Skip to content
BY-NC-ND 3.0 license Open Access Published by De Gruyter Open Access June 17, 2012

Monte Carlo analysis of polymer translocation with deterministic and noisy electric fields

Davide Valenti, Giovanni Denaro, Dominique Adorno, Nicola Pizzolato, Salvatore Zammito and Bernardo Spagnolo
From the journal Open Physics

Abstract

Polymer translocation through the nanochannel is studied by means of a Monte Carlo approach, in the presence of a static or oscillating external electric voltage. The polymer is described as a chain molecule according to the two-dimensional “bond fluctuation model”. It moves through a piecewise linear channel, which mimics a nanopore in a biological membrane. The monomers of the chain interact with the walls of the channel, modelled as a reflecting barrier. We analyze the polymer dynamics, concentrating on the translocation time through the channel, when an external electric field is applied. By introducing a source of coloured noise, we analyze the effect of correlated random fluctuations on the polymer translocation dynamics.

[1] A. Meller, L. Nivon, D. Branton, Phys. Rev. Lett. 86, 3435 (2001) http://dx.doi.org/10.1103/PhysRevLett.86.343510.1103/PhysRevLett.86.3435Search in Google Scholar

[2] A. Meller, J. Phys.: Condens. Matter 15, R581 (2003) http://dx.doi.org/10.1088/0953-8984/15/17/20210.1088/0953-8984/15/17/202Search in Google Scholar

[3] S. Adhya, C. Merril, Nature 443, 754 (2006) http://dx.doi.org/10.1038/443754a10.1038/443754aSearch in Google Scholar

[4] B. Hanss, E Leal-Pinto, L. A. Bruggeman, T. D. Copeland, Proc. Natl. Acad. Sci. USA 95, 1921 (1998) http://dx.doi.org/10.1073/pnas.95.4.192110.1073/pnas.95.4.1921Search in Google Scholar

[5] J. Han, S. W. Turner, H. G. Craighead, Phys. Rev. Lett. 83, 1688 (1999) http://dx.doi.org/10.1103/PhysRevLett.83.168810.1103/PhysRevLett.83.1688Search in Google Scholar

[6] J. Han, H. G. Craighead, Science 288, 1026 (2000) http://dx.doi.org/10.1126/science.288.5468.102610.1126/science.288.5468.1026Search in Google Scholar

[7] K. Luo, T. Ala-Nissila, S.-C. Ying, A. Bhattacharya, Phys. Rev. Lett. 99, 148102 (2007) http://dx.doi.org/10.1103/PhysRevLett.99.14810210.1103/PhysRevLett.99.148102Search in Google Scholar

[8] K. Luo, T. Ala-Nissila, S.-C. Ying, A. Bhattacharya, Phys. Rev. Lett. 100, 058101 (2008) http://dx.doi.org/10.1103/PhysRevLett.100.05810110.1103/PhysRevLett.100.058101Search in Google Scholar

[9] J. J. Kasianowicz, E. Brandin, D. Branton, D. W. Deamer, Proc. Natl. Acad. Sci. USA 93, 13770 (1996) http://dx.doi.org/10.1073/pnas.93.24.1377010.1073/pnas.93.24.13770Search in Google Scholar

[10] A. Meller, L. Nivon, E. Brandin, J. Golovchenko, D. Branton, Proc. Natl. Acad. Sci. USA 97, 1079 (2000) http://dx.doi.org/10.1073/pnas.97.3.107910.1073/pnas.97.3.1079Search in Google Scholar

[11] S. Matysiak, A. Montesi, M. Pasquali, A. B. Kolomeisky, C. Clementi, Phys. Rev. Lett. 96, 118103 (2006) http://dx.doi.org/10.1103/PhysRevLett.96.11810310.1103/PhysRevLett.96.118103Search in Google Scholar

[12] K. Luo, T. Ala-Nissila, S.-C. Ying, J. Chem. Phys. 124, 034714 (2006) http://dx.doi.org/10.1063/1.216118910.1063/1.2161189Search in Google Scholar

[13] K. Luo, T. Ala-Nissila, S.-C. Ying, J. Chem. Phys. 124, 114704 (2006) http://dx.doi.org/10.1063/1.217979210.1063/1.2179792Search in Google Scholar

[14] Z.-Y Yang, L.-X. Zhang, J. Cheng, Chin. J. Chem. Phys. 21, 555 (2008) http://dx.doi.org/10.1088/1674-0068/21/06/555-55910.1088/1674-0068/21/06/555-559Search in Google Scholar

