Polymer translocation through a nanopore induced by adsorption: Monte Carlo simulation of a coarse-grained model

The Journal of Chemical Physics
Andrey MilchevAniket Bhattacharya

Abstract

Dynamic Monte Carlo simulation of a bead-spring model of flexible macromolecules threading through a very narrow pore in a very thin rigid membrane are presented, assuming at the cis side of the membrane a purely repulsive monomer-wall interaction, while the trans side is attractive. Two choices of monomer-wall attraction epsilon are considered, one choice is slightly below and the other slightly above the "mushroom to pancake" adsorption threshold epsilon(c) for an infinitely long chain. Studying chain lengths N=32, 64, 128, and 256 and varying the number of monomers N(trans) (time t=0) that have already passed the pore when the simulation started, over a wide range, we find for epsilon<epsilon(c) (nonadsorbing case) that the translocation probability varies proportional to c(trans)=N(trans)(t=0)/N for small c(trans), while for epsilon>epsilon(c) a finite number N(trans)(t=0) suffices that the translocation probability is close to unity. In the case epsilon<epsilon(c), however, the time it takes for those chains to get through the pore to complete the translocation process scales as tau proportional, variant N(2.23+/-0.04). This result agrees with the suggestion of Chuang, Kantor, and Kardar [Phys. Rev. E 65, 011802 (2001)] th...Continue Reading

References

May 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·S M SimonG F Oster
Jan 1, 1969·Cold Spring Harbor Symposia on Quantitative Biology·D RekoshD Baltimore
Nov 26, 1996·Proceedings of the National Academy of Sciences of the United States of America·J J KasianowiczD W Deamer
Mar 13, 1995·Physical Review Letters·A Baumgärtner, J Skolnick
Oct 8, 1999·Biophysical Journal·D K Lubensky, D R Nelson
Feb 3, 2000·Proceedings of the National Academy of Sciences of the United States of America·A MellerD Branton
Sep 27, 2000·Physical Review Letters·S E HenricksonJ J Kasianowicz
Apr 6, 2001·Physical Review Letters·M Muthukumar
May 1, 2001·Physical Review Letters·A MellerD Branton
Jan 22, 2002·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Jeffrey ChuangMehran Kardar
Mar 23, 2002·Physical Review Letters·S W P TurnerH G Craighead
Sep 5, 2002·Electrophoresis·Chung Y Kong, Murugappan Muthukumar
Jul 10, 2003·Proceedings of the National Academy of Sciences of the United States of America·Roya ZandiWilliam M Gelbart
Jul 15, 2003·Physical Review Letters·Alexis F Sauer-BudgeDaniel Branton
Oct 6, 2005·Physical Biology·Ulrich GerlandTerence Hwa

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Citations

Apr 5, 2005·Journal of Molecular Modeling·Andrzej Sikorski, Piotr Romiszowski
Sep 15, 2010·Physical Chemistry Chemical Physics : PCCP·Li-Zhen SunMeng-Bo Luo
Jan 25, 2013·Physical Chemistry Chemical Physics : PCCP·Meng-Bo Luo, Chao Wang
Mar 28, 2009·The European Physical Journal. E, Soft Matter·S T T OllilaS-C Ying
Aug 12, 2009·The European Physical Journal. E, Soft Matter·A BhattacharyaK Binder
Nov 12, 2010·The European Physical Journal. E, Soft Matter·Hai-Jun WangXin-Wu Ba
Nov 26, 2009·The Journal of Chemical Physics·Li-Zhen SunMeng-Bo Luo
Jun 16, 2012·The Journal of Chemical Physics·Shuang Yang, Alexander V Neimark
Apr 21, 2007·The Journal of Chemical Physics·Kaifu LuoAniket Bhattacharya
Mar 25, 2006·The Journal of Chemical Physics·Kaifu LuoSee-Chen Ying
Sep 13, 2006·The Journal of Chemical Physics·Stanislav Kotsev, Anatoly B Kolomeisky
Oct 16, 2012·The Journal of Chemical Physics·Christopher J RasmussenAlexander V Neimark
Oct 4, 2006·The Journal of Chemical Physics·Ilkka HuopaniemiSee-Chen Ying
May 10, 2013·The Journal of Chemical Physics·James M Polson, Anthony C M McCaffrey
Dec 5, 2012·The Journal of Chemical Physics·Jack A CohenRamin Golestanian
Aug 2, 2013·The Journal of Chemical Physics·Shuang ZhangMeng-Bo Luo
Mar 1, 2012·The Journal of Chemical Physics·Christopher M EdmondsSankar Nair
Aug 18, 2012·The Journal of Chemical Physics·Stephen MirigianMurugappan Muthukumar
May 13, 2010·The Journal of Chemical Physics·Issei Nakamura, An-Chang Shi
Aug 7, 2009·The Journal of Chemical Physics·Alexandros G KoutsioubasChris Toprakcioglu
Aug 4, 2007·The Journal of Chemical Physics·Ying-Cai ChenMeng-Bo Luo
Jun 8, 2007·The Journal of Chemical Physics·Dongshan WeiQi Liao
Jan 17, 2013·The Journal of Chemical Physics·James M PolsonAnthony McCaffrey
Aug 3, 2012·The Journal of Chemical Physics·Zhen ZhangZhonghuai Hou
Jun 8, 2013·The Journal of Chemical Physics·Ramesh Adhikari, Aniket Bhattacharya
Oct 2, 2007·The Journal of Chemical Physics·David B WellsAleksei Aksimentiev
Nov 21, 2007·The Journal of Chemical Physics·Stanislav Kotsev, Anatoly B Kolomeisky
Aug 24, 2010·The Journal of Chemical Physics·Arash Nikoubashman, Christos N Likos
May 17, 2014·The Journal of Chemical Physics·James M Polson, Taylor R Dunn
Dec 24, 2015·The Journal of Chemical Physics·Chao WangMeng-Bo Luo
Oct 30, 2007·Biophysical Journal·Anatoly B Kolomeisky
Sep 4, 2007·The Journal of Chemical Physics·Chwen-Yang ShewKenichi Yoshikawa
Oct 11, 2014·Soft Matter·Vladimir V PalyulinRalf Metzler
Nov 16, 2018·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Li-Zhen SunMeng-Bo Luo
May 5, 2009·Physical Biology·Malcolm McCauleyRalf Bundschuh
Dec 31, 2005·Physical Review Letters·Ralf Bundschuh, Ulrich Gerland
Apr 7, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·V V LehtolaK Kaski
Dec 21, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Li-Zhen SunMeng-Bo Luo
Sep 13, 2013·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Debabrata PanjaAnatoly B Kolomeisky
Jun 11, 2015·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Maria Fyta
Jul 25, 2017·The Journal of Chemical Physics·Meng-Bo LuoLi-Zhen Sun
Jan 3, 2019·The Journal of Chemical Physics·Seulki Kwon, Bong June Sung

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