a.Department of Physics, Taizhou University, Taizhou 318000, China
b.Department of Physics, Zhejiang University, Hangzhou 310027, China
chaowang0606@126.com
收稿:2022-03-10,
修回:2022-4-5,
录用:2022-4-20,
网络首发:2022-07-20,
纸质出版:2022-12-01
Scan QR Code
Wang, C.; Hu, H. X.; Zhou, Y. L.; Zhao, B.; Luo, M. B. Translocation of a self-propelled polymer through a narrow pore. Chinese J. Polym. Sci. 2022, 40, 1670–1678
Chao Wang, Han-Xian Hu, Yan-Li Zhou, et al. Translocation of a Self-propelled Polymer through a Narrow Pore[J]. Chinese Journal of Polymer Science, 2022, 40(12): 1670-1678.
Wang, C.; Hu, H. X.; Zhou, Y. L.; Zhao, B.; Luo, M. B. Translocation of a self-propelled polymer through a narrow pore. Chinese J. Polym. Sci. 2022, 40, 1670–1678 DOI: 10.1007/s10118-022-2768-3.
Chao Wang, Han-Xian Hu, Yan-Li Zhou, et al. Translocation of a Self-propelled Polymer through a Narrow Pore[J]. Chinese Journal of Polymer Science, 2022, 40(12): 1670-1678. DOI: 10.1007/s10118-022-2768-3.
Under the driving of the tangential active force
the semiflexible polymer translocates through the narrow pore in a railway motion manner
resulting that the translocation time is independent of the rigidity of the polymer but is proportional to the polymer length and the reciprocal of the active force.
Recent studies indicate that active polymers often show curious conformational and dynamical properties. Specially
rigid polymers with self-propelled tangential forces can move directionally and even push a cargo. Motivated by this
the translocation of an active bead-spring polymer through a narrow pore is studied simulationly in this work. Each bead of the polymer is propelled by a tangential active force (
f
a
) along the contour of the polymer. Simulation results show that the active polymer translocates through the pore in a railway-motion manner. The translocation velocity
ν
of the polymer is determined only by
f
a
resulting that the translocation time (
τ
) as a function of the polymer length (
N
) and the active force
f
a
can be expressed as
$$ \tau \propto N{f}_{\mathrm{a}}^{-1} $$
http://html.publish.founderss.cn/rc-pub/api/common/picture?pictureId=36805591&type=
which is independent of the rigidity of the polymer. Our results indicate that the translocation dynamics of active polymers is quite different from that of passive polymers.
Simon, S. M.; Blobe, G . A protein-conducting channel in the endoplasmic reticulum . Cell , 1991 . 65 371 - 380 . DOI: 10.1016/0092-8674(91)90455-8 http://doi.org/10.1016/0092-8674(91)90455-8 .
Gabashvili, I. S.; Gregory, S. T.; Valle, M.; Grassucci, R.; Worbs, M.; Wahl, M. C.; Dahlberg, A. E.; Frank, J . The polypeptide tunnel system in the ribosome and its gating in erythromycin resistance mutants of L4 and L22 . Mol. Cell , 2001 . 8 181 - 188 . DOI: 10.1016/S1097-2765(01)00293-3 http://doi.org/10.1016/S1097-2765(01)00293-3 .
Helenius, J.; Ng, D. T. W.; Marolda, C. L.; Walter, P.; Valvano, M. A.; Aebi, M . Translocation of lipid-linked oligosaccharides across the ER membrane requires Rft1 protein . Nature , 2002 . 415 447 - 450 . DOI: 10.1038/415447a http://doi.org/10.1038/415447a .
Smith, D. E.; Tans, S. J.; Smith, S. B.; Grimes, S.; Anderson, D. L.; Bustamante, C . The bacteriophage φ 29 portal motor can package DNA against a large internal force . Nature , 2001 . 413 748 - 752 . DOI: 10.1038/35099581 http://doi.org/10.1038/35099581 .
Fuller, D. N.; Raymer, D. M.; Kottadiel, V. I.; Rao, V. B.; Smith, D. E . Single phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability . Proc. Natl. Acad. Sci. U.S.A. , 2007 . 104 16868 - 16873 . DOI: 10.1073/pnas.0704008104 http://doi.org/10.1073/pnas.0704008104 .
