Multiscale analysis of the effect of surface charge pattern on a nanopore's rectification and selectivity properties: From all-atom model to Poisson-Nernst-Planck.

We report a multiscale modeling study for charged cylindrical nanopores using three modeling levels that include (1) an all-atom explicit-water model studied with molecular dynamics, and reduced models with implicit water containing (2) hard-sphere ions studied with the Local Equilibrium Monte Carlo simulation method (computing ionic correlations accurately), and (3) point ions studied with Poisson-Nernst-Planck theory (mean-field approximation). We show that reduced models are able to reproduce device functions (rectification and selectivity) for a wide variety of charge patterns, that is, reduced models are useful in understanding the mesoscale physics of the device (i.e., how the current is produced). We also analyze the relationship of the reduced implicit-water models with the explicit-water model and show that diffusion coefficients in the reduced models can be used as adjustable parameters with which the results of the explicit- and implicit-water models can be related. We find that the values of the diffusion coefficients are sensitive to the net charge of the pore but are relatively transferable to different voltages and charge patterns with the same total charge.

Multiscale modeling of a rectifying bipolar nanopore: explicit-water versus implicit-water simulations.

In a multiscale modeling approach, we present computer simulation results for a rectifying bipolar nanopore at two modeling levels. In an all-atom model, we use explicit water to simulate ion transport directly with the molecular dynamics technique. In a reduced model, we use implicit water and apply the Local Equilibrium Monte Carlo method together with the Nernst-Planck transport equation. This hybrid method makes the fast calculation of ion transport possible at the price of lost details. We show that the implicit-water model is an appropriate representation of the explicit-water model when we look at the system at the device (i.e., input vs. output) level. The two models produce qualitatively similar behavior of the electrical current for different voltages and model parameters. Looking at the details of concentration and potential profiles, we find profound differences between the two models. These differences, however, do not influence the basic behavior of the model as a device because they do not influence the z-dependence of the concentration profiles which are the main determinants of current. These results then address an old paradox: how do reduced models, whose assumptions should break down in a nanoscale device, predict experimental data? Our simulations show that reduced models can still capture the overall device physics correctly, even though they get some important aspects of the molecular-scale physics quite wrong; reduced models work because they include the physics that is necessary from the point of view of device function. Therefore, reduced models can suffice for general device understanding and device design, but more detailed models might be needed for molecular level understanding.

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).

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.

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.

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.

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 H(2)O, CO, H(2), CH(4) 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.

Current and selectivity in a model sodium channel under physiological conditions: Dynamic Monte Carlo simulations.

A reduced model of a sodium channel is analyzed using Dynamic Monte Carlo simulations. These include the first simulations of ionic current under approximately physiological ionic conditions through a model sodium channel and an analysis of how mutations of the sodium channel's DEKA selectivity filter motif transform the channel from being Na(+) selective to being Ca(2+) selective. Even though the model of the pore, amino acids, and permeant ions is simplified, the model reproduces the fundamental properties of a sodium channel (e.g., 10 to 1 Na(+) over K(+) selectivity, Ca(2+) exclusion, and Ca(2+) selectivity after several point mutations). In this model pore, ions move through the pore one at a time by simple diffusion and Na(+) versus K(+) selectivity is due to both the larger K(+) not fitting well into the selectivity filter that contains amino acid terminal groups and K(+) moving more slowly (compared to Na(+)) when it is in the selectivity filter.

Simulation-assisted evidence for the existence of two stable kaolinite/potassium acetate intercalate complexes.

Recent molecular simulation findings with several kaolinite intercalate complexes raised the question of the existence of more than one stable state, which has not been confirmed by experimental observations yet. Kaolinite/potassium acetate intercalate complexes were synthesized and examined by X-ray diffraction, and a molecular simulation study was performed for the system. Consistent with the suggestion from the simulations, an additional stable basal spacing was found experimentally at d(001)=1.168nm besides the well-known one at d(001)=1.403nm.

Dynamic Monte Carlo simulation in mixtures.

