Abstract
We review transport equations and their usage for the modeling and simulation of nanopores. First, the significance of nanopores and the experimental progress in this area are summarized. Then the starting point of all classical and semiclassical considerations is the Boltzmann transport equation as the most general transport equation. The derivation of the drift-diffusion equations from the Boltzmann equation is reviewed as well as the derivation of the Navier–Stokes equations. Nanopores can also be viewed as a special case of a confined structure and hence as giving rise to a multiscale problem, and therefore we review the derivation of a transport equation from the Boltzmann equation for such confined structures. Finally, the state of the art in the simulation of nanopores is summarized.
Similar content being viewed by others
References
Pennisi, E.: Search for pore-fection. Science 336(6081), 534–537 (2012)
Branton, D., et al.: The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26(10), 1146–1153 (2008)
Wanunu, M.: Nanopores: a journey towards DNA sequencing. Phys. Life Rev. 9(2), 125–158 (2012)
Hall, A.R., Scott, A., Rotem, D., Mehta, K.K., Bayley, H., Dekker, C.: Hybrid pore formation by directed insertion of \(\alpha \)-haemolysin into solid-state nanopores. Nat. Nanotechnol. 5, 874–877 (2010)
Bell, N.A.W., Engst, C.R., Ablay, M., Divitini, G., Ducati, C., Liedl, T., Keyser, U.F.: DNA origami nanopores. Nano Lett. 12(1), 512–517 (2012)
Burns, J.R., Stulz, E., Howorka, S.: Self-assembled DNA nanopores that span lipid bilayers. Nano Lett. 13(6), 2351–2356 (2013)
Cercignani, C.: The Boltzmann Equation and Its Applications. Springer-Verlag, New York (1988)
Maxwell, J.C.: On the dynamical theory of gases. Phil. Trans. Roy. Soc. (London) 157, 49–88 (1867)
Cercignani, C., Illner, R., Pulvirenti, M.: The Mathematical Theory of Dilute Gases. Springer-Verlag, Berlin (1994)
Ben Abdallah, N.: On a hierarchy of macroscopic models for semiconductors. J. Math. Phys. 37(7), 3306–3333 (1996)
Ben Abdallah, N., Degond, P., Génieys, S.: An energy-transport model for semiconductors derived from the Boltzmann equation. J. Statist. Phys. 84(1–2), 205–231 (1996)
Heitzinger, Clemens, Ringhofer, Christian: A transport equation for confined structures derived from the Boltzmann equation. Commun. Math. Sci. 9(3), 829–857 (2011)
Ben Abdallah, N., Degond, P., Markowich, P., Schmeiser, C.: High field approximations of the spherical harmonics expansion model for semiconductors. Z. Angew. Math. Phys. 52(2), 201–230 (2001)
Markowich, P.A., Ringhofer, C.A., Schmeiser, C.: Semiconductor Equations. Springer-Verlag, Wien (1990)
Anile, A.M., Allegretto, W., Ringhofer, C.: Mathematical Problems in Semiconductor Physics. Springer-Verlag, Berlin (2003)
Baumgartner, Stefan, Heitzinger, Clemens: Existence and local uniqueness for 3d self-consistent multiscale models for field-effect sensors. Commun. Math. Sci. 10(2), 693–716 (2012)
Markowich, P.A.: The Stationary Semiconductor Device Equations. Springer-Verlag, Wien (1986)
Degond, P., Méhats, F., Ringhofer, C.: Quantum energy-transport and drift-diffusion models. J. Statist. Phys. 118, 625–667 (2005)
Baumgartner, Stefan, Heitzinger, Clemens: A one-level FETI method for the drift-diffusion-Poisson system with discontinuities at an interface. J. Comput. Phys. 243, 74–86 (June 2013)
Rubinstein, I.: Electro-Diffusion of Lons. SIAM, Philadelpha, PA (1990)
Ramírez, P., Mafé, S., Aguilella, V.M., Alcaraz, A.: Synthetic nanopores with fixed charges: an electrodiffusion model for ionic transport. Phys. Rev. E (3), 68(1):011910/1-8, (July 2003)
