Skip to main content
SpringerLink
Log in

Translocation of a Self-propelled Polymer through a Narrow Pore

  • Research Article
  • Published:
Chinese Journal of Polymer Science Aims and scope Submit manuscript

Abstract

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 (fa) 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 fa, resulting that the translocation time (τ) as a function of the polymer length (N) and the active force fa can be expressed as τ∝Nf −1a , 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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Simon, S. M.; Blobe, G. A protein-conducting channel in the endoplasmic reticulum. Cell 1991, 65, 371–380.

    Article  CAS  Google Scholar 

  2. 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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  4. Smith, D. E.; Tans, S. J.; Smith, S. B.; Grimes, S.; Anderson, D. L.; Bustamante, C. The bacteriophage φ29 portal motor can package DNA against a large internal force. Nature 2001, 413, 748–752.

    Article  CAS  Google Scholar 

  5. 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.

    Article  CAS  Google Scholar 

  6. 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 φ29. Biophys. J. 2008, 94, 159–167.

    Article  CAS  Google Scholar 

  7. 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.

    Article  CAS  Google Scholar 

  8. 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.

    Article  CAS  Google Scholar 

  9. Deamer, D.; Akeson, M.; Branton, D. Three decades of nanopore sequencing. Nat. Biotechnol. 2016, 34, 518–524.

    Article  CAS  Google Scholar 

  10. 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.

    Article  CAS  Google Scholar 

  11. Han, J.; Craighead, H. G. Separation of long DNA molecules in a microfabricated entropic trap array. Science 2000, 288, 1026–1029.

    Article  CAS  Google Scholar 

  12. 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.

    Article  Google Scholar 

  13. 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.

    Article  CAS  Google Scholar 

  14. 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.

    Article  CAS  Google Scholar 

  15. 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.

    Article  CAS  Google Scholar 

  16. Meller, A.; Branton, D. Single molecule measurements of DNA transport through a nanopore. Electrophoresis 2002, 23, 2583–2591.

    Article  CAS  Google Scholar 

  17. 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.

    Article  Google Scholar 

  18. 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.

    Article  CAS  Google Scholar 

  19. Anderson, B. N.; Muthukumar, M.; Meller, A. pH tuning of DNA translocation time through organically functionalized nanopores. ACS Nano 2013, 7, 1408–1414.

    Article  CAS  Google Scholar 

  20. Muthukumar, M. Polymer escape through a nanopore. J. Chem. Phys. 2003, 118, 5174–5184.

    Article  CAS  Google Scholar 

  21. Luo, K. F.; Ala-Nissila, T.; Ying, S. C.; Bhattacharya, B. Influence of polymer-pore interactions on translocation. Phys. Rev. Lett. 2007, 99, 148102.

    Article  Google Scholar 

  22. Luo, M. B. Translocation of polymer chains through interacting nanopores. Polymer 2007, 48, 7679–7686.

    Article  CAS  Google Scholar 

  23. 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.

    Article  Google Scholar 

  24. 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.

    Article  Google Scholar 

  25. 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.

    Article  CAS  Google Scholar 

  26. Ding, M.; Duan, X.; Shi, T. Flow-induced translocation of star polymers through a nanopore. Soft Matter 2016, 12, 2851–2857.

    Article  CAS  Google Scholar 

  27. Katkar, H. H.; Muthukumar, M. Single molecule electrophoresis of star polymers through nanopores: simulations. J. Chem. Phys. 2018, 149, 163306.

    Article  CAS  Google Scholar 

  28. 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.

    Article  Google Scholar 

  29. Huopaniemi, I.; Luo, K.; Ala-Nissila, T.; Ying, S. C. Langevin dynamics simulations of polymer translocation through nanopores. J. Chem. Phys. 2006, 125, 124901.

    Article  Google Scholar 

  30. 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.