Rickgauer, J. P.; Fuller, D. N.; Grimes, S.; Jardine, P. J.; Anderson, D. L.; Smith, D. E . Portal motor velocity and internal force resisting viral DNA packaging in bacteriophage φ 29 . Biophys. J. , 2008 . 94 159 - 167 . DOI: 10.1529/biophysj.107.104612 http://doi.org/10.1529/biophysj.107.104612 .
Wang, C.; Wu, F.; Zhao, B.; Chen, Y. C.; Luo, M. B . Spontaneous injection of polymer into a spherical cavity from a narrow tube . Macromolecules , 2020 . 53 1694 - 1700 . DOI: 10.1021/acs.macromol.9b02645 http://doi.org/10.1021/acs.macromol.9b02645 .
Kasianowicz, J. J.; Brandin, E.; Branton, D.; Deamer, D. W . Characterization of individual polynucleotide molecules using a membrane channel . Proc. Natl. Acad. Sci. U. S. A. , 1996 . 93 13770 - 13773 . DOI: 10.1073/pnas.93.24.13770 http://doi.org/10.1073/pnas.93.24.13770 .
Deamer, D.; Akeson, M.; Branton, D . Three decades of nanopore sequencing . Nat. Biotechnol. , 2016 . 34 518 - 524 . DOI: 10.1038/nbt.3423 http://doi.org/10.1038/nbt.3423 .
Wang, C.; Chen, Y. C.; Zhang, S.; Luo, M. B . Translocation of diblock copolymer through compound channels: a Monte Carlo simulation study . Macromolecules , 2014 . 47 7215 - 7220 . DOI: 10.1021/ma501308h http://doi.org/10.1021/ma501308h .
Han, J.; Craighead, H. G . Separation of long DNA molecules in a microfabricated entropic trap array . Science , 2000 . 288 1026 - 1029 . DOI: 10.1126/science.288.5468.1026 http://doi.org/10.1126/science.288.5468.1026 .
Wang, C.; Zhou, Y. L.; Sun, L. Z.; Chen, Y. C.; Luo, M. B . Simulation study on the migration of diblock copolymers in periodically patterned slits . J. Chem. Phys. , 2019 . 150 164904 DOI: 10.1063/1.5093791 http://doi.org/10.1063/1.5093791 .
Ouldali, H.; Sarthak, K.; Ensslen, T.; Piguet, F.; Manivet, P.; Pelta, J.; Behrends, J . C.; Aksimentiev, A.; Oukhaled, A. Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore . Nat. Biotechnol. , 2020 . 38 176 - 181 . DOI: 10.1038/s41587-019-0345-2 http://doi.org/10.1038/s41587-019-0345-2 .
Brinkerhoff, H.; Kang, A. S . W.; Liu, J.; Aksimentiev, A.; Dekker, C. Multiple rereads of single proteins at single-amino acid resolution using nanopores . Science , 2021 . 374 1509 - 1513 . DOI: 10.1126/science.abl4381 http://doi.org/10.1126/science.abl4381 .
Lam, E. T.; Hastie, A.; Lin, C.; Ehrlich, D.; Das, S. K.; Austin, M. D.; Deshpande, P.; Cao, H.; Nagarajan, N.; Xiao, M.; Kwok, P. Y . Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly . Nat. Biotechnol. , 2012 . 30 771 - 776 . DOI: 10.1038/nbt.2303 http://doi.org/10.1038/nbt.2303 .
Meller, A.; Branton, D . Single molecule measurements of DNA transport through a nanopore . Electrophoresis , 2002 . 23 2583 - 2591 . DOI: 10.1002/1522-2683(200208)23:16<2583::AID-ELPS2583>3.0.CO;2-H http://doi.org/10.1002/1522-2683(200208)23:16<2583::AID-ELPS2583>3.0.CO;2-H .
Luo, M. B.; Tsehay, D. A.; Sun, L. Z . Temperature dependence of the translocation time of polymer through repulsive nanopores . J. Chem. Phys. , 2017 . 147 034901 DOI: 10.1063/1.4993217 http://doi.org/10.1063/1.4993217 .
Edmonds, C. M.; Hesketh, P. J.; Nair, S . Polymer translocation in solid-state nanopores: dependence on hydrodynamic interactions and polymer configuration . Chem. Phys. , 2013 . 425 1 - 13 . DOI: 10.1016/j.chemphys.2013.07.016 http://doi.org/10.1016/j.chemphys.2013.07.016 .
