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

Abstract

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.

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

“…10 of Ref. [90]). If we are after "just" the device behavior, however, reduced models can be extremely handy.…”

“…These three methods have been presented in detail in our previous publications [49,50,51,90,47,48,91,52] Here, we briefly describe them focusing on the differences that are summarized in Table 1.…”

Comparison of a finite-element and finite-volume scheme for a degenerate cross-diffusion system for ion transport

“…Often, bipolar ion channels are modeled with asymmetric surface charge distributions on the channel walls. However, to fit these channels into the framework of our model, we follow the approach described in [17]. Similar to the first test case, we assume that there are eight confined molecules inside the channel, but this time four molecules are positively charged (+0.5e) and the other four molecules are negatively charged (−0.5e).…”

The effect of the charge pattern on the applicability of a nanopore as a sensor

“…This hybrid method, called NP+LEMC, was applied for various problems in the last couple of years. These problems include particle transport through model membranes [38,39], ion channels [40,41,42], and nanopores [43,44,15,45,46]. With this computational technique, we are able to simulate the effect of even a very low concentration of X + ions on the current through the nanopore [15].…”