Effects of interaction between nanopore and polymer on translocation time

Document Type : Full length research Paper


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


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.


Main Subjects

[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 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 dynamicsJournal of Computational Physics 117 1 (1995) 1-19. https://doi.org/10.1006/jcph.1995.1039
##[26] W. Humphrey, A. Dalke, K. Schulten, VMDvisual 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).