Anderson, B . N.; Muthukumar, M.; Meller, A. pH tuning of DNA translocation time through organically functionalized nanopores . ACS Nano , 2013 . 7 1408 - 1414 . DOI: 10.1021/nn3051677 http://doi.org/10.1021/nn3051677 .
Muthukumar, M . Polymer escape through a nanopore . J. Chem. Phys. , 2003 . 118 5174 - 5184 . DOI: 10.1063/1.1553753 http://doi.org/10.1063/1.1553753 .
Luo, K. F.; Ala-Nissila, T.; Ying, S. C.; Bhattacharya, B . Influence of polymer-pore interactions on translocation . Phys. Rev. Lett. , 2007 . 99 148102 DOI: 10.1103/PhysRevLett.99.148102 http://doi.org/10.1103/PhysRevLett.99.148102 .
Luo, M. B . Translocation of polymer chains through interacting nanopores . Polymer , 2007 . 48 7679 - 7686 . DOI: 10.1016/j.polymer.2007.10.041 http://doi.org/10.1016/j.polymer.2007.10.041 .
Chen, Y. C.; Wang, C.; Zhou, Y. L.; Luo, M. B . Effect of attractive polymer-pore interactions on translocation dynamics . J. Chem. Phys. , 2009 . 130 054902 DOI: 10.1063/1.3071198 http://doi.org/10.1063/1.3071198 .
Wang, C.; Chen, Y. C.; Zhou, Y. L.; Luo, M. B . Escape of polymer chains from an attractive channel under electrical force . J. Chem. Phys. , 2011 . 134 064905 DOI: 10.1063/1.3553261 http://doi.org/10.1063/1.3553261 .
Chen, J.; Chen, X.; Sun, L. Z.; Xu, X. J.; Luo, M. B . Translocation of a looped polymer threading through a nanopore . Soft Matter , 2021 . 17 4342 - 4351 . DOI: 10.1039/D1SM00007A http://doi.org/10.1039/D1SM00007A .
Ding, M.; Duan, X.; Shi, T . Flow-induced translocation of star polymers through a nanopore . Soft Matter , 2016 . 12 2851 - 2857 . DOI: 10.1039/C6SM00040A http://doi.org/10.1039/C6SM00040A .
Katkar, H. H.; Muthukumar, M . Single molecule electrophoresis of star polymers through nanopores: simulations . J. Chem. Phys. , 2018 . 149 163306 DOI: 10.1063/1.5029980 http://doi.org/10.1063/1.5029980 .
Sharma, R. K.; Agrawal, I.; Dai, L.; Doyle, P. S.; Garaj, S . Complex DNA knots detected with a nanopore sensor . Nat. Commun. , 2019 . 10 4473 DOI: 10.1038/s41467-019-12358-4 http://doi.org/10.1038/s41467-019-12358-4 .
Huopaniemi, I.; Luo, K.; Ala-Nissila, T.; Ying, S. C . Langevin dynamics simulations of polymer translocation through nanopores . J. Chem. Phys. , 2006 . 125 124901 DOI: 10.1063/1.2357118 http://doi.org/10.1063/1.2357118 .
Luo, K.; Huopaniemi, I.; Ala-Nissila, T.; Ying, S. C . Polymer translocation through a nanopore under an applied external field . J. Chem. Phys. , 2006 . 124 114704 DOI: 10.1063/1.2179792 http://doi.org/10.1063/1.2179792 .
Luo, K.; Metzler, R . Polymer translocation into a fluidic channel through a nanopore . Phys. Rev. E , 2010 . 82 021922 DOI: 10.1103/PhysRevE.82.021922 http://doi.org/10.1103/PhysRevE.82.021922 .
Sung, W.; Park, P. J . Polymer translocation through a pore in a membrane . Phys. Rev. Lett. , 1996 . 77 783 - 786 . DOI: 10.1103/PhysRevLett.77.783 http://doi.org/10.1103/PhysRevLett.77.783 .
Muthukumar, M . Polymer translocation through a hole . J. Chem. Phys. , 1999 . 111 10371 - 10374 . DOI: 10.1063/1.480386 http://doi.org/10.1063/1.480386 .
Chuang, J.; Kantor, Y.; Kardar, M . Anomalous dynamics of translocation . Phys. Rev. E , 2001 . 65 011802 .
