Translocation of Polymer Through a Nanopore Studied by Langevin Dynamics:Effect of the Friction Coefficient

Abstract

Abstract: The driven polymer translocation through a nanopore with unbiased initial configuration has been studied by using Langevin dynamics(LD) simulations.It is found that the scaling relationship between translocation time and the polymer chain length is strongly affected by the friction coefficient in LD and the driving force.However,there is no scaling relationship between the translocation time and the friction coefficient.The translocation time is almost inversely proportional to the driving force,which is in agreement with those obtained in biased translocation.The scaling relationship between gyration radius(R_g) of subchain at the trans side with the subchain length (L) is R_g～L^0.33 that is in good agreement with the limiting value for molten globule state,while the curve of R_g of subchain at the cis side has two distinct stages.During translocation,the subchain at the cis side is being stretched gradually,and the structure of the subchain transforms from sphere-like to rod-like.When the effect of stretching reaches the tail end,the subchain is at the most stretched state.Finally the subchain will rapidly restore to coil structure.According to the results of force analysis,the retarding force at the trans side is more crucial during the practical translocation.

Key words: translocation, Langevin dynamics, friction coefficient, polymer, nanopore

摘要： The driven polymer translocation through a nanopore with unbiased initial configuration has been studied by using Langevin dynamics(LD) simulations.It is found that the scaling relationship between translocation time and the polymer chain length is strongly affected by the friction coefficient in LD and the driving force.However,there is no scaling relationship between the translocation time and the friction coefficient.The translocation time is almost inversely proportional to the driving force,which is in agreement with those obtained in biased translocation.The scaling relationship between gyration radius(R_g) of subchain at the trans side with the subchain length (L) is R_g～L^0.33 that is in good agreement with the limiting value for molten globule state,while the curve of R_g of subchain at the cis side has two distinct stages.During translocation,the subchain at the cis side is being stretched gradually,and the structure of the subchain transforms from sphere-like to rod-like.When the effect of stretching reaches the tail end,the subchain is at the most stretched state.Finally the subchain will rapidly restore to coil structure.According to the results of force analysis,the retarding force at the trans side is more crucial during the practical translocation.

关键词: translocation, Langevin dynamics, friction coefficient, polymer, nanopore

FENG Jian, SHANG Yazhuo, ZHOU Lihui, LIU Honglai, HU Ying. Translocation of Polymer Through a Nanopore Studied by Langevin Dynamics:Effect of the Friction Coefficient[J]. Chin.J.Chem.Eng., 2012, 20(2): 231-238.

冯剑, 尚亚卓, 周丽绘, 刘洪来, 胡英. Translocation of Polymer Through a Nanopore Studied by Langevin Dynamics:Effect of the Friction Coefficient[J]. Chinese Journal of Chemical Engineering, 2012, 20(2): 231-238.

