Pure Molecular Dynamics Research Articles

A continuum–atomistic simulation of heat transfer in micro- and nano-flows

We develop a hybrid atomistic–continuum scheme for simulating micro- and nano-flows with heat transfer. The approach is based on spatial “domain decomposition” in which molecular dynamics (MD) is used in regions where atomistic details are important, while classical continuum fluid dynamics is used in the remaining regions. The two descriptions are matched in a coupling region where we ensure continuity of mass, momentum, energy and their fluxes. The scheme for including the energy equation is implemented in 1-D and 2-D, and used to study steady and unsteady heat transfer in channel flows with and without nano roughness. Good agreement between hybrid results and analytical or pure MD results is found, demonstrating the accuracy of this multiscale method and its potential applications in thermal engineering.

Density distribution for a dense hard-sphere gas in micro/nano-channels: Analytical and simulation results

We study the properties of a hard-sphere dense gas near the hard walls of micro and nano-channels. Analytical techniques, Monte Carlo (MC) methods and molecular dynamics (MD) simulation methods have been used to characterize the influence of the characteristic parameters such as number density, reduced density, width of the system and molecular diameter, on the equilibrium properties of the gas near the hard walls of micro and nano-channels. A mathematical model has been developed to characterize the density oscillations as the result of packing of molecules in case of a dense gas near the micro and nano-channels walls. The height and the position of the density oscillation peaks near the wall are characterized. These results are also confirmed by the MD and MC simulation results.Comparisons between MD and MC simulation results for particles having different diameter are also presented. For the same size of the particles and moderately dense gas, MC and MD results are similar, differences in the density profiles being limited only to the oscillatory region. For different particle sizes, MD and MC results are limited to a short distance near the wall for long size systems and moderately dense fluids. The effect of the boundary (particle size) on the simulation results is found to increase with η (reduced density) and it is very small in case of a dilute gas. For small η and small particle size (R) relative to the width of the system L, the height of the oscillation peaks is slowly increasing with R/L, and for high densities is always decreasing with R/L. The position of these peaks depends only on the size of the particles and when R is much smaller than L, it shows a small dependence on L. The deviations in the oscillatory region for the pure MC simulation results compared to pure MD simulation results are quantified, and more efficient hybrid MC–MD simulations are performed to reduce these deviations.

A structural mechanics study of single-walled carbon nanotubes generalized from atomisticsimulation

A new structural mechanics model is developed to closely duplicate the atomicconfiguration and behaviours of single-walled carbon nanotubes (SWCNTs). The SWCNTsare effectively represented by a space frame, where primary and secondary beams are usedto bridge the nearest and next-nearest carbon atoms, to mimic energies associated withbond stretching and angle variation, respectively. The elastic properties of the framecomponents are generalized from molecular dynamics (MD) simulation based on anaccurate ab initio force field, and numerical analyses of tension, bending, and torsion arecarried out on nine different SWCNTs. The space-frame model also closely duplicates thebuckling behaviours of SWCNTs in torsion and bending. In addition, by repeating thesame process with continuum shell and beam models, new elastic and sectionparameters are fitted from the MD benchmark experiments. As an application, all threemodels are employed to study the thermal vibration behaviours of SWCNTs,and excellent agreements with MD analyses are found. The present analysis is asystematic structural mechanics attempt to fit SWCNT properties for several basicdeformation modes and applicable to a variety of SWCNTs. The continuum models andfitted parameters may be used to effectively simulate the overall deformationbehaviours of SWCNTs at much larger length- and timescales than pure MD analysis.

Multiscale modeling of carbon nanotubes under axial tension and compression

In this paper, we study the elastic and plastic properties of single-walled carbon nanotubes (SWCNTs) under axial compression and tension. The present work employs molecular dynamics (MD) as well as a multiscale technique where a handshaking region between MD and tight-binding (TB) is described and implemented. The interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond-order potential, TB derived forces, as well as long-range Lennard-Jones potential. A smooth cutoff Lennard-Jones with switch function is also explored. The detection of sideway buckling due to the asymmetrical axial compression is reported and discussed. This sideway buckling phenomenon is observed when using both pure MD and MD/TB multiscale models. The viability of the presently developed handshaking region between MD and TB in CNTs under axial compression and tension is thus validated.

