References:
[1] Yan, S., Li, X., Zhang, P., et al. “Direct sequencing of 2′-deoxy-2′-fluoroarabinonucleic acid (FANA) using nanopore-induced phase-shift sequencing (NIPSS)”, Chemical Science, 10(10), pp. 3110-3117 (2019).
[2] Zascavage, R. R., Thorson, K., & Planz, J. V. “Nanopore sequencing: An enrichment‐free alternative to mitochondrial DNA sequencing”, Electrophoresis, 40(2), pp. 272-280 (2019).
[3] Qiu, Y., Arcadia, C., Alibakhshi, M. A., et al. “Nanopore fabrication in ultrathin HFO2 membranes for nanopore-based DNA sequencing”, Biophysical Journal, 114(3), 179a (2018).
[4] Rand, A. C., Jain, M., Eizenga, J. M., et al. “Mapping DNA methylation with high-throughput nanopore sequencing”. Nature methods, 14(4), pp. 411 (2017).
[5] Deamer, D., Akeson, M., & Branton, D. “Three decades of nanopore sequencing”, Nature biotechnology, 34(5), pp. 518, (2016)..
[6] Fuller, C. W., Kumar, S., Porel, M., et al.”Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array”, Proceedings of the National Academy of Sciences, 113(19), pp. 5233-5238, (2016).
[7] Castro-Wallace, S. L., Chiu, C. Y., John, K. K., et al. “Nanopore DNA sequencing and genome assembly on the International Space Station”, Scientific reports, 7(1), 18022, (2017).
[8] Jain, M., Koren, S., Miga, K. H., et al. “Nanopore sequencing and assembly of a human genome with ultra-long reads”, Nature biotechnology, 36(4), pp. 338, (2018).
[9] Johnson, S. S., Zaikova, E., Goerlitz, D. S., et al. “Real-time DNA sequencing in the Antarctic dry valleys using the Oxford Nanopore sequencer”, Journal of biomolecular techniques: JBT, 28(1), pp. 2, (2017).
[10] Shendure, J., Balasubramanian, S., Church, G. M., et al. “DNA sequencing at 40: past, present and future”, Nature, 550(7676), pp. 345, (2017).
[11] Fotouhi, B., Ahmadi, V., & Abasifard, M. “Controlling DNA translocation speed through graphene nanopore via plasmonic fields”, Scientia Iranica, 25(3), pp. 1849-1856, (2018).
[12] Fotouhi, B., Ahmadi, V., Abasifard, M., et al. “Petahertz-frequency plasmons in graphene nanopore and their application to nanoparticle sensing”, Scientia Iranica. Transaction F, Nanotechnology, 24(3), pp. 1669, (2017).
[13] Meller, A., Nivon, L., & Branton, D., “Voltage-driven DNA translocations through a nanopore”, Physical Review Letters, 86(15), pp. 3435, (2001).
[14] Wendell, D., Jing, P., Geng, J., et al. “Translocation of double-stranded DNA through membrane-adapted phi29 motor protein nanopores”, Nature nanotechnology, 4(11), pp. 765, (2009).
[15] Manrao, E. A., Derrington, I. M., Pavlenok, M., et al. “Nucleotide discrimination with DNA immobilized in the MspA nanopore”, PloS one, 6(10), pp. e25723, (2011).
[16] Li, J., Stein, D., McMullan, C., et al. “Ion-beam sculpting at nanometre length scales”, Nature, 412(6843), pp. 166, (2001).
[17] Storm, A. J., Chen, J. H., Ling, X. S., et al. “Electron-beam-induced deformations of SiO 2 nanostructures”, Journal of Applied Physics, 98(1), pp. 014307, (2005).
[18] Venkatesan, B. M., Shah, A. B., Zuo, J. M., et al. “DNA sensing using nanocrystalline surface‐enhanced Al2O3 nanopore sensors”, Advanced functional materials, 20(8), pp. 1266-1275, (2010).
[19] Schneider, G. F., Kowalczyk, S. W., Calado, V. E., et al. “DNA translocation through graphene nanopores” Nano letters, 10(8), pp. 3163-3167, (2010).
[20] Garaj, S., Hubbard, W., Reina, A., et al. “Graphene as a subnanometre trans-electrode membrane”, Nature, 467(7312), pp. 190, (2010).