[15] N. Pizzolato, A. Fiasconaro, B. Spagnolo, J. Stat. Mech.-Theory E., P01011 (2009) 10.1088/1742-5468/2009/01/P01011Search in Google Scholar

[16] N. Pizzolato, A. Fiasconaro, D. Persano Adorno, B. Spagnolo, Phys. Biol., 034001 (2010) 10.1088/1478-3975/7/3/034001Search in Google Scholar

[17] A. Fiasconaro, J.J. Mazo, F. Falo, Phys. Rev. E 82, 031803 (2010) http://dx.doi.org/10.1103/PhysRevE.82.03180310.1103/PhysRevE.82.031803Search in Google Scholar

[18] A. Mohan, A. B. Kolomeisky, M. Pasquali, J. Chem. Phys. 128, 125104 (2008) http://dx.doi.org/10.1063/1.286877710.1063/1.2868777Search in Google Scholar

[19] C. Tai, A. Wong, M. Muthukumar, J. Chem. Phys. 128, 154903 (2008) http://dx.doi.org/10.1063/1.289793210.1063/1.2897932Search in Google Scholar

[20] J. Deng, K. H. Schoenbach, E. S. Buescher, P. S. Hair, P. M. Fox, S. J. Beebe, Biophysical Journal 84, 2709 (2003) http://dx.doi.org/10.1016/S0006-3495(03)75076-010.1016/S0006-3495(03)75076-0Search in Google Scholar

[21] G. Sigalov, J. Comer, G. Timp, A. Aksimentiev, Nano Lett. 8, 56 (2008) http://dx.doi.org/10.1021/nl071890k10.1021/nl071890kSearch in Google Scholar

[22] A. Meller, D. Branton, Electrophoresis 23, 2583 (2002) http://dx.doi.org/10.1002/1522-2683(200208)23:16<2583::AID-ELPS2583>3.0.CO;2-H10.1002/1522-2683(200208)23:16<2583::AID-ELPS2583>3.0.CO;2-HSearch in Google Scholar

[23] P. E. Rouse Jr., J. Chem. Phys. 21, 1272 (1953) http://dx.doi.org/10.1063/1.169918010.1063/1.1699180Search in Google Scholar

[24] N. Metropolis, S. Ulam, J. Am. Stat. Assoc. 44, 335 (1949) http://dx.doi.org/10.1080/01621459.1949.1048331010.1080/01621459.1949.10483310Search in Google Scholar

[25] N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, E. Teller, J. Chem. Phys. 21, 1087 (1953) http://dx.doi.org/10.1063/1.169911410.1063/1.1699114Search in Google Scholar

[26] M. Muthukumar, P. Welch, Polymer 41, 8833 (2000) http://dx.doi.org/10.1016/S0032-3861(00)00226-310.1016/S0032-3861(00)00226-3Search in Google Scholar

[27] J. Tothova, B. Brotovsky, V. Lisy, Czech. J. Phys. 55, 221 (2005) http://dx.doi.org/10.1007/s10582-005-0033-y10.1007/s10582-005-0033-ySearch in Google Scholar

[28] B. Spagnolo, S. Spezia, L. Curcio, N. Pizzolato, A. Fiasconaro, D. Valenti, P. Lo Bue, E. Peri, S. Colazza, Eur. Phys. J. B 69, 133 (2009) http://dx.doi.org/10.1140/epjb/e2009-00162-y10.1140/epjb/e2009-00162-ySearch in Google Scholar

[29] G.-J. Zhao, J.-Y. Liu, L.-C. Zhou, K.-L. Han, J. Phys. Chem. B 111, 8940 (2007) http://dx.doi.org/10.1021/jp073453010.1021/jp0734530Search in Google Scholar

[30] G.-J. Zhao, K.-L. Han, Biophys. J. 94, 38 (2008) http://dx.doi.org/10.1529/biophysj.107.11373810.1529/biophysj.107.113738Search in Google Scholar

[31] G.-J. Zhao, K.-L. Han, Acc. Chem. Res., DOI: 10.1021/ar200135h 10.1021/ar200135hSearch in Google Scholar

[32] M. McCauley, R. Forties, U. Gerland, R. Bundschuh, Phys. Biol. 6, 036006 (2009) http://dx.doi.org/10.1088/1478-3975/6/3/03600610.1088/1478-3975/6/3/036006Search in Google Scholar

[33] C. W. Gardiner, Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences, 2nd edition, (Springer-Verlag, Berlin, 1985) 10.1007/978-3-662-02452-2Search in Google Scholar

Published Online: 2012-6-17
Published in Print: 2012-6-1

© 2012 Versita Warsaw

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Scroll Up Arrow