|Table of Contents|

[1] Chen Chen, Chen Yunfei, Sha Jingjie, et al. Molecular dynamics simulation of ion transportationthrough graphene nanochannels [J]. Journal of Southeast University (English Edition), 2017, 33 (2): 171-176. [doi:10.3969/j.issn.1003-7985.2017.02.008]
Copy

Molecular dynamics simulation of ion transportationthrough graphene nanochannels()
Share:

Journal of Southeast University (English Edition)[ISSN:1003-7985/CN:32-1325/N]

Volumn:
33
Issue:
2017 2
Page:
171-176
Research Field:
Materials Sciences and Engineering
Publishing date:
2017-06-30

Info

Title:
Molecular dynamics simulation of ion transportationthrough graphene nanochannels
Author(s):
Chen Chen1 2 Chen Yunfei1 2 Sha Jingjie1 2 Wu Gensheng3 Ma Jian1 2 Li Kun1 2 Ji Anping1 2
1School of Mechanical Engineering, Southeast University, Nanjing 211189, China
2Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
3School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China
Keywords:
molecular dynamics simulation ion transportation graphene nanochannels ionic conductance
PACS:
TB383
DOI:
10.3969/j.issn.1003-7985.2017.02.008
Abstract:
The model of ion transportation through graphene nanochannels is established by the molecular dynamics simulation method. Statistics of the electric potential and charge distribution are made, respectively, on both sides of graphene nanopore with various diameters. Then, their changing relationship with respect to the nanopore diameter is determined. When applying a uniform electric field, polar water molecules are rearranged so that the corresponding relationship between the polarized degree of these molecules and the nanopore diameter can be created. Based on the theoretical model of ion transportation through nanochannels, the changing relationship between the concentration of anions/cations in nanochannels and bulk solution concentration is quantitatively analyzed. The results show that the increase of potential drop and charge accumulation, as well as a more obvious water polarization, will occur with the decrease of nanopore diameter. In addition, hydrogen ion concentration has a large proportion in nanochannels with a sodium chloride(NaCl)solution at a relative low concentration. As the NaCl concentration increases, the concentration appreciation of sodium ions tends to be far greater than the concentration drop of chloride ions. Therefore, sodium ion concentration makes more contribution to ionic conductance.

References:

[1] Thomas M, Corry B, Hilder T A. What have we learnt about the mechanisms of rapid water transport, ion rejection and selectivity in nanopores from molecular simulation?[J]. Small, 2014, 10(8): 1453-1465. DOI:10.1002/smll.201302968.
[2] Fornasiero F, Park H G, Holt J K, et al. Ion exclusion by sub-2-nm carbon nanotube pores [J]. Proceedings of the National Academy of Sciences, 2008, 105(45): 17250-17255. DOI:10.1073/pnas.0710437105.
[3] Stevens B J, Swift H. RNA transport from nucleus to cytoplasm in Chironomus salivary glands [J]. The Journal of Cell Biology, 1966, 31(1): 55-77. DOI:10.1083/jcb.31.1.55.
[4] Ying Y L, Zhang J, Gao R, et al. Nanopore-based sequencing and detection of nucleic acids [J]. Angewandte Chemie International Edition, 2013, 52(50): 13154-13161. DOI:10.1002/anie.201303529.
[5] Aksimentiev A. Deciphering ionic current signatures of DNA transport through a nanopore [J]. Nanoscale, 2010, 2(4): 468-483. DOI:10.1039/b9nr00275h.
[6] Bustamante C, Smith S B, Liphardt J, et al. Single-molecule studies of DNA mechanics [J]. Current Opinion in Structural Biology, 2000, 10(3): 279-285. DOI:10.1016/s0959-440x(00)00085-3.
[7] Cao R, Thapa R, Kim H, et al. Promotion of oxygen reduction by a bio-inspired tethered iron phthalocyanine carbon nanotube-based catalyst [J]. Nature Communications, 2013, 4: 2076. DOI:10.1038/ncomms3076.
[8] Zhu F, Schulten K. Water and proton conduction through carbon nanotubes as models for biological channels [J]. BiophysicalJournal, 2003, 85(1): 236-244. DOI:10.1016/S0006-3495(03)74469-5.
[9] Cao C, Ying Y L, Hu Z L, et al. Discrimination of oligonucleotides of different lengths with a wild-type aerolysin nanopore [J]. Nature Nanotechnology, 2016, 11(8): 713-718. DOI:10.1038/nnano.2016.66.
[10] de la Escosura-Muñiz A, Merkoçi A. Nanochannels preparation and application in biosensing [J]. ACS Nano, 2012, 6(9): 7556-7583. DOI:10.1021/nn301368z.
[11] Fologea D, Gershow M, Ledden B, et al. Detecting single stranded DNA with a solid state nanopore [J]. Nano Letters, 2005, 5(10): 1905-1909. DOI:10.1021/nl051199m.
[12] Gamble T, Decker K, Plett T S, et al. Rectification of ion current in nanopores depends on the type of monovalent cations: experiments and modeling [J]. The Journal of Physical Chemistry C, 2014, 118(18): 9809-9819. DOI:10.1021/jp501492g.
[13] Schoch R B, Han J, Renaud P. Transport phenomena in nanofluidics [J]. Reviews of Modern Physics, 2008, 80(3): 839-883. DOI:10.1103/revmodphys.80.839.
[14] Novoselov K S, Geim A K, Morozov S V, et al. Electric field effect in atomically thin carbon films[J]. Science, 2004, 306(5696): 666-669. DOI:10.1126/science.1102896.
[15] Lee C, Wei X, Kysar J W, et al. Measurement of the elastic properties and intrinsic strength of monolayer graphene [J]. Science, 2008, 321: 385-388. DOI:10.1126/science.1157996.
[16] Schedin F, Geim A K, Morozov S V, et al. Detection of individual gas molecules adsorbed on graphene [J]. Nature Materials, 2007, 6(9): 652-655. DOI:10.1038/nmat1967.
[17] Nair R R, Blake P, Grigorenko A N, et al. Fine structure constant defines visual transparency of graphene[J].Science, 2008, 320(5881): 1308. DOI:10.1126/science.1156965.
[18] Balandin A A, Ghosh S, Bao W, et al. Superior thermal conductivity of single-layer graphene [J]. Nano Letters, 2008, 8(3): 902-907. DOI:10.1021/nl0731872.
[19] Ferrari A C, Bonaccorso F, Fal’ko V, et al. Science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems [J]. Nanoscale, 2015, 7(11): 4598-4810. DOI:10.1039/c4nr01600a.
[20] Holt J K, Park H G, Wang Y, et al. Fast mass transport through sub-2-nanometer carbon nanotubes [J]. Science, 2006, 312(5776): 1034-1037. DOI:10.1126/science.1126298.
[21] Plecis A, Schoch R B, Renaud P. Ionic transport phenomena in nanofluidics: Experimental and theoretical study of the exclusion-enrichment effect on a chip [J]. Nano Letters, 2005, 5(6):1147-1155. DOI:10.1021/nl050265h.
[22] Aksimentiev A, Schulten K. Imaging α-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability, and the electrostatic potential map [J]. Biophysical Journal, 2005, 88(6): 3745-3761. DOI:10.1529/biophysj.104.058727.
[23] Mark P, Nilsson L. Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298K [J]. The Journal of Physical Chemistry A, 2001, 105(43): 9954-9960. DOI:10.1021/jp003020w.
[24] Smeets R M M, Keyser U F, Krapf D, et al. Salt dependence of ion transport and DNA translocation through solid-state nanopores [J]. Nano Letters, 2006, 6(1): 89-95. DOI:10.1021/nl052107w.
[25] Si W, Sha J J, Liu L, et al. Effect of nanopore size on poly(dt)30 translocation through silicon nitride membrane [J]. Science China Technological Sciences, 2013, 56(10): 2398-2402. DOI:10.1007/s11431-013-5330-2.
[26] Ashkenasy N, Sánchez-Quesada J, Bayley H, et al. Recognizing a single base in an individual DNA strand: A step toward DNA sequencing in nanopores [J]. Angewandte Chemie, 2005, 117(9): 1425-1428. DOI: 10.1002/ange.200462114.
[27] Parsegian A. Energy of an ion crossing a low dielectric membrane: Solutions to four relevant electrostatic problems [J]. Nature, 1969, 221(5183): 844-846. DOI:10.1038/221844a0.
[28] Israelachvili J, Wennerström H. Role of hydration and water structure in biological and colloidal interactions[J]. Nature, 1996, 379(6562): 219-225. DOI:10.1038/379219a0.
[29] Sabbah S, Lerner A, Erlick C, et al. Under water polarization vision—A physical examination [J]. Recent Research Developments in Experimental and Theoretical Biology, 2005, 1: 123-176.
[30] Pal S K, Zhao L, Zewail A H. Water at DNA surfaces: Ultrafast dynamics in minor groove recognition [J]. Proceedings of the National Academy of Sciences, 2003, 100(14): 8113-8118. DOI:10.1073/pnas.1433066100.
[31] Duan C, Majumdar A. Anomalous ion transport in 2-nm hydrophilic nanochannels[J]. Nature Nanotechnology, 2010, 5(12): 848-852. DOI:10.1038/nnano.2010.233.
[32] Hunter R J. Zeta potential in colloid science: Principles and applications[M]. San Diego, CA, USA:Academic Press, 2013.
[33] Baldessari F. Santiago J G. Electrokinetics in nanochannels: Part Ⅰ. Electric double layer overlap and channel-to-well equilibrium[J]. Journal of Colloid and Interface Science, 2008, 325(2): 526-538. DOI:10.1016/j.jcis.2008.06.007.
[34] Stein D, Kruithof M, Dekker C. Surface-charge-governed ion transport in nanofluidic channels[J]. Physical Review Letters, 2004, 93(3): 035901. DOI:10.1103/PhysRevLett.93.035901.
[35] Karnik R, Fan R, Yue M, et al. Electrostatic control of ions and molecules in nanofluidic transistors[J]. Nano Letters, 2005, 5(5): 943-948. DOI:10.1021/nl050493b.

Memo

Memo:
Biographies: Chen Chen(1991—), male, graduate; Chen Yunfei(corresponding author), male, doctor, professor, yunfeichen@seu.edu.cn.
Foundation items: The National Basic Research Program of China(973 Program)(No.2011CB707600), the National Natural Science Foundation of China(No.51435003, 51375092), the Natural Science Foundation of Jiangsu Province(No.BK20160935), the Natural Science Foundation of Higher Education Institutions of Jiangsu Province(No.16KJB460015).
Citation: Chen Chen, Chen Yunfei, Sha Jingjie, et al.Molecular dynamics simulation of ion transportation through graphene nanochannels[J].Journal of Southeast University(English Edition), 2017, 33(2):171-176.DOI:10.3969/j.issn.1003-7985.2017.02.008.
Last Update: 2017-06-20