The dynamic Monte Carlo technique is a widely used simulation tool but the parameters of the calculation have to be tuned to reflect the same dynamics as the corresponding molecular dynamics simulation. As the direct calibration of the dynamic Monte Carlo with molecular dynamics is a laborious task, we propose a new method that allows the standard dynamic Monte Carlo to realize the correct time proportionality in many-component systems without the need of corresponding molecular dynamics calculation. The method has been tested in various systems and the dynamic Monte Carlo results obtained by the proposed method were found to be in good agreement with the results of the control molecular dynamics simulations.

Simulation and experimental study of intercalation of urea in kaolinite.

Experimental measurements and molecular simulations were used to describe the characteristics of the kaolinite/urea intercalation compound. The intercalation compound was synthesized by a mechanochemical method and examined by X-ray diffraction and thermogravimetry. Additionally, a series of NpT (constant particle number-pressure-temperature) simulations was performed to identify thermodynamically stable basal spacings. From the simulations the most probable molecular orientations were determined for single and double layered arrangements of urea molecules that develop between the layers of kaolinite.

Magnetic properties in monolayers of a model polydisperse ferrofluid.

The influence of polydispersity on the equilibrium properties of monolayers of three-dimensional dipolar spheres with short-range repulsive interactions is studied by means of Monte Carlo simulations and a high field approximation perturbation theory. The particle distribution in the simulations is realized in the semigrand ensemble by tuning appropriately the underlying particle distribution density. The magnetization curves are calculated as functions of density and temperature, and the obtained results are compared with the data determined in a monodisperse equivalent of the system. In-plane and out-of-plane initial magnetic susceptibilities are determined using external fields applied parallel or normal to the monolayer plane. Susceptibility data for the true two- and three-dimensional counterparts of the system are also calculated for comparison. Our findings for the magnetic properties can partly be explained by the structural characteristics obtained from the simulations.

Heat capacity in a model polydisperse ferrofluid with narrow particle size distribution.

The influence of polydispersity on the phase equilibrium properties and the heat capacity of a dipolar system with additional short-range (repulsive + attractive) interactions (modeled by a shifted Lennard-Jones pair potential) is studied by means of a Monte Carlo scheme. The particle distribution of the investigated system is realized in the semigrand ensemble by tuning appropriately the underlying particle distribution density. The phase coexistence and heat capacity data are calculated with and without an applied magnetic field, and the obtained results are compared with the data determined in a monodisperse equivalent of the system.

Phase separation in mixtures of Yukawa and charged Yukawa particles from Gibbs ensemble Monte Carlo simulations and the mean spherical approximation.

The phase equilibrium of mixtures of Yukawa and charged Yukawa particles is studied by means of Gibbs ensemble Monte Carlo (GEMC) simulation method and the mean spherical approximation (MSA). The strength of the Coulomb energy compared to that of the Yukawa attraction is characterized by a coupling constant. For low coupling constants a classical vapor--liquid phase separation appears with a good agreement between GEMC and the MSA. For high coupling constant, a phase separation between a salt poor and a salt rich phase occurs that resembles the phase equilibrium behavior of the solvent primitive model.

Phase separation in model polydisperse ferrofluids.

The influence of polydispersity on the phase equilibrium properties of a dipolar system with additional short-range (repulsive+attractive) interactions (modeled by a shifted Lennard-Jones pair potential) is studied by means of Gibbs ensemble Monte Carlo simulations. The critical temperature and density as well as the magnetization at the critical point are calculated as a function of the applied magnetic field, and the obtained results are compared with the data determined in a monodisperse equivalent of the system.

Magnetic properties and structure of polydisperse ferrofluid models.

The influence of polydispersity on the equilibrium properties of dipolar systems with short range repulsive interactions (modeled by a shifted and truncated Lennard-Jones pair potential) is studied by means of canonical Monte Carlo simulation and a high field approximation perturbation theory. The particle concentrations and the average magnetic moments of the investigated systems are typical of real ferrofluids. The magnetization curves are calculated and the microstructures are analyzed as a function of density, and the obtained results are compared with the data determined in the monodisperse equivalents of the systems. At weak and moderate magnetic fields the magnetization is found to be generally higher in the polydisperse system than in the corresponding monodisperse one. Our findings for the magnetic properties can partly be explained by the structural characteristics obtained from the simulations.