A Parallel Algorithm for Nonequilibrium Molecular Dynamics Simulation of Shear Flow on Distributed Memory Machines

A mean-field anisotropic diffusion model for unentangled polymeric liquids and semi-dilute solutions: Model development and comparison with experimental and simulation data

Atomic-level characterization of the human immunodeficiency virus type 1 envelope glycoproteins using molecular dynamic simulations.

We present nonequilibrium molecular dynamics (NEMD) simulation results for the miscibility, structural properties, and melt rheological behavior of polymeric blends under shear flow. The polymeric blends consist of chemically identical linear polymer chains (187 monomers per chain) and dendrimer polymers of generations g = 1-4. The number fraction x of the dendrimer species is varied (4%, 8%, and 12%) in the blend melt. The miscibility of blend species is measured, using the pair distribution functions gDL, gLL, and gDD. All the studied systems form miscible blend melts under the conditions investigated. We also study the effect of shear rate γ̇ and dendrimer generation on inter-penetration between blend species for different blend systems. The results reveal that shear flow increases the interpenetration of linear chains toward the core of the dendrimers. We also calculate the shear-rate dependent radius of gyration and ratios of the eigenvalues of the gyration tensor to study the shear-induced deformation of the molecules in the blend. Melt rheological properties including the shear viscosity and first and second normal stress coefficients obtained from NEMD simulations at constant pressure are found to fall into the range between those of pure dendrimer and pure linear polymer melts.

Investigation of the thermal behaviors of folded graphene by non-equilibrium molecular dynamics simulation

Determination of the absolute binding free energies of HIV-1 protease inhibitors using non-equilibrium molecular dynamics simulations

Individual molecule dynamics have been shown to influence significantly the bulk rheological and microstructural properties of short-chain, unentangled, linear polyethylene liquids undergoing high strain-rate flows. The objective of this work was to extend this analysis to a linear polyethylene composed of macromolecules of a much greater length and entanglement density; i.e., a liquid consisting of C400H802 molecules, with approximately ten kinks per chain at equilibrium, as calculated by the Z1 code of Kröger [Comput. Phys. Commun. 168, 209–232 (2005)]. To achieve this, we performed nonequilibrium molecular dynamics (NEMD) simulations of a model system using the well-established potential model of Siepmann et al. [Nature 365, 330–332 (1993)] for a wide range of Weissenberg numbers (Wi) under steady shear flow. A recent study by Baig et al. [Macromolecules 43, 6886–6902 (2010)] examined this same system using NEMD simulations, but focused on the bulk rheological and microstructural properties as calculated from ensemble averages of the chains comprising the macromolecular liquids. In so doing, some key features of the system dynamics were not fully elucidated, which this article aims to highlight. Specifically, it was found that this polyethylene liquid displays multiple timescales associated with not only the decorrelation of the end-to-end vector (commonly related to the Rouse time or disengagement time, depending on the entanglement density of the liquid), but also ones associated with the retraction and rotation cycles of the individual molecules. Furthermore, when accounting for these individual chain dynamics, the “longest” relaxation time of the system was higher by a factor of 1.7, independent of shear rate, when calculated self-consistently due to the coupling of relaxation modes. Brownian dynamics (BD) simulations were also performed on an analogous free-draining bead-rod chain model to compare the rotation and retraction dynamics of a single chain in dilute solution with individual molecular motions in the melt. These BD simulations revealed that the dynamics of the free-draining chain are qualitatively and quantitatively similar to those of the individual chains comprising the polyethylene melt at strain rates in excess of Wi ≈ 50, implying a possible breakdown of reptation theory in the high shear limit. An examination of the bulk-average properties revealed the effects of the chain rotation and retraction cycles upon commonly modeled microstructural properties, such as the distribution function of the chain end-to-end vector and the entanglement number density.

In this work, we study the impact of the phonon thermal conductivity of Silver (Ag) and Gold (Au) on the interface resistance of metal-nonmetal contacts at room temperature. The thermal conductivity of both metals is determined for bulk and thin films of varying thickness using non-equilibrium molecular dynamics (NEMD) simulations. Likewise, we determine the thermal interface resistance due to phonons of metal films embedded in a nonmetal layer composed of Silicon (Si). Based on a two-temperature model (TTM) for electrons and phonons, we determine the thermal resistance due to electron-phonon interactions and the variation of the film resistance of Ag and Au layers as a function of their thickness. The latter considering the estimated phonon contribution to the thermal conductivity of the studied metals obtained with our NEMD simulations. Two important results are presented in this work. First, we have found for the studied metals that at room temperature phonons contribute less than 1.0 % to the bulk thermal conductivity; and that their relative contribution to the conductivity and its variation with the film thickness significantly impacts the overall film resistance of metallic films.

