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

Matejczyk, Bartłomiej; Valiskó, Mónika; Wolfram, Marie-Thérèse; Pietschmann, Jan‐Frederik; Boda, Dezső

doi:10.1063/1.4978942

Cited by 30 publications

(61 citation statements)

References 75 publications

(82 reference statements)

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“…In this pure theory study, the particular choice does not qualitatively affect our conclusions so long as the pore is the highest resistance element. We used an infinite dilution value of 1.334 · 10 −9 m 2 /s for both ions in the bulk, while the value inside the pore is ten times smaller as in our earlier works [43,50,19]. The value inside the pore just scales the current and do not influence rectification, because it scales the current in the ON and OFF states the same way.…”

Section: Models and Methodsmentioning

confidence: 99%

Scaling Behavior of Bipolar Nanopore Rectification with Multivalent Ions

et al. 2019

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We present a scaling behavior of a rectifying bipolar nanopore as a function of the parameter ξ = R P /(λ z if ), where R P is the radius of the pore, λ is the characteristic screening length of the electrolyte filling the pore, and z if = z + |z − | is a scaling factor that makes scaling work for electrolytes containing multivalent ions (z + and z − are cation and the anion valences). By scaling we mean that the rectification of the pore (defined as the ratio of currents in the forward and reversed biased states) depends on pore radius, concentration, c, and ion valences via the parameter ξ implicitly. This feature is based on the fact that rectification depends on the voltage-sensitive appearance of depletion zones that, in turn, depend on the relation of R P to the rescaled screening length λ z if . In this modeling study, we use the Poisson-Nernst-Planck (PNP) theory and a particle simulation method, the Local Equilibrium Monte Carlo (LEMC). The latter can compute ion correlations that are ignored in the mean-field treatment of PNP and that are very important for multivalent ions (we show results for 1:1, 2:1, 3:1, and 2:2 electrolytes). In addition to the z if factor, we show that one must choose a screening length appropriate to the system, in our case the Debye length for λ for PNP and the screening length given by the Mean Spherical Approximation for LEMC.

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Section: Models and Methodsmentioning

confidence: 99%

Scaling Behavior of Bipolar Nanopore Rectification with Multivalent Ions

et al. 2019

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“…Because the shapes of the I−U curves are similar for every case, we can characterize the ON and OFF states by two chosen voltages, ±200 mV as in our previous studies [44,45,1,48]. Therefore, we define our device functions as the ON-…”

Section: Resultsmentioning

confidence: 99%

“…The bulk value is experimental (D bulk K + = 1.849 × 10 −9 m 2 s −1 and D bulk Cl − = D bulk X = 2.032 × 10 −9 m 2 s −1 ), while D pore i just scales the current without influencing the I/I 0 ratio. Following our previous studies [45,8,46,47] here we set the relation D…”

Section: Interparticle Potentialsmentioning

confidence: 99%

“…Thus, the NP and the continuity equations together with LEMC form a self-consistent system. The advantage over the widely used Poisson-Nernst-Planck theory is that the statistical mechanical component is an accurate particle simulation method instead of an approximate mean-field theory (Poisson-Boltzmann) [45,47,48]. Details are found in earlier papers [39,41].…”

Section: Np+lemcmentioning

confidence: 99%

“…We apply the Nernst-Planck (NP) transport equation and couple it to LEMC resulting in a hybrid method, called NP+LEMC. This method was successfully applied for various problems in the last couple of years such as particle transport through model membranes [39,40], ion channels [41,42,43], and nanopores [44,45,8,46,47,1,48].…”

Section: Introductionmentioning

confidence: 99%

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

Mádai

Valiskó

Boda

2019

Phys. Chem. Chem. Phys.

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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 carries a bipolar charge pattern with a larger positive buffer region determining the anions as the main charge carriers and the 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 to the Nernst-Planck equation) we show that we can create a sensor whose underlying mechanisms are based on the changes of the local electric field as a response to changing thermodynamic conditions. The change of the electric field results in changes in the local ionic concentrations (depletion zones), and, thus, changes in ionic currents.

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

Mádai

Valiskó

Boda

2019

Journal of Molecular Liquids

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We investigate a model nanopore sensor that is able to detect analyte ions that are present in the electrolyte solution in very small concentrations. The nanopore selectively binds the analyte ions with which the local concentrations of the ions of the background electrolyte (KCl), and, thus, the ionic current flowing through the pore is changed. Analyte concentration can be determined from calibration curves. In our previous study (Mádai et al. J. Chem. Phys., 147(24):244702, 2017.), we proposed a symmetric model (surface charge is negative all along the pore). The mechanism of sensing was a competition between K + and positive analyte ions, so increasing analyte concentration decreased K + current. Here we allow asymmetric charge patterns on the pore wall (positive/negative/neutral along the pore), thus, gaining an additional device function, rectification, resulting in a dual responsive device. We find that a bipolar nanopore is an efficient geometry with Cl − ions being the main charge carriers. The mechanism of sensing is that more positive analyte ions attract more Cl − ions into the pore thus increasing the current. Also they make the pore less asymmetric and, thus, decrease rectification. We use a hybrid computer simulation method, where a generalization of the grand canonical Monte Carlo method to non-equilibrium (Local Equilibrium Monte Carlo) is coupled to the Nernst-Planck equation with which the flux is computed.

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

Cited by 30 publications

References 75 publications

Scaling Behavior of Bipolar Nanopore Rectification with Multivalent Ions

Scaling Behavior of Bipolar Nanopore Rectification with Multivalent Ions

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

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

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