Grand canonical steady-state simulation of nucleation

ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multicenter rigid potential models based on Lennard-Jones sites, point charges, and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, such as fluids at interfaces, as well as nonequilibrium molecular dynamics simulation of heat and mass transfer.

Ion fluxes through nanopores and transmembrane channels

We introduce an implicit solvent Molecular Dynamics approach for calculating ionic fluxes through narrow nanopores and transmembrane channels. The method relies on a dual-control-volume grand-canonical molecular dynamics (DCV-GCMD) simulation and the analytical solution for the electrostatic potential inside a cylindrical nanopore recently obtained by Levin [Europhys. Lett. 76, 163 (2006)]. The theory is used to calculate the ionic fluxes through an artificial transmembrane channel which mimics the antibacterial gramicidin A channel. Both current-voltage and current-concentration relations are calculated under various experimental conditions. We show that our results are comparable to the characteristics associated to the gramicidin A pore, especially the existence of two binding sites inside the pore and the observed saturation in the current-concentration profiles.

Thermodynamic properties of a symmetrical binary mixture in the coexistence region

A three-dimensional symmetric binary fluid is studied, as a function of temperature, in the two-phase (liquid-liquid) coexistence region via Monte Carlo simulations. Particular focus has been in the understanding of curvature-dependent interfacial tension, which is observed to vary as σ(R) = σ(∞)/[1+2(ℓ/R)(2)], implying that a Tolman length is zero in the limit R → ∞. The length ℓ is found to have a critical divergence the same as the correlation length, but its amplitude is significantly larger (ℓ ~/= 4ξ). Our findings hence imply that the barrier against homogeneous nucleation is significantly reduced (in comparison with the classical nucleation theory) in the critical region. We also report results for the critical behavior of the flat interfacial tension σ(∞) and the concentration susceptibility, as well as the amplitude ratios involving these thermodynamic quantities. Noting that the interatomic potential in our model is described by the Lennard-Jones form that decays faster that 1/r(3), all of our results for critical phenomena are expectedly consistent with the Ising universality class of three spatial dimensions.