Harmonic behavior of silicon nanowire by molecular dynamics

Silicon nanowires (SiNW) have attracted increasing interests as potential core parts for nanoscale devices due to their distinguished mechanical and electrical properties. Using molecular dynamics (MD) method, we investigated the vibration behaviors of SiNW on the atomic scale, including the fundamental mode frequency and quality factor. The quality factor as low as 120 is attributed to the energy loss process coming from atomic friction and nonlinearity. We also found that the energy of lattice vibration (phonon energy) is much larger than the macroscale beam vibration energy. And both the energies are less than the surface relaxation energy of the beam. The comparison between MD and FEM has been made to discuss the validity of continuum approximation for the study of SiNW.     

A reversible problem in non-equilibrium thermodynamics: Hamiltonian evolution equations for non-equilibrium molecular dynamics simulations

The reversible contribution to contemporary theories of non-equilibrium thermodynamics is reviewed as a methodology for attacking difficult, conservative problems in complex fluid dynamics. Several examples of past successes are discussed, and a new application is addressed: non-equilibrium molecular dynamics (NEMD) simulations. NEMD simulations of fluids are generally based on either a DOLLS or SLLOD tensor algorithm. The former is always considered to be a Hamiltonian system, but not particularly useful in high strain rate flow simulations, while the latter is considered not to be a Hamiltonian system, but much more practical and accurate in flow simulations. We demonstrate herein using non-canonical transformations of the particle momenta of the system that the SLLOD equations, when written in terms of appropriate non-canonical variables, are completely Hamiltonian, whereas the DOLLS equations are not so. A modified set of DOLLS equations in terms of the non-canonical variables which again is completely Hamiltonian is also derived. Both algorithms then lead to a phase space distribution function which is canonical in both the coordinates and momenta.     

Size and temperature effects on the fracture mechanisms of silicon nanowires: Molecular dynamics simulations

We present molecular dynamics simulations of [1 1 0]-oriented Si nanowires (NWs) under a constant strain rate in tension until failure, using the modified embedded-atom-method (MEAM) potential. The fracture behavior of the NWs depends on both temperature and NW diameter. For NWs of diameter larger than 4 nm, cleavage fracture on the transverse (1 1 0) plane are predominantly observed at temperatures below 1000 K. At higher temperatures, the same NWs shear extensively on inclined {1 1 1} planes prior to fracture, analogous to the brittle-to-ductile transition (BDT) in bulk Si. Surprisingly, NWs with diameter less than 4 nm fail by shear regardless of temperature. Detailed analysis reveals that cleavage fracture is initiated by the nucleation of a crack, while shear failure is initiated by the nucleation of a dislocation, both from the surface. While dislocation mobility is believed to be the controlling factor of BDT in bulk Si, our analysis showed that the change of failure mechanism in Si NWs with decreasing diameters is nucleation controlled. Our results are compared with a recent in situ tensile experiment of Si NWs showing ductile failure at room temperature.     

Large-scale molecular dynamics simulations of dense plasmas: The Cimarron Project

We describe the status of a new time-dependent simulation capability for dense plasmas. The backbone of this multi-institutional effort – the Cimarron Project – is the massively parallel molecular dynamics (MD) code “ddcMD,” developed at Lawrence Livermore National Laboratory. The project’s focus is material conditions such as exist in inertial confinement fusion experiments, and in many stellar interiors: high temperatures, high densities, significant electromagnetic fields, mixtures of high- and low-Z elements, and non-Maxwellian particle distributions. Of particular importance is our ability to incorporate into this classical MD code key atomic, radiative, and nuclear processes, so that their interacting effects under non-ideal plasma conditions can be investigated. This paper summarizes progress in computational methodology, discusses strengths and weaknesses of quantum statistical potentials as effective interactions for MD, explains the model used for quantum events possibly occurring in a collision, describes two new experimental efforts that play a central role in our validation work, highlights some significant results obtained to date, outlines concepts now being explored to deal more efficiently with the very disparate dynamical timescales that arise in fusion plasmas, and provides a careful comparison of quantum effects on electron trajectories predicted by more elaborate dynamical methods.     

