Abstract
Ion channels are part of nature’s solution for regulating biological environments. Every ion channel consists of a chain of amino acids carrying a strong and sharply varying permanent charge, folded in such a way that it creates a nanoscopic aqueous pore spanning the otherwise mostly impermeable membranes of biological cells. These naturally occurring proteins are particularly interesting to device engineers seeking to understand how such nanoscale systems realize device-like functions. Availability of high-resolution structural information from X-ray crystallography, as well as large-scale computational resources, makes it possible to conduct realistic ion channel simulations. In general, a hierarchy of simulation methodologies is needed to study different aspects of a biological system like ion channels. Biology Monte Carlo (BioMOCA), a three-dimensional coarse-grained particle ion channel simulator, offers a powerful and general approach to study ion channel permeation. BioMOCA is based on the Boltzmann Transport Monte Carlo (BTMC) and Particle-Particle-Particle-Mesh (P3M) methodologies developed at the University of Illinois at Urbana-Champaign. In this paper we briefly discuss the various approaches to simulating ion flow in channel systems that are currently being pursued by the biophysics and engineering communities, and present the effect of having anisotropic dielectric constants on ion flow through a number of nanopores with different effective diameters.
Similar content being viewed by others
References
Hille, B.: Ionic Channels of Excitable Membranes. Sinauer, Sunderland (2001)
Ashcroft, F.M.: Ion Channels and Disease. Academic Press, New York (1999)
Eisenberg, B.: J. Comput. Electron. 2, 245 (2003)
Sambrook, J., Russell, D.W.: Molecular Cloning: A Laboratory Manual, 3rd edn. Cold Spring Harbor, New York (2001)
Watson, J.D., Baker, T.A., Bell, S.P., Gann, A., Levine, M., Losick, R.: Molecular Biology of the Gene, 5th edn. Benjamin-Cummings, Redwood City (2003)
Tieleman, D.P., Biggin, P.C., Smith, G.R., Sansom, M.S.: Q. Rev. Biophys. 34, 473 (2001)
van der Straaten, T.A., Kathawala, G., Ravaioli, U.: J. Comput. Theor. Nanosci. 3, 1 (2006)
Roux, B., Allen, T., Berneche, S., Im, W.: Q. Rev. Biophys. 37, 15 (2004)
Pauling, L., Wilson, E.B. Jr.: Introduction to Quantum Mechanics with Applications to Chemistry. Dover, New York (1985)
Guillet, V., Roblin, P., Werner, S., Coraiola, M., Menestrina, G., Monteil, H., Prevost, G., Mourey, L.: J. Biol. Chem. 279, 41028 (2004)
MacKerell, A.D. Jr., Bashford, D., Bellott, M., Dunbrack, R.L. Jr., Evanseck, J., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph, D., Kuchnir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, W.E. III, Roux, B., Schlenkrich, M., Smith, J., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., Karplus, M.: J. Phys. Chem. B 102, 3586 (1998)
MacKerell, A.D. Jr., Brooks, B., Brooks, C.B. III, Nilsson, L., Roux, B., Won, Y., Karplus, M.: CHARMM: the energy function and its parametrization with an overview of the program. In: Schleyer, P.v.R., Allinger, N.L., Clark, T., Gasteiger, J., Kollman, P.A., Schaefer, H.F. III, Schreiner, P.R. (eds.) Encyclopedia of Computational Chemistry, vol. 1, p. 271. Wiley, Chichester (1998)
MacKerell, A.D. Jr., Bashford, D., Bellott, M., Dunbrack, R.L. Jr., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph, D., Kuchnir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Roux, B., Schlenkrich, M., Smith, J., Stote, R., Straub, J., Wiorkiewicz-Kuczera, J., Karplus, M.: FASEB J. 6, A143 (1992)
Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M. Jr., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W., Kollman, P.A.: J. Am. Chem. Soc. 117, 5179 (1995)
http://amber.scripps.edu/doc8/amber8.pdf, and references within
Jorgensen, W.L.: OPLS force fields. In: Schleyer, P.v.R. (ed.) The Encyclopedia of Computational Chemistry. Wiley, Athens (1998)
Jorgensen, W.L., Tirado-Rives, J.: J. Am. Chem. Soc. 110, 1657 (1988)
Sitkoff, D., Sharp, K.A., Honig, B.: J. Phys. Chem. 98, 1978 (1994)
van der Straaten, T.A., Kathawala, G., Trellakis, A., Eisenberg, R.S., Ravaioli, U.: Mol. Simul. 31, 151 (2005)
Li, S.C., Hoyles, M., Kuyucak, S., Chung, S.H.: Biophys. J. 74, 37 (1998)
Chung, S.H., Hoyles, M., Allen, T.W., Kuyucak, S.: Biophys. J. 75, 793 (1998)
Jacoboni, C., Lugli, P.: The Monte Carlo Method for Semiconductor Device Simulation. Springer, New York (1989)
Hockney, R., Eastwood, J.: Computer Simulation Using Particles. McGraw-Hill, New York (1981)
Warshel, A., Russell, S.T.: Q. Rev. Biol. 17, 283 (1984)
Schutz, C.N., Warshel, A.: Proteins 44, 400 (2001)
Warshel, A., Papazyan, A.: Curr. Opin. Struct. Biol. 8, 211 (1998)
Baker, N.A., Sept, D., Holst, M.J., McCammon, J.A.: IBM J. Res. Dev. 45, 427 (2001)
Corry, B., Kuyucak, S., Chung, S.H.: Biophys. J. 78, 2364 (2000)
Chen, D.P., Lear, J., Eisenberg, R.S.: Biophys. J. 72, 97 (1997)
Noskov, S.Y., Im, W., Roux, B.: Biophys. J. 87, 2299 (2004)
Rosenfeld, Y.: J. Chem. Phys. 98, 8126 (1993)
Gillespie, D., Nonner, W., Eisenberg, R.S.: J. Phys., Condens. Matter 14, 12129 (2002)
Im, W., Roux, B.: J. Mol. Biol. 322, 851 (2002)
van der Straaten, T.A., Tang, J.M., Ravaioli, U., Eisenberg, R.S., Aluru, N.: J. Comput. Electron. 2, 29 (2003)
Selberherr, S.: Analysis and Simulation of Semiconductor Devices. Springer, New York (1984)
Joseph, S., Mashl, R.J., Jakobsson, E.: Nano Lett. 3(10), 1399 (2003)
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Toghraee, R., Mashl, R.J., Lee, K.I. et al. Simulation of charge transport in ion channels and nanopores with anisotropic permittivity. J Comput Electron 8, 98–109 (2009). https://doi.org/10.1007/s10825-009-0272-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10825-009-0272-4