AUTHORS: Marıa Daniela Barrios Perez, Patrick Senet, Vincent Meunier, Adrien Nicola

Download as PDF

ABSTRACT: Solid-state nanopores have emerged as versatile devices for probing single molecules. Because the channel conductance of the ionic flow through nanopores scales inversely with the membrane thickness, few-atoms thick materials are ideal candidates with an expected high signal-to-noise ratio. On one hand, graphene nanopores have been extensively studied because they exhibit the highest signal. However, they also exhibit high noise. On the other hand, transition metal dichalcogenides such as molybdenum disulfide (MoS2) are potentially advantageous due to their rich optoelectronic and mechanical properties. In this paper, we investigate the dynamics of KCl ions through MoS2 nanopores using non-equilibrium molecular dynamics (MD) simulations. MoS2 nanopores with different diameters, from 1.0 to 3.0 nm and nanoporous membranes with different thicknesses, from single-layer to trilayers MoS2 are studied. The structural properties of ions and water inside MoS2 nanopores are discussed and the performance of MoS2 nanopores to conduct ions at low voltages is quantified by computing I-V curves in order to extract open pore conductance and by comparing MD data to analytical models. This comparison reveals that ionic conductance and effective geometrical parameters for MoS2 nanoporous membranes extracted from models are overestimated. We provide open pore benchmark signals for further translocation simulations/experiments using MoS2 nanopores.

KEYWORDS: nanopores, MoS2, MD simulations, open pore conductance, bulk conductivity, effective diameter, effective thickness

REFERENCES:

[1] C. Dekker, Solid-state nanopores, Nat. Nanotechnol. 2, 2007, pp. 209–215.

[2] H. Arjmandi-Tash, L. Belyaeva and G. Schneider, Single molecule detection with graphene and other two-dimensional materials: nanopores and beyond, Chem. Soc. Rev. 45, 2016, pp. 476–493.

[3] J. K. Rosenstein, M. Wanunu, C. A. Merchant, M. Drndic, K. L. Shepard, Integrated nanopore ´ sensing platform with sub-microsecond temporal resolution, Nat. Methods 9, 2012, pp. 487–492.

[4] J. Rodr´ıguez-Manzo, M. Puster, A. Nicola¨ı, V. Meunier, M. Drndic, DNA translocation ´ in nanometer thick silicon nanopores, ACS. Nano 9, 2015, pp. 6555–6564.

[5] S. W. Kowalczyk, A. Y. Grosberg, Y. Rabin and C. Dekker. Modeling the conductance and DNA blockade of solid-state nanopores, Nanotechnology 22, 2011, pp. 315101.

[6] M. Wanunu, T. Dadosh, V. Ray, J. Jin, L. McReynolds, M. Drndic, Rapid electronic ´ detection of probe-specific microRNAs using thin nanopore sensors, Nat. Nanotechnol., 5, 2010, pp. 807–814.

[7] K. Venta, G. Shemer, M. Puster, J. A. Rodr´ıguez-Manzo, A. Balan, J. K. Rosenstein, K. Shepard, M. Drndic,´ Differentiation of short, single-stranded DNA homopolymers in solid-state nanopores, ACS Nano, 7, 2013, pp. 4629–4636.

[8] E. A. Manrao, I. M. Derrington, A. H. Laszlo, K. W. Langford, M. K. Hopper, N. Gillgren, M. Pavlenok, M. Niederweis, J. H. Gundlach, Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase, Nat. Biotechnol. 30, 2012, pp. 349-353.

[9] C. A. Merchant, K. Healy, M. Wanunu, R. Vishva, N. Peterman, J. Bartel, M. D. Fischbein, K. Venta, Z. Luo, A. T. C. Johnson, M. Drndic, DNA translocation ´ through graphene nanopores, Nano Lett. 10, 2010, pp. 2915–2921.

[10] G. F. Schneider, S. W. Kowalczyk, V. E. Calado, G. Pandraud, H. W. Zandbergen, L. M. K. Vandersypen, C. Dekker, DNA translocation through graphene nanopores, Nano Lett. 10, 2010, pp. 3163-3167.

[11] S. Garaj, W. Hubbard, A. Reina, J. Kong, D. Branton, J. A. Golovchenko, Graphene as a sub-nanometer trans-electrode membrane, Nature 467, 2010, pp. 190–193.