Effect of interfacial structures on ionic conductivity in particle-dispersed composite electrolytes

Mechanism of Enhanced Mechanical Stability of Retroviral Kissing-Loops Elucidated by Non-Equilibrium Molecular Dynamics Simulations

Phonon thermal transport is a key feature for the operation of thermoelectric materials, but it is challenging to accurately calculate the thermal conductivity of materials with strong anharmonicity or large cells. In this work, a deep neural network potential (NNP) is developed using a dataset based on density functional theory (DFT) and applied to describe the lattice dynamics of Sb2Te3 and Bi2Te3/Sb2Te3 superlattices. The lattice thermal conductivities of Sb2Te3 are first predicted using equilibrium molecular dynamics (EMD) simulations combined with an NNP and the results match well with experimental values. Then, through further exploration of weighted phase spaces and the Grüneisen parameter, we find that there is a stronger anharmonicity in the out-of-plane direction in Sb2Te3, which is the reason why the thermal conductivities are overestimated more in the out-of-plane direction than in the in-plane direction by solving the phonon Boltzmann transport equation (BTE) with only three-phonon scattering processes being considered. More importantly, the lattice thermal conductivities of Bi2Te3/Sb2Te3 superlattices with different periods are accurately predicted using non-equilibrium molecular dynamics (NEMD) simulations together with an NNP, which serves as a good example to explore the thermal transport physics of superlattices using a deep neural network potential.

The shear viscosity of molten NaCl and KCl was calculated through equilibrium (EMD) and nonequilibrium molecular-dynamics (NEMD) simulations in the canonical (N,V,T) ensemble. Two rigid-ion potentials were investigated, namely, the Born-Mayer-Huggins-Tosi-Fumi potential and the Michielsen-Woerlee-Graaf-Ketelaar potential with the parameters proposed by Ladd. The NEMD simulations were performed using the SLLOD equations of motion [D. J. Evans and G. P. Morriss, Phys. Rev. A 30, 1528 (1984)] with a Gaussian isokinetic thermostat and the results are compared with those obtained from Green-Kubo EMD (N,V,T) simulations and experimental shear viscosity data. The NEMD zero strain rate shear viscosity, eta(0), was obtained by fitting a simplified Carreau-type equation and by application of mode-coupling theory, i.e., a eta-gamma(1/2) linear relationship. The values obtained from the first method are found to be significantly lower than those predicted by the second. The agreement between the EMD and NEMD results with experimental data is satisfactory for the two potentials investigated. The ion-ion radial distribution functions obtained with the two rigid-ion potentials for both molten salts are discussed in terms of the differences between the two models.

In this work, nonequilibrium molecular dynamics (MD) simulations were performed to investigate uniform liquid argon flow past a carbon nanotube. In the simulation, nanotubes were modeled as rigid cylinders of carbon atoms. Both argon-argon and argon-carbon interactions were calculated based on Lennard-Jones potential. Simulated drag coefficients were compared with (i) published empirical equation which was based on experiments conducted with macroscale cylinders and (ii) finite element (FE) analyses based on Navier-Stokes equation for flow past a circular cylinder using the same dimensionless parameters used in MD simulations. Results show that classical continuum mechanics cannot be used to calculate drag on a nanotube. In slow flows, the drag coefficients on a single-walled nanotube calculated from MD simulations were larger than those from the empirical equation or FE analysis. The difference increased as the flow velocity decreased. For higher velocity flows, slippage on the surface of the nanotube was identified which resulted in lower drag coefficient from MD simulation. This explains why the drag coefficient from MD dropped faster than those from the empirical equation or FE simulation as the flow velocity increased. It was also found that the drag forces are almost equal for single- and double-walled nanotubes with the same outer diameter, implying that inner tubes do not interact with fluid molecules.

It is known that polystyrene melts behave anomalously in fast elongational flows insofar as the steady-state elongational viscosity keeps decreasing with increasing stretching rate ε̇, without showing the typical upturn at ε̇τR ≈ 1, with τR the Rouse time. The authors have recently suggested that such an anomalous behavior might be due to a decrease of the monomeric friction coefficient brought about by alignment of the Kuhn segments of the polymer to the stretching direction. Here we perform a quantitative analysis of such a possibility by first determining from existing stress–optical data how such a reduction should correlate to the order parameter of the Kuhn segments and then by performing nonequilibrium molecular dynamics (NEMD) simulations over a sequence of styrene oligomers. We have used NEMD not only to obtain diffusion coefficients of those oligomers but also, for what seems to be the first time, friction coefficients. Indeed, it is well-known that the Einstein relationship linking friction to diffusion does not hold true far from equilibrium. The friction coefficients so obtained correlate to the order parameter of the monomers in much the same way as in the polymeric case, and by increasing the length (or mass) of the oligomer, they appear to approach a similar characteristic curve.

Cellulose-reinforced polypropylene bionanocomposites can show improved elastic properties over their pure polypropylene counterparts. We have used equilibrium and non-equilibrium molecular dynamics (MD) simulations to study the elastic properties of polypropylene bionanocomposite systems composed of cellulose nanofibrils (CNF), polypropylene (PP) matrix, and maleic anhydride (MAH) coupling agent. The components of the bionanocomposite were parametrized for compatibility with the AMBER14SB force fields. The elastic properties of pure PP systems converge for the chains with at least 20 monomers. The ratio of cellulose in CNF-PP bionanocomposites strongly affects their elastic properties. The elastic modulus of CNF-PP bionanocomposites shows small improvement when the adhesion between hydrophobic and hydrophilic components is facilitated by a MAH coupling agent. The results demonstrate how fully-atomistic MD simulations can be systematically used to evaluate the elastic properties of CNF-PP bionanocomposites and to make predictions that are in agreement with experiments.

Thermal conductivity of amorphous and crystalline thin films by molecular dynamics simulation