    Article  Google Scholar 

  31. Luo, K.; Metzler, R. Polymer translocation into a fluidic channel through a nanopore. Phys. Rev. E 2010, 82, 021922.

    Article  Google Scholar 

  32. Sung, W.; Park, P. J. Polymer translocation through a pore in a membrane. Phys. Rev. Lett. 1996, 77, 783–786.

    Article  CAS  Google Scholar 

  33. Muthukumar, M. Polymer translocation through a hole. J. Chem. Phys. 1999, 111, 10371–10374.

    Article  CAS  Google Scholar 

  34. Chuang, J.; Kantor, Y.; Kardar, M. Anomalous dynamics of translocation. Phys. Rev. E 2001, 65, 011802.

    Article  Google Scholar 

  35. Kantor, Y.; Kardar, M. Anomalous dynamics of forced translocation. Phys. Rev. E 2004, 69, 021806.

    Article  Google Scholar 

  36. Tian, P.; Smith, G. D. Translocation of a polymer chain across a nanopore: a Brownian dynamics simulation study. J. Chem. Phys. 2003, 119, 11475.

    Article  CAS  Google Scholar 

  37. 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.

    Article  Google Scholar 

  38. 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.

    Article  Google Scholar 

  39. 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.

    Article  CAS  Google Scholar 

  40. 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).

    Article  Google Scholar 

  41. Luo, K.; Ala-Nissila, T.; Ying, S. C.; Bhattacharya, A. Heteropolymer translocation through nanopores. J. Chem. Phys. 2007, 126, 145101.

    Article  Google Scholar 

  42. 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.

    Article  CAS  Google Scholar 

  43. 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.

    Article  Google Scholar 

  44. 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.

    Article  CAS  Google Scholar 

  45. 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.

    Article  CAS  Google Scholar 

  46. Liu, L.; Tüzel, E.; Ross, J. L. Loop formation of microtubules during gliding at high density. J. Phys.: Condens. Matter 2011, 23, 374104.

    Google Scholar 

  47. 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.

    Article  CAS  Google Scholar 

  48. Man, Y.; Kanso, E. Morphological transitions of axially-driven microfilaments. Soft Matter 2019, 15, 5163–5173.

    Article  CAS  Google Scholar 

  49. 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.

    Article  CAS  Google Scholar 

  50. Bianco, V.; Locatelli, E.; Malgaretti, P. Globulelike conformation and enhanced diffusion of active polymers. Phys. Rev. Lett. 2018, 121, 217802.

    Article  CAS  Google Scholar 

  51. Locatelli, E.; Bianco, V.; Malgaretti, P. Activity-induced collapse and arrest of active polymer rings. Phys. Rev. Lett. 2021, 126, 097801.

    Article  CAS  Google Scholar 

  52. 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.

    Article  Google Scholar 

  53. 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.

    Article  Google Scholar 

  54. 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.

    Article  CAS  Google Scholar 

  55. 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.

    Article  CAS  Google Scholar 

  56. 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.

    Article  Google Scholar 

  57. 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.

    Article  CAS  Google Scholar 

  58. Manna, R. K.; Kumar, P.; Adhikari, R. Colloidal transport by active filaments. J. Chem. Phys. 2017, 146, 024901.

    Article  Google Scholar 

  59. 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.

    Article  CAS  Google Scholar 

  60. 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.

    Article  CAS  Google Scholar 

  61. 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.

    Article  CAS  Google Scholar 

  62. 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.

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was financially supported by the Zhejiang Provincial Natural Science Foundation of China (No. LY20A040004) and the National Natural Science Foundation of China (Nos. 11604232 and 11974305).

Author information

Authors and Affiliations

  1. Department of Physics, Taizhou University, Taizhou, 318000, China

    Chao Wang, Yan-Li Zhou & Bin Zhao

  2. Department of Physics, Zhejiang University, Hangzhou, 310027, China

    Han-Xian Hu & Meng-Bo Luo

Authors
  1. Chao Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Han-Xian Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yan-Li Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Bin Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Meng-Bo Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Chao Wang.

Additional information

Notes

The authors declare no competing financial interest.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, C., Hu, HX., Zhou, YL. et al. Translocation of a Self-propelled Polymer through a Narrow Pore. Chin J Polym Sci 40, 1670–1678 (2022). https://doi.org/10.1007/s10118-022-2768-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10118-022-2768-3

Keywords

Search

Navigation