[12] S. J. Heerema, G. F. Schneider, M. Rozemuller, L. Vicarelli, H. W. Zandbergen, C. Dekker, 1/f noise in graphene nanopores, Nanotechnology 26, 2015, pp. 074001.

[13] A. Aksimentiev, Deciphering ionic current signatures of DNA transport through a nanopore, Nanoscale 2, 2010, pp. 468–483.

[14] C. Sathe, X. Zou, J.-P. Leburton, K. Schulten, Computational investigation of DNA detection using graphene nanopores, ACS Nano 5, 2011, pp. 8842–8851.

[15] D. B. Wells, M. Belkin, J. Comer, A. Aksimentiev, Assessing graphene nanopores for sequencing DNA, Nano Lett. 12, 2012, pp. 4117–4123.

[16] W. Lv, S. Liu, X. Li, R. Wu, Spatial blockage of ionic current for electrophoretic translocation of DNA through a graphene nanopore, Electrophoresis 35, 2014, pp. 1144–1151.

[17] R. Lv, J. A. Robinson, R. E. Schaak, D. Sun, Y. Sun, T. E. Mallouk, M. Terrones, Transition Metal Dichalcogenides and Beyond: Synthesis, Properties, and Applications of Single- and Few-Layer Nanosheets, Acc. Chem. Res. 48, 2015, pp. 56–64.

[18] K. Liu, J. Feng, A. Kis, A. Radenovic, Atomically thin molybdenum disulfide nanopores with high sensitivity for DNA translocation, ACS Nano 8, 2014, pp. 2504–2511.

[19] A. B. Farimani, K. Min, N. R. Aluru, DNA base detection using a single-layer MoS2, ACS Nano 8, 2014, pp. 7914-7922.

[20] J. W. Jiang, Parametrization of Stillinger-Weber potential based on valence force field model: application to single-layer MoS2 and black phosphorus, Nanotechnology 26, 2015, pp. 315706.

[21] W. L. Jorgensen, J. Chandrasekhar, J. Madura, R. W. Impey, M. L. Klein, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 79, 1983, pp. 926–935.

[22] I. S. Joung, T. E. Cheatham, Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations, J. Phys. Chem. B 112, 2008, pp. 9020–9041.

[23] T. Liang, S. R. Phillpot, S. B. Sinnott, Parametrization of a reactive many-body potential for Mo-S systems, Phys. Rev. B 79, 2009, pp. 245110.

[24] M. Heiranian, A. B. Farimani, N. R. Aluru, Water desalination with a single-layer MoS2 nanopore, Nat. Commun. 6:8616, 2015.

[25] J. Tersoff, New empirical approach for the structure and energy of covalent systems, Phys. Rev. B 37, 1988, pp. 6991–7000.

[26] R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M. S. Dresselhaus, Anomalous potential barrier of double-wall carbon nanotube, Chem. Phys. Lett. 348, 2001, pp. 187–193.

[27] S. Plimpton, Fast parallel algorithms for short-range molecular dynamics, J. Comp. Phys. 117, 1995, pp. 1–19.

[28] W. C. Swope, H. C. Andersen, P. H. Berens, K. R. Wilson, A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters, J. Chem. Phys. 76, 1982, pp. 637–649.

[29] S. Nose, A unified formulation of the constant ´ temperature molecular-dynamics methods, J. Chem. Phys. 81, 1984, pp. 511–519.

[30] W. G. Hoover, Canonical dynamics: Equilibrium phase-space distributions, Phys. Rev. A 31, 1985, pp. 1695-1697.

[31] R. W. Hockney, J. W. Eastwood, Computer Simulation Using Particles, Adam–Hilger, New York 1989.

[32] J.-P. Ryckaert, G. Ciccotti, H. J. C. Berendsen, Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, J. Comp. Phys. 23, 1977, pp. 327-341.

[33] E. R. Cruz-Chu, A. Aksimentiev, K. Schulten, Ionic current rectification through silica nanopores, J. Phys. Chem. C 113, 2009, pp. 1850-1862.

[34] T. Sumikama, Origin of the shape of current-voltage curve through nanopores: a molecular dynamics study, Sci. Rep. 6, 2016, pp.25750.

[35] M. E. Suk, N. R. Aluru, Ion transport in sub-5-nm graphene nanopores, J. Chem. Phys. 140, 2014, pp. 084707.