Effects of interaction between nanopore and polymer on translocation time

Document Type : Full length research Paper

Authors

Department of Physics, Faculty of Science, Iran University of Science and Technology, Tehran, Iran

Abstract

Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and different pore diameters. Our results show that in both non-equilibrium and equilibrium initial conditions, translocation time will always increase by increasing binding energy and or increasing pore diameter. Moreover, scaling exponent of time versus force is -0.9531 in accordance to our predecessors. The comparison between equilibrium and non- equilibrium initial condition shows that the translocation time is very sensitive to the initial condition. Translocation time of the relaxed polymers for interaction energy of 8𝑘𝐵 𝑇 is smaller from the non- equilibrium case even in the small energy of 1𝑘𝐵 𝑇. Moreover, our simulation results show that the translocation velocity decrease by increasing the nanopore diameter from 3𝜎 to 5𝜎, where 𝜎 is the size of a monomer.

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References

[1] B. Alberts, et al., Molecular Biology of the Cell )2002( Garland Publishing.
##[2] A. Guyton, a.J.H., Textbook of Medical Physiology. 7th ed. (2005) Saunders.
##[3] D.C. Chang, Guide to Electroporation and Electrofusion. (1992) New York Academic.
##[4] A. Meller, Dynamics of polynucleotide transport through nanometer-scale pores. Journal of Physics: Condensed Matter 15 (2003) R581-R607. https://doi.org/10.1088/0953-8984/15/17/202
##[5] R. Balasubramanian, et al. DNA Translocation through Hybrid Bilayer Nanopores, The Journal of Physical Chemistry C 123 18 (2019) ‏11908-11916. https://doi.org/10.1021/acs.jpcc.9b00399
##[6] M. Magill, E. Waller, H.W. de Haan. A sequential nanopore-channel device for polymer separation, The Journal of chemical physics 149 17 (2018) 174903.‏ https://doi.org/10.1063/1.5037449
##[7] M. Muthukumar, Polymer Translocation (2011) CRC Press.
##[8] M. Muthukumar, Polymer translocation through a hole, Journal of Chemical Physics, 111 22 (1999) 10371-10374. https://doi.org/10.1063/1.480386
##[9] V.V. Palyulin, T. Ala-Nissila, R. Metzler, Polymer translocation: the first two decades and the recent diversification, Soft Matter 10 45 (2014) 9016-9037. https://doi.org/10.1039/C4SM01819B
##[10] D. Tomkiewicz, N. Nouwen, A.J.M. Driessen, Pushing, pulling and trapping–Modes of motor protein supported protein translocation, Federation of European Biochemical Societies 581 15 (2007) 2820–2828. https://doi.org/10.1016/j.febslet.2007.04.015
##[11] R. Haji Abdolvahab, M.R. Ejtehadi, R. Metzler, Sequence dependence of the binding energy in chaperone-driven polymer translocation through a nanopore, Physical Review E 83 1 (2011) 011902. https://doi.org/10.1103/PhysRevE.83.011902
##[12] R. Haji Abdolvahab, Chaperone-driven polymer translocation through nanopore: Spatial distribution and binding energy, European Physical Journal E 40 4 (2017) 41.              https://doi.org/10.1140/epje/i2017-11528-2
##[13] P. Suhonen, and R. Linna, Chaperone-assisted translocation of flexible polymers in three dimensions, Physical Review E 93 1 (2016) 012406. https://doi.org/10.1103/PhysRevE.93.012406
##[14] W. Yu, K. Luo, Polymer translocation through a nanopore driven by binding particles: Influence of chain rigidity, Physical Review E 90 4 (2014) 042708. https://doi.org/10.1103/PhysRevE.90.042708
##[15] W. Yu, K. Luo, Chaperone-assisted translocation of a polymer through a nanopore, Journal of the American Chemical Society 133 34 (2011) 13565-13570.        https://doi.org/10.1021/ja204892z
##[16] J. Sarabadani, et al. Dynamics of end-pulled polymer translocation through a nanopore, Europhysics Letters 120 3 (2018) 38004.‏                  https://doi.org/10.1209/0295-5075/120/38004
##[17] I. Huopaniemi, K. Luo, T. Ala-Nissila, Langevin dynamics simulations of polymer translocation through nanopores, Journal of Chemical Physics 125 12 )2006.( https://doi.org/10.1063/1.2357118
##[18] I. Huopaniemi, et al., Polymer translocation through a nanopore under a pulling force, Physical Review E 75 6 (2007). https://doi.org/10.1103/PhysRevE.75.061912
##[19] M Magill, C. Falconer, E. Waller, H.W. de Haan, Translocation Time through a Nanopore with an Internal Cavity Is Minimal for Polymers of Intermediate Length, Physical Review Letter 117 24 (2016) 247802. https://doi.org/10.1103/PhysRevLett.117.247802
##[20] V. Lehtola, R. Linna, K Kaski, Critical evaluation of the computational methods used in the forced polymer translocation, Physical Review E 78 (2008) 061803. https://doi.org/10.1103/PhysRevE.78.061803
##[21] A. Bhattacharya, et al., Scaling exponents of forced polymer translocation through a nanopore, European Physical Journal E 29 4 (2009) 423-429. https://doi.org/10.1140/epje/i2009-10495-5
##[22] K. Luo, T. Ala-Nissila, S. Yingand, R. Metzler, Driven polymer translocation through nanopores: Slow-vs.-fast dynamics, Europhysics Letters 88) 2009( 68006. https://doi.org/10.1209/0295-5075/88/68006
 ##[23] J. Wang, Y. Wang, K. Luo, Dynamics of polymer translocation through kinked nanopores, Journal of Chemical Physics 142 8 (2015) 084901. https://doi.org/10.1063/1.4913468
##[24] T. Menais, Polymer translocation under a pulling force: Scaling arguments and threshold forces, Physical Review E 97 2 (2018) 022501. https://doi.org/10.1103/PhysRevE.97.022501
##[25] S. Plimpton, Fast parallel algorithms for short-range molecular dynamics‏, Journal of Computational Physics 117 1 (1995) 1-19. https://doi.org/10.1006/jcph.1995.1039
##[26] W. Humphrey, A. Dalke, K. Schulten, VMD: visual molecular dynamics, Journal of molecular graphics 14 1 (1996) 33-38. https://doi.org/10.1016/0263-7855(96)00018-5
##[27] T. Williams, C. Kelley, Gnuplot 4.4: an interactive plotting program (2010).

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History

  • Receive Date: 09 October 2018
  • Revise Date: 29 September 2019
  • Accept Date: 20 December 2019

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