Iranian Journal of Mechanical Engineering Transactions of the ISME

Iranian Journal of Mechanical Engineering Transactions of the ISME

A Simulation Study on Ionic Current in Cylindrical Hydrophobic Nanopores

Document Type : Research Paper

Authors
Ali Shafiei Souderjani 1
Mohammad Hassan Saidi 2
1 M.Sc., Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran
2 Professor, Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran
10.30506/jmee.2024.2014715.1326
Abstract
The ionic current and electroosmotic flow (EOF) are studied in hydrophobic nanopores numerically. The Poisson, Stokes, and Nernst-Planck equations were solved simultaneously by finite element method. For the characterization of hydrophobic nanopores, the Navier-slip boundary condition was replaced the no-slip boundary condition on the surface of the nanopore, and a wide range of slip lengths is used in order to cover all the possible hydrophobic conditions. The effect of hydrophobicity on different ionic current mechanisms is investigated. Also, the effects of voltage difference, electrolyte concentration, and radius of nanopore on the ionic current in hydrophobic nanopores are studied. The results show that nanopore hydrophobicity affects the convective and electrophoretic ionic current significantly. Due to the EOF enhancement by increasing the nanopore’s slip length, the convective ionic current signifies, and the electrophoretic ionic current dwindles.
Keywords
Nanopore
Hydrophobicity
Ionic current
Eletroosmotic flow
Creeping flow
Subjects
[1]        I. M. Derrington, T.Z. Butler, M.D. Collins, E. Manrao, M. Pavlenok, M. Niederweis, and J.H. Gundlach, "Nanopore DNA Sequencing with MspA," Proceedings of the National Academy of Sciences, Vol. 107, No. 37, pp. 16060-16065, 2010, Doi: https://doi.org/10.1073/pnas.1001831107.
 
[2]        J. Clarke, H.-C. Wu, L. Jayasinghe, A. Patel, S. Reid, and H. Bayley, "Continuous Base Identification for Single-molecule Nanopore DNA Sequencing," Nature Nanotechnology, Vol. 4, No. 4, pp. 265-270, 2009, Doi: https://doi.org/10.1038/nnano.2009.12.
 
[3]        G. F. Schneider and C. Dekker, "DNA Sequencing with Nanopores," Nature Biotechnology, Vol. 30, No. 4, pp. 326-328, 2012, Doi: https://doi.org/10.1038/nbt.2181.
 
[4]        T. Z. Butler, M. Pavlenok, I. M. Derrington, M. Niederweis, and J. H. Gundlach, "Single-molecule DNA Detection with an Engineered MspA Protein Nanopore," Proceedings of the National Academy of Sciences, Vol. 105, No. 52, pp. 20647-20652, 2008, Doi: https://doi.org/10.1073/pnas.0807514106.
 
[5]        A. Fanget, F. Traversi, S. Khlybov, P. Granjon, A. Magrez, L. Forró, and A. Radenovic, "Nanopore Integrated Nanogaps for DNA Detection," Nano Letters, Vol. 14, No. 1, pp. 244-249, 2014, Doi: https://doi.org/10.1021/nl403849g.
 
[6]        A. Barati Farimani, P. Dibaeinia, and N. R. Aluru, "DNA Origami–graphene Hybrid Nanopore for DNA Detection," ACS Applied Materials & Interfaces, Vol. 9, No. 1, pp. 92-100, 2017, Doi: https://doi.org/10.1021/acsami.6b11001.
 
[7]        Z. Liu, X. Shi, and H. Wu, "Coarse-grained Molecular Dynamics Study of Wettability Influence on Protein Translocation Through Solid Nanopores," Nanotechnology, Vol. 30, No. 16, p. 165701, 2019, Doi: 10.1088/1361-6528/aafdd7.
 
[8]        M. Waugh, K. Briggs, D. Gunn, M. Gibeault, S. King, Q. Ingram, A.M. Jimenez, S. Berryman, D. Lomovtsev, L. Andrzejewski, and V. Tabard-Cossa, "Solid-state Nanopore Fabrication by Automated Controlled Breakdown," Nature Protocols, Vol. 15, No. 1, pp. 122-143, 2020, Doi: https://doi.org/10.1038/s41596-019-0255-2.
[9] A. Storm, J. Chen, X. Ling, H. Zandbergen, and C. Dekker, "Fabrication of Solid-state Nanopores with Single-nanometre Precision," Nature Materials, Vol. 2, No. 8, pp. 537-540, 2003, Doi: https://doi.org/10.1038/nmat941.
 
[10] Y. Goto, I. Yanagi, K. Matsui, T. Yokoi, and K.-i. Takeda, "Integrated Solid-state Nanopore Platform for Nanopore Fabrication Via Dielectric Breakdown, DNA-speed Deceleration and Noise Reduction," Scientific Reports, Vol. 6, No. 1, p. 31324, 2016, Doi: https://doi.org/10.1038/srep31324.
 
[11] R. Dela Torre, J. Larkin, A. Singer, and A. Meller, "Fabrication and Characterization of Solid-state Nanopore Arrays for High-throughput DNA Sequencing," Nanotechnology, Vol. 23, No. 38, p. 385308, 2012, Doi: 10.1088/0957-4484/23/38/385308.
 
[12] M. Wanunu and A. Meller, "Chemically Modified Solid-state Nanopores," Nano Letters, Vol. 7, No. 6, pp. 1580-1585, 2007, Doi: https://doi.org/10.1021/nl070462b.
 