References

1 Muthukumar,M.,“Mechanism of DNA transport through pores”,Annu.Rev.Biophys.Biomol.Struct.,36,435-450(2007).
2 Branton,D.,Deamer,D.,Marziali,A.,Bayley,H.,Benner,S.A.,Butler,T.,Ventra,M.D.,“The potential and challenges of nanopore sequencing”,Nat.Biotech.,26(10),1146-1153(2008).
3 Movileanu,L.,“Interrogating single proteins through nanopores:challenges and opportunities”,Trends in Biotechnology,27(6),333-341 (2009).
4 Wickner,W.T.,Lodish,H.F.,“Multiple mechanisms of protein insertion into and across membranes”,Science,230,400-407(1985).
5 Kasianowicz,J.J.,Brandin,E.,Branton,D.,Deaner,D.W.,“Characterization of individual polynucleotide molecules using a membrane channel”,Proc.Natl.Acad.Sci.U.S.A.,93,13770-13733(1996).
6 Meller,A.,Nivon,L.,Branton,D.,“Voltage-driven DNA translocations through a nanopore”,Phys.Rev.Lett.,86(15),3435-3438(2001).
7 Robertson,J.W.F.,Rodrigues,C.G.,Standford,V.M.,Rubinson,K.A.,Krasilnikov,O.V.,Kasianowicz,J.J.,“Single-molecule mass spectrometry in solution using a solitary nanopore”,Proc.Natl.Acad.Sci.U.S.A.,104,8207-8211(2007).
8 Krasilnikov,O.V.,Rodrigues,C.G.,Bezrukov,S.M.,“Single polymer molecules in a protein nanopore in the limit of a strong polymer-pore attraction”,Phys.Rev.Lett.,97,018301(2006).
9 Zhao,Q.T.,Jayawardhana,D.A.,Wang,D.Q.,Guan,X.Y.,“Study of peptide transport through engineered protein channels”,J.Phys.Chem.B,113(11),3572-3578(2009).
10 de Zoysa,R.S.S.,Jayawardhana,D.A.,Zhao,Q.,Wang,D.,Armstrong,D.W.,Guan,X.,“Slowing DNA translocation through nanopores using a solution containing organic salts”,J.Phys.Chem.B,113,13332-13336(2009).
11 Li,J.L.,Stein,D.,McMullan,C.,Branton,D.,Aziz,M.J.,Golovchenko,J.A.,“Ion-beam sculpting at nanometre length scales”,Nature,412,166-169(2001).
12 Li,J.L.,Gershow,M.,Stein,D.,Brandin,E.,Golovchenko,J.A.,“DNA molecules and configurations in a solid-state nanopore microscope”,Natural Material,2,611-615(2003).
13 Storm,A.J.,Chen,J.H.,Zandbergen,H.W.,Dekker,C.,“Translocation of double-strand DNA through a silicon oxide nanopore”,Phys.Rev.E,71,051903(2005).
14 Storm,A.J.,Storm,C.,Chen,J.,Zandbergen,H.,Joanny,J.F.,Dekker,C.,“Fast DNA translocation through a solid-state nanopore”,Nano Lett.,5(7),1193-1197(2005).
15 Muthukumar,M.,“Polymer translocation through a hole”,J.Chem.Phys.,111,10371-10374(1999).
16 Ghosal,S.,“Electrophoresis of a polyelectrolyte through a nanopore”,Phys.Rev.E,74,041901(2006).
17 Dubbeldam,J.L.A.,Milchev,A.,Rostiashvili,V.G.,Vilgis,T.A., “Polymer translocation through a nanopore:A showcase of anomalous diffusion”,Phys.Rev.E,76,010801(2007).
18 Wong,C.T.A.,Muthukumar,M.,“Polymer capture by electro-osmotic flow of oppositely charged nanopores”,J.Chem.Phys.,126,164903(2007).
19 Gopinathan,A.,Kim,Y.W.,“Polymer translocation in crowded environments”,Phys.Rev.Lett.,99,228106(2007).
20 Lagerqvist,J.,Zwolak,M.,Ventra,M.D.,“Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport”,Biophys.J.,93(7),2384-2390(2007).
21 Tai,C.,Wong,C.,Muthukumara,M.,“Polymer translocation through a cylindrical channel”,J.Chem.Phys.,128,154903(2008).
22 ten Bosch,A.,Cheyssac,P.,“Translocation of a stiff polymer in a microchannel”,Phys.Rev.E,79,011903(2009).
23 Luo,K.F.,Ala-Nissila,T.,Ying,S.C.,“Polymer translocation through a nanopore:A two-dimensional Monte Carlo study”,J. Chem.Phys.,124,034714(2006).