Kantor, Y.; Kardar, M . Anomalous dynamics of forced translocation . Phys. Rev. E , 2004 . 69 021806 DOI: 10.1103/PhysRevE.69.021806 http://doi.org/10.1103/PhysRevE.69.021806 .
Tian, P.; Smith, G. D . Translocation of a polymer chain across a nanopore: a Brownian dynamics simulation study . J. Chem. Phys. , 2003 . 119 11475 DOI: 10.1063/1.1621614 http://doi.org/10.1063/1.1621614 .
Wei, D.; Yang, W.; Jin, X.; Liao, Q . Unforced translocation of a polymer chain through a nanopore: the solvent effect . J. Chem. Phys. , 2007 . 126 204901 DOI: 10.1063/1.2735627 http://doi.org/10.1063/1.2735627 .
Luo, K.; Ala-Nissila, T.; Ying, S. C . Polymer translocation through a nanopore: a two-dimensional Monte Carlo study . J. Chem. Phys. , 2006 . 124 034714 DOI: 10.1063/1.2161189 http://doi.org/10.1063/1.2161189 .
Milchev, A.; Binder, K.; Bhattacharya, A . Polymer translocation through a nanopore induced by adsorption: Monte Carlo simulation of a coarse-grained model . J. Chem. Phys. , 2004 . 121 6042 - 6051 . DOI: 10.1063/1.1785776 http://doi.org/10.1063/1.1785776 .
Luo, K.; 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 2008 , 78 , 050901(R).
Luo, K.; Ala-Nissila, T.; Ying, S. C.; Bhattacharya, A . Heteropolymer translocation through nanopores . J. Chem. Phys. , 2007 . 126 145101 DOI: 10.1063/1.2719198 http://doi.org/10.1063/1.2719198 .
Chen, X.; Chen, J.; Zhuo, B. Y.; Yang, X.; Luo, M. B . Simulation study for the pulling translocation of a polymer globule . Polym. J. , 2021 . 53 1047 - 1056 . DOI: 10.1038/s41428-021-00502-1 http://doi.org/10.1038/s41428-021-00502-1 .
Luo, M. B.; Cao, W. P . Influence of polymer-pore interaction on the translocation of a polymer through a nanopore . Phys. Rev. E , 2012 . 86 031914 DOI: 10.1103/PhysRevE.86.031914 http://doi.org/10.1103/PhysRevE.86.031914 .
Wu, F.; Fu, Y.; Yang, X.; Sun, L. Z.; Luo, M. B . Driven translocation of semiflexible polyelectrolyte through a nanopore . J. Polym. Sci. Part B Polym. Phys. , 2019 . 57 912 - 921 . DOI: 10.1002/polb.24846 http://doi.org/10.1002/polb.24846 .
Kron, S. J.; Spudich, J. A . Fluorescent actin filaments move on myosin fixed to a glass surface . Proc. Natl. Acad. Sci. U. S. A. , 1986 . 83 6272 - 6276 . DOI: 10.1073/pnas.83.17.6272 http://doi.org/10.1073/pnas.83.17.6272 .
Liu, L.; Tüzel, E.; Ross, J. L . Loop formation of microtubules during gliding at high density . J. Phys.: Condens. Matter , 2011 . 23 374104 DOI: 10.1088/0953-8984/23/37/374104 http://doi.org/10.1088/0953-8984/23/37/374104 .
Isele-Holder, R . E.; Elgeti, J.; Gompper, G. Self-propelled worm-like filaments: spontaneous spiral formation, structure, and dynamics . Soft Matter , 2015 . 11 7181 - 7190 . DOI: 10.1039/C5SM01683E http://doi.org/10.1039/C5SM01683E .
Man, Y.; Kanso, E . Morphological transitions of axially-driven microfilaments . Soft Matter , 2019 . 15 5163 - 5173 . DOI: 10.1039/C8SM02397B http://doi.org/10.1039/C8SM02397B .
Wu, J. C.; Lin, F. J.; Ai, B. Q . Absolute negative mobility of active polymer chains in steady laminar flows . Soft Matter , 2022 . 18 1194 - 1200 . DOI: 10.1039/D1SM01664D http://doi.org/10.1039/D1SM01664D .
