10.1007/s40097-020-00336-y

Mechanism of rectification of polymer motion in an asymmetric nano-channel

  • Maedeh Heidari1,
  • Mahdieh Mikani1,
  • Narges Nikoofard*1,
  1. Institute of Nanoscience and Nanotechnology, University of Kashan, Kashan, 51167-87317, IR

Published in Issue 02-03-2020

How to Cite

Heidari, M., Mikani, M., & Nikoofard, N. (2020). Mechanism of rectification of polymer motion in an asymmetric nano-channel. Journal of Nanostructure in Chemistry, 10(2 (June 2020). https://doi.org/10.1007/s40097-020-00336-y
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Abstract

Abstract Separation is an important process in science and technology. Nano-structures are being used widely to improve the resolution and speed of the separation process. For this purpose, the motion of a charged polymer in an asymmetric nano-channel under constant and alternating applied electric fields are studied in this manuscript. Computer simulations and theoretical considerations are used to find the optimal condition for the nano-channel as a separation device. It is shown recently that an asymmetric channel acts as an entropic rectifier for polymers in an alternating electric field. Here, the mechanism of polymer motion in the channel, composed of consecutive nano-cones, is investigated based on the role of entropic traps. Entropic traps are referred to the narrow constrictions before the cones. It is shown that the characteristic time for the polymers to put their monomers in front of narrow constrictions (trapping time) becomes determining, in smaller electric fields. Dependence of the polymer velocity in the channel on the strength of the electric field, the cone angle and the time period of the electric field is discussed. Finally, the difference between velocities of polymers of various lengths is considered, which is an important parameter for the separation purposes. Graphic abstract

Keywords

  • Asymmetric nano-channel,
  • Entropic rectifier,
  • Polymer separation,
  • Entropic trapping

