Zoltán Ható

Simulation of steady-state diffusion: Driving force ensured by dual control volumes or local equilibrium Monte Carlo

We provide a systematic comparative analysis of various simulation methods for studying steady-state diffusive transport of molecular systems. The methods differ in two respects: (1) the actual method with which the dynamics of the system is handled can be a direct simulation technique [molecular dynamics (MD) and dynamic Monte Carlo (DMC)] or can be an indirect transport equation [the Nernst-Planck (NP) equation], while (2) the driving force of the steady-state transport can be maintained with control cells on the two sides of the transport region [dual control volume (DCV) technique] or it can be maintained in the whole simulation domain with the local equilibrium Monte Carlo (LEMC) technique, where the space is divided into small subvolumes, different chemical potentials are assigned to each, and grand canonical Monte Carlo simulations are performed for them separately. The various combinations of the transport-methods with the driving-force methods have advantages and disadvantages. The MD+DCV and DMC+DCV methods are widely used to study membrane transport. The LEMC method has been introduced with the NP+LEMC technique, which was proved to be a fast, but somewhat empirical method to study diffusion [D. Boda and D. Gillespie, J. Chem. Theor. Comput. 8, 824 (2012)]. In this paper, we introduce the DMC+LEMC method and show that the resulting DMC+LEMC technique has the advantage over the DMC+DCV method that it provides better sampling for the flux, while it has the advantage over the NP+LEMC method that it simulates dynamics directly instead of hiding it in an external adjustable parameter, the diffusion coefficient. The information gained from the DMC+LEMC simulation can be used to construct diffusion coefficient profiles for the NP+LEMC calculations, so a simultaneous application of the two methods is advantageous.

Water-mediated potassium acetate intercalation in kaolinite as revealed by molecular simulation.

Molecular simulations are suitable tools to study the adsorption and intercalation of molecules in clays. In this work, a recently proposed thermodynamically consistent force field for inorganic compounds (INTERFACE, Heinz H, Lin TJ, Mishra RK, Emami FS (2013) Langmuir 29:1754–1765), which enables accurate simulations of inorganic–organic interfaces, was tested for a two-sheet type clay mineral. All-atom NpT molecular dynamics simulations were used to describe the characteristics (basal spacing, loading, molecular orientation) of some intercalate complexes of kaolinite with potassium acetate and the results were compared with the available experimental data. The most probable structural configurations of the kaolinite/potassium acetate intercalate complexes were determined from the simulations. Our examinations confirmed some supposed (single- or double-layered) arrangements of guest molecules. The need of interlayer water in the intercalate complex, which can be produced by the basic synthesis procedure in air atmosphere, was verified.

Characterization of kaolinite–ammonium acetate complexes prepared by one-step homogenization method

Although kaolinite-ammonium acetate complexes are of interest in the area of kaolinite nanocomposites, the structures of these complexes have remained largely elusive. Experimental and molecular simulation analysis is used to investigate their structures, revealing that two types of water-containing kaolinite-ammonium acetate complex exist. A cost-efficient one-step homogenization method was used to synthesize these complexes. The effect of the aging time and the amount of reagents on the intercalation were characterized experimentally by X-ray diffraction, thermogravimetry, Fourier transform infrared spectroscopy and scanning electron microscopy. The optimal degree of intercalation was obtained by using two orders of magnitude lower amount of reagents than in the case of the solution method. It was found that the so far less investigated 1.7-nm complex has higher water content than the 1.4-nm one. For both complexes, our molecular simulations predict the double-layered structure of the acetate ions, which is usually assumed in the case of the kaolinite-acetate complexes. For the 1.7-nm complex, however, a quasi-triple-layered structure of water molecules instead of the double-layered one was calculated.

Molecular simulation of water removal from simple gases with zeolite NaA

Water vapor removal from some simple gases using zeolite NaA was studied by molecular simulation. The equilibrium adsorption properties of H2O, CO, H2, CH4 and their mixtures in dehydrated zeolite NaA were computed by grand canonical Monte Carlo simulations. The simulations employed Lennard-Jones + Coulomb type effective pair potential models, which are suitable for the reproduction of thermodynamic properties of pure substances. Based on the comparison of the simulation results with experimental data for single-component adsorption at different temperatures and pressures, a modified interaction potential model for the zeolite is proposed. In the adsorption simulations with mixtures presented here, zeolite exhibits extremely high selectivity of water to the investigated weakly polar/non-polar gases demonstrating the excellent dehydration ability of zeolite NaA in engineering applications.

A simple method for the simulation of steady-state diffusion through membranes: pressure-tuned, boundary-driven molecular dynamics

We present a novel molecular dynamics-based simulation technique for investigating gas transport through membranes. In our simulations, the main control parameters are the partial pressure for the components on the input side of the membrane and the total pressure on the output side. The essential point of our scheme is that this pressure control should be realised by adjusting the particle numbers in the input and output side control cells indirectly. Although this perturbation is applied sufficiently far from the membrane, the bulk-phase properties are well controlled in a simulation cell of common size. Numerical results are given for silicalite-1 membrane with permeating CH4, CO2, H2 and N2 gases as well as with binary mixtures of CO2 with the other three components. To describe interactions between particles, we used the simple shifted and cut Lennard–Jones potential with parameters available in the literature. It is expected that the proposed technique can be applied to several other types of membranes and transported fluids in order to support the development of a deeper understanding of separation processes.

Simulation study of a rectifying bipolar ion channel: detailed model versus reduced model

We study a rectifying mutant of the OmpF porin ion channel using both all-atom and reduced models. The mutant was created by Miedema et al. [Nano Lett., 2007, 7, 2886] on the basis of the N-P semiconductor diode, in which an N-P junction is formed. The mutant contains a pore region with positive amino acids on the left-hand side and negative amino acids on the right-hand side. Experiments show that this mutant rectifies. Although we do not know the structure of this mutant, we can build an all-atom model for it on the basis of the structure of the wild type channel. Interestingly, molecular dynamics simulations for this all-atom model do not produce rectification. A reduced model that contains only the important degrees of freedom (the positive and negative amino acids and free ions in an implicit solvent), on the other hand, exhibits rectification. Our calculations for the reduced model (using the Nernst-Planck equation coupled to Local Equilibrium Monte Carlo simulations) reveal a rectification mechanism that is different from that seen for semiconductor diodes. The basic reason is that the ions are different in nature from electrons and holes (they do not recombine). We provide explanations for the failure of the all-atom model including the effect of all the other atoms in the system as a noise that inhibits the response of ions (that would be necessary for rectification) to the polarizing external field.

Communication: Molecular simulation study of kaolinite intercalation with realistic layer size

Intercalation phenomena of kaolinite in aqueous potassium acetate and in hexyl-amine solutions are studied by large scale molecular dynamics simulations. The simulated kaolinite particle is constructed from ~6.5 × 10(6) atoms, producing a particle size of ~100 nm × 100 nm × 10 nm. The simulation with potassium acetate results in a stable kaolinite-potassium acetate complex, with a basal spacing that is in close agreement with experimental data. The simulation with hexyl-amine shows signs of the experimentally observed delamination of kaolinite (the initial phase of the formation of nanoscrolls from the external layers).