[13] J. Kudr, J. Kudr, S. Skalickova, L. Nejdl, A. Moulick, B. Ruttkay–Nedecky, V. Adam, and R. Kizek "Fabrication of Solid‐state Nanopores and Its Perspectives," Electrophoresis, Vol. 36, No. 19, pp. 2367-2379, 2015, Doi: https://doi.org/10.1002/elps.201400612.
 
[14] K. Briggs, H. Kwok, and V. Tabard‐Cossa, "Automated Fabrication of 2‐nm Solid‐State Nanopores for Nucleic Acid Analysis," Small, Vol. 10, No. 10, pp. 2077-2086, 2014, Doi: https://doi.org/10.1002/smll.201303602.
 
[15] J.-Y. Jung, P. Joshi, L. Petrossian, T. J. Thornton, and J. D. Posner, "Electromigration Current Rectification in a Cylindrical Nanopore Due to Asymmetric Concentration Polarization," Analytical Chemistry, Vol. 81, No. 8, pp. 3128-3133, 2009, Doi: https://doi.org/10.1021/ac900318j.
 
[16] S. Balme, S. Balme, F. Picaud, M. Manghi, J. Palmeri, M. Bechelany, S. Cabello-Aguilar, A. Abou-Chaaya, P. Miele, E. Balanzat, and J. M. Janot, "Ionic Transport Through Sub-10 nm Diameter Hydrophobic High-aspect Ratio Nanopores: Experiment, Theory and Simulation," Scientific Reports, Vol. 5, No. 1, p. 10135, 2015, Doi: https://doi.org/10.1038/srep10135.
 
[17] M. R. Powell, L. Cleary, M. Davenport, K. J. Shea, and Z. S. Siwy, "Electric-field-induced Wetting and Dewetting in Single Hydrophobic Nanopores," Nature Nanotechnology, Vol. 6, No. 12, pp. 798-802, 2011, Doi: https://doi.org/10.1038/nnano.2011.189.
 
[18] J. Polster, E. T. Acar, T. A. Pham, and Z. S. Siwy, "Gating of Hydrophobic Nanopores with Large Anions," Biophysical Journal, Vol. 118, No. 3, pp. 158a-159a, 2020, Doi: https://doi.org/10.1021/acsnano.9b09777.
 
[19] T. Haynes, I. P. Smith, E. J. Wallace, J. L. Trick, M. S. Sansom, and S. Khalid, "Electric-field-driven Translocation of ssDNA Through Hydrophobic Nanopores," ACS Nano, Vol. 12, No. 8, pp. 8208-8213, 2018, Doi: https://doi.org/10.1021/acsnano.8b03365.
 
[20] A. Asatekin and K. K. Gleason, "Polymeric Nanopore Membranes for Hydrophobicity-based Separations by Conformal Initiated Chemical Vapor Deposition," Nano Letters, Vol. 11, No. 2, pp. 677-686, 2011, Doi: https://doi.org/10.1021/nl103799d.
 
[21] A. Shafiei Souderjani, M. Bakouei, M. H. Saidi, and M. Taghipoor, "Electrophoretic motion of hydrophobic spherical particles in nanopore: Characteristics, Separation, and Resistive Pulse Sensing," Physics of Fluids, Vol. 35, No. 2, 2023, Doi: https://doi.org/10.1063/5.0136454.
 
[22] A. V. Belyaev and O. I. Vinogradova, "Electro-osmosis on Anisotropic Superhydrophobic Surfaces," Physical Review Letters, Vol. 107, No. 9, p. 098301, 2011, Doi: https://doi.org/10.1103/PhysRevLett.107.098301.
 
[23] M. Manghi, J. Palmeri, K. Yazda, F. Henn, and V. Jourdain, "Role of Charge Regulation and Flow Slip in the Ionic Conductance of Nanopores: An Analytical Approach," Physical Review E, Vol. 98, No. 1, p. 012605, 2018, Doi: https://doi.org/10.1103/PhysRevE.98.012605.
 
[24] D. Pandey and S. Bhattacharyya, "Impact of Surface Hydrophobicity and Ion Steric Effects on the Electroosmotic Flow and Ion Selectivity of a Conical Nanopore," Applied Mathematical Modelling, Vol. 94, pp. 721-736, 2021, Doi: https://doi.org/10.1016/j.apm.2021.01.035.
 
[25] A. Velasco, S. Friedman, M. Pevarnik, Z. Siwy, and P. Taborek, "Pressure-driven Flow Through a Single Nanopore," Physical Review E, Vol. 86, No. 2, p. 025302, 2012, Doi: https://doi.org/10.1103/PhysRevE.86.025302.
 
[26] S. Movahed and D. Li, "Electrokinetic Motion of a Rectangular Nanoparticle in a Nanochannel," Journal of Nanoparticle Research, Vol. 14, pp. 1-15, 2012, Doi: https://doi.org/10.1007/s11051-012-1032-0.
 
[27] Y. Qiu, I. Vlassiouk, Y. Chen, and Z. S. Siwy, "Direction Dependence of Resistive-pulse Amplitude in Conically Shaped Mesopores," Analytical Chemistry, Vol. 88, No. 9, pp. 4917-4925, 2016, Doi: https://doi.org/10.1021/acs.analchem.6b00796.