[21] Postma, H. W. C. “Rapid sequencing of individual DNA molecules in graphene nanogaps”, Nano letters, 10(2), pp. 420-425, (2010).
[22] Heerema, S. J., & Dekker, C. “Graphene nanodevices for DNA sequencing”, Nature nanotechnology, 11(2), pp. 127, (2016).
[23] Storm, A. J., Chen, J. H., Ling, X. S., et al. “Fabrication of solid-state nanopores with single-nanometre precision”, Nature materials, 2(8), pp. 537, (2003).
[24] Cao, Y., Dong, S., Liu, S., et al. “Building High‐Throughput Molecular Junctions Using Indented Graphene Point Contacts”, Angewandte Chemie, 124(49), pp. 12394-12398, (2012).
[25] Island, J. O., Holovchenko, A., Koole, M., et al. “Fabrication of hybrid molecular devices using multi-layer graphene break junctions”, Journal of Physics: Condensed Matter, 26(47), pp. 474205, (2014).
[26] Min, S. K., Kim, W. Y., Cho, Y., et al. “Fast DNA sequencing with a graphene-based nanochannel device”, Nature nanotechnology, 6(3), pp. 162, (2011).
[27] Kim, Y., Kim, K. S., Kounovsky, K. L., et al. “Nanochannel confinement: DNA stretch approaching full contour length”, Lab on a Chip, 11(10), pp. 1721-1729, (2011).
[28] Kasianowicz, J. J., Brandin, E., Branton, D., et al. “Characterization of individual polynucleotide molecules using a membrane channel”, Proceedings of the National Academy of Sciences, 93(24), pp. 13770-13773, (1996).
[29] Deamer, D. W., & Branton, D. “Characterization of nucleic acids by nanopore analysis”, Accounts of chemical research, 35(10), pp. 817-825, (2002).
[30] Fologea, D., Gershow, M., Ledden, B., et al. “Detecting single stranded DNA with a solid state nanopore”, Nano letters, 5(10), pp. 1905-1909, (2005).
[31] Schneider, G. F., Kowalczyk, S. W., Calado, V. E., et al. “DNA translocation through graphene nanopores”, Nano letters, 10(8), pp. 3163-3167, (2010).
[32] Zwolak, M., & Di Ventra, M. “Electronic signature of DNA nucleotides via transverse transport”, Nano letters, 5(3), pp. 421-424, (2005).
[33] Lagerqvist, J., Zwolak, M., & Di Ventra, M. “Fast DNA sequencing via transverse electronic transport”, Nano letters, 6(4), pp. 779-782, (2006).
[34] Ivanov, A. P., Instuli, E., McGilvery, C. M., et al. “DNA tunneling detector embedded in a nanopore”, Nano letters, 11(1), pp. 279-285, (2010).
[35] Chen, X., Rungger, I., Pemmaraju, C. D., et al. “First-principles study of high-conductance DNA sequencing with carbon nanotube electrodes”, Physical Review B, 85(11), pp. 115436, (2012).
[36] Zwolak, M., & Di Ventra, M. “Colloquium: Physical approaches to DNA sequencing and detection”, Reviews of Modern Physics, 80(1), pp. 141, (2008).
[37] Lagerqvist, J., Zwolak, M., & Di Ventra, M. “Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport”, Biophysical journal, 93(7), pp. 2384-2390, (2007).
[38] Postma, H. W. C. “Rapid sequencing of individual DNA molecules in graphene nanogaps” Nano letters, 10(2), pp. 420-425, (2010).
[39] Gracheva, M. E., Xiong, A., Aksimentiev, A., et al. “Simulation of the electric response of DNA translocation through a semiconductor nanopore–capacitor” Nanotechnology, 17(3), pp. 622, (2006).
[40] Gracheva, M. E., Aksimentiev, A., & Leburton, J. P. “Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor”, Nanotechnology, 17(13), pp. 3160, (2006).
[41] Ohshiro, T., & Umezawa, Y. “Complementary base-pair-facilitated electron tunneling for electrically pinpointing complementary nucleobases”, Proceedings of the National Academy of Sciences, 103(1), pp. 10-14, (2006).
