• Modeling and Simulation of Complex Molecular Systems

Modeling ion transport

Ion transport through ion channels and nanopores

This project aims modeling natural (ion channels) and synthetic nanopores that cross a natural (biological bilayer) or synthetic (plastic or solid state) membranes. Nanopores facilitate the transport of ions between two bulk electrolytes in a regulated manner that makes nanopores essential building blocks of nanodevices. Peculiar behavior (selectivity, rectification, switching) of nanopores arises from the fact that the radius of the pore is measurable to the Debye screening length of the electrolyte, so the opposing double layers at the nanopore’s wall overlap.

We are interested in device behavior, namely, in how the nanopore responds to an input signal and what are the basic characteristics that need to be built into a reduced model that can reproduce device behavior, namely, the relation of the input and output signals. Useful reduced models are created by keeping only those degrees of freedom in the model that are necessary to describe the device. For this purpose, reduced models are validated against detailed all-atom models, while the parameters of the reduced models are calibrated against experiments. We work in a multiscale approach [13,14,19] that is based on developing models of different resolutions and studying them with appropriate computational methods [6,7,11].

Systems that we study include ion channels [2,4,5,8,10,12,24], selective nanopores [1,3,19,24], rectifying annopores [12,13,14,19,21,23,24] nanopore-based sensors [15,17,20,22], transistors [16,21], and transporters [9].

Video clip showing a rectifying bipolar nanopore in the ON and OFF states:

SI snapshot

Multiscale modeling scheme


Selected publications

[24] D. Boda, M. Valiskó, D. Gillespie. Modeling the device behavior of biological andsynthetic nanopores with reduced models. Entropy, submitted, 2020. IF: 2.494 [PDF] [Supplementary Info]

[23] D. Fertig, M. Valiskó, D. Boda. Rectification of bipolar nanopores in multivalent electrolytes: effect of charge inversion and strong ionic correlations. Phys. Chem. Chem. Phys. 22(34):19033-19045, 2020. IF: 3.567 [PDF]

[22] B. Hohl, E. Mádai, D. Boda, M. Valiskó. Modeling of a pH-tunable dual-response nanopore sensor. J. Mol. LIq. 310: 112946, 2020. IF: 4.513 [PDF]

[21] D. Fertig, B. Matejczyk, M. Valiskó, D. Gillespie, D. Boda. Scaling Behavior of Bipolar Nanopore Rectification with Multivalent Ions. J. Phys. Chem. C. 123(47): 28985-28996, 2019, IF: 4.484 [PDF]

[20] E. Mádai, M. Valiskó, D. Boda. Application of a bipolar nanopore as a sensor: rectification as an additional device function. Phys. Chem. Chem. Phys. 117(20):2793-2801, 2019. IF:3.567 [PDF]

[19] M. Valiskó, B. Matejczyk, Z. Ható, T. Kristóf, E. Mádai, D. Fertig, D. Gillespie, D. Boda. 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. J. Chem. Phys. 150(14):144703, 2019. IF: 2.843 [PDF]

[18] D. Fertig, M. Valiskó, D. Boda. Controlling ionic current through a nanopore by tuning pH: a Local Equilibrium Monte Carlo study. Mol. Phys. 117(20):2793-2801, 2019. IF: 1.704 [PDF]

[17] E. Mádai, M. Valiskó, D. Boda. The effect of the charge pattern on the applicability of a nanopore as a sensor. J. Mol. Liq. 283:391-398, 2019. IF: 4.513 [PDF]

[16] E. Mádai, B. Matejczyk, A. Dallos, M. Valiskó, D. Boda. Controlling ion transport through nanopores: modeling transistor behavior. Phys. Chem. Chem. Phys. 20(37):24156-24167, 2018. IF: 3.906 [PDF]

[15] E. Mádai, M. Valiskó, A. Dallos, D. Boda. Simulation of a model nanopore sensor: ion competition underlies device behavior.  J. Chem. Phys. 147(24):244702, 2017.

