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

Mass Transfer through Vapor-Liquid Interfaces Studied by Non-Stationary Molecular Dynamics Simulations

Molecular dynamics (MD) simulations are highly attractive for studying the influence of interfacial effects, such as the enrichment of components, on the mass transfer through the interface. In a recent work, we have presented a steady-state MD simulation method for investigating this phenomenon and tested it using model mixtures with and without interfacial enrichment. The present study extends this work by introducing a non-stationary MD simulation method. A rectangular simulation box that contains a mixture of two components 1 + 2 with a vapor phase in the middle and two liquid phases on both sides is used. Starting from a vapor-liquid equilibrium state, a non-stationary molar flux of component 2 is induced by inserting particles of component 2 into the center of the vapor phase in a pulse-like manner. During the isothermal relaxation process, particles of component 2 pass through the vapor phase, cross the vapor-liquid interface, and enter the liquid phase. The system thereby relaxes into a new vapor-liquid equilibrium state. During the relaxation process, spatially resolved responses for the component densities, fluxes, and pressure are sampled. To reduce the noise and provide measures for the uncertainty of the observables, a set of replicas of simulations is carried out. The new simulation method was applied to study mass transfer in two binary Lennard-Jones mixtures: one that exhibits a strong enrichment of the low-boiling component 2 at the vapor-liquid interface and one that shows no enrichment. Even though both mixtures have similar transport coefficients in the bulk phases, the results for mass transfer differ significantly, indicating that the interfacial enrichment influences the mass transfer.

Corrosion Behavior of Al Modified with Zn in Chloride Solution

Aluminum-based alloys have been considered candidate materials for cathodic protection anodes. However, the Al-based alloys can form a layer of alumina, which is a drawback in a sacrificial anode. The anodes must exhibit uniform corrosion to achieve better performance. Aluminum can be alloyed with Zn to improve their performance. In this sense, in the present research, the electrochemical corrosion performance of Al-xZn alloys (x = 1.5, 3.5, and 5 at.% Zn) exposed to 3.5 wt.% NaCl for 24 h was evaluated. Polarization curves, linear polarization resistance (LPR), and electrochemical impedance spectroscopy (EIS) were used to identify the electrochemical behavior. The microstructure of the samples before the corrosion assessment was characterized by means of X-ray diffraction analyses (XRD) and scanning electron microscopy (SEM). In addition, microstructures of the corroded surfaces were characterized using X-ray mappings via SEM. Polarization curves indicated that Zn additions changed the pseudo-passivation behavior from what pure Al exhibited in a uniform dissolution regime. Furthermore, the addition of Zn shifted the corrosion potential to the active side and increased the corrosion rate. This behavior was consistent with the proportional decrease in polarization resistance (R_p) and charge transfer resistance (R_ct) in the EIS. The analysis of EIS was done using a mathematical model related to an adsorption electrochemical mechanism. The adsorption of chloride at the Al-Zn alloy surface formed aluminum chloride intermediates, which controlled the rate of the process. The rate constants of the reactions of a proposed chemical mechanism were evaluated.

Modulation of P2X4 pore closure by magnesium, potassium, and ATP

The P2X4 receptor plays a prominent role in cellular responses to extracellular ATP. Through classical all-atom molecular dynamics (MD) simulations totaling 24 μs we have investigated how metal-complexed ATP stabilizes the channel's open state and prevents its closing. We have identified two metal-binding sites, Mg2+ and potassium K+, one at the intersection of the three subunits in the ectodomain (MBS1) and the second one near the ATP-binding site (MBS2), similar to those characterized in Gulf Coast P2X. Our data indicate that when Mg2+ and K+ ions are complexed with ATP, the channel is locked into an open state. Interestingly, irrespective of the number of bound ATP molecules, Mg2+ ions bound to the MBS2 impeded the collapse of the open-state protein to a closed state by stabilizing the ATP-protein interactions. However, when Mg2+ in the MBS2 was replaced with K+ ions, as might be expected when in equilibrium with an extracellular solution, the interactions between the subunits were weakened and the pore collapsed. This collapse was apparent when fewer than two ATPs were bound to MBS2 in the presence of K+. Therefore, the different capacities of common cations to stabilize the channel may underlie a mechanism governing P2X4 channel gating in physiological systems. This study therefore provides structural insights into the differential modulation of ATP activation of P2X4 by Mg2+ and K+.

Modeling the Device Behavior of Biological and Synthetic Nanopores with Reduced Models

Biological ion channels and synthetic nanopores are responsible for passive transport of ions through a membrane between two compartments. Modeling these ionic currents is especially amenable to reduced models because the device functions of these pores, the relation of input parameters (e.g., applied voltage, bath concentrations) and output parameters (e.g., current, rectification, selectivity), are well defined. Reduced models focus on the physics that produces the device functions (i.e., the physics of how inputs become outputs) rather than the atomic/molecular-scale physics inside the pore. Here, we propose four rules of thumb for constructing good reduced models of ion channels and nanopores. They are about (1) the importance of the axial concentration profiles, (2) the importance of the pore charges, (3) choosing the right explicit degrees of freedom, and (4) creating the proper response functions. We provide examples for how each rule of thumb helps in creating a reduced model of device behavior.

