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.     

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.     

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.     

Microstructural evolution and mechanical properties of FeCoCrNiCu high entropy alloys: a microstructure-based constitutive model and a molecular dynamics simulation study

High entropy alloys(HEAs) attract remarkable attention due to the excellent mechanical performance. However, the origins of their high strength and toughness compared with those of the traditional alloys are still hardly revealed. Here, using a microstructure-based constitutive model and molecular dynamics(MD) simulation, we investigate the unique mechanical behavior and microstructure evolution of FeCoCrNiCu HEAs during the indentation. Due to the interaction between the dislocation and solution,the high dislocation density in FeCoCrNiCu leads to strong work hardening. Plentiful slip systems are stimulated, leading to the good plasticity of FeCoCrNiCu. The plastic deformation of FeCoCrNiCu is basically affected by the motion of dislocation loops. The prismatic dislocation loops inside FeCoCrNiCu are formed by the dislocations with the Burgers vectors of a/6[■] and a/6[■], which interact with each other, and then emit along the ■slip direction. In addition, the mechanical properties of FeCoCrNiCu HEA can be predicted by constructing the microstructure-based constitutive model, which is identified according to the evolution of the dislocation density and the stress-strain curve.Strong dislocation strengthening and remarkable lattice distortion strengthening occur in the deformation process of FeCoCrNiCu, and improve the strength. Therefore, the origins of high strength and high toughness in FeCoCrNiCu HEAs come from lattice distortion strengthening and the more activable slip systems compared with Cu. These results accelerate the discovery of HEAs with excellent mechanical properties, and provide a valuable reference for the industrial application of HEAs.     

Effect of short chain branching in molecular dimensions and Newtonian viscosity of ethylene/1-hexene copolymers: matching conformational and rheological experimental properties and atomistic simulations

The molecular dimensions in dilute solution and the linear viscoelastic melt properties of a series of linear ethylene/1-hexene random copolymers with variable short chain branching content are reported. The results obtained from size exclusion chromatography and viscosimetry in dilute solution show a molecular contraction as the branching level increases. Additionally, a clear dependence of the Newtonian viscosity with the short chain branching content at T = 463 K is obtained. Both experimental observations are in agreement with previous experimental results found in ethylene/α-olefin copolymers, but more interestingly with recent full atomistic simulations made in our group in this type of macromolecular systems. The dependences observed can be related to the changes observed in the macromolecular conformational features and also in the equilibration entanglement time and the molecular weight between entanglements as the number of short chain branches increases.     

Rotational dynamics in dipolar colloidal suspensions: video microscopy experiments and simulations results

The dynamics of field-induced structures in very dilute dipolar colloidal suspensions subject to rotating magnetic fields have been experimentally studied using video microscopy. When a rotating field is imposed the chain-like aggregates rotate with the magnetic field frequency. We found that the size of the induced structures at small rotational frequencies is larger than at zero rotating frequency, i.e. when an uniaxial magnetic field is applied. At higher frequencies, the average size of the aggregates decreases with frequency following a power law with exponent −0.5 as the hydrodynamic friction forces overcome the dipolar magnetic forces, causing the chains break up. A non-thermal molecular dynamics simulations are also reported, showing good agreement with the experiments.     

On the dynamics of tapping mode atomic force microscope probes

A?mathematical model is developed to investigate the grazing dynamics of tapping mode atomic force microscopes (AFM) subjected to a base harmonic excitation. A?multimode Galerkin approximation is utilized to discretize the nonlinear partial differential equation of motion governing the cantilever response and associated boundary conditions and obtain a set of nonlinearly coupled ordinary differential equations governing the time evolution of the system dynamics. A?comprehensive numerical analysis is performed for a wide range of the excitation amplitude and frequency. The tip oscillations are examined using nonlinear dynamic tools through several examples. The non-smoothness in the tip/sample interaction model is treated rigorously. A?higher-mode Galerkin analysis indicates that period doubling bifurcations and chaotic vibrations are possible in tapping mode microscopy for certain operating parameters. It is also found that a single-mode Galerkin approximation, which accurately predicts the tip nonlinear responses far from the sample, is not adequate for predicting all of the nonlinear phenomena exhibited by an AFM, such as grazing bifurcations, and leads to both quantitative and qualitative errors.