     

Simulation of screw dislocation motion in iron by molecular dynamics simulations

Molecular dynamics (MD) simulations are used to investigate the response of a/2<111> screw dislocation in iron submitted to pure shear strain. The dislocation glides and remains in a (110) plane; the motion occurs exclusively through the nucleation and propagation of double kinks. The critical stress is calculated as a function of the temperature. A new method is developed and used to determine the activation energy of the double kink mechanism from MD simulations. It is shown that the differences between experimental and simulation conditions lead to a significant difference in activation energy. These differences are explained, and the method developed provides the link between MD and mesoscopic simulations.     

Multi-scale molecular dynamics simulations and applications on mechanosensitive proteins of integrins

Molecular dynamics simulation(MDS)is a powerful technology for investigating evolution dynamics of target proteins,and it is used widely in various fields from materials to biology.This mini-review introduced the principles,main preforming procedures,and advances of MDS,as well as its applications on the studies of conformational and allosteric dynamics of proteins especially on that of the mechanosensitive integrins.Future perspectives were also proposed.This review could provide clues in understanding the potentiality of MD simulations in structure–function relationship investigation of biological proteins.