24 Luo,K.F.,Huopaniemi,I.,Ala-Nissila,T.,Ying,S.C.,“Polymer translocation through a nanopore under an applied external field”,J. Chem.Phys.,124,114704(2006).
25 Huopaniemi,I.,Luo,K.F.,Ala-Nissila,T.,Ying,S.C.,“Langevin dynamics simulations of polymer translocation through nanopores”, J.Chem.Phys.,125,124901(2006).
26 Forrey,C.,Muthukumara,M.,“Langevin dynamics simulations of ds-DNA translocation through synthetic nanopores”,J.Chem.Phys.,127,015102(2007).
27 Luo,K.F.,Ala-Nissila,T.,Ying,S.C.,Bhattacharya,A.,“Influence of polymer-pore interactions on translocation”,Phys.Rev.Lett.,99,148102(2007).
28 Luo,K.F.,Ala-Nissila,T.,Ying,S.C.,Bhattacharya,A.,“Heteropoly- mer translocation through nanopores”,J.Chem.Phys.,126,145101 (2007).
29 Luo,K.F.,Ollila,S.T.T.,Huopaniemi,I.,Ala-Nissila,T.,Pomorski, P.,Karttunen,M.,Ying,S.C.,Bhattacharya,A.,“Dynamical scaling exponents for polymer translocation through a nanopore”,Phys.Rev. E,78,050901(2008).
30 Luo,K.F.,Ala-Nissila,T.,Ying,S.C.,Bhattacharya,A.,“Sequence dependence of DNA translocation through a nanopore”,Phys.Rev. Lett.,100,058101(2008).
31 Luo,K.F.,Ala-Nissila,T.,Ying,S.C.,Bhattacharya,A.,“Dynamics of DNA translocation through an attractive nanopore”,Phys.Rev.E,78,061911(2008).
32 Luo,K.F.,Ala-Nissila,T.,Ying,S.C.,Bhattacharya,A.,“Transloca- tion dynamics with attractive nanopore-polymer interactions”,Phys. Rev.E,78,061918(2008).
33 Gauthier,M.G.,Slater,G.W.,“Molecular dynamics simulation of a polymer chain translocating through a nanoscopic pore-hydrodynamic interactions versus pore radius”,Eur.Phys.J.E,25,17-23(2008).
34 Gauthier,M.G..,Slater,G.W.,“A Monte Carlo algorithm to study polymer translocation through nanopores.II.scaling laws”,J.Chem. Phys.,128,205103(2008).
35 Gauthier,M.G.,Slater,G.W.,“Sequence effects on the forced trans- location of heteropolymers through a small channel”,J.Chem.Phys.,128,175103(2008).
36 Izmitli,A.,Schwartz,D.C.,Graham,M.D.,de Pablo,J.J.,“The ef- fect of hydrodynamic interactions on the dynamics of DNA translo- cation through pores”,J.Chem.Phys.,128,085102(2008).
37 Lehtola,V.V.,Linna,R.P.,Kaski,K.,“Critical evaluation of the computational methods used in the forced polymer translocation”, Phys.Rev.E,78,061803(2008).
38 Feng,J.,Ge,X.T.,Shang,Y.Z.,Zhou,L.H.,Liu,H.L.,Hu,Y., “Translocation of polymer through a nanopore studied by dissipative particle dynamics”,Fluid Phase Equilibrium,302,26-31(2011).
39 Leach,A.R.,Molecular Modelling:Principles and Applications,2nd edition,Pearson Education,England,331-334(2001).
40 Luo,K.F.,Ala-Nissila,T.,Ying,S.C.,Metzler,R.,“Driven polymer translocation through nanopores:Slow-vs.-fast dynamics”,EPL,88,68006(2009).
41 Yang,Z.,Li,S.,Zhang,L.,Ur Rehman,A.,Liang,H.,“Transloca- tion ofα-helix chains through a nanopore”,J.Chem.Phys.,133(22),154903(2010).
42 Bhattacharya,A.,Morrison,W.H.,Luo,K.F.,Ala-Nissila,T.,Ying,S.C., Milchev,A.,Binder,K.,“Scaling exponents of forced polymer translocation through a nanopore”,Eur.Phys.J.E,29,423-429(2009).
43 Kapahnke,F.,Schmidt,U.,Heermann,D.W.,Weiss,M.,“Polymer translocation through a nanopore:The effect of solvent conditions”, J.Chem.Phys.,132,164904(2010).
44 Feng,J.,Liu,H.L.,Hu,Y.,“Molecular dynamics simulations of polyampholytes inside a slit”,Mol.Simul.,31(10),731-738(2005).

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