[14] Z. Ható, M. Valiskó, T. Kristóf, D. Gillespie, D. Boda. Multiscale modeling of a rectifying bipolar nanopore: explicit-water versus implicit-water simulations.   Phys. Chem. Chem. Phys. 19(27):17816-17826, 2017.

[13] B. Matejczyk, M. Valiskó, M.-T. Wolfram, J.-F. Pietschmannn, D. Boda. Multiscale modeling of a rectifying bipolar nanopore: Comparing Poisson-Nernst-Planck to Monte Carlo. J. Chem. Phys. 146(12):124125, 2017.

[12] Z. Ható, D. Boda, D. Gillespie, J. Vrabec, G. Rutkai, T. Kristóf. Simulation study of a rectifying bipolar ion channel: detailed model versus reduced model. Condens. Matt. Phys. 19(1):13802, 2016.

[11] C. Berti, S. Furini, D. Gillespie, D. Boda, R. S. Eisenberg, E. Sangiorgi, C. Fiegna. A 3-D Brownian Dynamics simulator for the study of ion permeation through membrane pores J. Chem. Theory Comp., 10(8):2911-2926, 2014.

[10] D. Boda. Monte Carlo simulation of electrolyte solutions in biology: in and out of equilibrium. Ann. Rep. Comp. Chem., Editor R. A. Wheeler, volume 10, pages 127–163. Elsevier, 2014.

[9] D. Boda, É. Csányi, D. Gillespie, T. Kristóf. Dynamic Monte Carlo simulation of coupled transport through a narrow multiply-occupied pore J. Phys. Chem. C, 118(1):700-707, 2014.

[8] D. Boda, R. Kovács, D. Gillespie, T. Kristóf. Selective transport through a model calcium channel studied by Local Equilibrium Monte Carlo simulations coupled to the Nernst-Planck equation J. Mol. Liq., 189:100, 2014.

[7] Z. Ható, D. Boda, T. Kristóf. Simulation of Steady-State Diffusion: Driving Force Ensured by Dual Control Volumes or Local Equilibrium Monte Carlo. J. Chem. Phys., 137(5):054109, 2012.

[6] D. Boda, D. Gillespie. Steady state electrodiffusion from the Nernst-Planck equation coupled to Local Equilibrium Monte Carlo simulations. J. Chem. Theory Comp., 8(3):824-829, 2012.

[5] É. Csányi, D. Boda, D. Gillespie, and T. Kristóf. Current and selectivity in a model sodium channel under physiological conditions: Dynamic Monte Carlo simulations. Biochim. et Biophys. Acta - Biomembranes, 1818(3):592-600, 2012.

[4] G. Rutkai, D. Boda, and T. Kristóf. Relating binding affinity to dynamical selectivity from dynamic Monte Carlo simulations of a model calcium channel. J. Phys. Chem. Lett., 1(14):2179-2184, 2010.

[3] Y. He, D. Gillespie, D. Boda, I. Vlassiouk, R. S. Eisenberg, and Z. S. Siwy. Tuning transport properties of nano-fluidic devices with local charge inversion. JACS, 131(14):5194-5202, 2009.

[2] D. Gillespie and D. Boda. The anomalous mole fraction effect in calcium channels: A measure of preferential selectivity. Biophys. J., 95(6):2658-2672, 2008.

[1] D. Gillespie, D. Boda, Y. He, P. Apel, and Z.S. Siwy. Synthetic nanopores as a test case for ion channel theories: The anomalous mole fraction effect without single filing. Biophys. J., 95(2):609-619, 2008.

Selected talks

[2] Boda et al. Simulating ion transport in a multiscale approach: from molecular dynamics to continuum theories and in between, CECAM Workshop “Multiscale modelling in electrophysiology: from atoms to organs” Lugano, Switzerland, 2018.03.26-28.

[1] Boda et al. Multiscale modeling of ion transport through nanopores: the case study of a rectifying bipolar nanofluidic diode, Hybrid Methods in Molecular Simulation, Cagliari, Italy, 2017.04.03-04.