Explicit solvent molecular dynamics simulations of chaperonin-assisted rhodanese folding

Chaperonins are known to facilitate the productive folding of numerous misfolded proteins, Despite their established importance, the mechanism of chaperonin-assisted protein folding remains unknown. In the present article, all-atom explicit solvent molecular dynamics (MD) simulations have been performed for the first time on rhodanese folding in a series of cavity-size and cavity-charge chaperonin mutants. A compromise between stability and flexibility of chaperonin structure during the substrate folding has been observed and the key factors affecting this dynamic process are discussed.     

On the energy conservation during the active deformation in molecular dynamics simulations

In this paper, we examined the energy conservation for the current schemes of applying active deformation in molecular dynamics (MD) simulations. Specifically, two methods are examined. One is scaling the dimension of the simulation box and the atom positions via an affine transformation, suitable for the periodic system. The other is moving the rigid walls that interact with the atoms in the system, suitable for the non-periodic system. Based on the calculation of the external work and the internal energy change, we present that the atom velocities also need to be updated in the first deformation method; otherwise the energy conservation cannot be satisfied. The classic updating scheme is examined, in which any atom crossing the periodic boundary experiences a velocity delta that is equal to the velocity difference between the opposite boundaries. In addition, a new scheme which scales the velocities of all the atoms according to the strain increment is proposed, which is more efficient and realistic than the classic scheme. It is also demonstrated that the Virial stress instead of its interaction part is the correct stress definition that corresponds to Cauchy stress in the continuum mechanics.     

金属材料辐照缺陷演化的分子动力学研究进展

辐照条件下,高能粒子在金属材料内部引人稠密的辐照缺陷,导致材料力学性能严重退化,缩短材料服役寿命,是辐照材料研究的关键问题.辐照缺陷多处在纳米尺度,故分子动力学方法是模拟辐照缺陷的有力工具,近年来被广泛用于研究辐照缺陷演化.论文总结了金属材料中辐照缺陷演化的分子动力学研究进展,介绍了级联碰撞、点缺陷、空洞、氦泡、Frank位错环、层错四面体等辐照缺陷,及其与位错、晶界等微结构的相互作用.分子动力学方法揭示的机制与模型,深化了学界对辐照效应的认识,有助于提高辐照材料力学性能和设计耐辐照材料.     

金属材料辐照缺陷演化的分子动力学研究进展

辐照条件下,高能粒子在金属材料内部引入稠密的辐照缺陷,导致材料力学性能严重退化,缩短材料服役寿命,是辐照材料研究的关键问题。辐照缺陷多处在纳米尺度,故分子动力学方法是模拟辐照缺陷的有力工具,近年来被广泛用于研究辐照缺陷演化。本文总结了金属材料中辐照缺陷演化的分子动力学研究进展,介绍了级联碰撞、点缺陷、空洞、氦泡、Frank位错环、层错四面体等辐照缺陷,及其与位错、晶界等微结构的相互作用。分子动力学方法揭示的机制与模型,深化了学界对辐照效应的认识,有助于提高辐照材料力学性能和设计耐辐照材料。     

A study on the measurement of mean velocity and its convergence in molecular dynamics simulations

In many particle‐based simulations, measurement of local mean flow velocity and other continuum‐based properties are of utmost importance. Macroscopic quantities, such as mean flow velocity, temperature, and density, can be estimated by averaging the corresponding microscopic behavior of the particles. The two main subjects that should be considered in the averaging over the particles in a specific problem are spatial and temporal behaviors of them. In this paper, we study the latter. Because of the chaotic nature of the collisions among the molecules and consequently their random path, extracted macroscopic values fluctuate about their average values causing statistical errors. In this paper, an averaging method called SAM‐Modified‐CAM (SMC) will be proposed for the measurement of mean velocity that reduces statistical errors in its calculation. This proposal is based on the study conducted here on the implementations of two common averaging methods, sample‐averaged measurement (SAM) and cumulative average measurement (CAM) in molecular dynamics. In addition, convergence of mean flow velocity measurement is thoroughly discussed, and a convergence criterion is proposed for this purpose. Implementation of the proposed method in different test cases has approved its reliable performance. Copyright © 2010 John Wiley & Sons, Ltd.     