Rectification of bipolar nanopores in multivalent electrolytes: effect of charge inversion and strong ionic correlations

Bipolar nanopores have powerful rectification properties due to the asymmetry in the charge pattern on the wall of the nanopore. In particular, bipolar nanopores have positive and negative surface charges along the pore axis. Rectification is strong if the radius of the nanopore is small compared to the screening length of the electrolyte so that both cations and anions have depletion zones in the respective regions. The depths of these depletion zones is sensitive to sign of the external voltage. In this work, we are interested in the effect of the presence of strong ionic correlations (both between ions and between ions and surface charge) due to the presence of multivalent ions and large surface charges. We show that strong ionic correlations cause leakage of the coions, a phenomenon that is absent in mean field theories. In this modeling study, we use both the mean-field Poisson-Nernst-Planck (PNP) theory and a particle simulation method, Local Equilibrium Monte Carlo (LEMC), to show that phenomena such as overcharging and charge inversion cannot be reproduced with PNP, while LEMC is able to produce nonmonotonic dependence of currents and rectification as a function of surface charge strength.

Separation Selectivity of CH4/CO2 Gas Mixtures in the ZIF-8 Membrane Explored by Dynamic Monte Carlo Simulations

Here we report a series of nonequilibrium dynamic Monte Carlo simulations combined with dual control volume (DCV-DMC) to explore the separation selectivity of CH₄/CO₂ gas mixtures in the ZIF-8 membrane with a thickness of up to about 20 nm. Meanwhile, an improved DCV-DMC approach coupled with the corresponding potential map (PM-DCV-DMC) is further developed to speed up the computational efficiency of conventional DCV-DMC simulations. Our simulation results provide the molecular-level density and selectivity profiles along the permeation direction of both CH₄ and CO₂ molecules in the ZIF-8 membrane, indicating that the parts near membrane surfaces at both ends play a key role in determining the separation selectivity. All densities initially show a sharp increase in the individual maximum within the first outermost unit cell at the feed side and follow a long fluctuating decrease process. Accordingly, the corresponding selectivity profiles initially display a long fluctuating increase in the individual maximum and follow a sharp decrease near the membrane surface at the permeation side. Furthermore, the effects of feed composition, temperature, and pressure on the relevant separation selectivity are also discussed in detail, where the temperature has a greater influence on the separation selectivity than the feed composition and pressure. More importantly, the predicted separation selectivities from our PM-DCV-DMC simulations are well consistent with previous experimental results.

Application of a bipolar nanopore as a sensor: rectification as an additional device function

We model and simulate a nanopore sensor that selectively binds analyte ions. This binding leads to the modulation of the local concentrations of the ions of the background electrolyte (KCl), and, thus, to the modulation of the ionic current flowing through the pore. The nanopore's wall has a bipolar charge pattern with a larger positive buffer region determining the anions as the main charge carriers and a smaller negative binding region containing binding sites. This charge pattern proved to be an appropriate one as shown by a previous comparative study of varying charge patterns (Mádai et al. J. Mol. Liq., 2019, 283, 391-398.). Binding of the positive analyte ions attracts more anions in the pore thus increasing the current. The asymmetric nature of the pore results in an additional device function, rectification. Our model, therefore, is a dual response device. Using a reduced model of the nanopore studied by a hybrid computer simulation method (Local Equilibrium Monte Carlo coupled with the Nernst-Planck equation) we show that we can create a sensor whose underlying mechanisms are based on the changes in the local electric field as a response to changing thermodynamic conditions. The change in the electric field results in changes in the local ionic concentrations (depletion zones), and, thus, changes in ionic currents.

Controlling ion transport through nanopores: modeling transistor behavior

We present a modeling study of a nanopore-based transistor computed by a mean-field continuum theory (Poisson–Nernst–Planck, PNP) and a hybrid method including particle simulation (Local Equilibrium Monte Carlo, LEMC) that is able to take ionic correlations into account including the finite size of ions.

Multiscale modeling of a rectifying bipolar nanopore: Comparing Poisson-Nernst-Planck to Monte Carlo

In the framework of a multiscale modeling approach, we present a systematic study of a bipolar rectifying nanopore using a continuum and a particle simulation method. The common ground in the two methods is the application of the Nernst-Planck (NP) equation to compute ion transport in the framework of the implicit-water electrolytemodel. The difference is that the Poisson-Boltzmann theory is used in the Poisson-Nernst-Planck (PNP) approach, while the Local Equilibrium Monte Carlo (LEMC) method is used in the particle simulation approach (NP+LEMC) to relate the concentration profile to the electrochemical potential profile. Since we consider a bipolar pore which is short and narrow, we perform simulations using two-dimensional PNP. In addition, results of a non-linear version of PNP that takes crowding of ions into account are shown. We observe that the mean field approximation applied in PNP is appropriate to reproduce the basic behavior of the bipolar nanopore (e.g., rectification) for varying parameters of the system (voltage, surface charge,electrolyte concentration, and pore radius). We present current data that characterize the nanopore's behavior as a device, as well as concentration, electrical potential, and electrochemical potential profiles.