References

  1. Rahong et al. (2014) Ultrafast and wide range analysis of DNA molecules using rigid network structure of solid nanowires https://doi.org/10.1038/srep05252
  2. Viefhues et al. (2013) Fast and continuous-flow separation of DNA-complexes and topological DNA variants in microfluidic chip format 138(1) (pp. 186-196) https://doi.org/10.1039/C2AN36056J
  3. Nikoofard and Mashaghi (2016) Topology sorting and characterization of folded polymers using nano-pores 8(8) (pp. 4643-4649) https://doi.org/10.1039/C5NR08828C
  4. Duan et al. (2017) Continuous-flow electrophoresis of DNA and proteins in a two-dimensional capillary-well sieve 89(18) (pp. 10022-10028) https://doi.org/10.1021/acs.analchem.7b02484
  5. Nivedita and Papautsky (2013) Continuous separation of blood cells in spiral microfluidic devices 7(5) https://doi.org/10.1063/1.4819275
  6. Agrawal et al. (2018) Entropic trap purification of long DNA 18(6) (pp. 955-964) https://doi.org/10.1039/C7LC01355H
  7. Ding et al. (2017) Flow-induced polymer separation through a nanopore: effects of solvent quality 13(40) (pp. 7239-7243) https://doi.org/10.1039/C7SM00784A
  8. Marenda et al. (2017) Sorting ring polymers by knot type with modulated nanochannels 13(4) (pp. 795-802) https://doi.org/10.1039/C6SM02551J
  9. Li et al. (2019) A nanofluidic ion regulation membrane with aligned cellulose nanofibers 5(2) https://doi.org/10.1126/sciadv.aau4238
  10. Gao et al. (2017) Nanofluidics in two-dimensional layered materials: inspirations from nature 46(17) (pp. 5400-5424) https://doi.org/10.1039/C7CS00369B
  11. Skaug et al. (2018) Nanofluidic rocking Brownian motors 359(6383) (pp. 1505-1508) https://doi.org/10.1126/science.aal3271
  12. Masaeli et al. (2012) Continuous inertial focusing and separation of particles by shape 2(3)
  13. Costanzo et al. (2014) Motility-sorting of self-propelled particles in microchannels 107(3) https://doi.org/10.1209/0295-5075/107/36003
  14. Stein D., van den Heuvel, M.G.L., Dekker, C.: Chapter 1: transport of ions, DNA polymers, and microtubules in the nanofluidic regime. In: Nanofluidics, pp. 1–36. The Royal Society of Chemistry, London (2016)
  15. Ding et al. (2015) Entropic transport without external force in confined channel with oscillatory boundary 143(24) https://doi.org/10.1063/1.4939081
  16. Ko et al. (2017) Nanofluidic device for continuous multiparameter quality assurance of biologics 12(8) https://doi.org/10.1038/nnano.2017.74
  17. Wang et al. (2017) Wafer-scale integration of sacrificial nanofluidic chips for detecting and manipulating single DNA molecules 8(1) (pp. 1-9) https://doi.org/10.1038/s41467-016-0009-6
  18. Haywood et al. (2015) Fundamental studies of nanofluidics: nanopores, nanochannels, and nanopipets 87(1) (pp. 172-187) https://doi.org/10.1021/ac504180h
  19. Fu et al. (2006) Molecular sieving in periodic free-energy landscapes created by patterned nanofilter arrays 97(1) https://doi.org/10.1103/PhysRevLett.97.018103
  20. Yasui et al. (2015) Arrangement of a nanostructure array to control equilibrium and nonequilibrium transports of macromolecules 15(5) (pp. 3445-3451) https://doi.org/10.1021/acs.nanolett.5b00783
  21. Ouyang et al. (2017) Nanofluidic crystals: nanofluidics in a close-packed nanoparticle array 17(18) (pp. 3006-3025) https://doi.org/10.1039/C7LC00588A
  22. Matthias and Muller (2003) Asymmetric pores in a silicon membrane acting as massively parallel brownian ratchets 424(6944) https://doi.org/10.1038/nature01736
  23. Shaw et al. (2007) Geometry-induced asymmetric diffusion 104(23) (pp. 9580-9584) https://doi.org/10.1073/pnas.0703280104
  24. Mahmud et al. (2009) Directing cell motions on micropatterned ratchets 5(8) (pp. 606-612) https://doi.org/10.1038/nphys1306
  25. Leonardo et al. (2010) Bacterial ratchet motors 107(21) (pp. 9541-9545) https://doi.org/10.1073/pnas.0910426107
  26. Slater et al. (1997) Bidirectional transport of polyelectrolytes using self-modulating entropic ratchets 78(6) https://doi.org/10.1103/PhysRevLett.78.1170
  27. Polson et al. (2010) Dynamics of a polymer in a Brownian ratchet 82(5) https://doi.org/10.1103/PhysRevE.82.051931
  28. Wang et al. (2013) Net motion of a charged macromolecule in a ratchet-slit 9(46) (pp. 11107-11112) https://doi.org/10.1039/c3sm52011k
  29. Mondal and Muthukumar (2016) Ratchet rectification effect on the translocation of a flexible polyelectrolyte chain 145(8) https://doi.org/10.1063/1.4961505
  30. Reguera et al. (2012) Entropic splitter for particle separation 108(2) https://doi.org/10.1103/PhysRevLett.108.020604
  31. Nikoofard and Fazli (2012) Electric-field-driven polymer entry into asymmetric nanoscale channels 85(2) https://doi.org/10.1103/PhysRevE.85.021804
  32. Hoseinpoor et al. (2016) Accuracy limits of the blob model for a flexible polymer confined inside a cylindrical nano-channel 163(3) (pp. 593-603) https://doi.org/10.1007/s10955-016-1489-9
  33. Nikoofard et al. (2014) Accuracy of the blob model for single flexible polymers inside nanoslits that are a few monomer sizes wide 90(6) https://doi.org/10.1103/PhysRevE.90.062603
  34. Rubinstein and Colby (2003) Oxford University Press
  35. Nikoofard and Fazli (2011) Free-energy barrier for electric-field-driven polymer entry into nanoscale channels 83(5) https://doi.org/10.1103/PhysRevE.83.050801
  36. Han et al. (1999) Entropic trapping and escape of long DNA molecules at submicron size constriction 83(8) (pp. 1688-1691) https://doi.org/10.1103/PhysRevLett.83.1688
  37. Nikoofard and Fazli (2015) A flexible polymer confined inside a cone-shaped nano-channel 11(24) (pp. 4879-4887) https://doi.org/10.1039/C5SM00818B
  38. Nikoofard et al. (2013) Directed translocation of a flexible polymer through a cone-shaped nano-channel 139(7) https://doi.org/10.1063/1.4818419
  39. Limbach et al. (2006) ESPResSo—an extensible simulation package for research on soft matter systems 174(9) (pp. 704-727) https://doi.org/10.1016/j.cpc.2005.10.005