Bianco, V.; Locatelli, E.; Malgaretti, P . Globulelike conformation and enhanced diffusion of active polymers . Phys. Rev. Lett. , 2018 . 121 217802 DOI: 10.1103/PhysRevLett.121.217802 http://doi.org/10.1103/PhysRevLett.121.217802 .
Locatelli, E.; Bianco, V.; Malgaretti, P . Activity-induced collapse and arrest of active polymer rings . Phys. Rev. Lett. , 2021 . 126 097801 DOI: 10.1103/PhysRevLett.126.097801 http://doi.org/10.1103/PhysRevLett.126.097801 .
Chelakkot, R.; Gopinath, A.; Mahadevan, L.; Hagan, M. F . Flagellar dynamics of a connected chain of active, polar, Brownian particles . J. R. Soc. Interface , 2014 . 11 20130884 DOI: 10.1098/rsif.2013.0884 http://doi.org/10.1098/rsif.2013.0884 .
Fily, Y.; Subramanian, P.; Schneider, T . M.; Chelakkot, R.; Gopinath, A. Buckling instabilities and spatio-temporal dynamics of active elastic filaments . J. R. Soc. Interface , 2020 . 17 20190794 DOI: 10.1098/rsif.2019.0794 http://doi.org/10.1098/rsif.2019.0794 .
Sekimoto, K.; Mori, N.; Tawada, K.; Toyoshima, Y. Y . Symmetry breaking instabihties of an in vitro biological system . Phys. Rev. Lett. , 1995 . 75 172 - 175 . DOI: 10.1103/PhysRevLett.75.172 http://doi.org/10.1103/PhysRevLett.75.172 .
Bourdieu, L.; Duke, T.; Elowitz, M. B.; Winkelmann, D . A.; Leibler, S.; Libchabe, A. Spiral defects in motility assays: a measure of motor protein force . Phys. Rev. Lett. , 1995 . 75 176 - 179 . DOI: 10.1103/PhysRevLett.75.176 http://doi.org/10.1103/PhysRevLett.75.176 .
Laskar, A.; Singh, R.; Ghose, S.; Jayaraman, G.; Kumar, P. B. S.; Adhikari, R . Hydrodynamic instabilities provide a generic route to spontaneous biomimetic oscillations in hemomechanically active filaments . Sci. Rep. , 2013 . 3 1964 DOI: 10.1038/srep01964 http://doi.org/10.1038/srep01964 .
Isele-Holder, R . E.; Jäger, J.; Saggiorato, G.; Elgeti, J.; Gompper, G. Dynamics of self-propelled filaments pushing aload . Soft Matter , 2016 . 12 8495 - 8505 . DOI: 10.1039/C6SM01094F http://doi.org/10.1039/C6SM01094F .
Manna, R . K.; Kumar, P.; Adhikari, R. Colloidal transport by active filaments . J. Chem. Phys. , 2017 . 146 024901 DOI: 10.1063/1.4972010 http://doi.org/10.1063/1.4972010 .
Shen, C.; Qin, C. R.; Xu, T. L.; Chen, K.; Tian, W. D . Structure and dynamics of an active polymer adsorbed on the surface of a cylinder . Soft Matter , 2022 . 18 1489 - 1497 . DOI: 10.1039/D1SM01658J http://doi.org/10.1039/D1SM01658J .
Xu, G. H.; Li, F. G.; Wu, J. C.; Ai, B. Q . Rectification of an active polymer chain with chirality in a transversal asymmetric channel . Phys. A: Statist. Mechan. Applic. , 2021 . 575 126051 DOI: 10.1016/j.physa.2021.126051 http://doi.org/10.1016/j.physa.2021.126051 .
Wang, F. H.; Wu, Y. Y.; Tan, Z. J . Salt contribution to the flexibility of single-stranded nucleic acid of finite length . Biopolymers , 2013 . 99 370 - 381 . DOI: 10.1002/bip.22189 http://doi.org/10.1002/bip.22189 .
Fu, Y; Wu, F; Huang, J. H.; Chen, Y. C.; Luo, M. B . Simulation study on the extension of semi-flexible polymer chains in cylindrical channel . Chinese J. Polym. Sci. , 2019 . 37 1290 - 1297 . DOI: 10.1007/s10118-019-2291-3 http://doi.org/10.1007/s10118-019-2291-3 .
0
浏览量
184
Downloads
0
CSCD
关联资源
相关文章
相关作者
相关机构
京公网安备11010802046900号