Научная электронная библиотека ULRICH'S Periodicals Directory

Сибирский государственный университет
науки и технологий имени академика М.Ф. Решетнева

Сибирский аэрокосмический журнал
ISSN 2712-8970 (Print) ISSN 2782-5760 (on-line)

Сведения об образовательной организации

UDK UDC 537.21, 539.217, 620.3+004.942 Doi: 10.31772/2587-6066-2018-19-4-677-682
MATHEMATICAL MODEL OF CONDUCTING NANOPORE FOR MOLECULAR DYNAMICS SIMULATIONS
V. E. Zalizniak, O. A. Zolotov, O. P. Zolotova
Siberian Federal University, 79, Svobodny Av., Krasnoyarsk, 660041, Russian Federation; Reshetnev Siberian State University of Science and Technology, 31, Krasnoyarsky Rabochy Av., Krasnoyarsk, 660037, Russian Federation
An electrostatic model of conducting nanopore is presented in the paper. The model does not require solution of the Poisson equation for the potential. This model is intended for use in simulation of transport phenomena of charged particles in conducting nanopores by the method of molecular dynamics. This method is based on Newton’s equations of motion and it allows one to determine the variation of position, velocity and acceleration of particles with time. The electric field from the charge distributed over the nanopore surface is approximated by the field from fictitious point charges on the same surface. To verify the proposed model of fictitious charges system capacitance is calculated. The obtained values of capacitance are compared with classical results for conducting tubule and with the results obtained by the other similar method. The comparison shows that relative discrepancy between results is less than 10 %. There is a need to further develop the proposed model both in case of a large number of fictitious charges and in case when charged particles are in close proximity to the nanopore surface. The proposed method can be easily applied to an arbitrary shape nanopore. The model can be used in the development of various nanodevices, among them the devices used in life support systems of manned space vehicles.
Keywords: conducting nanopore, ion transport, molecular dynamics.
References

1. Dekker C. Solid-state nanopores. Nature Nanotechnology. 2007, Vol. 2, No. 4, P. 209–215. DOI: 10.1038/nnano.2007.27.

2. Thomas M., Corry B., Hilder T. A. What have we learnt about the mechanisms of rapid water transport, ion rejection and selectivity in nanopores from molecular simulation? Small. 2014, Vol. 10, No. 8, P. 1453–1465. DOI: 10.1002/smll.201302968.

3. Daiguji H. Ion transport in nanofluidic channels. Chemical Society Reviews. 2010, Vol. 39, No. 3, P. 901–911. DOI: 10.1039/B820556F.

4. Majd S., Yusko E. C., Billeh Y. N. et. al. Applications of biological pores in nanomedicine, sensing, and nanoelectronics. Current Opinion in Biotechnology. 2010, Vol. 21, No. 4, P. 439–476. DOI: 10.1016/j.copbio.2010.05.002.

5. Singer A., Rapireddy S., Ly D. H., Meller A. Electronic barcoding of a viral gene at the single-molecule level. Nano Letters. 2012, Vol. 12, No. 3, P. 1722–1728. DOI: 10.1021/nl300372a.

6. Hou X., Zhang H., Jiang L. Building bio-inspired artificial functional nanochannels: from symmetric to asymmetric modification. Angewandte Chemie International Edition. 2012, Vol. 51, No. 22, P. 5296–5307. DOI: 10.1002/anie.201104904.

7. Zhang Y., Kong X. Y., Gao L. et. al. Fabrication of nanochannels. Materials. 2015, Vol. 8, No. 9, P. 6277–6308. DOI: 10.3390/ma8095304.

8. Kasi J. K., Kasi A. K., Wongwiriyapan W. et. al. Synthesis of carbon nanotube and carbon nanofiber in nanopore of anodic aluminum oxide template by chemical vapor deposition at atmospheric pressure. Advanced Materials Research – Trans Tech Publications. 2012, Vol. 557–559, P. 544–549. DOI: 10.4028/www.scientific.net/AMR.557-559.544.

9. Choi W., Ulissi Z. W., Shimizu S. F. et. al. Diameter- dependent ion transport through the interior of isolated single-walled carbon nanotubes. Nature Communications. 2013, Vol. 4, P. 2397. DOI: 10.1038/ncomms3397.

10. Simunin M. M., Khartov S. V., Shiverskii A. V. et. al. Structures based on graphitized nanotubulenes with a common electrode in a matrix of porous anodic alumina for the purpose of forming electrically switchable membranes. Technical Physics Letters. 2015, Vol. 41, No. 11, P. 1047–1050. DOI: 10.1134/S1063785015110103.

11. Levin Y. Electrostatics of ions inside the nanopores and trans-membrane channels. Europhysics Letters. 2006, Vol. 76, No. 1, P. 163–169. DOI: 10.1209/epl/i2006-10240-4.

12. Modi N., Winterhalter M., Kleinekathoefer U. Computational modeling of ion transport through nanopores. Nanoscale. 2012, Vol. 4, No. 20, P. 6166–6180. DOI: 10.1039/b000000x.

13. Hilder T. A., Gordon D., Chung S. H. Computational modeling of transport in synthetic nanotubes. Nanomedicine: Nanotechnology, Biology and Medicine. 2011, Vol. 7, No. 6, P. 702–709. DOI: 10.1016/j.nano.2011.02.011.

14. Iossel Yu. Ya., Kochanov E. S., Strunsky M. G. Raschet elektricheskoy emkosti [Calculation of Electric Power]. Leningrad, Energoizdat, 1981, 288 p. (In Russ.).

15. Zolotov O. A, Zalizniak V. E. Simple mathematical model of conducting nanopore. Zhurnal Sibirskogo federal’nogo universiteta. Seriya Matematika i fizika. 2018, Vol. 11, No. 4, P. 505–512. DOI: 10.17516/1997-1397-2018-11-4-505-512.


Zalizniak Viktor Evgen’evich – Cand. Sc., Docent, Department of Mathematic modeling and management activities,

Institute of Mathematics and Computer Science, Siberian Federal University. Е-mail: vzalizniak@mail.ru.

Zolotov Oleg Aleksandrovich – Cand. Sc., Docent, Department of Mathematic modeling and management activities,

Institute of Mathematics and Computer Science, Siberian Federal University. Е-mail: ozolot_@mail.ru.

Zolotova Olga Pavlovna – Cand. Sc., Docent, Department of Technical Physics, Reshetnev Siberian State University

of Science and Technology. Е-mail: zolotova@sibsau.ru.


  MATHEMATICAL MODEL OF CONDUCTING NANOPORE FOR MOLECULAR DYNAMICS SIMULATIONS