Bin size determination for the measurement of mean flow velocity in molecular dynamics simulations

Extracting macroscopic properties from molecular simulation of fluids is required in most of the molecular dynamics problems. However, methods used for this purpose, their accuracy, and their dependence on the sampling and averaging schemes are still ambiguous. Macroscopic properties at any point of a molecular domain can be extracted via sampling and averaging of molecular behavior within a control region around that point, called a bin. The size of this bin has a significant impact on the accuracy of the macroscopic properties' measurement. In this research, we will focus on the measurement of mean flow velocity using ‘binning method’. On the basis of the results of this study, the most appropriate range of the bin size in which mean velocity can be measured accurately is determined. Although this range is determined based on the measurement of mean flow velocity, we believe that it can be used to estimate the proper range for the measurement of other flow quantities as well. Copyright © 2012 John Wiley & Sons, Ltd.     

Insight into the interaction between water and surfactant aerosol particles based on molecular dynamics simulations

The ubiquitous surfactant significantly influences the hygroscopic growth of atmospheric aerosol particles. However, knowledge on the morphology of surfactant particles after the adsorption of water is insufficient. In this study, the interaction between water and particles composed of surface active malonic acid (MA) or adipic acid (AA) are simulated based on the molecular dynamics method. The key point is the combined effect of temperature and water content on the structural properties of particles and the surface propensity of surfactants at the equilibrium state. Results show that demixed structure 1 with the adsorption of water clusters on acid grain, mixed structure and demixed structure 2 with acids coating on water droplet can be observed. With temperature increasing from 160 K to 330 K the surface propensity of MA and AA increases first and then weakens. Near the standard atmospheric temperature (280–330 K), the surface propensity of MA and AA increases with increasing water content and alkyl group, and its sensitivity to temperature and water content varies regularly. Moreover, all surfactants at the particle surface orient their hydrophobic groups toward the gas. These findings improve our insight into the surfactant partitioning and further assist in more accurate prediction of the particle hygroscopic growth.     

Predicting EXAFS signals from shock compressed iron by use of molecular dynamics simulations

Simulated EXAFS signals from ab initio models and configurational averaging of molecular dynamics (MD) data are compared for α-Fe, and configurationally averaged MD EXAFS signals are compared with experimental data for iron shock compressed to pressures above the α–ε transition pressure. It is shown that molecular dynamics potentials and ab initio models capable of recreating similar vibrational density of states lead to EXAFS signals in good mutual agreement. The effects of the classical nature of the phonon distribution in the MD and the anharmonicity of the potential give rise to noticeable differences between ab initio models and configurational averaging of MD data. However, the greatest influence on the spectra is the form of the potential itself. We discuss the importance of these effects in simulating EXAFS spectra for shock compressed polycrystalline iron. It is shown that EXAFS is an insensitive probe for determining the nature of the close packed product phase in this system.     

Analysis of semi-classical potentials for molecular dynamics and Monte Carlo simulations of warm dense matter

Effective, semi-classical potentials may present a powerful tool for the determination of properties of warm dense matter, systems characterized by both moderate coupling and moderate degeneracy. However, this requires the use of these potentials in a regime where the approximations employed in their derivation begin to break down. This work presents a careful analysis of the methodology and approximations used to derive semi-classical potentials for Coulomb systems. Particular attention is paid to the appearance of many-body effects and the techniques that may be used to model them. Analytical arguments and simple examples indicate that the role of many-body effects cannot be ignored in the warm dense matter regime, and those semi-classical Coulomb potentials that focus on the pair interaction do not adequately treat many-body effects.     