Hybrid method coupling molecular dynamics and Monte Carlo simulations to study the properties of gases in microchannels and nanochannels

We combine molecular dynamics (MD) and Monte Carlo (MC) simulations to study the properties of gas molecules confined between two hard walls of a microchannel or nanochannel. The coupling between MD and MC simulations is introduced by performing MD near the boundaries for accuracy and MC in the bulk because of the low computational cost. We characterize the influence of different densities and molecule sizes on the equilibrium properties of the gas in the microchannel. The effect of the particle size on the simulation results is very small in the case of a dilute gas and increases with the density. The hybrid MD-MC simulation method is validated by comparing the results for density and temperature profiles with those of pure MD and pure MC simulations. These results compare well for pure MD and pure MC, as well as hybrid MD-MC, both in the bulk and near the boundaries, when hard-sphere interactions are used. When Lennard-Jones potentials are used to accurately model the interactions between the gas and wall molecules instead, the results of pure MD simulations differ significantly from the pure MC simulations near the boundaries, but the results of the hybrid method compare well with the pure MD results near the wall, and with the pure MC and pure MD results in the middle of the channel. The hybrid method also very accurately simulates the interface between the MD and MC simulation domains. Comparisons between MD, MC, and hybrid MD-MC computational costs are outlined. The speedup when using 50% of the domain for MD simulations and 50% for MC simulations is very small compared to pure MD simulations times, but this speedup increases drastically for more realistic situations where the region near the wall is small compared to the bulk region.

Investigations on the chain conformation of weakly charged polyelectrolyte in solvents by using efficient hybrid molecular simulations

We have investigated the microstructural properties of a weakly charged polyelectrolyte modeled with both Hookean spring and Debye-Huckel potential, by employing a novel hybrid scheme of molecular dynamics (MD) and Monte Carlo (MC) simulations. Although the off-lattice pivot step facilitates the earlier computations stage, it gives rise to oscillations and hinders the stable equilibrium state. In order to overcome this problem, we adopt the MC off-lattice pivot step in early stage only, and then switch the computation to a pure MD step. The result shows that the computational speed-up compared to the previous method is entirely above 10 to 50, without loss of the accuracy. We examined the conformations of polyelectrolyte in solvents in terms of the end-to-end distance, radius of gyration, and structure factor with variations of the screening effects of solvent and the monomer charges. The emphasis can favorably be given on the elongation behavior of a polyelectrolyte chain, with observing the simultaneous snapshots.

Fourier acceleration of Langevin molecular dynamics

Fourier acceleration has been successfully applied to the simulation of lattice field theories for more than a decade. In this paper, we extend the method to the dynamics of discrete particles moving in a continuum. Although our method is based on a mapping of the particles' dynamics to a regular grid so that discrete Fourier transforms may be taken, it should be emphasized that the introduction of the grid is a purely algorithmic device and that no smoothing, coarse-graining, or mean-field approximations are made. The method thus can be applied to the equations of motion of molecular dynamics (MD) or its Langevin or Brownian variants. For example, in Langevin MD simulations our acceleration technique permits a straightforward spectral decomposition of forces so that the long-wavelength modes are integrated with a longer time step, thereby reducing the time required to reach equilibrium or to decorrelate the system in equilibrium. Speedup factors of up to 30 are observed relative to pure (unaccelerated) Langevin MD. As with acceleration of critical lattice models, even further gains relative to the unaccelerated method are expected for larger systems. Preliminary results for Fourier-accelerated molecular dynamics are presented in order to illustrate the basic concepts. Possible extensions of the method and further lines of research are discussed.

Simulation of a single polymer chain in solution by combining lattice Boltzmann and molecular dynamics

In this paper we establish a new efficient method for simulating polymer–solvent systems which combines a lattice Boltzmann approach for the fluid with a continuum molecular-dynamics (MD) model for the polymer chain. The two parts are coupled by a simple dissipative force while the system is driven by stochastic forces added to both the fluid and the polymer. Extensive tests of the new method for the case of a single polymer chain in a solvent are performed. The dynamic and static scaling properties predicted by analytical theory are validated. In this context, the influence of the finite size of the simulation box is discussed. While usually the finite size corrections scale as L−1 (L denoting the linear dimension of the box), the decay rate of the Rouse modes is only subject to an L−3 finite size effect. Furthermore, the mapping to an existing MD simulation of the same system is done so that all physical input values for the new method can be derived from pure MD simulation. Both methods can thus be compared quantitatively, showing that the new method allows for much larger time steps. Comparison of the results for both methods indicates systematic deviations due to nonperfect match of the static chain conformations.

ISOTHERMAL MOLECULAR DYNAMICS: A PRACTICAL STUDY

In a molecular dynamics simulation, trapping of the phase space trajectory can occur at low energy for long time intervals. To untrap that evolution and recover the canonical ensemble description, at regular clock hits, all particle velocities are randomly redistributed according to the Maxwell statistics. The organization of this hybrid evolution mixing molecular dynamics and random number generation leads to a fully parallel and synchronous algorithm. An illustration of this approach on the one-dimensional jellium is presented. For large values of the coupling λ for which the evolution at constant energy is trapped, the hybrid method allows to reproduce the exact Boltzmann statistical description. Computer simulations show that the Nosé-Hoover method does not really improve the pure molecular dynamics for the one dimensional jellium.