[42] Prasongkit, J., Grigoriev, A., Pathak, B., et al. “Theoretical study of electronic transport through DNA nucleotides in a double-functionalized graphene nanogap”, The Journal of Physical Chemistry C, 117(29), pp. 15421-15428, (2013).
[43] He, Y., Scheicher, R. H., Grigoriev, A., et al. “Enhanced DNA Sequencing Performance Through Edge‐Hydrogenation of Graphene Electrodes”, Advanced Functional Materials, 21(14), pp. 2674-2679, (2011).
[44] Gu, L. Q., Braha, O., Conlan, S., et al. “Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter”, Nature, 398(6729), pp. 686, (1999).
[45] Astier, Y., Braha, O., & Bayley, H. “Toward single molecule DNA sequencing: direct identification of ribonucleoside and deoxyribonucleoside 5 ‘-monophosphates by using an engineered protein nanopore equipped with a molecular adapter”, Journal of the American Chemical Society, 128(5), pp. 1705-1710, (2006).
[46] Lee, J. W., & Meller, A. “Rapid DNA sequencing by direct nanoscale reading of nucleotide bases on individual DNA chains”, Perspectives in Bioanalysis, 2, pp. 245-263, (2007).
[47] Keyser, U. F., Koeleman, B. N., Van Dorp, S., et al. “Direct force measurements on DNA in a solid-state nanopore”, Nature Physics, 2(7), pp. 473, (2006).
[48] Qiu, H., & Guo, W. “Detecting ssDNA at single-nucleotide resolution by sub-2-nanometer pore in monoatomic graphene: A molecular dynamics study”, Applied Physics Letters, 100(8), pp. 083106, (2012).
[49] Qamar, S., Williams, P. M., & Lindsay, S. M. “Can an atomic force microscope sequence DNA using a nanopore?” Biophysical journal, 94(4), pp. 1233-1240, (2008).
[50] Luan, B., & Aksimentiev, A. “Control and reversal of the electrophoretic force on DNA in a charged nanopore”, Journal of Physics: Condensed Matter, 22(45), pp. 454123, (2010).
[51] Luan, B., Martyna, G., & Stolovitzky, G. “Characterizing and controlling the motion of ssDNA in a solid-state nanopore”, Biophysical journal, 101(9), pp. 2214-2222, (2011).
[52] Harris, S. A., & Laughton, C. A. “A simple physical description of DNA dynamics: quasi-harmonic analysis as a route to the configurational entropy”, Journal of Physics: Condensed Matter, 19(7), pp. 076103, (2007).
[53] Peyrard, M. “Nonlinear dynamics and statistical physics of DNA”, Nonlinearity, 17(2), pp. R1, (2004).
[54] Kalé, L., Skeel, R., Bhandarkar, et al. “NAMD2: greater scalability for parallel molecular dynamics”, Journal of Computational Physics, 151(1), pp. 283-312, (1999).
[55] Humphrey, W., Dalke, A., & Schulten, K. “VMD: visual molecular dynamics. Journal of molecular graphics”, 14(1), pp. 33-38, (1996).
[56] Lu, X. J., & Olson, W. K. “3DNA: a software package for the analysis, rebuilding and visualization of three‐dimensional nucleic acid structures”, Nucleic acids research, 31(17), pp. 5108-5121, (2003).
[57] MacKerell Jr, A. D., Bashford, D., Bellott, M. L. D. R., et al. “All-atom empirical potential for molecular modeling and dynamics studies of proteins”, The journal of physical chemistry B, 102(18), pp. 3586-3616, (1998).
[58] Pu, Q., Leng, Y., Zhao, X., et al. “Molecular simulations of stretching gold nanowires in solvents. Nanotechnology”, 18(42), pp. 424007, (2007).59] Allen, M. P., & Tildesley, D. J. “Computer simulation of liquids”, Oxford university press, (2017).
[60] Essmann, U., Perera, L., Berkowitz, M. L., et al. “A smooth particle mesh Ewald method”, The Journal of chemical physics, 103(19), pp. 8577-8593, (1995).
[61] Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. “Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes”, Journal of computational physics, 23(3), pp. 327-341, (1977).
[62] Grigorescu, A. E., & Hagen, C. W. “Resists for sub-20-nm electron beam lithography with a focus on HSQ: state of the art”, Nanotechnology, 20(29), pp. 292001, (2009).
)