Rheology of dense model fluids via nonequilibrium molecular dynamics: Shear thinning and ordering transition

Nonequilibrium molecular dynamics computer simulations are employed to investigate the rheology of dense simple model fluids. Besides the non-Newtonian behavior of the viscosity functions a shear-induced ordering transition is an essential feature of this presentation. Its occurrence in the simulation is supported by a hydrodynamic stability analysis. To illustrate the scenario preceding the instability, density and velocity profiles of the flow are considered as well as the static structure factor which enables a comparison with recent experimental results for dense suspensions. Problems related to experimental evidence of the ordering transition into layers are discussed in light of the derived stability criterion.

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Zusammenfassung Nichtgleichgewichts-Molekulardynamik Computersimulationen werden zur Untersuchung der rheologischen Eigenschaften von dichten einfachen Modell-Fluiden herangezogen. Neben dem nicht-Newtonschen Verhalten der Viskositätsfunktionen steht ein scherinduzierter Ordnungsübergang im Vordergrund der Betrachtungen. Sein Auftreten in der Simulation wird durch eine hydrodynamische Stabilitätsanalyse untermauert. Dichte- und Geschwindigkeitsprofile der Strömung werden zur Veranschaulichung des der Instabilität vorausgehenden Szenarios ebenso herangezogen wie der statische Strukturfaktor, der einen Vergleich mit neuen experimentellen Beobachtungen an dichten Suspensionen ermöglicht. Probleme beim experimentellen Nachweis dieses sich als Schichtenbildung manifestierenden Ordnungsüberganges werden anhand des abgeleiteten Stabilitätskriteriums diskutiert.

     

Plasticity of metal wires in torsion: Molecular dynamics and dislocation dynamics simulations

The orientation dependent plasticity in metal nanowires is investigated using molecular dynamics and dislocation dynamics simulations. Molecular dynamics simulations show that the orientation of single crystal metal wires controls the mechanisms of plastic deformation. For wires oriented along , dislocations nucleate along the axis of the wire, making the deformation homogeneous. These wires also maintain most of their strength after yield. In contrast, wires oriented along and directions deform through the formation of twist boundaries and tend not to recover when high angle twist boundaries are formed. The stability of the dislocation structures observed in molecular dynamics simulations are investigated using analytical and dislocation dynamics models.     

The application of nonlocal theory method in the coarse-grained molecular dynamics simulations of long-chain polylactic acid

The micro-capsules used for drug delivery are fabricated using polylactic acid(PLA),which is a biomedical material approved by the FDA.A coarse-grained model of long-chain PLA was built,and molecular dynamics(MD)simulations of the model were performed using a MARTINI force field.Based on the nonlocal theory,the formula for the initial elastic modulus of polymers considering the nonlocal effect was derived,and the scaling law of internal characteristic length of polymers was proposed,which was used to adjust the cut-off radius in the MD simulations of PLA.The results show that the elastic modulus should be computed using nonlinear regression.The nonlocal effect has a certain influence on the simulation results of PLA.According to the scaling law,the cut-off radius was determined and applied to the MD simulations,the results of which reflect the influence of the molecular weight change on the elastic moduli of PLA,and are in agreement with the experimental outcome.     

固体塑性实验室时间尺度的分子动力学模拟概述

随着超级计算机软硬件的飞速提升,基于经验势函数的分子动力学模拟在解析固体塑性的微观机制方面发挥着关键作用.但是,由于传统分子动力学基于牛顿运动方程数值积分,积分时间步长通常为飞秒量级,其模拟的时间尺度通常限于纳秒量级,从而为模拟长时间尺度固体塑性机制带来了巨大的挑战.本文从分子动力学模拟的时间尺度限制切入,介绍目前国际...