van der Straaten, T.A., Tang, J.M., Ravaioli, U., Eisenberg, R.S., Aluru, N.R.: Simulating ion permeation through the ompF porin ion channel using three-dimensional drift-diffusion theory. J. Comp. Electron. 2, 29–47 (2003)
Gardner, C.L., Nonner, W., Eisenberg, R.S.: Electrodiffusion model simulation of ionic channels: 1D simulations. J. Comput. Electron. 3, 25–31 (2004)
Coalson, R.D., Kurnikova, M.G.: Poisson–Nernst–Planck theory approach to the calculation of current through biological ion channels. IEEE Trans. Nanobiosci. 4(1), 81–93 (2005)
Cervera, J., Schiedt, B., Ramírez, P.: A Poisson/Nernst–Planck model for ionic transport through synthetic conical nanopores. Europhys. Lett. 71(1), 35–41 (2005)
Liu, Y., Sauer, J., Dutton, R.W.: Effect of electro-diffusion current flow on electrostatic screening in aqueous pores. J. Appl. Phys. 103, 084701 (2008)
Cervera, J., Ramírez, P., Manzanares, J.A., Mafé, S.: Incorporating ionic size in the transport equations for charged nanopores. Microfluid. Nanofluid. 9(1), 41–53 (2010)
Gardner, C.L., Jones, J.R.: Electrodiffusion model simulation of the potassium channel. J. Theoret. Biol. 291, 10–13 (2011)
Lu, B., Hoogerheide, D.P., Zhao, Q., Yu, D.: Effective driving force applied on DNA inside a solid-state nanopore. Phys. Rev. E 86(1), 011921 (2012)
Gummel, H.K.: A self-consistent iterative scheme for one-dimensional steady state transistor calculations. IEEE Trans. Electron Devices ED–11, 455–465 (1964)
Scharfetter, D.L., Gummel, H.K.: Large-signal analysis of a silicon read diode oscillator. IEEE Trans. Electron Devices ED 16(1), 64–77 (1969)
Kerkhoven, T.: A proof of convergence of Gummel’s algorithm for realistic device geometries. SIAM J. Numer. Anal. 23(6), 1121–1137 (1986)
Gartland Jr, E.C.: On the uniform convergence of the Scharfetter–Gummel discretization in one dimension. SIAM J. Numer. Anal. 30(3), 749–758 (1993)
Mao, M., Ghosal, S., Hu, G.: Hydrodynamic flow in the vicinity of a nanopore induced by an applied voltage. Nanotechnology 24(24), 245202 (2013)
Ai, Y., Qian, S.: Electrokinetic particle translocation through a nanopore. Phys. Chem. Chem. Phys. 13(9), 4060–4071 (2011)
van Dorp, S., Keyser, U.F., Dekker, N.H., Dekker, C., Lemay, S.G.: Origin of the electrophoretic force on DNA in solid-state nanopores. Nat. Phys. 5, 347–351 (2009)
Jubery, T.Z., Prabhu, A.S., Kim, M.J., Dutta, P.: Modeling and simulation of nanoparticle separation through a solid-state nanopore. Electrophoresis 33(2), 325–333 (2012)
Bearden, S., Zhang, G.: The effects of the electrical double layer on giant ionic currents through single-walled carbon nanotubes. Nanotechnology 24(12), 125204 (2013)
Liu, Y., Huber, D.E., Tabard-Cossa, V., Dutton, R.W.: Descreening of field effect in electrically gated nanopores. Appl. Phys. Lett. 97(1–3), 143109 (2010)
Bhatia, S., Nicholson, D.: Molecular transport in nanopores. J. Chem. Phys. 119(3), 1719–1730 (2013)
Joseph, S., Guan, W., Reed, M.A., Krstic, P.S.: A long DNA segment in a linear nanoscale Paul trap. Nanotechnology 21(1), 015103 (2010)
Wei, G.-W., Zheng, Q., Chen, Z., Xia, K.: Variational multiscale models for charge transport. SIAM Rev. 54(4), 699–754 (2012)
Acknowledgments
The first author acknowledges support by the FWF (Austrian Science Fund) START project No. Y660 PDE Models for Nanotechnology. The second author acknowledges support by NSF Grant 11-07465 (KI-Net).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Heitzinger, C., Ringhofer, C. Hierarchies of transport equations for nanopores. J Comput Electron 13, 801–817 (2014). https://doi.org/10.1007/s10825-014-0586-8
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10825-014-0586-8