arXiv subjects

Dezső Boda

Publications and source records attributed to Dezső Boda.

24 records · Page 2Linked to original sources

arXiv2017

Simulation of a model nanopore sensor: ion competition underlies device behavior

We study a model nanopore sensor with which a very low concentration of analyte molecules can be detected on the basis of the selective binding of the analyte molecules to the binding sites on the pore wall. The bound analyte ions partially replace the current-carrier cations in a thermodynamic competition. This competition depends both on the properties of the nanopore and the concentrations of the competing ions (through their chemical potentials). The output signal given by the device is the current reduction caused by the presence of the analyte ions. The concentration of the analyte ions can be determined through calibration curves. We model the binding site with the square-well potential and the electrolyte as charged hard spheres in an implicit background solvent. We study the system with a hybrid method in which we compute the ion flux with the Nernst-Planck (NP) equation coupled with the Local Equilibrium Monte Carlo (LEMC) simulation technique. The resulting NP+LEMC method is able to handle both strong ionic correlations inside the pore (including finite size of ions) and bulk concentrations as low as micromolar. We analyze the effect of bulk ion concentrations, pore parameters, binding site parameters, electrolyte properties, and voltage on the behavior of the device.

physics.app-ph↗

arXiv2017

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 on 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 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.

cond-mat.mes-hall↗

arXiv2017

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 electrolyte model. 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.

cond-mat.soft↗

arXiv2017

Activity coefficients of individual ions in LaCl$_{3}$ from the II+IW theory

We investigate the individual activity coefficients of ions in LaCl$_{3}$ using our theory that is based on the competition of ion-ion (II) and ion-water (IW) interactions (Vincze et al., J. Chem. Phys. 133, 154507, 2010). The II term is computed from Grand Canonical Monte Carlo simulations on the basis of the implicit solvent model of electrolytes using hard sphere ions with Pauling radii. The IW term is computed on the basis of Born's treatment of solvation using experimental hydration free energies. This agreement is remarkable considering the facts that (i) the result is the balance of two terms that are large in absolute value (up to $20 kT$) but opposite in sign, and (ii) that our model does not contain any adjustable parameter. All the parameters used in the model are taken from experiments: concentration dependent dielectric constant, hydration free energies, Pauling radii.

physics.chem-ph↗

arXiv2014

Unraveling the behavior of the individual ionic activity coefficients on the basis of the balance of ion-ion and ion-water interactions

We investigate the individual activity coefficients of pure 1:1 and 2:1 electrolytes using our theory that is based on the competition of ion-ion (II) and ion-water (IW) interactions (Vincze et al., J. Chem. Phys. 133, 154507, 2010). The II term is computed from Grand Canonical Monte Carlo simulations on the basis of the implicit solvent model of electrolytes using hard sphere ions with Pauling radii. The IW term is computed on the basis of Born's treatment of solvation using experimental hydration free energies. The two terms are coupled through the concentration-dependent dielectric constant of the electrolyte. With this approach we are able to reproduce the nonmonotonic concentration dependence of the mean activity coefficient of pure electrolytes qualitatively without using adjustable parameters. In this paper, we show that the theory can provide valuable insight into the behavior of individual activity coefficients too. We compare our theoretical predictions against experimental data measured by electrochemical cells containing ion-specific electrodes. As in the case of the mean activity coefficients, we find good agreement for 2:1 electrolytes, while the accuracy of our model is worse for 1:1 systems. This deviation in accuracy is explained by the fact that the two competing terms (II and IW) are much larger in the 2:1 case so errors in the two separate terms have less effects. The difference of the excess chemical potentials of cations and anions (the ratio of activity coefficients) is determined by asymmetries in the properties of the two ions: charge, radius, and hydration free energies.

cond-mat.stat-mech↗

arXiv2013

Dynamic Monte Carlo simulation of coupled transport through a narrow multiply-occupied pore

Dynamic Monte Carlo simulations are used to study coupled transport (co-transport) through sub-nanometer-diameter pores. In this classic Hodgkin-Keynes mechanism, an ion species uses the large flux of an abundant ion species to move against its concentration gradient. The efficiency of co-transport is examined for various pore parameters so that synthetic nanopores can be engineered to maximize this effect. In general, the pore must be narrow enough that ions cannot pass each other and the charge of the pore large enough to attract many ions so that they exchange momentum. Co-transport efficiency increases as pore length increases, but even very short pores exhibit co-transport, in contradiction to the usual perception that long pores are necessary. The parameter ranges where co-transport occurs is consistent with current and near-future synthetic nanopore geometry parameters, suggesting that co-transport of ions may be a new application of nanopores.

cond-mat.soft↗